cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Dominant Rio1 kinase/ATPase catalytic mutant induces trapping of late pre-40S biogenesis factors in 80S-like ribosomes
Creators: name: Ferreira-Cerca, Sébastien
name: Kiburu, Irene
name: Thomson, Emma
name: LaRonde, Nicole
name: Hurt, Ed
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: 570 Biowissenschaften, Biologie

description: During eukaryotic ribosome biogenesis, members of the conserved atypical serine/threonine protein kinase family, the RIO kinases (Rio1, Rio2 and Rio3) function in small ribosomal subunit biogenesis. Structural analysis of Rio2 indicated a role as a conformation-sensing ATPase rather than a kinase to regulate its dynamic association with the pre-40S subunit. However, it remained elusive at which step and by which mechanism the other RIO kinase members act. Here, we have determined the crystal structure of the human Rio1-ATP-Mg2+ complex carrying a phosphoaspartate in the active site indicative of ATPase activity. Structure-based mutations in yeast showed that Rio1's catalytic activity regulates its pre-40S association. Furthermore, we provide evidence that Rio1 associates with a very late pre-40S via its conserved C-terminal domain. Moreover, a rio1 dominant-negative mutant defective in ATP hydrolysis induced trapping of late biogenesis factors in pre-ribosomal particles, which turned out not to be pre-40S but 80S-like ribosomes. Thus, the RIO kinase fold generates a versatile ATPase enzyme, which in the case of Rio1 is activated following the Rio2 step to regulate one of the final 40S maturation events, at which time the 60S subunit is recruited for final quality control check.
Reversible Fluorination of Graphene: towards a Two-Dimensional Wide Bandgap Semiconductor
Creators: name: Cheng, S. -H.
name: Zou, K.
name: Okino, F.
name: Gutierrez, H. R.
name: Gupta, A.
name: Shen, N.
name: Eklund, P. C.
name: Sofo, J. O.
name: Zhu, J.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report the synthesis and evidence of graphene fluoride, a two-dimensional wide bandgap semiconductor derived from graphene. Graphene fluoride exhibits hexagonal crystalline order and strongly insulating behavior with resistance exceeding 10 G$Ω$ at room temperature. Electron transport in graphene fluoride is well described by variable-range hopping in two dimensions due to the presence of localized states in the band gap. Graphene obtained through the reduction of graphene fluoride is highly conductive, exhibiting a resistivity of less than 100 k$Ω$ at room temperature. Our approach provides a new path to reversibly engineer the band structure and conductivity of graphene for electronic and optical applications.
description: 7 pages, 5 figures, revtex, to appear in PRB
Quantum mechanics of composite objects with internal entanglement
Creators: name: Suzuki, Fumika
Publisher: name: University of British Columbia
Year: 2017

description: Although many quantum mechanics problems of a point particle have been well understood, the realistic physical model is often a composite object consisting of particles bound together, and its quantum mechanics is an important problem with applications in many areas of physics. Unlike a point particle, a composite object possesses internal structure described by some degrees of freedom which are often entangled with each other. We call the entanglement among these degrees of freedom ``internal entanglement'', to distinguish it from any other entanglement they may share with an external object. Examples of internal entanglement include the entanglement between a vibrational and a rotational mode of a molecule, and that between its position and its internal clock-state etc. In this thesis, we study quantum mechanics of composite objects by focusing on the effects of internal entanglement. We first look at the tunnelling of a diatomic molecule type composite object through a half-silvered mirror in continuum space and observe that its spatial superposition state made by the mirror can decohere by emission of radiation due to the fact that its internal degrees of freedom are entangled with radiation fields, and that there exists entanglement between its position and its internal (i.e., relative position) degrees of freedom. Secondly, we study its lattice analog in molecular crystals, namely we replace the diatomic molecule by a biexicton, and the mirror by an impurity. We find that discreteness of a lattice makes the wave vector of a biexicton and the relative distance between two excitons of it entangled with each other. We investigate how this inseparability affects the creation of the biexciton-impurity bound states and the entanglement dynamics. Finally we propose a possible application of our study of internal entanglement to the Anderson model of a composite quasiparticle.
Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction.
Creators: name: Dümcke, Sebastian
name: Bräuer, Johannes
name: Anchang, Benedict Nchang
name: Spang, Rainer
name: Beerenwinkel, Niko
name: Tresch, Achim
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Algorithms
subject: Animals
subject: Cell Differentiation
subject: Embryonic Stem Cells/metabolism
subject: Feedback, Physiological
subject: Gene Expression
subject: Mice
subject: Probability
subject: RNA Interference
subject: Signal Transduction

