cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Maximum margin learning of t-SPNs for cell classification with filtered input
Creators: name: Kang, Haeyong
name: Yoo, Chang D.
name: Na, Yongcheon
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: An algorithm based on a deep probabilistic architecture referred to as a tree-structured sum-product network (t-SPN) is considered for cell classification. The t-SPN is constructed such that the unnormalized probability is represented as conditional probabilities of a subset of most similar cell classes. The constructed t-SPN architecture is learned by maximizing the margin, which is the difference in the conditional probability between the true and the most competitive false label. To enhance the generalization ability of the architecture, L2-regularization (REG) is considered along with the maximum margin (MM) criterion in the learning process. To highlight cell features, this paper investigates the effectiveness of two generic high-pass filters: ideal high-pass filtering and the Laplacian of Gaussian (LOG) filtering. On both HEp-2 and Feulgen benchmark datasets, the t-SPN architecture learned based on the max-margin criterion with regularization produced the highest accuracy rate compared to other state-of-the-art algorithms that include convolutional neural network (CNN) based algorithms. The ideal high-pass filter was more effective on the HEp-2 dataset, which is based on immunofluorescence staining, while the LOG was more effective on the Feulgen dataset, which is based on Feulgen staining.
The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics
Creators: name: Threadgill, David W.
name: Wang, Wei
name: Pardo-Manuel de Villena, Fernando
name: McMillan, Leonard
name: Roberts, Adam
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Mouse genetic resources include inbred strains, recombinant inbred lines, chromosome substitution strains, heterogeneous stocks, and the Collaborative Cross (CC). These resources were generated through various breeding designs that potentially produce different genetic architectures, including the level of diversity represented, the spatial distribution of the variation, and the allele frequencies within the resource. By combining sequencing data for 16 inbred strains and the recorded history of related strains, the architecture of genetic variation in mouse resources was determined. The most commonly used resources harbor only a fraction of the genetic diversity of Mus musculus, which is not uniformly distributed thus resulting in many blind spots. Only resources that include wild-derived inbred strains from subspecies other than M. m. domesticus have no blind spots and a uniform distribution of the variation. Unlike other resources that are primarily suited for gene discovery, the CC is the only resource that can support genome-wide network analysis, which is the foundation of systems genetics. The CC captures significantly more genetic diversity with no blind spots and has a more uniform distribution of the variation than all other resources. Furthermore, the distribution of allele frequencies in the CC resembles that seen in natural populations like humans in which many variants are found at low frequencies and only a minority of variants are common. We conclude that the CC represents a dramatic improvement over existing genetic resources for mammalian systems biology applications.
An imputed genotype resource for the laboratory mouse
Creators: name: Hutchins, Lucie
name: Churchill, Gary A.
name: Beane, Glen L.
name: Szatkiewicz, Jin P.
name: Pardo-Manuel de Villena, Fernando
name: Ding, Yueming
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: We have created a high-density SNP resource encompassing 7.87 million polymorphic loci across 49 inbred mouse strains of the laboratory mouse by combining data available from public databases and training a hidden Markov model to impute missing genotypes in the combined data. The strong linkage disequilibrium found in dense sets of SNP markers in the laboratory mouse provides the basis for accurate imputation. Using genotypes from eight independent SNP resources, we empirically validated the quality of the imputed genotypes and demonstrate that they are highly reliable for most inbred strains. The imputed SNP resource will be useful for studies of natural variation and complex traits. It will facilitate association study designs by providing high density SNP genotypes for large numbers of mouse strains. We anticipate that this resource will continue to evolve as new genotype data become available for laboratory mouse strains. The data are available for bulk download or query at http://cgd.jax.org/.
Unidirectional magnetoelectric-field multiresonant tunneling
Creators: name: Kamenetskii, E. O.
name: Hollander, E.
name: Joffe, R.
name: Shavit, R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Unidirectional multi-resonant tunneling of the magneto-electric (ME)-field excitations through a sub wavelength (regarding the scales of regular electromagnetic radiation) vacuum or isotropic-dielectric regions has been observed in two-port microwave structures having a quasi-2D ferrite disk with magnetic-dipolar-mode (MDM) oscillations. The excitations manifest themselves as the Fano-resonance peaks in the scattering-matrix parameters at the stationary states of the MDM spectrum. The ME near-field excitations are quasi magnetostatic fields with non-zero helicity parameter. Topological-phase properties of ME fields are determined by edge chiral currents of MDM oscillations. We show that while for a given direction of a bias magnetic field (in other words, for a given direction of time), the ME-field excitations are considered as forward tunneling processes, in the opposite direction of a bias magnetic field (the opposite direction of time), there are backward tunneling processes. Unidirectional ME-field resonant tunneling is observed due to distinguishable topology of the forward and backward ME-field excitations. We establish a close connection between the Fano-resonance unidirectional tunneling and topology of ME fields in different microwave structures.
Crossover from Super- to Sub-Diffusive Motion and Memory Effects in Crystalline Organic Semiconductors
Creators: name: De Filippis, G.
name: Cataudella, V.
name: Mishchenko, A. S.
name: Nagaosa, N.
name: Fierro, A.
name: de Candia, A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The transport properties at finite temperature of crystalline organic semiconductors are investigated, within the Su-Schrieffer-Heeger model, by combining exact diagonalization technique, Monte Carlo approaches, and maximum entropy method. The temperature-dependent mobility data measured in single crystals of rubrene are successfully reproduced: a crossover from super- to sub-diffusive motion occurs in the range $150 \leq T \leq 200$ K, where the mean free path becomes of the order of the lattice parameter and strong memory effects start to appear. We provide an effective model which can successfully explain low frequencies features of the absorption spectra. The observed response to slowly varying electric field is interpreted by means of a simple model where the interaction between the charge carrier and lattice polarization modes is simulated by a harmonic interaction between a fictitious particle and an electron embedded in a viscous fluid.
The Collaborative Cross at Oak Ridge National Laboratory: developing a powerful resource for systems genetics
Creators: name: Branstetter, Lisa R.
name: Threadgill, David W.
name: Williams, Robert W.
name: Chesler, Elissa J.
name: Galloway, Leslie D.
name: Philip, Vivek M.
name: Johnson, Dabney K.
name: Churchill, Gary A.
name: Jackson, Barbara L.
name: Culiat, Cymbeline T.
name: Voy, Brynn H.
name: Miller, Darla R.
name: Manly, Kenneth F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Complex traits and disease comorbidity in humans and in model organisms are the result of naturally occurring polymorphisms that interact with each other and with the environment. To ensure the availability of resources needed to investigate biomolecular networks and systems-level phenotypes underlying complex traits, we have initiated breeding of a new genetic reference population of mice, the Collaborative Cross. This population has been designed to optimally support systems genetics analysis. Its novel and important features include a high level of genetic diversity, a large population size to ensure sufficient power in high-dimensional studies, and high mapping precision through accumulation of independent recombination events. Implementation of the Collaborative Cross has been ongoing at the Oak Ridge National Laboratory (ORNL) since May 2005. Production has been systematically managed using a software-assisted breeding program with fully traceable lineages, performed in a controlled environment. Currently, there are 650 lines in production, and close to 200 lines are now beyond their seventh generation of inbreeding. Retired breeders enter a high-throughput phenotyping protocol and DNA samples are banked for analyses of recombination history, allele drift and loss, and population structure. Herein we present a progress report of the Collaborative Cross breeding program at ORNL and a description of the kinds of investigations that this resource will support.
Murine models of colorectal cancer
Creators: name: Uronis, Joshua M.
name: Threadgill, David W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Colorectal cancer is one of the most prevalent cancers of humans. To experimentally investigate this common disease, numerous murine models have been established. These models accurately recapitulate the molecular and pathological characteristics of human colorectal cancer including activation of MYC, which has recently been suggested to be a key mediator of colorectal cancer development. This review focuses on the variety of murine models of human colorectal cancer that are available to the research community and on their use to identify common and distinct characteristics of colorectal cancer.
Additional file 3 of Comparison of catastrophic out-of-pocket medical expenditure among older adults in the United States and South Korea: what affects the apparent difference?
Creators: name: Kim, Narae
name: Jacobson, Mireille
Publisher: name: figshare
Year: 2022
Subjects: Medicine
Science Policy
Computational Biology

