cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The parallel replica method for computing equilibrium averages of Markov chains
Creators: name: Aristoff, David
Publisher: name: arXiv
Year: 2015
Subjects: subject: Numerical Analysis (math.NA)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 65C05, 65C20, 65C40, 60J22, 65Y05

description: An algorithm is proposed for computing equilibrium averages of Markov chains which suffer from metastability -- the tendency to remain in one or more subsets of state space for long time intervals. The algorithm, called the parallel replica method (or ParRep), uses many parallel processors to explore these subsets more efficiently. Numerical simulations on a simple model demonstrate consistency of the method. A proof of consistency is given in an idealized setting. The parallel replica method can be considered a generalization of A.F. Voter's parallel replica dynamics, originally developed to efficiently simulate metastable Langevin stochastic dynamics.
description: 25 pages, 7 figures
CROR: Coding-Aware Opportunistic Routing in Multi-Channel Cognitive Radio Networks
Creators: name: Zhong, Xiaoxiong
name: Qin, Yang
name: Yang, Yuanyuan
name: Li, Li
Publisher: name: arXiv
Year: 2015
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: Cognitive radio (CR) is a promising technology to improve spectrum utilization. However, spectrum availability is uncertain which mainly depends on primary user's (PU's) behaviors. This makes it more difficult for most existing CR routing protocols to achieve high throughput in multi-channel cognitive radio networks (CRNs). Inter-session network coding and opportunistic routing can leverage the broadcast nature of the wireless channel to improve the performance for CRNs. In this paper we present a coding aware opportunistic routing protocol for multi-channel CRNs, cognitive radio opportunistic routing (CROR) protocol, which jointly considers the probability of successful spectrum utilization, packet loss rate, and coding opportunities. We evaluate and compare the proposed scheme against three other opportunistic routing protocols with multichannel. It is shown that the CROR, by integrating opportunistic routing with network coding, can obtain much better results, with respect to throughput, the probability of PU-SU packet collision and spectrum utilization efficiency.
description: 6 pages, 8 figures, to appear in Proc. of IEEE GlobeCom 2014
MALT-45: A 7 mm survey of the southern Galaxy - I. Techniques and spectral line data
Creators: name: Jordan, Christopher H.
name: Walsh, Andrew J.
name: Lowe, Vicki
name: Voronkov, Maxim A.
name: Ellingsen, Simon P.
name: Breen, Shari L.
name: Purcell, Cormac R.
name: Barnes, Peter J.
name: Burton, Michael G.
name: Cunningham, Maria R.
name: Hill, Tracey
name: Jackson, James M.
name: Longmore, Steven N.
name: Peretto, Nicolas
name: Urquhart, James S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present the first results from the MALT-45 (Millimetre Astronomer's Legacy Team - 45 GHz) Galactic Plane survey. We have observed 5 square-degrees ($l = 330 - 335$, $b = \pm0.5$) for spectral lines in the 7 mm band (42-44 and 48-49 GHz), including $\text{CS}$ $(1-0)$, class I $\text{CH}_3\text{OH}$ masers in the $7(0,7)-6(1,6)$ $\text{A}^{+}$ transition and $\text{SiO}$ $(1-0)$ $v=0,1,2,3$. MALT-45 is the first unbiased, large-scale, sensitive spectral line survey in this frequency range. In this paper, we present data from the survey as well as a few intriguing results; rigorous analyses of these science cases are reserved for future publications. Across the survey region, we detected 77 class I $\text{CH}_3\text{OH}$ masers, of which 58 are new detections, along with many sites of thermal and maser $\text{SiO}$ emission and thermal $\text{CS}$. We found that 35 class I $\text{CH}_3\text{OH}$ masers were associated with the published locations of class II $\text{CH}_3\text{OH}$, $\text{H}_2\text{O}$ and $\text{OH}$ masers but 42 have no known masers within 60 arcsec. We compared the MALT-45 $\text{CS}$ with $\text{NH}_3$ (1,1) to reveal regions of $\text{CS}$ depletion and high opacity, as well as evolved star-forming regions with a high ratio of $\text{CS}$ to $\text{NH}_3$. All $\text{SiO}$ masers are new detections, and appear to be associated with evolved stars from the $\it{Spitzer}$ Galactic Legacy Infrared Mid-Plane Survey Extraordinaire (GLIMPSE). Generally, within $\text{SiO}$ regions of multiple vibrational modes, the intensity decreases as $v=1,2,3$, but there are a few exceptions where $v=2$ is stronger than $v=1$.