description: MOTIVATION: For biological pathways, it is common to measure a gene expression time series after various knockdowns of genes that are putatively involved in the process of interest. These interventional time-resolved data are most suitable for the elucidation of dynamic causal relationships in signaling networks. Even with this kind of data it is still a major and largely unsolved challenge to infer the topology and interaction logic of the underlying regulatory network. RESULTS: In this work, we present a novel model-based approach involving Boolean networks to reconstruct small to medium-sized regulatory networks. In particular, we solve the problem of exact likelihood computation in Boolean networks with probabilistic exponential time delays. Simulations demonstrate the high accuracy of our approach. We apply our method to data of Ivanova et al. (2006), where RNA interference knockdown experiments were used to build a network of the key regulatory genes governing mouse stem cell maintenance and differentiation. In contrast to previous analyses of that data set, our method can identify feedback loops and provides new insights into the interplay of some master regulators in embryonic stem cell development. Availability and implementation: The algorithm is implemented in the statistical language R. Code and documentation are available at Bioinformatics online.
DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases.
Creators: name: Aryee, Martin J.
name: Liu, Wennuan
name: Engelmann, Julia C.
name: Nuhn, Philipp
name: Gurel, Meltem
name: Haffner, Michael C.
name: Esopi, David
name: Irizarry, Rafael A.
name: Getzenberg, Robert H.
name: Nelson, William G.
name: Luo, Jun
name: Xu, Jianfeng
name: Isaacs, William B.
name: Bova, G. Steven
name: Yegnasubramanian, Srinivasan
Publisher: name: Universität Regensburg
Year: 2013
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Alleles
subject: Clone Cells
subject: DNA Methylation/genetics
subject: DNA-Binding Proteins/genetics
subject: Epigenesis, Genetic
subject: Gene Expression Regulation, Neoplastic
subject: Genetic Heterogeneity
subject: Genomics
subject: Humans
subject: Male
subject: Neoplasm Metastasis
subject: Polymorphism, Single Nucleotide/genetics
subject: Prostatic Neoplasms/pathology
subject: Protein Structure, Tertiary

description: Human cancers almost ubiquitously harbor epigenetic alterations. Although such alterations in epigenetic marks, including DNA methylation, are potentially heritable, they can also be dynamically altered. Given this potential for plasticity, the degree to which epigenetic changes can be subject to selection and act as drivers of neoplasia has been questioned. We carried out genome-scale analyses of DNA methylation alterations in lethal metastatic prostate cancer and created DNA methylation "cityscape" plots to visualize these complex data. We show that somatic DNA methylation alterations, despite showing marked interindividual heterogeneity among men with lethal metastatic prostate cancer, were maintained across all metastases within the same individual. The overall extent of maintenance in DNA methylation changes was comparable to that of genetic copy number alterations. Regions that were frequently hypermethylated across individuals were markedly enriched for cancer- and development/differentiation-related genes. Additionally, regions exhibiting high consistency of hypermethylation across metastases within individuals, even if variably hypermethylated across individuals, showed enrichment for cancer-related genes. Whereas some regions showed intraindividual metastatic tumor heterogeneity in promoter methylation, such methylation alterations were generally not correlated with gene expression. This was despite a general tendency for promoter methylation patterns to be strongly correlated with gene expression, particularly at regions that were variably methylated across individuals. These findings suggest that DNA methylation alterations have the potential for producing selectable driver events in carcinogenesis and disease progression and highlight the possibility of targeting such epigenome alterations for development of longitudinal markers and therapeutic strategies.
Higher rank stable pairs on K3 surfaces
Creators: name: Bakker, Benjamin
name: Jorza, Andrei
Publisher: name: arXiv
Year: 2011
Subjects: subject: Algebraic Geometry (math.AG)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 14N35, 14J28, 14D20

