cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The performance of the bolometer array and readout system during the 2012/2013 flight of the E and B experiment (EBEX)
Creators: name: MacDermid, Kevin
name: Aboobaker, Asad M.
name: Ade, Peter
name: Aubin, Francois
name: Baccigalupi, Carlo
name: Bandura, Kevin
name: Bao, Chaoyun
name: Borrill, Julian
name: Chapman, Daniel
name: Didier, Joy
name: Dobbs, Matt
name: Grain, Julien
name: Grainger, Will
name: Hanany, Shaul
name: Helson, Kyle
name: Hillbrand, Seth
name: Hilton, Gene
name: Hubmayr, Hannes
name: Irwin, Kent
name: Johnson, Bradley
name: Jaffe, Andrew
name: Jones, Terry
name: Kisner, Ted
name: Klein, Jeff
name: Korotkov, Andrei
name: Lee, Adrian
name: Levinson, Lorne
name: Limon, Michele
name: Miller, Amber
name: Milligan, Michael
name: Pascale, Enzo
name: Raach, Kate
name: Reichborn-Kjennerud, Britt
name: Reintsema, Carl
name: Sagiv, Ilan
name: Smecher, Graeme
name: Stompor, Radek
name: Tristram, Matthieu
name: Tucker, Greg
name: Westbrook, Ben
name: Zilic, Kyle
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: EBEX is a balloon-borne telescope designed to measure the polarization of the cosmic microwave background radiation. During its eleven day science flight in the Austral Summer of 2012, it operated 955 spider-web transition edge sensor (TES) bolometers separated into bands at 150, 250 and 410 GHz. This is the first time that an array of TES bolometers has been used on a balloon platform to conduct science observations. Polarization sensitivity was provided by a wire grid and continuously rotating half-wave plate. The balloon implementation of the bolometer array and readout electronics presented unique development requirements. Here we present an outline of the readout system, the remote tuning of the bolometers and Superconducting QUantum Interference Device (SQUID) amplifiers, and preliminary current noise of the bolometer array and readout system.
description: 15 pages, 12 figures, SPIE conference proceedings
Inferring Ecological Processes from Taxonomic, Phylogenetic and Functional Trait β-Diversity
Creators: name: Stegen, James C.
name: Hurlbert, Allen H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Understanding the influences of dispersal limitation and environmental filtering on the structure of ecological communities is a major challenge in ecology. Insight may be gained by combining phylogenetic, functional and taxonomic data to characterize spatial turnover in community structure (β-diversity). We develop a framework that allows rigorous inference of the strengths of dispersal limitation and environmental filtering by combining these three types of β-diversity. Our framework provides model-generated expectations for patterns of taxonomic, phylogenetic and functional β-diversity across biologically relevant combinations of dispersal limitation and environmental filtering. After developing the framework we compared the model-generated expectations to the commonly used “intuitive” expectation that the variance explained by the environment or by space will, respectively, increase monotonically with the strength of environmental filtering or dispersal limitation. The model-generated expectations strongly departed from these intuitive expectations: the variance explained by the environment or by space was often a unimodal function of the strength of environmental filtering or dispersal limitation, respectively. Therefore, although it is commonly done in the literature, one cannot assume that the strength of an underlying process is a monotonic function of explained variance. To infer the strength of underlying processes, one must instead compare explained variances to model-generated expectations. Our framework provides these expectations. We show that by combining the three types of β-diversity with model-generated expectations our framework is able to provide rigorous inferences of the relative and absolute strengths of dispersal limitation and environmental filtering. Phylogenetic, functional and taxonomic β-diversity can therefore be used simultaneously to infer processes by comparing their empirical patterns to the expectations generated by frameworks similar to the one developed here.
Pitch-angle scattering of energetic particles with adiabatic focusing
Creators: name: Tautz, R. C.
name: Shalchi, A.
name: Dosch, A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Understanding turbulent transport of charged particles in magnetized plasmas often requires a model for the description of random variations in the particle's pitch angle. The Fokker-Planck coefficient of pitch-angle scattering, which is used to describe scattering parallel to the mean magnetic field, is therefore of central importance. Whereas quasi-linear theory assumes a homogeneous mean magnetic field, such a condition is often not fulfilled, especially for high-energy particles. Here, a new derivation of the quasi-linear approach is given that is based on the unperturbed orbit found for an adiabatically focused mean magnetic field. The results show that, depending on the ratio of the focusing length and the particle's Larmor radius, the Fokker-Planck coefficient is significantly modified but agrees with the classical expression in the limit of a homogeneous mean magnetic field.
description: 10 pages, 6 figures, accepted for publication in ApJ
Inhibition of Fried Meat-Induced Colorectal DNA Damage and Altered Systemic Genotoxicity in Humans by Crucifera, Chlorophyllin, and Yogurt
Creators: name: Swank, Adam E.
name: MacIntosh, Beth
name: Sandler, Robert S.
name: Knize, Mark G.
name: Schliebe, Barbara
name: Matthews, Peggy P.
name: Taylor, Jack A.
name: Gangarosa, Lisa M.
name: Shaughnessy, Daniel T.
name: Umbach, David M.
name: DeMarini, David M.