description: Accepted by Monthly Notices of the Royal Astronomical Society on 2015 January 23. Appendices will be published with MNRAS
Qualitative and analytical results of the bifurcation thresholds to halo orbits
Creators: name: Bucciarelli, Sara
name: Ceccaroni, Marta
name: Celletti, Alessandra
name: Pucacco, Giuseppe
Publisher: name: arXiv
Year: 2015
Subjects: subject: Dynamical Systems (math.DS)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 37N05, 70F15, 37L10

description: We study the dynamics in the neighborhood of the collinear Lagrangian points in the spatial, circular, restricted three--body problem. We consider the case in which one of the primaries is a radiating body and the other is oblate (although the latter is a minor effect). Beside having an intrinsic mathematical interest, this model is particularly suited for the description of a mission of a spacecraft (e.g., a solar sail) to an asteroid. The aim of our study is to investigate the occurrence of bifurcations to halo orbits, which take place as the energy level is varied. The estimate of the bifurcation thresholds is performed by analytical and numerical methods: we find a remarkable agreement between the two approaches. As a side result, we also evaluate the influence of the different parameters, most notably the solar radiation pressure coefficient, on the dynamical behavior of the model. To perform the analytical and numerical computations, we start by implementing a center manifold reduction. Next, we estimate the bifurcation values using qualitative techniques (e.g. Poincaré surfaces, frequency analysis, FLIs). Concerning the analytical approach, following \cite{CPS} we implement a resonant normal form, we transform to suitable action-angle variables and we introduce a detuning parameter measuring the displacement from the synchronous resonance. The bifurcation thresholds are then determined as series expansions in the detuning. Three concrete examples are considered and we find in all cases a very good agreement between the analytical and numerical results.
3D Human Activity Recognition with Reconfigurable Convolutional Neural Networks
Creators: name: Wang, Keze
name: Wang, Xiaolong
name: Lin, Liang
name: Wang, Meng
name: Zuo, Wangmeng
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences
subject: I.4
subject: 68U01

description: Human activity understanding with 3D/depth sensors has received increasing attention in multimedia processing and interactions. This work targets on developing a novel deep model for automatic activity recognition from RGB-D videos. We represent each human activity as an ensemble of cubic-like video segments, and learn to discover the temporal structures for a category of activities, i.e. how the activities to be decomposed in terms of classification. Our model can be regarded as a structured deep architecture, as it extends the convolutional neural networks (CNNs) by incorporating structure alternatives. Specifically, we build the network consisting of 3D convolutions and max-pooling operators over the video segments, and introduce the latent variables in each convolutional layer manipulating the activation of neurons. Our model thus advances existing approaches in two aspects: (i) it acts directly on the raw inputs (grayscale-depth data) to conduct recognition instead of relying on hand-crafted features, and (ii) the model structure can be dynamically adjusted accounting for the temporal variations of human activities, i.e. the network configuration is allowed to be partially activated during inference. For model training, we propose an EM-type optimization method that iteratively (i) discovers the latent structure by determining the decomposed actions for each training example, and (ii) learns the network parameters by using the back-propagation algorithm. Our approach is validated in challenging scenarios, and outperforms state-of-the-art methods. A large human activity database of RGB-D videos is presented in addition.
description: This manuscript has 10 pages with 9 figures, and a preliminary version was published in ACM MM'14 conference
A Germline Clone Screen on the X Chromosome Reveals Novel Meiotic Mutants in Drosophila melanogaster
Creators: name: McClurken, Cailey M.
name: Kohl, Kathryn P.
name: Callicoat, Jonathon G.
name: Hawley, R. Scott
name: Lake, Cathleen M.
name: Collins, Kimberly A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: In an effort to isolate novel meiotic mutants that are severely defective in chromosome segregation and/or exchange, we employed a germline clone screen of the X chromosome of Drosophila melanogaster. We screened over 120,000 EMS-mutagenized chromosomes and isolated 19 mutants, which comprised nine complementation groups. Four of these complementation groups mapped to known meiotic genes, including mei-217, mei-218, mei-9, and nod. Importantly, we have identified two novel complementation groups with strong meiotic phenotypes, as assayed by X chromosome nondisjunction. One complementation group is defined by three alleles, and the second novel complementation group is defined by a single allele. All 19 mutants are homozygous viable, fertile, and fully recessive. Of the 9 mutants that have been molecularly characterized, 5 are canonical EMS-induced transitions, and the remaining 4 are transversions. In sum, we have identified two new genes that are defined by novel meiotic mutants, in addition to isolating new alleles of mei-217, mei-218, mei-9, and nod.
Accelerating the Inbreeding of Multi-Parental Recombinant Inbred Lines Generated By Sibling Matings
Creators: name: McMillan, Leonard
name: Welsh, Catherine E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Inbred model organisms are powerful tools for genetic studies because they provide reproducible genomes for use in mapping and genetic manipulation. Generating inbred lines via sibling matings, however, is a costly undertaking that requires many successive generations of breeding, during which time many lines fail. We evaluated several approaches for accelerating inbreeding, including the systematic use of back-crosses and marker-assisted breeder selection, which we contrasted with randomized sib-matings. Using simulations, we explored several alternative breeder-selection methods and monitored the gain and loss of genetic diversity, measured by the number of recombination-induced founder intervals, as a function of generation. For each approach we simulated 100,000 independent lines to estimate distributions of generations to achieve full-fixation as well as to achieve a mean heterozygosity level equal to 20 generations of randomized sib-mating. Our analyses suggest that the number of generations to fully inbred status can be substantially reduced with minimal impact on genetic diversity through combinations of parental backcrossing and marker-assisted inbreeding. Although simulations do not consider all confounding factors underlying the inbreeding process, such as a loss of fecundity, our models suggest many viable alternatives for accelerating the inbreeding process.