description: Additional file 3: Table 1. Odds of Being Exposed to Catastrophic Health Spending in the US and South Korea with 20% threshold.
Multiple-access Fading Channel with Wireless Power Transfer and Energy Harvesting
Creators: name: Hadzi-Velkov, Zoran
name: Zlatanov, Nikola
name: Schober, Robert
Publisher: name: arXiv
Year: 2014
Subjects: subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences

description: We consider the achievable average rates of a multiple-access system, which consists of N energy-harvesting users (EHUs) that transmit information over a block fading multiple-access channel (MAC) and a base station (BS) that broadcasts radio frequency (RF) energy to the EHUs for wireless power transfer. The information (over the uplink) and power (over the downlink) can be transmitted either in time division duplex or frequency division duplex. For the case when the EHUs battery capacities and the number of transmission slots are both infinite, we determine the optimal power allocation for the BS and the optimal rates and power allocations for the EHUs that maximize the achievable rate region of the MAC. The resulting online solution is asymptotically optimal, and also applicable for a finite number of transmission slots and finite battery capacities.
description: 4 pages, 1 figure
The origin of optical emission lines in the soft state of X-ray binary outbursts: the case of MAXI J1820+070
Creators: name: Koljonen, K. I. I.
name: Long, K. S.
name: Matthews, J. H.
name: Knigge, C.
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The optical emission line spectra of X-ray binaries (XRBs) are thought to be produced in an irradiated atmosphere, possibly the base of a wind, located above the outer accretion disc. However, the physical nature of - and physical conditions in - the line-forming region remain poorly understood. Here, we test the idea that the optical spectrum is formed in the transition region between the cool, geometrically thin part of the disc near the mid-plane and a hot, vertically extended atmosphere or outflow produced by X-ray irradiation. We first present a VLT X-Shooter spectrum of XRB MAXI J1820+070 in the soft state associated with its 2018 outburst, which displays a rich set of double-peaked hydrogen and helium recombination lines. Aided by ancillary X-ray spectra and reddening estimates, we then model this spectrum with the Monte Carlo radiative transfer code Python, using a simple biconical disc wind model inspired by radiation-hydrodynamic simulations of irradiation-driven outflows from XRB discs. Such a model can qualitatively reproduce the observed features; nearly all of the optical emission arising from the transonic 'transition region' near the base of the wind. In this region, characteristic electron densities are on the order of 10$^{12-13}$ cm$^{-3}$, in line with the observed flat Balmer decrement (H$α$/H$β\approx 1.3$). We conclude that strong irradiation can naturally give rise to both the optical line-forming layer in XRB discs and an overlying outflow/atmosphere that produces X-ray absorption lines.
description: 17 pages, 11 figures. This article has been accepted for publication in MNRAS published by Oxford University Press on behalf of the Royal Astronomical Society
Trophic level interactions in Australian reservoirs: Evidence from plankton and fisheries acoustics
Creators: name: Matveev, Vladimir
name: Matveeva, Lilian
Publisher: name: La Trobe
Year: 2023