name: Xu, Zongli
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Dietary exposures implicated as reducing or causing risk for colorectal cancer may reduce or cause DNA damage in colon tissue; however, no one has assessed this hypothesis directly in humans. Thus, we enrolled 16 healthy volunteers in a 4-week controlled feeding study where 8 subjects were randomly assigned to dietary regimens containing meat cooked at either low (100°C) or high temperature (250°C), each for 2 weeks in a crossover design. The other 8 subjects were randomly assigned to dietary regimens containing the high-temperature meat diet alone or in combination with 3 putative mutagen inhibitors: cruciferous vegetables, yogurt, and chlorophyllin tablets, also in a crossover design. Subjects were nonsmokers, at least 18 years old, and not currently taking prescription drugs or antibiotics. We used the Salmonella assay to analyze the meat, urine, and feces for mutagenicity, and the comet assay to analyze rectal biopsies and peripheral blood lymphocytes for DNA damage. Low-temperature meat had undetectable levels of heterocyclic amines (HCAs) and was not mutagenic, whereas high-temperature meat had high HCA levels and was highly mutagenic. The high-temperature meat diet increased the mutagenicity of hydrolyzed urine and feces compared to the low-temperature meat diet. The mutagenicity of hydrolyzed urine was increased nearly twofold by the inhibitor diet, indicating that the inhibitors enhanced conjugation. Inhibitors decreased significantly the mutagenicity of un-hydrolyzed and hydrolyzed feces. The diets did not alter the levels of DNA damage in non-target white blood cells, but the inhibitor diet decreased nearly twofold the DNA damage in target colorectal cells. To our knowledge, this is the first demonstration that dietary factors can reduce DNA damage in the target tissue of fried-meat associated carcinogenesis.
Kaiser Family Foundation Poll: April Kaiser Health Tracking Poll
Creators: name: Kaiser Family Foundation
Publisher: name: Roper Center for Public Opinion Research
Year: 2020

description: Favorability of Affordable Care Act (1); Congress acting on ACA (1); levels of government implementing law (2); benefits of ACA (4); drawbacks of ACA (4); amount of people enrolling in health insurance marketplaces (2); problems with open enrollment (1); private health insurance coverage birth control (2); news stories followed closely (11); ads about ACA (6); where purchased insurance (2); reasons for not having insurance (3); trying to get insurance (6); paying fine for not having health insurance (1); expected cost of health insurance (1); cost of health insurance fine (1); pre-existing condition (1).
Interleukin-6 Induces Gr-1+CD11b+ Myeloid Cells to Suppress CD8+ T Cell-Mediated Liver Injury in Mice
Creators: name: Xing, Qiao
name: Cheng, Liang
name: Li, Xiaozhu
name: Wang, Shengdian
name: Du, Peishuang
name: Wang, Jun
name: Su, Lishan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Agonist antibodies against CD137 (4–1BB) on T lymphocytes are used to increase host anti-tumor immunity, but often leading to severe liver injury in treated mice or in patients during clinical trials. Interleukin-6 (IL-6) has been reported to protect hepatocyte death, but the role of IL-6 in protecting chronic T cell-induced liver diseases is not clearly defined due to lack of relevant animal models. We aimed to define the role of IL-6 in CD8+ T cell-mediated liver injury induced by a CD137 agonistic mAb (clone 2A) in mice.
Kaiser Family Foundation Poll: May Kaiser Health Tracking Poll
Creators: name: Kaiser Family Foundation
Publisher: name: Roper Center for Public Opinion Research
Year: 2020

description: Most important congressional issues (2); favorability of Affordable Care Act (1); Congress handling ACA (1); most important ACA improvement (1); Republican alternative to ACA (1); ACA personal benefits and drawbacks (3); various ACA experiences (4); attention paid to election campaign (1); factors affecting congressional candidate preference (4); Congress debating ACA (1); private insurance covering birth control (2); news stories followed closely (10); insurance from government marketplace (2); most important reason to have insurance (1); rating insurance coverage (2); value of insurance (1); satisfaction with various insurance aspects (7).
Latitudinal Gradients in Degradation of Marine Dissolved Organic Carbon
Creators: name: Ziervogel, Kai
name: Steen, Andrew D.
name: Jeffrey, Wade H.
name: Ghobrial, Sherif
name: Arnosti, Carol
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Heterotrophic microbial communities cycle nearly half of net primary productivity in the ocean, and play a particularly important role in transformations of dissolved organic carbon (DOC). The specific means by which these communities mediate the transformations of organic carbon are largely unknown, since the vast majority of marine bacteria have not been isolated in culture, and most measurements of DOC degradation rates have focused on uptake and metabolism of either bulk DOC or of simple model compounds (e.g. specific amino acids or sugars). Genomic investigations provide information about the potential capabilities of organisms and communities but not the extent to which such potential is expressed. We tested directly the capabilities of heterotrophic microbial communities in surface ocean waters at 32 stations spanning latitudes from 76°S to 79°N to hydrolyze a range of high molecular weight organic substrates and thereby initiate organic matter degradation. These data demonstrate the existence of a latitudinal gradient in the range of complex substrates available to heterotrophic microbial communities, paralleling the global gradient in bacterial species richness. As changing climate increasingly affects the marine environment, changes in the spectrum of substrates accessible by microbial communities may lead to shifts in the location and rate at which marine DOC is respired. Since the inventory of DOC in the ocean is comparable in magnitude to the atmospheric CO2 reservoir, such a change could profoundly affect the global carbon cycle.