Rescattering effects in laser-assisted electron-atom bremsstrahlung
Creators: name: Zheltukhin, A. N.
name: Flegel, A. V.
name: Frolov, M. V.
name: Manakov, N. L.
name: Starace, Anthony F.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Rescattering effects in nonresonant spontaneous laser-assisted electron-atom bremsstrahlung (LABrS) are analyzed within the framework of time-dependent effective-range (TDER) theory. It is shown that high energy LABrS spectra exhibit rescattering plateau structures that are similar to those that are well-known in strong field laser-induced processes as well as those that have been predicted theoretically in laser-assisted collision processes. In the limit of a low-frequency laser field, an analytic description of LABrS is obtained from a rigorous quantum analysis of the exact TDER results for the LABrS amplitude. This amplitude is represented as a sum of factorized terms involving three factors, each having a clear physical meaning. The first two factors are the exact field-free amplitudes for electron-atom bremsstrahlung and for electron-atom scattering, and the third factor describes free electron motion in the laser field along a closed trajectory between the first (scattering) and second (rescattering) collision events. Finally, a generalization of these TDER results to the case of LABrS in a Coulomb field is discussed.
Differentiation-Driven Nucleolar Association of the Mouse Imprinted Kcnq1 Locus
Creators: name: Calabrese, J. Mauro
name: Magnuson, Terry
name: Fedoriw, Andrew M.
name: Mu, Weipeng
name: Yee, Della
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The organization of the genome within the mammalian nucleus is nonrandom, with physiologic processes often concentrated in specific three-dimensional domains. This organization may be functionally related to gene regulation and, as such, may play a role in normal development and human disease processes. However, the mechanisms that participate in nuclear organization are poorly understood. Here, we present data characterizing localization of the imprinted Kcnq1 alleles. We show that nucleolar association of the paternal allele (1) is stimulated during the differentiation of trophoblast stem cells, (ii) is dependent upon the Kcnq1ot1 noncoding RNA, (3) does not require polycomb repressive complex 2, and (4) is not sufficient to preclude transcription of imprinted genes. Although nucleolar positioning has been proposed as a mechanism to related to gene silencing, we find that silencing and perinucleolar localization through the Kcnq1ot1 noncoding RNA are separable events.
Investment in U.S. Public Agricultural Research and Development Has Fallen by a Third Over Past Two Decades, Lags Major Trade Competitors
Creators: name: Nelson, Kelly
name: Fuglie, Keith
name: Nelson, Kelly
name: Fuglie, Keith
Publisher: name: Unknown
Year: 2022

description: In the United States, public agricultural research and development (R&D), which includes any agricultural R&D conducted at universities or Government laboratories regardless of funding source, is supported through Federal-State partnerships. These partnerships provide an important complement to business R&D, providing scientific and technological innovations that raise U.S. agri-food system productivity.
Expression Quantitative Trait Loci for Extreme Host Response to Influenza A in Pre-Collaborative Cross Mice
Creators: name: Aylor, David L.
name: Bottomly, Daniel
name: Rosenzweig, Elizabeth
name: Haagmans, Bart L.
name: Bradel-Tretheway, Birgit G.
name: Ferris, Martin T.
name: McWeeney, Shannon K.
name: de Villena, Fernando Pardo-Manuel
name: Threadgill, David W.
name: Katze, Michael G.
name: Aicher, Lauri D.
name: Bryan, Janine T.
name: Gralinski, Lisa E.
name: Whitmore, Alan
name: Baric, Ralph S.
name: Heise, Mark
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Outbreaks of influenza occur on a yearly basis, causing a wide range of symptoms across the human population. Although evidence exists that the host response to influenza infection is influenced by genetic differences in the host, this has not been studied in a system with genetic diversity mirroring that of the human population. Here we used mice from 44 influenza-infected pre-Collaborative Cross lines determined to have extreme phenotypes with regard to the host response to influenza A virus infection. Global transcriptome profiling identified 2671 transcripts that were significantly differentially expressed between mice that showed a severe (“high”) and mild (“low”) response to infection. Expression quantitative trait loci mapping was performed on those transcripts that were differentially expressed because of differences in host response phenotype to identify putative regulatory regions potentially controlling their expression. Twenty-one significant expression quantitative trait loci were identified, which allowed direct examination of genes associated with regulation of host response to infection. To perform initial validation of our findings, quantitative polymerase chain reaction was performed in the infected founder strains, and we were able to confirm or partially confirm more than 70% of those tested. In addition, we explored putative causal and reactive (downstream) relationships between the significantly regulated genes and others in the high or low response groups using structural equation modeling. By using systems approaches and a genetically diverse population, we were able to develop a novel framework for identifying the underlying biological subnetworks under host genetic control during influenza virus infection.