description: La Trobe University Faculty of Science, Technology and Engineering Murray Darling Freshwater Research Centre

MDFRC item.

Indirect evidence is presented in support of the view that significant trophic level interactions between pelagic fish, Daphnia and phytoplankton may occur in Australian reservoirs.
Additional file 1 of A novel injectable boron doped-mesoporous nano bioactive glass loaded-alginate composite hydrogel as a pulpotomy filling biomaterial for dentin regeneration
Creators: name: Naga, Marwa S.
name: Helal, Hala M.
name: Kamoun, Elbadawy A.
name: Moaty, Maha Abdel
name: Omar, Samia S. Abdel Rehim
name: Ghareeb, Ahmed Z.
name: El-Fakharany, Esmail M.
name: El Din, Mona Mohy
Publisher: name: figshare
Year: 2024
Subjects: Biochemistry
Space Science
Medicine
Pharmacology
Biotechnology
Environmental Sciences not elsewhere classified
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified

description: Supplementary Material 1
Monmouth University Poll: October 2015 Iowa Caucuses
Creators: name: Monmouth University Polling Institute
Publisher: name: Roper Center for Public Opinion Research
Year: 2022

description: Registered to vote (1); voter likelihood (1); Republican/Democratic presidential caucus (2); switch party registration to vote in caucus (2); Republican presidential caucus choice (5); favorability of Republican presidential candidates (11); Republican/Democratic Party job performance (2); met/seen presidential candidates this year (4); Democratic presidential caucus choice (5); favorability of Democratic presidential candidates (4); Democratic Party job approval of representing voters like you (1); Tea Party (1).
(:unas) unassigned
Creators: name: (:Unkn) Unknown
Publisher: name: Universita' degli Studi di Salerno
Year: 2024

description: In questo saggio si applicherà la nozione di fenomeno performático all’opera del cantautore Claudio Baglioni, offrendo un focus sulle sue drammaturgie visive e sulle modalità di messa in scena, che si configurano come agenti di scrittura attivi a livello testuale sulla sua produzione. Dall’analisi emerge come la forma-canzone si configuri, oggi, come un crocevia di intersezioni e di stratificazioni complesse, in cui la performance, in quanto elemento fondativo della sua ontologia, gioca un ruolo chiave, configurandosi come un fattore di scrittura soggettivo e autoriale.
description: In this essay we will apply the notion of performatic phenomenon to the work of the singersongwriter Claudio Baglioni, offering a focus on his visual dramaturgies and on his methods of staging, that are active like writing agents. It will emerge how the song-form is configured, today, as a crossroads of intersections and complex stratifications, in which the performance, as a founding element of its ontology, plays a key role, configuring itself as a subjective writing factor and authorial.
Beam-beam and impedance
Creators: name: White, S.
name: Buffat, X.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Accelerator Physics (physics.acc-ph)
subject: FOS: Physical sciences

description: As two counter-rotating beams interact they can give rise to coherent dipole modes. Under the influence of impedance these coherent beam-beam modes can couple to higher order head-tail modes and lead to strong instabilities. A fully self-consistent approach including beam-beam and impedance was used to characterize this new coupled mode instability and study possible cures such as a transverse damper and high chromaticity.
description: 9 pages, contribution to the ICFA Mini-Workshop on Beam-Beam Effects in Hadron Colliders, CERN, Geneva, Switzerland, 18-22 Mar 2013
Realism and Empirical Evidence
Creators: name: Schmelzer, Ilja
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: 83D05
subject: 83A0