Kaiser Family Foundation Poll: June Kaiser Health Tracking Poll--Affordable Care Act/Wellness Programs
Creators: name: Kaiser Family Foundation
Publisher: name: Roper Center for Public Opinion Research
Year: 2020

description: Favorability of Affordable Care Act (1); source of ACA impression (1); enough information about ACA (1); effects of ACA on various groups (5); quality of Veterans Affairs health care (2); news stories followed closely (8); VA waiting times as common or isolated (1); Eric Shinseki resigned or was fired (1); source of health insurance (2); health insurance offering wellness programs (2); paying more for not meeting health goals (3); types of wellness programs offered (1); participation in wellness programs (1).
Magnesium-vacancy optical centers in diamond
Creators: name: Corte, Emilio
name: Andrini, Greta
name: Hernández, Elena Nieto
name: Pugliese, Vanna
name: Costa, Ângelo
name: Magchiels, Goele
name: Moens, Janni
name: Tunhuma, Shandirai Malven
name: Villarreal, Renan
name: Pereira, Lino M. C.
name: Vantomme, André
name: Correia, João Guilherme
name: Bernardi, Ettore
name: Traina, Paolo
name: Degiovanni, Ivo Pietro
name: Moreva, Ekaterina
name: Genovese, Marco
name: Tchernij, Sviatoslav Ditalia
name: Olivero, Paolo
name: Wahl, Ulrich
name: Forneris, Jacopo
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We provide the first systematic characterization of the structural and photoluminescence properties of optically active defect centers fabricated upon implantation of 30-100 keV Mg+ ions in artificial diamond. The structural configurations of Mg-related defects were studied by the emission channeling technique for 27Mg implantations performed both at room-temperature and 800 °C, which allowed the identification of a major fraction of Mg atoms (~30-42%) in sites which are compatible with the split-vacancy structure of the MgV complex. A smaller fraction of Mg atoms (~13-17%) was found on substitutional sites. The photoluminescence emission was investigated both at the ensemble and individual defect level in a temperature range comprised between 5 K and 300 K, offering a detailed picture of the MgV-related emission properties and revealing the occurrence of previously unreported spectral features. The optical excitability of the MgV center was also studied as a function of the optical excitation wavelength enabling to identify the optimal conditions for photostable and intense emission. The results are discussed in the context of the preliminary experimental data and the theoretical models available in the literature, with appealing perspectives for the utilization of the tunable properties of the MgV center for quantum information processing applications.
description: 7 figures
Modeling Symmetric Macromolecular Structures in Rosetta3
Creators: name: Baker, David
name: Bradley, Phil
name: Leaver-Fay, Andrew
name: DiMaio, Frank
name: André, Ingemar
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Symmetric protein assemblies play important roles in many biochemical processes. However, the large size of such systems is challenging for traditional structure modeling methods. This paper describes the implementation of a general framework for modeling arbitrary symmetric systems in Rosetta3. We describe the various types of symmetries relevant to the study of protein structure that may be modeled using Rosetta's symmetric framework. We then describe how this symmetric framework is efficiently implemented within Rosetta, which restricts the conformational search space by sampling only symmetric degrees of freedom, and explicitly simulates only a subset of the interacting monomers. Finally, we describe structure prediction and design applications that utilize the Rosetta3 symmetric modeling capabilities, and provide a guide to running simulations on symmetric systems.
One-Way Optical Transition based on Causality in Momentum Space
Creators: name: Yu, Sunkyu
name: Piao, Xianji
name: Yoo, KyungWan
name: Shin, Jonghwa
name: Park, Namkyoo
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The concept of parity-time (PT) symmetry has been used to identify a novel route to nonreciprocal dynamics in optical momentum space, imposing the directionality on the flow of light. Whereas PT-symmetric potentials have been implemented under the requirement of V(x) = V*(-x), this precondition has only been interpreted within the mathematical frame for the symmetry of Hamiltonians and has not been directly linked to nonreciprocity. Here, within the context of light-matter interactions, we develop an alternative route to nonreciprocity in momentum space by employing the concept of causality. We demonstrate that potentials with real and causal momentum spectra produce unidirectional transitions of optical states inside the k-continuum, which corresponds to an exceptional point on the degree of PT-symmetry. Our analysis reveals a critical link between non-Hermitian problems and spectral theory and enables the multi-dimensional manipulation of optical states, in contrast to one-dimensional control from the use of a Schrodinger-like equation in previous PT-symmetric optics.
Kaiser Family Foundation Poll: July Kaiser Health Tracking Poll--Affordable Care Act
Creators: name: Kaiser Family Foundation
Publisher: name: Roper Center for Public Opinion Research
Year: 2020

description: Government attention paid to various issues (11); most important congressional issues (2); Affordable Care Act favorability (1); repealing or improving ACA (1); effects of ACA on family (3); conversations about ACA (2); ACA insurance choices (1); news stories followed closely (11); ACA-related advertisements (6); ACA news coverage (1); 2014 election campaign (1); birth control coverage (3); feeling toward Supreme Court birth control decisions (1); Supreme Court ruling affecting voter participation (1); Supreme Court decision related to ACA (2); factors affecting Supreme Court decision (7); Supreme Court decision affecting birth control availability (1); who's responsible for birth control coverage (1); denying other health care services based on religious objections (1); United States progress on HIV/AIDS (1); concern about HIV infection (1); discussions about HIV/AIDS (3); anti-retroviral medications impacting HIV transmission (1); medication to lower HIV risk (1); comfort with HIV- positive roommate (1); knowledge of people with HIV (6); know anyone who passed from HIV/AIDS (1); tested for HIV/AIDS (2); sexual orientation (2).