description: We define and compute higher rank analogs of Pandharipande-Thomas stable pair invariants in primitive classes for K3 surfaces. Higher rank stable pair invariants for Calabi-Yau threefolds have been defined by Sheshmani \cite{shesh1,shesh2} using moduli of pairs of the form $Ø^n\into \F$ for $\F$ purely one-dimensional and computed via wall-crossing techniques. These invariants may be thought of as virtually counting embedded curves decorated with a $(n-1)$-dimensional linear system. We treat invariants counting pairs $Ø^n\into \E$ on a $\K3$ surface for $\E$ an arbitrary stable sheaf of a fixed numerical type ("coherent systems" in the language of \cite{KY}) whose first Chern class is primitive, and fully compute them geometrically. The ordinary stable pair theory of $\K3$ surfaces is treated by \cite{MPT}; there they prove the KKV conjecture in primitive classes by showing the resulting partition functions are governed by quasimodular forms. We prove a "higher" KKV conjecture by showing that our higher rank partition functions are modular forms.
Poisson Reduction
Creators: name: Esposito, Chiara
Publisher: name: arXiv
Year: 2011
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics

description: In this paper we develope a theory of reduction for classical systems with Poisson Lie groups symmetries using the notion of momentum map introduced by Lu. The local description of Poisson manifolds and Poisson Lie groups and the properties of Lu's momentum map allow us to define a Poisson reduced space.
description: 13 pages
N-cadherin promoter polymorphisms and risk of osteoarthritis
Creators: name: Ruedel, Anke
name: Stark, Klaus
name: Kaufmann, Simone
name: Bauer, Richard
name: Reinders, Jörg
name: Rovensky, Jozef
name: Blazicková, Stanislava
name: Oefner, Peter J.
name: Bosserhoff, Anja Katrin
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: CDH2; genetic association study; hnRNP K; rs11564299
subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Adult
subject: Aged
subject: Aged, 80 and over
subject: Binding Sites/physiology
subject: Cadherins/genetics
subject: Cells, Cultured
subject: Chromatin Immunoprecipitation
subject: Electrophoretic Mobility Shift Assay
subject: Enzyme-Linked Immunosorbent Assay
subject: Female
subject: Genotype
subject: Humans
subject: Male
subject: Middle Aged
subject: Osteoarthritis/genetics
subject: Polymorphism, Genetic/genetics
subject: Promoter Regions, Genetic/genetics
subject: Reverse Transcriptase Polymerase Chain Reaction
subject: Young Adult

description: Osteoarthritis (OA) is the most common form of arthritis. It is characterized by cartilage destruction and bone remodeling, mediated in part by synovial fibroblasts (SFs). Given the functional significance of cadherins in these cells, we aimed at determining the role of genetic variants of N-cadherin (CDH2) in OA of the knee and hip. Six single-nucleotide polymorphisms in the genomic region of the CDH2 gene were genotyped in 312 patients with OA and 259 healthy control subjects. Gene expression of CDH2 was analyzed by qRT-PCR. Liquid chromatography-mass spectrometry was used to identify a transcription factor isolated by DNA pulldown. Its potential for binding to gene variants was examined by electrophoretic mobility shift assay, enzyme-linked immunosorbent assay, and chromatin immunoprecipitation. Genetic analysis identified a polymorphism located in the CDH2 promoter region to be associated with risk of OA. The minor allele of rs11564299 had a protective effect against OA. Compared to carriers of the major allele, carriers of the minor allele of rs11564299 displayed increased N-cadherin levels in SFs. Based on in silico analysis, the minor allele was predicted to generate a novel transcription factor binding site, Direct-binding assays and mass spectrometric analysis identified hnRNP K as binding selectively to the minor allele. In summary, a CDH2 promoter polymorphism influences the risk of OA, and hnRNP K was found to be involved in the regulation of elevated N-cadherin expression in patients with OA carrying the minor allele of rs11564299.
GRB 050502B optical afterglow: a jet break at high redshift
Creators: name: Afonso, P.
name: Greiner, J.
name: Pian, E.
name: Covino, S.
name: Malesani, D.
name: Yoldaş, A. Küpcü
name: Krühler, T.
name: Clemens, C.
name: McBreen, S.
name: Rau, A.
name: Giannios, D.
name: Hjorth, J.
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Aims: GRB 050502B is well known for the very bright flare displayed in its X-ray light curve. Despite extensive studies, however, the optical light curve has never been discussed and its redshift is unconstrained. Possible correlations between optical and X-ray data are analysed. Methods: Photometric data from TNG in the R and I bands were used to compare the optical afterglow with the X-ray light curve. The HyperZ package and a late time VLT host observation were used to derive redshift estimates. Results: The I-band afterglow decay followed a power-law of index α = 2.1 $\pm$ 0.6, after a late break at ~ $1.3 \times 10^5$ s. The R - I color is remarkably red and the broadband spectral index β_OX = $0.9 \pm 0.1$ is consistent with the X-ray spectral slope β_X. Although a photometric redshift of z > 4 is the most conservative result to consider, a photometric redshift of z = 5.2 $\pm$ 0.3 is suggested with no extinction in the host, based on which an isotropic energy E_γ,iso = $(3.8 \pm 0.7) \times 10^52$ erg and a jet opening angle θ ~ $3.7^{\circ}$ are subsequently derived. Conclusions: The combined X-ray and optical data suggest an achromatic break, which we interpret as a jet break. The post jet break slope obeys roughly the closure relation for the jet slow cooling model. Because of the afterglow's very red color, in order for the redshift to be low (z < 1), extinction, if present in the host, must be significantly high. Since the optical-to-X-ray index is consistent with the X-ray spectrum, and there is no XRT evidence for excess N_H, GRB 050502B was likely at high redshift.
Wood grain direction measurement from spatial reflection with linear method
Creators: name: Pan, Qi
Publisher: name: University of British Columbia
Year: 2017