description: We define realism using a slightly modified version of the EPR criterion of reality. This version is strong enough to show that relativity is incomplete.We show that this definition of realism is nonetheless compatible with the general principles of causality and canonical quantum theory as well as with experimental evidence in the (special and general) relativistic domain. We show that the realistic theories we present here, compared with the standard relativistic theories, have higher empirical content in the strong sense defined by Popper's methodology.
Additional file 4 of Comparison of catastrophic out-of-pocket medical expenditure among older adults in the United States and South Korea: what affects the apparent difference?
Creators: name: Kim, Narae
name: Jacobson, Mireille
Publisher: name: figshare
Year: 2022
Subjects: Medicine
Science Policy
Computational Biology

description: Additional file 4: Table 2. US-South Korea Decomposition for Probability of Being Exposed to Catastrophic Out-of-Pocket Medical Expenditure with 20% Threshold.
Numerical simulation of the surface hardening of steel
Creators: name: Fuhrmann, Jürgen
name: Hömberg, Dietmar
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: finite volume method
subject: heat treatment
subject: induction hardening
subject: laser hardening
subject: phase transitions
subject: 35K20
subject: 65C20
subject: 65N30

description: We discuss a model that is capable of describing the solid-solid phase transitions in steel. It consists of a system of ordinary differential equations for the volume fractions of the occuring phases coupled with a nonlinear energy balance equation to take care of the latent heats of the phase changes. This model is applied to simulate surface heat treatments, which play an important role in the manufacturing of steel. Two different technologies are considered: laser and induction hardening. In the latter case the model has to be extended by Maxwell's equations. Finally, we present numerical simulations of laser and surface hardening applied to the steel 42 CrMo 4.
Replication and narrowing of gene expression quantitative trait loci using inbred mice
Creators: name: Wright, Fred A.
name: Gatti, Daniel M.
name: Harrill, Alison H.
name: Rusyn, Ivan
name: Threadgill, David W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Gene expression quantitative trait locus (eQTL) mapping has become a powerful tool in systems biology. While many authors have made important discoveries using this approach, one persistent challenge in eQTL studies is the selection of loci and genes that should receive further biological investigation. In this study, we compared eQTL generated from gene expression profiling in the livers of two panels of mouse strains, 41 BXD recombinant inbred and 36 mouse diversity panel (MDP) strains. Cis-eQTL, loci in which the transcript and its maximum QTL are co-located, have been shown to be more reproducible than trans-eQTL, which are not co-located with the transcript. We observed that 9.9% of cis-eQTL and 2.0% of trans-eQTL replicated between the two panels. Notably, a significant eQTL hotspot on distal chromosome 12 observed in the BXD panel was reproduced in the MDP. Furthermore, the shorter linkage disequilibrium in the MDP strains allowed us to considerably narrow the locus and limit the number of candidate genes to a cluster of Serpin genes, which code for extracellular proteases. We conclude that this strategy has some utility in increasing confidence and resolution in eQTL mapping studies; however, due to the high false positive rate in the MDP, eQTL mapping in inbred strains is best carried out in combination with an eQTL linkage study.
Dissonant heritage and memory wars: communication battles on Facebook
Creators: name: Armakauskaite, Donata
Publisher: name: Zenodo
Year: 2023
Subjects: Dissonant heritage, soviet period, monument, public space, memory actyvism

description: After the restoration of independence, a wave of destruction of Soviet period monuments passed. Nevertheless, even after three decades, some public spaces, heritage objects and memory sights are still discussed. Cultural heritage objects, especially the ones related to the traumatic and difficult past, become objects for discussions in media and social networks. In some cases, debates on social networks are ruthless and turn into arguments that can be named “memory wars”. The subject of this study is the discussions on Facebook related to heritage sites, urban areas, public places and institutions of memory, which are subject to mixed interpretations, and the participants of these discussions. The research aims to extract the main narratives echoed by the participants of the "memory wars" and to understand and reveal the identity formed by the participants of the discussions in the social networks through these narratives.
Additional file 5 of Comparison of catastrophic out-of-pocket medical expenditure among older adults in the United States and South Korea: what affects the apparent difference?
Creators: name: Kim, Narae
name: Jacobson, Mireille
Publisher: name: figshare
Year: 2022
Subjects: Medicine
Science Policy
Computational Biology