The Extension of Unital Completely Positive Semigroups on Operator Systems to Semigroups on $C^*$-algebras
Creators: name: Yashin, V. I.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Operator Algebras (math.OA)
subject: Quantum Physics (quant-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 46L07, 47L25, 47D06, 81P45

description: The study of open quantum systems relies on the notion of unital completely positive semigroups on $C^*$-algebras representing physical systems. The natural generalisation would be to consider the unital completely positive semigroups on operator systems. We show that any continuous unital completely positive semigroup on matricial system can be extended to a semigroup on a finite-dimensional $C^*$-algebra, which is an injective envelope of the matricial system. In case the semigroup is invertible, this extension is unique.
description: 21 pages, 1 figure, typos corrected, journal reference added
Preliminary results of excavations at Langlands Iron Foundry and Stooke’s Shipping Butchers, 556−560 Flinders Street, Melbourne
Creators: name: Mallett, Tom
name: Myers, Sarah
name: Mirams, Sarah
name: Coleman, Felicity
name: Shanahan, Fiona
Publisher: name: La Trobe
Year: 2023

description: Archaeology Program, La Trobe University
Molecular Malaria Epidemiology: Mapping and Burden Estimates for the Democratic Republic of the Congo, 2007
Creators: name: Taylor, Steve M.
name: Hand, Carla C.
name: Meshnick, Steven R.
name: Messina, Jane P.
name: Emch, Michael
name: Juliano, Jonathan J.
name: Muwonga, Jeremie
name: Tshefu, Antoinette K.
name: Atua, Benjamin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: BackgroundEpidemiologic data on malaria are scant in many high-burden countries including the Democratic Republic of the Congo (DRC), which suffers the second-highest global burden of malaria. Malaria control efforts in regions with challenging infrastructure require reproducible and efficient surveillance. We employed new high-throughput molecular testing to characterize the state of malaria control in the DRC and estimate childhood mortality attributable to excess malaria transmission.Methods and FindingsThe Demographic and Health Survey was a cross-sectional, population-based cluster household survey of adults aged 15–59 years in 2007 employing structured questionnaires and dried blood spot collection. Parasitemia was detected by real-time PCR, and survey responses measured adoption of malaria control measures and under-5 health indices. The response rate was 99% at the household level, and 8,886 households were surveyed in 300 clusters; from 8,838 respondents molecular results were available. The overall prevalence of parasitemia was 33.5% (95% confidence interval [C.I.] 32–34.9); P. falciparum was the most prevalent species, either as monoinfection (90.4%; 95% C.I. 88.8–92.1) or combined with P. malariae (4.9%; 95% C.I. 3.7–5.9) or P. ovale (0.6%; 95% C.I. 0.1–0.9). Only 7.7% (95% CI 6.8–8.6) of households with children under 5 owned an insecticide-treated bednet (ITN), and only 6.8% (95% CI 6.1–7.5) of under-fives slept under an ITN the preceding night. The overall under-5 mortality rate was 147 deaths per 1,000 live births (95% C.I. 141–153) and between clusters was associated with increased P. falciparum prevalence; based on the population attributable fraction, 26,488 yearly under-5 deaths were attributable to excess malaria transmission.ConclusionsAdult P. falciparum prevalence is substantial in the DRC and is associated with under-5 mortality. Molecular testing offers a new, generalizable, and efficient approach to characterizing malaria endemicity in underserved countries.
Public Opinion in Panama - # 5
Creators: name: CID/Gallup, Costa Rica
Publisher: name: Roper Center for Public Opinion Research
Year: 2019

description: Sources of information(3); opinion about media(2); economic situation(5); safety issues(2); Panama Canal(2); party ID(1); evaluation of government performance(1); opinion about political leaders(3); opinion about political parties(3); opinion about P.D.C.(7); most important issue(1); voting intentions(2); opinion about U.S.(2); "social" debt(2); U.S. troops(1); national issues(3); "Ford" plan(1); integration to Central America(3); drug-trafficking issue(4); consumer habits(1); opinion about Panama's people(3); opinion about Chase Manhattan Bank(5).
Mucin Variable Number Tandem Repeat Polymorphisms and Severity of Cystic Fibrosis Lung Disease: Significant Association with MUC5AC
Creators: name: Dang, Anthony T.
name: Harris, Ann
name: Pace, Rhonda G.
name: Stonebraker, Jaclyn R.
name: Swallow, Dallas M.
name: Zou, Fei
name: O'Neal, Wanda K.
name: Knowles, Michael R.
name: Commander, Clayton W.
name: Wright, Fred A.