title: The banker's duty of confidentiality
Creators: name: Anthony. Stokes, Robert
Publisher: name: University of Liverpool Repository
Year: 2023

description: The scheme of doctoral research is concerned with the banker's duty of confidentiality, something traditionally recognized as forming the cornerstone of the banker-client relationship. However, the law relating to banking confidentiality has undergone an active period of reform since the judicial recognition of such a duty. Indeed, the duty (or perhaps more accurately, the exceptions to the duty) has developed through retrospective incremental reforms, facilitated through both judicial decisions and through statute. The aim of the research is to analyse and explore the existing law, looking particularly at the development of the relevant practice and law, and consider whether it is true to suggest confidentiality is the exception rather than the rule. In order to successfully ground the importance of this scheme of research in the modern banking climate, the genesis and early development of the duty of confidentiality shall be analysed, before considering the development of the obligation through the Twentieth Century. Consequently, this study will concentrate upon the establishment of the duty of confidentiality through the decision in Tournier v. National Provincial and Union Bank of England1 , and consider the four heads of exception that Bankes L.J., discussed. The growth of these four heads of exception needs to be analysed, for, as the Jack Committee lamented in their final report, "the last two decades have seen a torrent of new legislation, which has since become a spate in the past few years, requiring or permitting bankers, in a wide range of specified situations, to disclose confidential information in the public interest".2 Since the presentation of the Jack Report this 'spate' has continued, and the scope of the various exceptions to the duty arising from,for example, the Proceeds of Crime Act 2002 (as amended) and the Money Laundering Regulations 2003 will need to be analysed. The thesis will also investigate certain key issues which are currently affecting the scope and nature of the banker's duty of confidentiality, including, the growth of the domestic anti-money laundering regime; the emergence of the criminal confiscation and civil recovery systems and associated investigatory powers and the dawn of the Human Rights Act era coupled with the growth of data protection considerations under the Data Protection Act 1998. These issues, whilst only coming to the fore in recent times, are all likely to play an important role in the future development and direction of the banker's duty of confidentiality, and are as such worthy of academic consideration.
Genetic Analysis of Hematological Parameters in Incipient Lines of the Collaborative Cross
Creators: name: Miller, Darla R.
name: Aylor, David L.
name: Kelada, Samir N. P.
name: Pardo-Manuel de Villena, Fernando
name: Chesler, Elissa J.
name: Collins, Francis S.
name: Threadgill, David W.
name: Tavarez, Urraca
name: Ryan, Joseph F.
name: Churchill, Gary A.
name: Peck, Bailey C. E.
name: Buus, Ryan J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Hematological parameters, including red and white blood cell counts and hemoglobin concentration, are widely used clinical indicators of health and disease. These traits are tightly regulated in healthy individuals and are under genetic control. Mutations in key genes that affect hematological parameters have important phenotypic consequences, including multiple variants that affect susceptibility to malarial disease. However, most variation in hematological traits is continuous and is presumably influenced by multiple loci and variants with small phenotypic effects. We used a newly developed mouse resource population, the Collaborative Cross (CC), to identify genetic determinants of hematological parameters. We surveyed the eight founder strains of the CC and performed a mapping study using 131 incipient lines of the CC. Genome scans identified quantitative trait loci for several hematological parameters, including mean red cell volume (Chr 7 and Chr 14), white blood cell count (Chr 18), percent neutrophils/lymphocytes (Chr 11), and monocyte number (Chr 1). We used evolutionary principles and unique bioinformatics resources to reduce the size of candidate intervals and to view functional variation in the context of phylogeny. Many quantitative trait loci regions could be narrowed sufficiently to identify a small number of promising candidate genes. This approach not only expands our knowledge about hematological traits but also demonstrates the unique ability of the CC to elucidate the genetic architecture of complex traits.
Factors affecting performance in elite finger-spin bowling
Creators: name: Sanders, Liam
Publisher: name: Loughborough University
Year: 2019
Subjects: subject: 119999 Medical and Health Sciences not elsewhere classified
subject: FOS: Other medical sciences

description: Full-body three-dimensional kinematics, passive joint range of motion and bowling parameters from match play were calculated to enable the analysis of elite finger spin bowling technique and delivery mechanics. Specifically, the effect of kinematic parameters and passive joint range of motion contributing to the production of spin were examined whilst ball trajectory parameters in international test match cricket were assessed and the extent to which these parameters may impact match performance. Kinematic and passive range of motion data were collected for a group of 23 elite finger spin bowlers, describing elements of finger spin bowling technique with the effect of these parameters on ball spin rate addressed using linear regression. Ball trajectory data were collected using a Hawk-eyeTM ball tracking system for 36 elite finger spin bowlers competing in international test match cricket between 2006 – 2015. Parameters were calculated describing elements of ball trajectory with the effect of these parameters on bowling average and economy addressed using linear regression. Kinematic analysis suggests the bowlers imparting the most spin adopted a mid-way pelvis orientation angle, a larger pelvis-shoulder separation angle and a shoulder orientation short of side-on at FFC. The orientation of the pelvis at FFC was shown to be the most important technique parameter explaining 43.1% of the variance in ball spin rate. Higher ball spin rates were also associated with a larger internal rotation of the rear hip and bowling shoulder, whilst the total arc of rotation of the non-dominant hip (front leg) was found to be the best predictor of ball spin rate, explaining 26% of the observed variance in spin rate. Side to side differences were also observed with greater external rotation and lesser internal rotation in the bowling shoulder, and greater internal rotation in the non-dominant hip. Linear regressions of bowling parameters in test match competition revealed bowling length, bowing line and release velocity as the biggest predictors of bowling economy, predicting 54.4% of the observed variance. Findings suggest bowlers conceding the least runs released the ball at higher ball release speeds, bowled straight bowling lines and pitched the ball 4 – 5m in length. Whilst no parameters were predictive of bowling average, results indicate that deliveries deviating away from the opposing batsman concede less runs and takes more wickets, when compared to deviating toward.