description: Additional file 5: Table 3. US-South Korea Decomposition with Health Conditions Variables for Probability of Being Exposed to Catastrophic Out-of-Pocket Medical Expenditure.
MIGHTEE-\HI: Possible interactions with the galaxy NGC~895
Creators: name: Namumba, Brenda
name: Román, Javier
name: Barroso, Jesus Falcon
name: Knapen, Johan H.
name: Roger, Ianjamasimanana
name: Naluminsa, Elizabeth
name: Jozsa, Gyula I. G.
name: Korsaga, Marie
name: Maddox, Natasha
name: Frank, Brad
name: Sikhosana, Sinenhlanhla
name: Legodi, Samuel
name: Carignan, Claude
name: Ponomareva, Anastasia A.
name: Jarrett, Tom
name: Lucero, Danielle
name: Smirnov, Oleg M.
name: van der Hulst, Thijs
name: Pisano, D. J.
name: Malek, kasia
name: Marchetti, Lucia
name: Vaccari, Mattia
name: Jarvis, Matt
name: Baes, Maarten
name: Meyer, Martin
name: Adams, Elizabeth A. K.
name: Delhaize, Jacinta
name: Chen, Hao
name: Rajohnson, Sambatriniaina
name: Kurapati, Sushma
name: Heywood, Ian
name: Verdes-Montenegro, Lourdes
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The transformation and evolution of a galaxy is strongly influenced by interactions with its environment. Neutral hydrogen (\HI) is an excellent way to trace these interactions. Here, we present \HI\ observations of the spiral galaxy NGC~895, which was previously thought to be isolated. High-sensitivity \HI\ observations from the MeerKAT large survey project MIGHTEE reveal possible interaction features, such as extended spiral arms, and the two newly discovered \HI\ companions, that drive us to change the narrative that it is an isolated galaxy. We combine these observations with deep optical images from the Hyper Suprime Camera to show an absence of tidal debris between NGC 895 and its companions. We do find an excess of light in the outer parts of the companion galaxy MGTH$\_$J022138.1-052631 which could be an indication of external perturbation and thus possible sign of interactions. Our analysis shows that NGC~895 is an actively star-forming galaxy with a SFR of $\mathrm{1.75 \pm 0.09 [M_{\odot}/yr]}$, a value typical for high stellar mass galaxies on the star forming main sequence. It is reasonable to state that different mechanisms may have contributed to the observed features in NGC~895 and this emphasizes the need to revisit the target with more detailed observations. Our work shows the high potential and synergy of using state-of-the-art data in both \HI\ and optical to reveal a more complete picture of galaxy environments.
description: 14 pages, 10 figures. Accepted for publication in MNRAS
A rigorous numerical method for the optimal design of binary gratings
Creators: name: Elschner, Johannes
name: Schmidt, Gunther
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: Diffraction problems
subject: Helmholtz equation
subject: transmission problem
subject: strongly elliptic variational formulation
subject: generalized FEM
subject: gradient methods
subject: 78-05
subject: 78A45
subject: 35J20
subject: 65N30
subject: 49J20

description: In this paper we describe recent developments in the application of mathematical and computational techniques to the problem of designing binary gratings on top of a multilayer stack in such a way that the propagating modes have a specified intensity or phase pattern for a chosen range of wavelengths or incidence angles. This optimal design problem is solved by a minimization algorithm based on gradient descent, the exact calculation of gradients of certain functionals with respect to the parameters of the grating profile and the thickness of the layers. For the computation of diffraction efficiencies and of the gradients we use a reliable finite element method which originates from variational formulations of the diffraction problems. We provide several numerical examples including polarisation gratings and beam splitters to demonstrate the efficiency of the algorithm.
The gastrointestinal microbiome: a malleable, third genome of mammals
Creators: name: Threadgill, Deborah S.
name: Carroll, Ian M.
name: Threadgill, David W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The nonpathogenic, mutualistic bacteria of the mammalian gastrointestinal tract provide a number of benefits to the host. Recent reports have shown how the aggregate genomes of gastrointestinal bacteria provide novel benefits by functioning as the third major genome in mammals along with the nuclear and mitochondrial genomes. Consequently, efforts are underway to elucidate the complexity of the organisms comprising the unique ecosystem of the gastrointestinal tract, as well as those associated with other epidermal surfaces. The current knowledge of the gastrointestinal microbiome, its relationship to human health and disease with a particular focus on mammalian physiology, and efforts to alter its composition as a novel therapeutic approach are reviewed.
A model of factors controlling orthophosphate removal in planted vertical flow wetlands
Creators: name: Lantzke, I. R
name: Mitchell, D. S
name: Heritage, A. D
name: Sharma, K. P
Publisher: name: La Trobe
Year: 2023

description: La Trobe University Faculty of Science, Technology and Engineering Murray Darling Freshwater Research Centre

MDFRC item.