name: Guo, XueLiang
name: Drumm, Mitchell L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Variability in cystic fibrosis (CF) lung disease is partially due to non-CFTR genetic modifiers. Mucin genes are very polymorphic, and mucins play a key role in the pathogenesis of CF lung disease; therefore, mucin genes are strong candidates as genetic modifiers. DNA from CF patients recruited for extremes of lung phenotype was analyzed by Southern blot or PCR to define variable number tandem repeat (VNTR) length polymorphisms for MUC1, MUC2, MUC5AC, and MUC7. VNTR length polymorphisms were tested for association with lung disease severity and for linkage disequilibrium (LD) with flanking single nucleotide polymorphisms (SNPs). No strong associations were found for MUC1, MUC2, or MUC7. A significant association was found between the overall distribution of MUC5AC VNTR length and CF lung disease severity (p = 0.025; n = 468 patients); plus, there was robust association of the specific 6.4 kb HinfI VNTR fragment with severity of lung disease (p = 6.2×10−4 after Bonferroni correction). There was strong LD between MUC5AC VNTR length modes and flanking SNPs. The severity-associated 6.4 kb VNTR allele of MUC5AC was confirmed to be genetically distinct from the 6.3 kb allele, as it showed significantly stronger association with nearby SNPs. These data provide detailed respiratory mucin gene VNTR allele distributions in CF patients. Our data also show a novel link between the MUC5AC 6.4 kb VNTR allele and severity of CF lung disease. The LD pattern with surrounding SNPs suggests that the 6.4 kb allele contains, or is linked to, important functional genetic variation.
Thermomechanical two-mode squeezing in an ultrahigh $Q$ membrane resonator
Creators: name: Patil, Y. S.
name: Chakram, S.
name: Chang, L.
name: Vengalattore, M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We realize a nondegenerate parametric amplifier in an ultrahigh $Q$ mechanical membrane resonator and demonstrate two-mode thermomechanical noise squeezing. Our measurements are accurately described by a two-mode model that attributes this nonlinear mechanical interaction to a substrate-mediated process which is dramatically enhanced by the quality factors of the individual modes. This realization of strong multimode nonlinearities in a mechanical platform compatible with quantum-limited optical detection and cooling makes this a powerful system for nonlinear approaches to quantum metrology, transduction between optical and phononic fields and the quantum manipulation of phononic degrees of freedom.
What does it take to solve the measurement problem?
Creators: name: Hance, Jonte R.
name: Hossenfelder, Sabine
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: History and Philosophy of Physics (physics.hist-ph)
subject: FOS: Physical sciences

description: We summarise different aspects of the measurement problem in quantum mechanics. We argue that it is a real problem which requires a solution, and identify the properties a theory needs to solve the problem. We show that no current interpretation of quantum mechanics solves the problem, and that, being interpretations rather than extensions of quantum mechanics, they cannot solve it. Finally, we speculate what a solution of the measurement problem might be good for.
description: 11 pages, no figures. Accepted for publication in Journal of Physics Communications
Multiple ATR-Chk1 Pathway Proteins Preferentially Associate with Checkpoint-Inducing DNA Substrates
Creators: name: Yilmaz, Seçil
name: Sancar, Aziz
name: Kemp, Michael G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The ATR-Chk1 DNA damage checkpoint pathway is a critical regulator of the cellular response to DNA damage and replication stress in human cells. The variety of environmental, chemotherapeutic, and carcinogenic agents that activate this signal transduction pathway do so primarily through the formation of bulky adducts in DNA and subsequent effects on DNA replication fork progression. Because there are many protein-protein and protein-DNA interactions proposed to be involved in activation and/or maintenance of ATR-Chk1 signaling in vivo, we systematically analyzed the association of a number of ATR-Chk1 pathway proteins with relevant checkpoint-inducing DNA structures in vitro. These DNA substrates included single-stranded DNA, branched DNA, and bulky adduct-containing DNA. We found that many checkpoint proteins show a preference for single-stranded, branched, and bulky adduct-containing DNA in comparison to undamaged, double-stranded DNA. We additionally found that the association of checkpoint proteins with bulky DNA damage relative to undamaged DNA was strongly influenced by the ionic strength of the binding reaction. Interestingly, among the checkpoint proteins analyzed the checkpoint mediator proteins Tipin and Claspin showed the greatest differential affinity for checkpoint-inducing DNA structures. We conclude that the association and accumulation of multiple checkpoint proteins with DNA structures indicative of DNA damage and replication stress likely contribute to optimal ATR-Chk1 DNA damage checkpoint responses.
APOBEC mutagenesis is a common process in normal human small intestine.
Creators: name: Wang, Yichen
name: Robinson, Philip S
name: Coorens, Tim HH
name: Moore, Luiza
name: Lee-Six, Henry
name: Noorani, Ayesha
name: Sanders, Mathijs A
name: Jung, Hyunchul
name: Katainen, Riku
name: Heuschkel, Robert
name: Brunton-Sim, Roxanne
name: Weston, Robyn
name: Read, Debbie
name: Nobbs, Beverley
name: Fitzgerald, Rebecca C
name: Saeb-Parsy, Kourosh
name: Martincorena, Iñigo
name: Campbell, Peter J
name: Rushbrook, Simon
name: Zilbauer, Matthias
name: Buczacki, Simon James Alexander
name: Stratton, Michael R
Publisher: name: Apollo - University of Cambridge Repository
Year: 2023
Subjects: Article
/631/208/212
/631/114/2164
/45
/45/23
/38/91
article

description: Funder: Core funding from the Wellcome Sanger Institute (Wellcome Trust, No. 206194).
description: Funder: Wellcome PhD Studentship (Wellcome Trust, No. 206194)
description: Funder: Wellcome Clinical PhD fellowship (Wellcome Trust, No. 206194)
description: Funder: Pathological Society of Great Britain and Ireland; doi: https://doi.org/10.13039/501100000672
description: Funder: Jean Shank/Pathological Society of Great Britain and Ireland Intermediate Clinical Fellowship(JSPS IF 2019 01)
description: Funder: Finnish Center of Excellence Program 2018–2025, No. 312041
description: Funder: NIHR Cambridge Biomedical Research Centre
description: Funder: Core funding from The Pharsalia Trust.