NERC-EL Guidelines for CEIL dataset
Creators: name: Penagos, Carlos Rodríguez
Publisher: name: Zenodo
Year: 2023

description: Annotation guidelines for NERC-EL CEIL dataset (https://huggingface.co/datasets/projecte-aina/ceil) This work was funded by the Departament de la Vicepresidència i de Polítiques Digitals i Territori de la Generalitat de Catalunya within the framework of Projecte AINA.
description: The dataset resides at: https://huggingface.co/datasets/projecte-aina/ceil This work was funded by the Departament de la Vicepresidència i de Polítiques Digitals i Territori de la Generalitat de Catalunya within the framework of Projecte AINA.
Intranight optical variability of radio-quiet BL Lacertae objects
Creators: name: Liu, Yuan
name: Zhang, Jin
name: Zhang, Shuang Nan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Aims: Intranight variation (or microvariation) is a common phenomenon of radio-loud BL Lac objects. However, it is not clear whether the recently found radio-quiet BL Lac objects have the same properties. The occurrence rate of intranight variation is helpful in distinguishing the mechanism of the continuum of radio-quiet BL Lac objects. Methods: We conducted a photometric monitoring of 8 radio-quiet BL Lac objects by the Xinglong 2.16m and Lijiang 2.4m telescopes. The differential light curves are calculated between each target and two comparison stars. To quantify the variation, the significance of variation is examined by a scaled $F$-test. Results: No significant variation is found in the 11 sessions of light curves of 8 radio-quiet BL Lac objects (one galactic source is excluded). The lack of microvariation in radio-quiet BL Lac objects is consistent with the detection rate of microvariation in normal radio-quiet AGNs, but much lower than for radio-loud AGNs. This result indicates that the continua of the radio-quiet BL Lac objects are not dominated by jets that will induce frequent microvariations.
description: Accepted for publication in Astronomy and Astrophysics; 7 pages, 1 figure, 3 tables
Genome-Wide Association Mapping of Quantitative Traits in Outbred Mice
Creators: name: Churchill, Gary A.
name: Staedtler, Frank
name: Harttman, Nicole
name: Korstanje, Ron
name: Zhang, Weidong
name: Thaisz, Jill
name: Yang, Hyuna
name: Feng, Minjie
name: Xu, Lingfei
name: Valdar, William
name: Yanas, Liane
name: DiPetrillo, Keith
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Recent developments in high-density genotyping and statistical analysis methods that have enabled genome-wide association studies in humans can also be applied to outbred mouse populations. Increased recombination in outbred populations is expected to provide greater mapping resolution than traditional inbred line crosses, improving prospects for identifying the causal genes. We carried out genome-wide association mapping by using 288 mice from a commercially available outbred stock; NMRI mice were genotyped with a high-density single-nucleotide polymorphism array to map loci influencing high-density lipoprotein cholesterol, systolic blood pressure, triglyceride levels, glucose, and urinary albumin-to-creatinine ratios. We found significant associations (P < 10−5) with high-density lipoprotein cholesterol and identified Apoa2 and Scarb1, both of which have been previously reported, as candidate genes for these associations. Additional suggestive associations (P < 10−3) identified in this study were also concordant with published quantitative trait loci, suggesting that we are sampling from a limited pool of genetic diversity that has already been well characterized. These findings dampen our enthusiasm for currently available commercial outbred stocks as genetic mapping resources and highlight the need for new outbred populations with greater genetic diversity. Despite the lack of novel associations in the NMRI population, our analysis strategy illustrates the utility of methods that could be applied to genome-wide association studies in humans.