Orthophosphate removal from wastewater by planted vertical-flow wetlands (VFWs) occurs through three parallel paths, with reaction rates of: sorption to substratum>biofilm assimilationmacrophyte uptake. Short term (one or two loadings) plant removal of phosphorus (P) is small but irreversible, whereas P removed by substratum sorption, or non-reactive P (NRP) formation, can be returned as reactive phosphorus (RP). The quantity of P removed by the three paths is substratum>macrophyte biofilm, in the short term, but macrophyte>substratumbiofilm, over months. Rhizosphere hydrology restricts P removal, the rate is limited by mass transfer without liquid mixing, but trebled by mixing. Evapotranspirational mixing alone is small and erratic. In small, above-ground, systems environmental temperature changes cause daily mixing, but prevailing soil temperature gradients limit below-ground mixing. A planted wetland, conceptual model, explains: (1) retention times: determined by initial RP removal rates, and operationally dependent on RP concentration and mixing. Aqueous phase cycling reduces retention times several fold; (2) minimum outflow concentrations: controlled by the gravel–PO4 sorption equilibrium; (3) sustainable annual P removal: the quantity harvested in the macrophytes. Substratum Fe(III) oxide–hydroxide sorption provides additional assimilation for some years. Specific, model derived, VFW design and operation recommendations are made.
Recommended nomenclature for five mammalian carboxylesterase gene families: human, mouse, and rat genes and proteins
Creators: name: Yokoi, Tsuyoshi
name: Holmes, Roger S.
name: Imai, Teruko
name: Perkins, Everett J.
name: Potter, Phillip M.
name: Yan, Bingfan
name: Hosokawa, Masakiyo
name: Yamashita, Tetsuro
name: Redinbo, Matthew R.
name: Zechner, Rudolf
name: Robert, Jacques
name: Ishibashi, Shun
name: Laulederkind, Stanley J. F.
name: Satoh, Tetsuo
name: Lehner, Richard
name: Wright, Matthew W.
name: Cox, Laura A.
name: Maltais, Lois J.
name: Miyazaki, Masao
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Mammalian carboxylesterase (CES or Ces) genes encode enzymes that participate in xenobiotic, drug, and lipid metabolism in the body and are members of at least five gene families. Tandem duplications have added more genes for some families, particularly for mouse and rat genomes, which has caused confusion in naming rodent Ces genes. This article describes a new nomenclature system for human, mouse, and rat carboxylesterase genes that identifies homolog gene families and allocates a unique name for each gene. The guidelines of human, mouse, and rat gene nomenclature committees were followed and “CES” (human) and “Ces” (mouse and rat) root symbols were used followed by the family number (e.g., human CES1). Where multiple genes were identified for a family or where a clash occurred with an existing gene name, a letter was added (e.g., human CES4A; mouse and rat Ces1a) that reflected gene relatedness among rodent species (e.g., mouse and rat Ces1a). Pseudogenes were named by adding “P” and a number to the human gene name (e.g., human CES1P1) or by using a new letter followed by ps for mouse and rat Ces pseudogenes (e.g., Ces2d-ps). Gene transcript isoforms were named by adding the GenBank accession ID to the gene symbol (e.g., human CES1_AB119995 or mouse Ces1e_BC019208). This nomenclature improves our understanding of human, mouse, and rat CES/Ces gene families and facilitates research into the structure, function, and evolution of these gene families. It also serves as a model for naming CES genes from other mammalian species.
Apparent bioaccumulation of Mn derived from paper-mill effluent by the freshwater crayfish Cherax destructor — the role of Mn oxidising bacteria
Creators: name: King, H. M
name: Baldwin, D. S
name: Rees, G. N
name: McDonald, S
Publisher: name: La Trobe
Year: 2023

description: La Trobe University Faculty of Science, Technology and Engineering Murray Darling Freshwater Research Centre

MDFRC item.

Bioaccumulation studies of wastewater from a thermo-mechanical paper mill using the freshwater crayfish (Cherax destructor) consistently demonstrated elevated levels of manganese. Most of the Mn appeared to be associated with the carapace of the animals. It is suggested that the elevated Mn levels are the result of Mn-oxidising bacteria forming biofilms on the carapace of the crayfish followed by Mn oxide precipitation rather than active uptake of Mn by the crayfish.
The probability approach to numerical solution of nonlinear parabolic equations
Creators: name: Milstein, Grigori N.
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: semilinear parabolicequations
subject: reaction-diffusion systems
subject: probabilistic representations for equations of mathematical physics
subject: weak approximation of solutions of stochastic differential equations
subject: 60H10
subject: 60H30
subject: 65M99