description: Wood grain direction is a very important quality control feature in wood industry because it is a good indicator of wood strength and uniformity. It is a three-dimensional quantity that is defined by its angles within and into the plane of the measured surface. These are respectively called the surface and dive angles. An interesting method to measure these angles involves measuring the spatial reflection from the wood surface when illuminated by concentrated light. The cellular shape of the wood microstructure causes the light reflection to be greatest perpendicular to the wood grain. This effect allows the surface and dive angles to be determined by analyzing the spatial variation of the reflected light. The conventional method for doing this involves sampling the reflection intensities around a circle above the wood surface. However, this method is effective only for small dive angles. A new method is described here where light reflection intensity variation is measured along two parallel lines on either side of the illuminated area. It is able to measure the full ranges of surface and dive angles that occur in practice. A laboratory device for making the required spatial reflection measurements is described and experimental results are presented. Based on the linear method, an equipment can be developed for industrial purpose, which consists of two parallel lines of sensors sparsely distributed along the longitudinal axis of lumber. To investigate this proposed arrangement of sensors, an interpolation study was undertaken on the associated low-resolution data, with the results compared with those from high-resolution full-field data. With the proposed sensor arrangement, grain angle measurements can be made at very high speed, which makes the equipment suitable for industrial use in sawmills and wood products factories.
Molecular classification of mature aggressive B-cell lymphoma using digital multiplexed gene expression on formalin-fixed paraffin-embedded biopsy specimens.
Creators: name: Masqué-Soler, Neus
name: Szczepanowski, Monika
name: Kohler, Christian
name: Spang, Rainer
name: Klapper, Wolfram
Publisher: name: Universität Regensburg
Year: 2013
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: B-Lymphocytes/pathology
subject: Biopsy
subject: Formaldehyde
subject: Gene Expression Profiling/methods
subject: Gene Expression Regulation, Neoplastic
subject: Humans
subject: Linear Models
subject: Lymphoma, B-Cell/pathology
subject: Paraffin Embedding
subject: Reproducibility of Results
subject: Tissue Fixation