Cryogenic Gaseous Photomultiplier for Position Reconstruction of Liquid Argon Scintillation Light
Creators: name: Paredes, B. Lopez
name: Azevedo, C. D. R.
name: Paganis, S.
name: Silva, A. L. M.
name: Spooner, N. J. C.
name: Veloso, J. F. C. A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: Presented here are first tests of a Gaseous Photomultiplier based on a cascade of Thick GEM structures intended for gamma-ray position reconstruction in liquid Argon. The detector has a MgF$_2$ window, transparent to VUV light, and a CsI photocathode deposited on the first THGEM. A gain of $8\cdot10^{5}$ per photoelectron and $\sim100\%$ photoelectron collection efficiency are measured at stable operation settings. The excellent position resolution capabilities of the detector (better than 100 $μ$m) at 100 kHz readout rate, is demonstrated at room temperature. Structural integrity tests of the detector and seals are successfully performed at cryogenic temperatures by immersing the detector in liquid Nitrogen, laying a good foundation for future operation tests in noble liquids.
description: 16 pages, 13 figures
Polarization in lines - a new method for measuring black hole masses in active galaxies
Creators: name: Afanasiev, Victor L.
name: Popovic, Luka C.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Measuring of the masses of galactic supermassive black holes (SMBHs) is an important task, since they correlate with the host galaxy properties and play an important role in evolution of galaxies. Here we present a new method for measuring of SMBH masses using the polarization of the broad lines emitted from active galactic nuclei (AGNs). We performed spectropolarometric observations of 9 AGNs and find that this method gives measured masses which are in a good agreement with reverberation measurements. An advantage of this method is that it can be used to measure the masses of SMBHs in a consistent way at different cosmological epochs.
description: ApJL accepted
Measurement of the Penetration Depth and Coherence Length of MgB$_\text{2}$ in All Directions Using Transmission Electron Microscopy
Creators: name: Loudon, J. C.
name: Yazdi, S.
name: Kasama, T.
name: Zhigadlo, N. D.
name: Karpinski, J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We demonstrate that images of flux vortices in a superconductor taken with a transmission electron microscope can be used to measure the penetration depth and coherence length in all directions at the same temperature and magnetic field. This is particularly useful for MgB$_2$, where these quantities vary with the applied magnetic field and values are difficult to obtain at low field or in the $c$-direction. We obtained images of flux vortices from an MgB$_2$ single crystal cut in the $ac$ plane by focussed ion beam milling and tilted to $45^\circ$ with respect to the electron beam about its $a$ axis. A new method was developed to simulate these images which accounted for vortices with a non-zero core in a thin, anisotropic superconductor and a simplex algorithm was used to make a quantitative comparison between the images and simulations to measure the penetration depths and coherence lengths. This gave penetration depths $Λ_{ab}=100\pm 35$ nm and $Λ_c=120\pm 15$ nm at 10.8 K in a field of 4.8 mT. The large error in $Λ_{ab}$ is a consequence of tilting the sample about $a$ and had it been tilted about $c$, the errors would be reversed. Thus, obtaining the most precise values requires taking images of the flux lattice with the sample tilted in more than one direction. In a previous paper, we obtained a more precise value using a sample cut in the $ab$ plane. Using this value gives $Λ_{ab}=107\pm 8$ nm, $Λ_c=120\pm 15$ nm, $ξ_{ab}=39\pm 11$ nm and $ξ_c=35\pm 10$ nm which agree well with measurements made using other techniques. The experiment required two days to conduct and does not require large-scale facilities. It was performed on a very small sample: $30\times 15$ microns and 200 nm thick so this method could prove useful for characterising new superconductors where only small single crystals are available.
description: 12 pages, 6 figures. Typos corrected and titles added to references. Accepted for publication in Physical Review B
HTreeQA: Using Semi-Perfect Phylogeny Trees in Quantitative Trait Loci Study on Genotype Data
Creators: name: Zhang, Xiang
name: Wang, Wei
name: Zhang, Zhaojun
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: With the advances in high-throughput genotyping technology, the study of quantitative trait loci (QTL) has emerged as a promising tool to understand the genetic basis of complex traits. Methodology development for the study of QTL recently has attracted significant research attention. Local phylogeny-based methods have been demonstrated to be powerful tools for uncovering significant associations between phenotypes and single-nucleotide polymorphism markers. However, most existing methods are designed for homozygous genotypes, and a separate haplotype reconstruction step is often needed to resolve heterozygous genotypes. This approach has limited power to detect nonadditive genetic effects and imposes an extensive computational burden. In this article, we propose a new method, HTreeQA, that uses a tristate semi-perfect phylogeny tree to approximate the perfect phylogeny used in existing methods. The semi-perfect phylogeny trees are used as high-level markers for association study. HTreeQA uses the genotype data as direct input without phasing. HTreeQA can handle complex local population structures. It is suitable for QTL mapping on any mouse populations, including the incipient Collaborative Cross lines. Applied HTreeQA, significant QTLs are found for two phenotypes of the PreCC lines, white head spot and running distance at day 5/6. These findings are consistent with known genes and QTL discovered in independent studies. Simulation studies under three different genetic models show that HTreeQA can detect a wider range of genetic effects and is more efficient than existing phylogeny-based approaches. We also provide rigorous theoretical analysis to show that HTreeQA has a lower error rate than alternative methods.