description: APOBEC mutational signatures SBS2 and SBS13 are common in many human cancer types. However, there is an incomplete understanding of its stimulus, when it occurs in the progression from normal to cancer cell and the APOBEC enzymes responsible. Here we whole-genome sequenced 342 microdissected normal epithelial crypts from the small intestines of 39 individuals and found that SBS2/SBS13 mutations were present in 17% of crypts, more frequent than most other normal tissues. Crypts with SBS2/SBS13 often had immediate crypt neighbors without SBS2/SBS13, suggesting that the underlying cause of SBS2/SBS13 is cell-intrinsic. APOBEC mutagenesis occurred in an episodic manner throughout the human lifespan, including in young children. APOBEC1 mRNA levels were very high in the small intestine epithelium, but low in the large intestine epithelium and other tissues. The results suggest that the high levels of SBS2/SBS13 in the small intestine are collateral damage from APOBEC1 fulfilling its physiological function of editing APOB mRNA.
Public Opinion in Nicaragua #4
Creators: name: CID/Gallup, Costa Rica
Publisher: name: Roper Center for Public Opinion Research
Year: 2019

description: Economic situation (7); national problems (1); security forces (2); property devolution (2); evaluation of government performance (2); labor unions (1); opinion about political leaders (14); party ID (1); opinion about businessmen (1); foreign assistance (4); opinion about media (2); ideology (1); expectations for future (1); opinion about political parties (1); voting record (1); consumer habits (7); trust in economic measures (1).
Nerve Agent Hydrolysis Activity Designed into a Human Drug Metabolism Enzyme
Creators: name: Lewis, Steven L.
name: Edwards, Jonathan S.
name: Redinbo, Matthew R.
name: Cadieux, C. Linn
name: Cerasoli, Douglas M.
name: Chica, Roberto A.
name: Otto, Tamara C.
name: Cashman, John R.
name: Wierdl, Monika
name: Kasten, Shane A.
name: Mayo, Stephen L.
name: Potter, Philip M.
name: Hemmert, Andrew C.
name: Tsurkan, Lyudmila
name: Edwards, Carol C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Organophosphorus (OP) nerve agents are potent suicide inhibitors of the essential neurotransmitter-regulating enzyme acetylcholinesterase. Due to their acute toxicity, there is significant interest in developing effective countermeasures to OP poisoning. Here we impart nerve agent hydrolysis activity into the human drug metabolism enzyme carboxylesterase 1. Using crystal structures of the target enzyme in complex with nerve agent as a guide, a pair of histidine and glutamic acid residues were designed proximal to the enzyme's native catalytic triad. The resultant variant protein demonstrated significantly increased rates of reactivation following exposure to sarin, soman, and cyclosarin. Importantly, the addition of these residues did not alter the high affinity binding of nerve agents to this protein. Thus, using two amino acid substitutions, a novel enzyme was created that efficiently converted a group of hemisubstrates, compounds that can start but not complete a reaction cycle, into bona fide substrates. Such approaches may lead to novel countermeasures for nerve agent poisoning.
Evolution of Prolate Molecular Clouds at HII Boundaries: I. Formation of fragment-core structures
Creators: name: Kinnear, Timothy M.
name: Miao, Jingqi
name: White, Glenn J.
name: Goodwin, Simon
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The evolution of a prolate cloud at an Hii boundary is investigated using Smoothed Particle Hydrodynamics (SPH). The prolate molecular clouds in our investigation are set with their semi-major axis perpendicular to the radiative direction of a plane parallel ionising Extreme Ultraviolet (EUV) flux. Simulations on three high mass prolate clouds reveal that EUV radiation can trigger distinctive high density core formation embedded in a final linear structure. This contrasts with results of the previous work in which only an isotropic Far Ultraviolet (FUV) interstellar background flux was applied. A systematic investigation on a group of prolate clouds of equal mass but different initial densities and geometric shapes finds that the distribution of the cores over the final linear structure changes with the initial conditions of the prolate cloud and the strength of the EUV radiation flux. These highly condensed cores may either scatter over the full length of the final linear structure or form two groups of high density cores at two foci, depending on the value of the ionising radiation penetration depth d_EUV, the ratio of the physical ionising radiation penetration depth to the minor axis of the cloud. Data anlysis on the total mass of the high density cores and the core formation time finds that the potential for EUV radiation triggered star formation efficiency is higher in prolate clouds with shallow ionisation penetration depth and intermediate major to minor axial ratio, for the physical environments investigated. Finally, it is suggested that the various fragment-core structures observed at Hii boundaries may result from the interaction between ionising radiation and pre-existing prolate clouds of different initial geometrical and physical conditions.
description: to be published in Monthly Notices of the Royal Astronomical Society, 16 pages, 16 figures, 5 tables
Neutrophil Extracellular Trap (NET)-Mediated Killing of Pseudomonas aeruginosa: Evidence of Acquired Resistance within the CF Airway, Independent of CFTR
Creators: name: Caceres, Silvia M.
name: Malcolm, Kenneth C.
name: Vasil, Michael L.
name: Taylor-Cousar, Jennifer L.
name: Poch, Katie R.
name: Nick, Jerry A.