description: The most frequent mature aggressive B-cell lymphomas are diffuse large B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL). Patients suffering from molecularly defined BL (mBL) but treated with a regimen developed for DLBCL show an unfavorable outcome compared with mBL treated with chemotherapy regimens for BL. Distinguishing BL from DLBCL by conventional histopathology is challenging in lymphomas that have features common to both diseases (aggressive B-cell lymphoma unclassifiable with features of DLBCL and BL [intermediates]). Moreover, DLBCLs are a heterogeneous group of lymphomas comprising distinct molecular subtypes: the activated B-cell–like (ABC), the germinal center B-cell–like (GCB), and the unclassifyable subtype as defined by gene expression profiling (GEP). Attempts to replace GEP with techniques applicable to formalin-fixed paraffin-embedded (FFPE) tissue led to algorithms for immunohistochemical staining (IHS).Disappointingly, the algorithms yielded conflicting results with respect to their prognostic potential, raising concerns about their validity. Furthermore, IHS algorithms did not provide a fully resolved classification: they did not identify mBL nor did they separate ABC from unclassified DLBCLs.
Lumbar Integrated Fixation Devices-Best Practices for Biomechanical Evaluation under Fatigue Loading
Creators: name: Regulatory Catalog
Publisher: name: Zenodo
Year: 2023

description: This tool provides recommended best practices for performing in vitro human cadaver based biomechanical evaluation of lumbar integrated fixation devices (IFDs) under fatigue loading. This tool also describes recommendations for performing multidirectional flexibility assessment of IFD constructs in the intact state, before and after the fatigue loading, to quantify the effect of the IFD on segmental range of motion (ROM). The tool Appendix describes recommendations for: Specimen preparation Study design Biomechanical testing Data analysis
Different patterns of Epstein-Barr virus latency in endemic Burkitt lymphoma (BL) lead to distinct variants within the BL-associated gene expression signature
Creators: name: Kelly, Gemma L
name: Stylianou, Julianna
name: Rasaiyaah, Jane
name: Wei, Wenbin
name: Thomas, Wendy
name: Croom-Carter, Deborah
name: Kohler, Christian
name: Spang, Rainer
name: Woodman, Ciaran
name: Kellam, Paul
name: Rickinson, Alan N.
name: Bell, Andrew I.
Publisher: name: Universität Regensburg
Year: 2013
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Antigens, Viral/biosynthesis
subject: Burkitt Lymphoma/virology
subject: Cell Line, Tumor
subject: DNA-Binding Proteins/genetics
subject: Down-Regulation
subject: Epstein-Barr Virus Nuclear Antigens/biosynthesis
subject: Gene Expression Profiling
subject: Gene Expression Regulation, Viral
subject: Herpesvirus 4, Human/physiology
subject: Humans
subject: Interferon Regulatory Factors/biosynthesis
subject: Repressor Proteins/biosynthesis
subject: Transcriptome
subject: Up-Regulation
subject: Viral Proteins/biosynthesis
subject: Virus Latency/genetics

description: Epstein-Barr virus (EBV) is present in all cases of endemic Burkitt lymphoma (BL) but in few European/North American sporadic BLs. Gene expression arrays of sporadic tumors have defined a consensus BL profile within which tumors are classifiable as "molecular BL" (mBL). Where endemic BLs fall relative to this profile remains unclear, since they not only carry EBV but also display one of two different forms of virus latency. Here, we use early-passage BL cell lines from different tumors, and BL subclones from a single tumor, to compare EBV-negative cells with EBV-positive cells displaying either classical latency I EBV infection (where EBNA1 is the only EBV antigen expressed from the wild-type EBV genome) or Wp-restricted latency (where an EBNA2 gene-deleted virus genome broadens antigen expression to include the EBNA3A, -3B, and -3C proteins and BHRF1). Expression arrays show that both types of endemic BL fall within the mBL classification. However, while EBV-negative and latency I BLs show overlapping profiles, Wp-restricted BLs form a distinct subgroup, characterized by a detectable downregulation of the germinal center (GC)-associated marker Bcl6 and upregulation of genes marking early plasmacytoid differentiation, notably IRF4 and BLIMP1. Importantly, these same changes can be induced in EBV-negative or latency I BL cells by infection with an EBNA2-knockout virus. Thus, we infer that the distinct gene profile of Wp-restricted BLs does not reflect differences in the identity of the tumor progenitor cell per se but differences imposed on a common progenitor by broadened EBV gene expression.
CASTRO: A New Compressible Astrophysical Solver. I. Hydrodynamics and Self-Gravity
Creators: name: Almgren, A. S.
name: Beckner, V. E.
name: Bell, J. B.
name: Day, M. S.
name: Howell, L. H.
name: Joggerst, C. C.
name: Lijewski, M. J.
name: Nonaka, A.
name: Singer, M.
name: Zingale, M.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We present a new code, CASTRO, that solves the multicomponent compressible hydrodynamic equations for astrophysical flows including self-gravity, nuclear reactions and radiation. CASTRO uses an Eulerian grid and incorporates adaptive mesh refinement (AMR). Our approach to AMR uses a nested hierarchy of logically-rectangular grids with simultaneous refinement in both space and time. The radiation component of CASTRO will be described in detail in the next paper, Part II, of this series.
description: accepted to Astrophysical Journal Suppliment (http://iop.org), 52 pages, 16 figures
Correlations between milk and plasma levels of amino and carboxylic acids in dairy cows.
Creators: name: Klein, Matthias S.
name: Almstetter, Martin F.
name: Nürnberger, Nadine
name: Sigl, Gregor
name: Gronwald, Wolfram
name: Wiedemann, Steffi
name: Dettmer, Katja
name: Oefner, Peter J.
Publisher: name: Universität Regensburg
Year: 2013
Subjects: subject: metabolomics; gas chromatography−mass spectrometry; plasma; milk; dairy cows
subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Amino Acids/metabolism
subject: Analysis of Variance
subject: Animals
subject: Carboxylic Acids/metabolism
subject: Cattle
subject: Female
subject: Gas Chromatography-Mass Spectrometry
subject: Metabolomics/methods
subject: Milk/metabolism