Impact of surface phenomena on direct bulk flexoelectric effect in finite samples
Creators: name: Yurkov, A. S.
name: Tagantsev, A. K.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: In the framework of a continuum theory, it is shown that the direct flexoelectric response of a finite sample essentially depends on the surface polarization energy, even in the thermodynamic limit where the body size tends to infinity. It is found that a modification of the surface energy can lead to a change of the polarization response by a factor of two. The origin of the effect is an electric field produced by surface dipoles induced by the strain gradient. The unexpected sensitivity of the polarization response to the surface energy in the thermodynamic limit is conditioned by the fact that the moments of the surface dipoles may scale as the body size.
In situ production and decay of marine viruses
Creators: name: Garza, Delfino Randy
Publisher: name: The University of Texas at Austin
Year: 1996
Subjects: subject: Synechococcales viruses
subject: Cyanobacteria viruses
subject: Cyanobacteria mortality
subject: Synechococcales mortality
subject: Bacteriophages
subject: Gulf of Mexico
subject: Marine viruses
subject: Synechococcales--Viruses--Mexico, Gulf of
subject: Cyanobacteria--Viruses--Mexico, Gulf of
subject: Synechococcales--Mortality--Mexico, Gulf of
subject: Cyanobacteria--Mortality--Mexico, Gulf of
subject: Bacteriophages--Mexico, Gulf of

description: Viruses which cause lysis of Synechococcus spp. were present in the western Gulf of Mexico and may be responsible for <1% to 8% of Synechococcus mortality throughout the year in the mixed layer. Solar-mediated decay rates of infectivity at the air/water interface of natural cyanophage communities ranged from undetectable to 0.335 h⁻¹, with the highest rate generally occurring during the summer. Decay rates of cyanophage isolates (SPWM-1 & SPWM-3) were similar in the spring and winter but were up to 2X greater than those of the natural community. These results indicate that natural cyanophage communities are more tolerant in summer to damage by solar radiation than cyanophage isolates. Moreover, decay rates of cyanophage infectivity were similar whether in the presence or absence of host cells, indicating that detectable cyanophage production did not occur during in situ incubations. The decay rates of virus isolates and natural cyanophage communities were examined in parallel incubations at several times during the year. Results from theses experiments showed that isolates predict decay rates of the natural communities during the winter. However, during the summer, isolates overestimated the decay rates of natural communities by as much as two-fold, indicating that surrogate viruses do not predict the decay processes of natural communities at all times
Mapping Six New Susceptibility to Colon Cancer ( Scc ) Loci Using a Mouse Interspecific Backcross
Creators: name: Threadgill, David W.
name: Pearsall, R. Scott
name: Eversley, Chevonne D.
name: Yuying, Xie
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Colorectal cancer (CRC) has a complex etiology resulting from the combination of multiple genetic and environmental factors, each with small effects. Interactions among susceptibility modifier loci make many of the loci difficult to detect in human genome-wide association studies. Previous analyses in mice have used classical inbred strains, which share large portions of their genomes due to common ancestry. Herein, we used an interspecific backcross between the Mus musculus strain A/J and the Mus spretus strain SPRET/EiJ to map 6 additional CRC modifier loci (Scc16-21) and 2 suggestive loci. Three loci modify the location of tumors along the proximal-distal axis of the colon. Six CRC modifiers previously mapped in intraspecific crosses were also replicated. This work confirms genetic models suggesting that CRC is caused by many small effect alleles and brings the catalog of reported CRC modifier loci to 23 spread across 13 chromosomes. Furthermore, this work provides the foundation for large population-level epistatic interaction tests to identify combinations of low effect alleles that may have large effects on CRC susceptibility.
Abundance Differences Between Exoplanet Binary Host Stars XO-2N and XO-2S -- Dependence on Stellar Parameters
Creators: name: Teske, Johanna K.
name: Ghezzi, Luan
name: Cunha, Katia
name: Smith, Verne V.
name: Schuler, Simon C.
name: Bergemann, Maria
Publisher: name: arXiv
Year: 2015
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The chemical composition of exoplanet host stars is an important factor in understanding the formation and characteristics of their orbiting planets. The best example of this to date is the planet-metallicity correlation. Other proposed correlations are thus far less robust, in part due to uncertainty in the chemical history of stars pre- and post-planet formation. Binary host stars of similar type present an opportunity to isolate the effects of planets on host star abundances. Here we present a differential elemental abundance analysis of the XO-2 stellar binary, in which both G9 stars host giant planets, one of which is transiting. Building on our previous work, we report 16 elemental abundances and compare the $Δ$(XO-2N-XO-S) values to elemental condensation temperatures. The $Δ$(N-S) values and slopes with condensation temperature resulting from four different pairs of stellar parameters are compared to explore the effects of changing the relative temperature and gravity of the stars. We find that most of the abundance differences between the stars depend on the chosen stellar parameters, but that Fe, Si, and potentially Ni are consistently enhanced in XO-2N regardless of the chosen stellar parameters. This study emphasizes the power of binary host star abundance analysis for probing the effects of giant planet formation, but also illustrates the potentially large uncertainties in abundance differences and slopes induced by changes in stellar temperature and gravity.