name: Young, Robert L.
name: Moskowitz, Samuel M.
name: Saavedra, Milene T.
name: Burns, Jane L.
name: Randell, Scott H.
name: Nichols, David P.
name: Kret, Jennifer E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The inability of neutrophils to eradicate Pseudomonas aeruginosa within the cystic fibrosis (CF) airway eventually results in chronic infection by the bacteria in nearly 80 percent of patients. Phagocytic killing of P. aeruginosa by CF neutrophils is impaired due to decreased cystic fibrosis transmembrane conductance regulator (CFTR) function and virulence factors acquired by the bacteria. Recently, neutrophil extracellular traps (NETs), extracellular structures composed of neutrophil chromatin complexed with granule contents, were identified as an alternative mechanism of pathogen killing. The hypothesis that NET-mediated killing of P. aeruginosa is impaired in the context of the CF airway was tested. P. aeruginosa induced NET formation by neutrophils from healthy donors in a bacterial density dependent fashion. When maintained in suspension through continuous rotation, P. aeruginosa became physically associated with NETs. Under these conditions, NETs were the predominant mechanism of killing, across a wide range of bacterial densities. Peripheral blood neutrophils isolated from CF patients demonstrated no impairment in NET formation or function against P. aeruginosa. However, isogenic clinical isolates of P. aeruginosa obtained from CF patients early and later in the course of infection demonstrated an acquired capacity to withstand NET-mediated killing in 8 of 9 isolates tested. This resistance correlated with development of the mucoid phenotype, but was not a direct result of the excess alginate production that is characteristic of mucoidy. Together, these results demonstrate that neutrophils can kill P. aeruginosa via NETs, and in vitro this response is most effective under non-stationary conditions with a low ratio of bacteria to neutrophils. NET-mediated killing is independent of CFTR function or bacterial opsonization. Failure of this response in the context of the CF airway may occur, in part, due to an acquired resistance against NET-mediated killing by CF strains of P. aeruginosa.
Dual CFT on Dyonic Kerr-Sen black hole and its gauged and ultraspinning counterparts
Creators: name: Sakti, Muhammad Fitrah Alfian Rangga
name: Burikham, Piyabut
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We demonstrate that rotating dyonic black holes in Einstein-Maxwell-Dilaton-Axion (EMDA) theory is holographically dual with 2D conformal field theory. We first investigate the duality on dyonic Kerr-Sen black hole with non-vanishing dilaton and axion charges. The near-horizon geometry of extremal dyonic Kerr-Sen spacetime possesses the $SL(2,R) \times U (1)$ isometry allowing to employ the asymptotic symmetry group method to find the corresponding central charge. We find two different branches of the mass which correspond to CFT with two different central charges $c_L=12am_+$ and $c_L=12am_-$. The exact agreement between the Bekenstain-Hawking entropy and entropy from CFT is then found also in two different branches of extremal entropy. Furthermore, we demonstrate that this duality is robust insofar for non-zero AdS length. We show that the duality holds for both dyonic Kerr-Sen-AdS black hole and its ultraspinning counterpart. In both cases, we obtain the expected entropy from CFT which matches exactly with the Bekenstein-Hawking entropy. Since dyonic and axion charges are proportional to $1/m$, we note that there are possibly more than two branches of the central charge for non-zero AdS length in terms of mass. When we turn off dyonic charge, the axion charge vanishes showing the results of Kerr-Sen-AdS black hole. Moreover, when we assume the equal electromagnetic charges, it recovers the results when the dilaton charge vanishes. In the end, we compare the results of dyonic Kerr-Sen-AdS black hole and its ultraspinning counterpart to those of the dyonic Kerr-Newman-AdS black hole and the ultraspinning counterpart. Depending on the dyonic charge parameters, it is found that extremal ultraspinning dyonic Kerr-Sen-AdS black hole is not always superentropic.
description: 22 pages, published
New Human Papilloma Virus E2 Transcription Factor Mimics: A Tripyrrole-Peptide Conjugate with Tight and Specific DNA-Recognition
Creators: name: Gallo, Mariana
name: Comin, Maria J.
name: Krajewski, Krzysztof
name: Wetzler, Diana E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: BackgroundHuman papillomavirus (HPV) is the main causative agent of cervical cancer, particularly high risk strains such us HPV-16, -18 and -31. The viral encoded E2 protein acts as a transcriptional modulator and exerts a key role in viral DNA replication. Thus, E2 constitutes an attractive target for developing antiviral agents. E2 is a homodimeric protein that interacts with the DNA target through an α-helix of each monomer. However, a peptide corresponding to the DNA recognition helix of HPV-16 E2 binds DNA with lower affinity than its full-length DNA binding domain. Therefore, in an attempt to promote the DNA binding of the isolated peptide, we have designed a conjugate compound of the E2 α-helix peptide and a derivative of the antibiotic distamycin, which involves simultaneous minor- and major-groove interactions.Methodology/Principal FindingsAn E2 α-helix peptide-distamycin conjugate was designed and synthesized. It was characterized by NMR and CD spectroscopy, and its DNA binding properties were investigated by CD, DNA melting and gel shift experiments. The coupling of E2 peptide with distamycin does not affect its structural properties. The conjugate improves significantly the affinity of the peptide for specific DNA. In addition, stoichiometric amounts of specific DNA increase meaningfully the helical population of the peptide. The conjugate enhances the DNA binding constant 50-fold, maintaining its specificity.Conclusions/SignificanceThese results demonstrate that peptide-distamycin conjugates are a promising tool to obtain compounds that bind the E2 target DNA-sequences with remarkable affinity and suggest that a bipartite major/minor groove binding scaffold can be a useful approach for therapeutic treatment of HPV infection.