description: The objective of this study was to investigate the relationship between the concentrations of 19 amino acids, glucose, and seven carboxylic acids in the blood and milk of dairy cows and their correlations with established markers of ketosis. To that end, blood plasma and milk specimens were collected throughout lactation in two breeds of dairy cows of different milk yield. Plasma concentrations of glucose, pyruvate, lactate, α-aminobutyrate, β-hydroxybutyrate (BHBA), and most amino acids, except for glutamate and aspartate, were on average 9.9-fold higher than their respective milk levels. In contrast, glutamate, aspartate, and the Krebs cycle intermediates succinate, fumarate, malate, and citrate were on average 9.1-fold higher in milk than in plasma. For most metabolites, with the exception of BHBA and threonine, no significant correlations were observed between their levels in plasma and milk. Additionally, milk levels of acetone showed significant direct relationships with the glycine-to-alanine ratio and the BHBA concentration in plasma. The marked decline in plasma concentrations of glucose, pyruvate, lactate, and alanine in cows with plasma BHBA levels above the diagnostic cutoff point for subclinical ketosis suggests that these animals fail to meet their glucose demand and, as a consequence, rely increasingly on ketone bodies as a source of energy. The concomitant increase in plasma glycine may reflect not only the excessive depletion of protein reserves but also a potential deficiency of vitamin B6.
Astrometric Effects of a Stochastic Gravitational Wave Background
Creators: name: Book, Laura G.
name: Flanagan, Éanna É.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: A stochastic gravitational wave background causes the apparent positions of distant sources to fluctuate, with angular deflections of order the characteristic strain amplitude of the gravitational waves. These fluctuations may be detectable with high precision astrometry, as first suggested by Braginsky et al. in 1990. Several researchers have made order of magnitude estimates of the upper limits obtainable on the gravitational wave spectrum Ω_gw(f), at frequencies of order f ~ 1 yr^-1, both for the future space-based optical interferometry missions GAIA and SIM, and for VLBI interferometry in radio wavelengths with the SKA. For GAIA, tracking N ~ 10^6 quasars over a time of T ~ 1 yr with an angular accuracy of Δθ~ 10 μas would yield a sensitivity level of Ω_gw ~ (Δθ)^2/(N T^2 H_0^2) ~ 10^-6, which would be comparable with pulsar timing. In this paper we take a first step toward firming up these estimates by computing in detail the statistical properties of the angular deflections caused by a stochastic background. We compute analytically the two point correlation function of the deflections on the sphere, and the spectrum as a function of frequency and angular scale. The fluctuations are concentrated at low frequencies (for a scale invariant stochastic background), and at large angular scales, starting with the quadrupole. The magnetic-type and electric-type pieces of the fluctuations have equal amounts of power.
description: 23 pages, 2 figures, references added and minor text corrections
Quantification of encapsulated bioburden in spacecraft polymer materials by cultivation-dependent and molecular methods
Creators: name: Bauermeister, Anja
name: Mahnert, Alexander
name: Auerbach, Anna
name: Böcker, Alexander
name: Flier, Niwin
name: Weber, Christina
name: Probst, Alexander J.
name: Haberer, Klaus
name: Moissl-Eichinger, Christine
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: 570 Biowissenschaften, Biologie