description: 11 pages, 2 figures Accepted in ApJL
Transcriptome Atlases of Mouse Brain Reveals Differential Expression Across Brain Regions and Genetic Backgrounds
Creators: name: McMillan, Leonard
name: Crowley, James J.
name: Zou, Fei
name: Wang, Jeremy
name: Buus, Ryan J.
name: Pardo-Manuel de Villena, Fernando
name: Wright, Fred A.
name: Miller, Darla R.
name: Lee, Seunggeun
name: Yun, Zaining
name: Sun, Wei
name: Zhabotynsky, Vasyl
name: Sullivan, Patrick F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Mouse models play a crucial role in the study of human behavioral traits and diseases. Variation of gene expression in brain may play a critical role in behavioral phenotypes, and thus it is of great importance to understand regulation of transcription in mouse brain. In this study, we analyzed the role of two important factors influencing steady-state transcriptional variation in mouse brain. First we considered the effect of assessing whole brain vs. discrete regions of the brain. Second, we investigated the genetic basis of strain effects on gene expression. We examined the transcriptome of three brain regions using Affymetrix expression arrays: whole brain, forebrain, and hindbrain in adult mice from two common inbred strains (C57BL/6J vs. NOD/ShiLtJ) with eight replicates for each brain region and strain combination. We observed significant differences between the transcriptomes of forebrain and hindbrain. In contrast, the transcriptomes of whole brain and forebrain were very similar. Using 4.3 million single-nucleotide polymorphisms identified through whole-genome sequencing of C57BL/6J and NOD/ShiLtJ strains, we investigated the relationship between strain effect in gene expression and DNA sequence similarity. We found that cis-regulatory effects play an important role in gene expression differences between strains and that the cis-regulatory elements are more often located in 5′ and/or 3′ transcript boundaries, with no apparent preference on either 5′ or 3′ ends.
Caenorhabditis elegans POT-1 and POT-2 Repress Telomere Maintenance Pathways
Creators: name: Simon, Matt
name: Shtessel, Ludmila
name: Lowden, Mia Rochelle
name: Ahmed, Shawn
name: Cheng, Chen
name: Wang, Kyle
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Telomeres are composed of simple tandem DNA repeats that protect the ends of linear chromosomes from replicative erosion or inappropriate DNA damage response mechanisms. The mammalian Protection Of Telomeres (POT1) protein interacts with single-stranded telomeric DNA and can exert positive and negative effects on telomere length. Of four distinct POT1 homologs in the roundworm Caenorhabditis elegans, deficiency for POT-1 or POT-2 resulted in progressive telomere elongation that occurred because both proteins negatively regulate telomerase. We created a POT-1::mCherry fusion protein that forms discrete foci at C. elegans telomeres, independent of POT-2, allowing for live analysis of telomere dynamics. Transgenic pot-1::mCherry repressed telomerase in pot-1 mutants. Animals deficient for pot-1, but not pot-2, displayed mildly enhanced telomere erosion rates in the absence of the telomerase reverse transcriptase, trt-1. However, trt-1; pot-1 double mutants exhibited delayed senescence in comparison to trt-1 animals, and senescence was further delayed in trt-1; pot-2; pot-1 triple mutants, some of which survived robustly in the absence of telomerase. Our results indicate that POT-1 and POT-2 play independent roles in suppressing a telomerase-independent telomere maintenance pathway but may function together to repress telomerase.
Embargoes From Past Avian Flu Outbreaks Reduced Demand for U.S. Chicken Meat
Creators: name: MacLachlan, Matthew
name: Zeng, Wendy
name: Padilla, Samantha
name: MacLachlan, Matthew
name: Zeng, Wendy
name: Padilla, Samantha
Publisher: name: Unknown
Year: 2022

description: On February 9, 2022, the USDA, Animal and Plant Health Inspection Service (APHIS) confirmed highly pathogenic avian influenza (HPAI) in a commercial turkey flock in Indiana. HPAI spreads rapidly, is transmittable across different species of birds, and is often lethal to infected birds. Since 2000, outbreaks of HPAI in the United States occurred in 2004 and again in 2014–15. More animals were lost in the 2014–15 outbreak than in any other infectious animal disease event in U.S. history. These events affected poultry commerce on a global scale, decimating international demand for U.S. poultry products and reducing incomes of affected U.S. producers as well as producers whose flocks did not contract HPAI. Government efforts to mitigate the disease were effective but costly.
An Action Principle for Relativistic MHD
Creators: name: D'Avignon, Eric
name: Morrison, Philip
name: Pegoraro, Francesco
Publisher: name: arXiv
Year: 2015
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: A covariant action principle for ideal relativistic magnetohydrodynamics (MHD) in terms of natural Eulerian field variables is given. This is done by generalizing the covariant Poisson bracket theory of Marsden et al., which uses a noncanonical bracket to effect constrained variations of an action functional. Various implications and extensions of this action principle are also discussed. Two significant by-products of this formalism are the introduction of a new divergence-free 4-vector variable for the magnetic field, and a new Lie-dragged form for the theory.