Structure and gap of low-$x$ (Ga$_{1-x}$In$_x$)$_2$O$_3$ alloys
Creators: name: Maccioni, M B
name: Ricci, F
name: Fiorentini, V
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We study the electronic and local structural properties of pure and In-substituted $β$-Ga$_2$O$_3$ using density functional theory (DFT). Our main result is that the structural energetics of In in Ga$_2$O$_3$ causes most sites to be essentially inaccessible to In substitution, thus reducing the maximum In content in thi to somewhere between 12 and 25 \% in this phase. We also find that the gap variation with doping is essentially due to "chemical pressure", i.e. volume variations with doping.
description: 4 pages, 3 figures
Three-laser coherent population trapping in a multi-lambda system: theory, experiment and applications
Creators: name: Barreto, Nicolás Nuñez
name: Drechsler, Martin
name: Schmiegelow, Christian Tomás
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Atomic Physics (physics.atom-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We present theoretical and experimental results of coherent population trapping spectra on a multi-level $^{40}$Ca$^+$-type configuration, adding a third beam to the standard two-laser $Λ$ system to avoid undesired optical pumping. We show that the extra laser can preserve the nature of the dark resonances or introduce decoherence depending on its power. Experiments are carried out using a single trapped $^{40}$Ca$^+$ ion in the $S_{1/2}-P_{1/2}-D_{3/2}$ manifold. Theoretically, the problem is solved with a Floquet-like expansion of the Liouvillian that correctly predicts all of the measured spectra without the need of full time integration. As a first application of the multilaser technique, we show that the richer spectra obtained can be used as a vectorial polarimeter of one of the beams, allowing one to measure the electrical field at the ion position in any spatial direction. We also explain how our setup could realize a thermometer with tunable sensitivity and no laser-linewidth dependence.
description: 11 pages, 8 figures
BO'LAJAK MUSIQA TA'LIMI O'QITUVCHILARIDA KOMMUNIKATIV KO'NIKMALARNI RIVOJLANTIRISH
Creators: name: Tursunaliyeva, Muxlisaxon
Publisher: name: Zenodo
Year: 2024

description: Ushbu tezisda "Bo‘lajak musiqa ta’limi o‘qituvchilarida kommunikativ ko‘nikmalarni rivojlantirish" mavzusi yoritilgan. Tezisda bo‘lajak musiqa o‘qituvchilarining professional faoliyatida kommunikativ ko‘nikmalarning ahamiyati, ularning ta’lim jarayonidagi o‘rni va rivojlantirish strategiyalari ko‘rib chiqiladi. Bo‘lajak o‘qituvchilarda kommunikativ ko‘nikmalarni samarali rivojlantirish uchun zamonaviy pedagogik metodlar, innovatsion texnologiyalar va amaliy mashg‘ulotlar muhokama qilinadi. Tezisda shuningdek, kommunikativ ko‘nikmalarning musiqa ta’limi sohasida ta’siri, o‘qituvchi va talaba o‘rtasidagi o‘zaro aloqaning yaxshilanishi, hamda ta’lim jarayonining samaradorligini oshirish uchun zaruriy choralar hamda tavsiyalar keltirilgan.
Performance of Genotype Imputation for Rare Variants Identified in Exons and Flanking Regions of Genes
Creators: name: Slater, Andrew J.
name: Li, Li
name: Aponte, Jennifer L.
name: Whittaker, John C.
name: Nelson, Matthew R.
name: Ehm, Margaret Gelder
name: Browning, Sharon R.
name: Li, Yun
name: Chissoe, Stephanie L.
name: Mooser, Vincent E.
name: Kong, Xiangyang
name: Browning, Brian L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Genotype imputation has the potential to assess human genetic variation at a lower cost than assaying the variants using laboratory techniques. The performance of imputation for rare variants has not been comprehensively studied. We utilized 8865 human samples with high depth resequencing data for the exons and flanking regions of 202 genes and Genome-Wide Association Study (GWAS) data to characterize the performance of genotype imputation for rare variants. We evaluated reference sets ranging from 100 to 3713 subjects for imputing into samples typed for the Affymetrix (500K and 6.0) and Illumina 550K GWAS panels. The proportion of variants that could be well imputed (true r2>0.7) with a reference panel of 3713 individuals was: 31% (Illumina 550K) or 25% (Affymetrix 500K) with MAF (Minor Allele Frequency) less than or equal 0.001, 48% or 35% with 0.001<MAF< = 0.005, 54% or 38% with 0.005<MAF< = 0.01, 78% or 57% with 0.01<MAF< = 0.05, and 97% or 86% with MAF>0.05. The performance for common SNPs (MAF>0.05) within exons and flanking regions is comparable to imputation of more uniformly distributed SNPs. The performance for rare SNPs (0.01<MAF< = 0.05) was much more dependent on the GWAS panel and the number of reference samples. These results suggest routine use of genotype imputation for extending the assessment of common variants identified in humans via targeted exon resequencing into additional samples with GWAS data, but imputation of very rare variants (MAF< = 0.005) will require reference panels with thousands of subjects.