description: Bioburden encapsulated in spacecraft polymers (such as adhesives and coatings) poses a potential risk to jeopardize scientific exploration of other celestial bodies. This is particularly critical for spacecraft components intended for hard landing. So far, it remained unclear if polymers are indeed a source of microbial contamination. In addition, data with respect to survival of microbes during the embedding/polymerization process are sparse. In this study we developed testing strategies to quantitatively examine encapsulated bioburden in five different polymers used frequently and in large quantities on spaceflight hardware. As quantitative extraction of the bioburden from polymerized (solid) materials did not prove feasible, contaminants were extracted from uncured precursors. Cultivation-based analyses revealed <0.1–2.5 colony forming units (cfu) per cm3 polymer, whereas quantitative PCR-based detection of contaminants indicated considerably higher values, despite low DNA extraction efficiency. Results obtained from this approach reflect the most conservative proxy for encapsulated bioburden, as they give the maximum bioburden of the polymers irrespective of any additional physical and chemical stress occurring during polymerization. To address the latter issue, we deployed an embedding model to elucidate and monitor the physiological status of embedded Bacillus safensis spores in a cured polymer. Staining approaches using AlexaFluor succinimidyl ester 488 (AF488), propidium monoazide (PMA), CTC (5-cyano-2,3-diotolyl tetrazolium chloride) demonstrated that embedded spores retained integrity, germination and cultivation ability even after polymerization of the adhesive Scotch-Weld 2216 B/A. Using the methods presented here, we were able to estimate the worst case contribution of encapsulated bioburden in different polymers to the bioburden of spacecraft. We demonstrated that spores were not affected by polymerization processes. Besides Planetary Protection considerations, our results could prove useful for the manufacturing of food packaging, pharmacy industry and implant technology.
Dynamics of Unitarization by Classicalization
Creators: name: Dvali, Gia
name: Pirtskhalava, David
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study dynamics of the classicalization phenomenon suggested in arXiv:1010.1415, according to which a class of non-renormalizable theories self-unitarizes at high-energies via creation of classical configurations (classicalons). We study this phenomenon in an explicit model of derivatively-self-coupled scalar that serves as a prototype for a Nambu-Goldstone-Stückelberg field. We prepare the initial state in form of a collapsing wave-packet of a small occupation number but of very high energy, and observe that the classical configuration indeed develops. Our results confirm the previous estimates, showing that because of self-sourcing the wave-packet forms a classicalon configuration with radius that increases with center of mass energy. Thanks to self-sourcing by energy, unlike solitons, the production of classicalons dominates the high-energy scattering. In order to confront classicalizing and non-classicalizing theories, we use a language in which the scattering cross section can be universally understood as a geometric cross section set by a classical radius down to which waves can propagate freely. The difference is, that in non-classicalizing examples this radius shrinks with increasing energy, whereas in classicalizing theories expands and becomes macroscopic. We study analogous scattering in a Galileon system and discover that classicalization is less efficient there. We thus observe, that classicalization is source-sensitive and that Goldstones pass the first test.
description: 20 pages
Wnt secretion is required to maintain high levels of Wnt activity in colon cancer cells
Creators: name: Voloshanenko, Oksana
name: Erdmann, Gerrit
name: Dubash, Taronish D.
name: Augustin, Iris
name: Metzig, Marie
name: Moffa, Giusi
name: Hundsrucker, Christian
name: Kerr, Grainne
name: Sandmann, Thomas
name: Anchang, Benedikt
name: Demir, Kubilay
name: Boehm, Christina
name: Leible, Svenja
name: Ball, Claudia R.
name: Glimm, Hanno
name: Spang, Rainer
name: Boutros, Michael
Publisher: name: Universität Regensburg
Year: 2013
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Adenocarcinoma/pathology
subject: Adenomatous Polyposis Coli Protein/metabolism
subject: Animals
subject: Cell Line, Tumor
subject: Cell Proliferation
subject: Colon/pathology
subject: Colonic Neoplasms/pathology
subject: Gene Expression Regulation, Neoplastic
subject: Humans
subject: Intracellular Signaling Peptides and Proteins/metabolism
subject: Mice
subject: Mice, Inbred NOD
subject: Mutation
subject: Neoplasm Transplantation
subject: Receptor, EphB2/metabolism
subject: Receptors, G-Protein-Coupled/metabolism
subject: Signal Transduction
subject: Wnt3 Protein/metabolism
subject: beta Catenin/metabolism