description: A number of new layer methods for solving semilinear parabolic equations and reaction-diffusion systems is derived by using probabilistic representations of their solutions. These methods exploit the ideas of weak sense numerical integration of stochastic differential equations. In spite of the probabilistic nature these methods are nevertheless deterministic. A convergence theorem is proved. Some numerical tests are presented.
Genetic determinants for intramuscular fat content and water-holding capacity in mice selected for high muscle mass
Creators: name: Brockmann, Gudrun A.
name: Schmitt, Armin O.
name: Cheng, Riyan
name: Kärst, Stefan
name: de Villena, Fernando Pardo Manuel
name: Yang, Hyuna
name: Palmer, Abraham A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Intramuscular fat content and water-holding capacity are important traits in livestock as they influence meat quality, nutritive value of the muscle, and animal health. As a model for livestock, two inbred lines of the Berlin Muscle Mouse population, which had been long-term selected for high muscle mass, were used to identify genomic regions affecting intramuscular fat content and water-holding capacity. The intramuscular fat content of the Musculus longissimus was on average 1.4 times higher in BMMI806 than in BMMI816 mice. This was accompanied by a 1.5 times lower water-holding capacity of the Musculus quadriceps in BMMI816 mice. Linkage analyses with 332 G3 animals of reciprocal crosses between these two lines revealed quantitative trait loci for intramuscular fat content on chromosome 7 and for water-holding capacity on chromosome 2. In part, the identified loci coincide with syntenic regions in pigs in which genetic effects for the same traits were found. Therefore, these muscle-weight-selected mouse lines and the produced intercross populations are valuable genetic resources to identify genes that could also contribute to meat quality in other species.
Canine models of Duchenne muscular dystrophy and their use in therapeutic strategies
Creators: name: Kornegay, Joe N.
name: Hoffman, Eric P.
name: Childers, Martin K.
name: Styner, Martin A.
name: Wang, Jiahui
name: Larsen, C. Aaron
name: Detwiler, David A.
name: Fan, Zheng
name: Tou, Sandra
name: Flanigan, Kevin M.
name: Nghiem, Peter
name: Howard, James F.
name: Li, Juan
name: Xiao, Xiao
name: Bhavaraju-Sanka, Ratna K.
name: Bogan, Janet R.
name: Schatzberg, Scott J.
name: Keene, Bruce P.
name: Grange, Robert W.
name: Bogan, Daniel J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder in which the loss of dystrophin causes progressive degeneration of skeletal and cardiac muscle. Potential therapies that carry substantial risk, such as gene and cell-based approaches, must first be tested in animal models, notably the mdx mouse and several dystrophin-deficient breeds of dogs, including golden retriever muscular dystrophy (GRMD). Affected dogs have a more severe phenotype, in keeping with that of DMD, so may better predict disease pathogenesis and treatment efficacy. We and others have developed various phenotypic tests to characterize disease progression in the GRMD model. These biomarkers range from measures of strength and joint contractures to magnetic resonance imaging. Some of these tests are routinely used in clinical veterinary practice, while others require specialized equipment and expertise. By comparing serial measurements from treated and untreated groups, one can document improvement or delayed progression of disease. Potential treatments for DMD may be broadly categorized as molecular, cellular, or pharmacologic. The GRMD model has increasingly been used to assess efficacy of a range of these therapies. While some of these studies have largely provided general proof-of-concept for the treatment under study, others have demonstrated efficacy using the biomarkers discussed. Importantly, just as symptoms in DMD vary among patients, GRMD dogs display remarkable phenotypic variation. While confounding statistical analysis in preclinical trials, this variation offers insight regarding the role that modifier genes play in disease pathogenesis. By correlating functional and mRNA profiling results, gene targets for therapy development can be identified.
Centralized mouse repositories
Creators: name: Lloyd, K. C. Kent
name: Donahue, Leah Rae
name: Obata, Yuichi
name: Magnuson, Terry
name: Davisson, Muriel T.
name: Hörlein, Andreas
name: Read, Stuart
name: Hagn, Michael
name: Franklin, Craig
name: Hrabe de Angelis, Martin
name: Wurst, Wolfgang
name: McKerlie, Colin
name: Nakagata, Naomi
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Because the mouse is used so widely for biomedical research and the number of mouse models being generated is increasing rapidly, centralized repositories are essential if the valuable mouse strains and models that have been developed are to be securely preserved and fully exploited. Ensuring the ongoing availability of these mouse strains preserves the investment made in creating and characterizing them and creates a global resource of enormous value. The establishment of centralized mouse repositories around the world for distributing and archiving these resources has provided critical access to and preservation of these strains. This article describes the common and specialized activities provided by major mouse repositories around the world.
Velocity measurement in the extensive [OIII] emission region 1.2° south-east of M31
Creators: name: Amram, P.
name: Adami, C.
name: Epinat, B.
name: Chemin, L.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The discovery of a broad, $\sim$1.5$^{\circ}$ long filamentary [OIII] 5007 emission $\sim$1.2$^{\circ}$ south-east of the M31 nucleus has recently been reported. More than 100 hours of exposures of a wide field (3.48$^{\circ} \times 2.32^{\circ}$) have allowed this pioneering detection based on 30 Å narrow-band filters and several small refractors equipped with large cameras. We report a first velocity measurement in this extensive [OIII] emission line region. We used the low-resolution spectrograph MISTRAL (R $\sim$ 750), a facility of the Haute-Provence Observatory 193 cm telescope. The velocity measurement is based on the H$α$, [NII], [SII] and [OIII] lines. The best solution to fit the spectrum indicates that the H$α$ and [OIII] emissions are at the same heliocentric line-of-sight velocity of -96$\pm$4 km s$^{-1}$. This was measured within an area of $\sim$250 arcsec$^2$ selected on a bright knot along the long filament of $\sim$1.5$^{\circ}$, together with a [OIII]5007 surface brightness of 4.2$\pm$2.1 10$^{-17}$ erg s$^{-1}$ cm$^{-2}$ arcsec$^{-2}$. This agrees moderately well with the previous measurement. We also estimated the H$α$/[NII] line ratio as $\sim$1.1. The radial velocities at which the H$α$ and [OIII] lines were detected seem to show that these hydrogen and oxygen atoms belong to the same layer, but we cannot exclude that another weaker [OIII] line, belonging to another structure, that is, at another velocity, is below our detection threshold. Different scenarios have been considered to explain this filamentary structure...
description: 8 pages, 5 figures, A&A letters, Accepted
Combined gene dosage requirement for SWI/SNF catalytic subunits during early mammalian development
Creators: name: Bultman, Scott J.
name: Smith-Roe, Stephanie L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Mammalian SWI/SNF complexes utilize either BRG1 or BRM as alternative catalytic subunits with DNA-dependent ATPase activity to remodel chromatin. Although the two proteins are 75% identical, broadly expressed, and have similar biochemical activities in vitro, BRG1 is essential for mouse embryonic development, while BRM is dispensable. To investigate whether BRG1 and BRM have overlapping functions during mouse embryogenesis, we performed double-heterozygous intercrosses using constitutive null mutations previously created by gene targeting. The progeny of these crosses had a distribution of genotypes that was significantly skewed relative to their combined gene dosage. This was most pronounced at the top and bottom of the gene dosage hierarchy with a 1.5-fold overrepresentation of Brg1+/+;Brm+/+ mice and a corresponding 1.6-fold underrepresentation of Brg1+/−;Brm−/− mice. To account for the underrepresentation of Brg1+/−;Brm−/− mice, timed matings and blastocyst outgrowth assays demonstrated that ~50% of these embryos failed to develop beyond the peri-implantation stage. These results challenge the idea that BRG1 is the exclusive catalytic subunit of SWI/SNF complexes in ES cells and suggest that BRM also interacts with the pluripotency transcription factors to facilitate self-renewal of the inner cell mass. In contrast to implantation, the Brm genotype did not influence an exencephaly phenotype that arises because of Brg1 haploinsufficiency during neural tube closure and that results in peri-natal lethality. Taken together, these results support the idea that BRG1 and BRM have overlapping functions for certain developmental processes but not others during embryogenesis.
On estimating a dynamic function of stochastic system with averaging
Creators: name: Liptser, Robert
name: Spokoiny, Vladimir
Publisher: name: Weierstrass Institute
Year: 1997
Subjects: subject: fast and slow components
subject: drift and diffusion coefficients
subject: ergodic property
subject: nonparametric estimation
subject: bandwidth selection
subject: 62G05
subject: 62M99

description: We consider a two-scaled diffusion system, when drift and diffusion parameters of a "slow" component are contaminated by an unobservable "fast" one. The goal is to estimate the dynamic function which is defined by averaging the drift coefficient of the "slow" component w.r.t. the stationary distribution of the "fast" one. For estimation we use a locally linear smoother with a data-driven choice of bandwidth. A procedure proposed is fully adaptive and nearly optimal up to a log log factor.
Ising quantum Hall ferromagnetism in Landau levels $\left\vert N\right\vert \geq 1$ of bilayer graphene
Creators: name: Luo, Wenchen
name: Côté, R.
name: Bédard-Vallée, Alexandre
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: A magnetic field applied perpendicularly to the chiral two-dimensional electron gas (C2DEG)\ in a Bernal-stacked bilayer graphene quantizes the kinetic energy into a discrete set of Landau levels $N=0,\pm 1,\pm 2,...$ While Landau level $N=0$ is eighfold degenerate, higher Landau levels ($ \left\vert N\right\vert \geq 1$) are fourfold degenerate when counting spin and valley degrees of freedom. In this work, the Hartree-Fock approximation is used to study the phase diagram of the C2DEG at integer fillings $ \widetilde{ν}=1,2,3$ of these higher Landau levels. At these filling factors, the C2DEG is a valley or spin Ising quantum Hall ferromagnet. At odd fillings, the C2DEG is spin polarized and has all its electrons in one valley or the other. There is no intervalley coherence in contrast with most of the the ground states in Landau level $N=0.$ At even filling, $\widetilde{ν}=2,$ the C2DEG is either fully spin polarized with electrons occupying both valleys or spin unpolarized with electron occupying one of the two valleys. A finite electric field (or bias) applied perpendicularly to the plane of the C2DEG induces a series of first-order phase transitions between these different ground states. The transport gap or its slope is discontinuous at the bias where a transition occurs. Such discontinuity may result in a change in the transport properties of the C2DEG at that bias.
description: 14 pages with 12 eps figures
Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse
Creators: name: de Villena, Fernando Pardo-Manuel
name: Didion, John P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: The laboratory mouse is an artificial construct with a complex relationship to its natural ancestors. In 2002, the mouse became the first mammalian model organism with a reference genome. Importantly, the mouse genome sequence was assembled from data on a single inbred laboratory strain, C57BL/6. Several large-scale genetic variant discovery efforts have been conducted, resulting in a catalog of tens of millions of SNPs and structural variants. High-density genotyping arrays covering a subset of those variants have been used to produce hundreds of millions of genotypes in laboratory stocks and a small number of wild mice. These landmark resources now enable us to determine relationships among laboratory mice, assign local ancestry at fine scale, resolve important controversies, and identify a new set of challenges—most importantly, the troubling scarcity of genetic data on the very natural populations from which the laboratory mouse was derived. Our aim with this review is to provide the reader with an historical context for the mouse as a model organism and to explain how practical decisions made in the past have influenced both the architecture of the laboratory mouse genome and the design and execution of current large-scale resources. We also provide examples on how the accomplishments of the past decade can be used by researchers to streamline the use of mice in their experiments and correctly interpret results. Finally, we propose future steps that will enable the mouse community to extend its successes in the decade to come.