description: Aberrant regulation of the Wnt/β-catenin pathway has an important role during the onset and progression of colorectal cancer, with over 90% of cases of sporadic colon cancer featuring mutations in APC or β-catenin. However, it has remained a point of controversy whether these mutations are sufficient to activate the pathway or require additional upstream signals. Here we show that colorectal tumours express elevated levels of Wnt3 and Evi/Wls/GPR177. We found that in colon cancer cells, even in the presence of mutations in APC or β-catenin, downstream signalling remains responsive to Wnt ligands and receptor proximal signalling. Furthermore, we demonstrate that truncated APC proteins bind β-catenin and key components of the destruction complex. These results indicate that cells with mutations in APC or β-catenin depend on Wnt ligands and their secretion for a sufficient level of β-catenin signalling, which potentially opens new avenues for therapeutic interventions by targeting Wnt secretion via Evi/Wls.
Quantitative modeling of the temperature-dependent internal Quantum Efficiency in InGaN light emitting diodes
Creators: name: Nirschl, Anna
name: Gomez-Iglesias, Alvaro
name: Sabathil, M.
name: Hartung, Georg
name: Off, Jürgen
name: Bougeard, Dominique
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: GaN; InGaN; internal quantum efficiency; light emitting diodes
subject: 530 Physik

description: The temperature dependence of the internal quantum efficiency (IQE) of blue InGaN-based light emitting diodes is analyzed both experimentally and theoretically with a drift-diffusion transport model. A high-performance reference structure and two improved epitaxial designs are compared at different operating temperatures. In contrast to a simple ABC model, the proposed approach allows for quantitative predictions of IQEs including optimizations regarding spatial carrier distributions at room temperature. At elevated temperatures, a moderate increase of the Auger coefficient gives a more precise agreement between experiment and simulations. The results show that the model is suitable to quantitatively predict the IQE for different structures and temperatures.
Image-based enhancement and tracking of an epidural needle in ultrasound using time-series analysis
Creators: name: Beigi, Parmida
Publisher: name: University of British Columbia
Year: 2017

description: Accurate placement of the needle to the target spot is crucial to the safety, efficiency and success of any ultrasound (US) guided procedures, e.g. epidurals. Real-time single-operator US guidance of epidurals is currently impractical with conventional 2D US and a standard needle. A novel 3D US imaging technology (3DUS+Epiguide) has been developed by our group to provide such capability, which comprises thick-slice rendering and a custom needle guide, Epiguide. This system aims to facilitate a single-operator real-time midline epidural needle insertion by visualizing the needle progression toward the epidural space. The visibility of the needle in US-guided procedures is, however, limited by dispersion of the needle's echoes away from the transducer. This makes needle visibility an ongoing challenge in US-guided procedures, e.g. epidurals. The aim of this thesis is to provide a software-based clinically-suitable solution to enhance needle visibility in US. In particular, we are interested in difficult cases, where the needle is invisible (i.e. minimal visibility) in an US image. To this end, we have developed frameworks to extract signatures from the needle using time-series analysis. We demonstrate that nearly invisible changes in motion dynamics of the needle can be revealed through spatio-temporal processing of the standard US image sequences. The extracted needle features are used to detect, track and localize a hand-held needle in a machine learning-based framework. Clinical, animal and phantom studies are designed to evaluate: 3DUS+Epiguide's capability to identify the needle puncture site for a midline insertion in the lumbar spine, and the capability of the proposed detection frameworks in localizing a needle within clinical acceptance. Methods are evaluated on the data from studies conducted at BC Women's Hospital and Jack Bell Research Facility, and are compared to the gold standard (GS). Results demonstrate that compared to the state-of-the-art needle detection methods using a finely-tuned Hough Transform, with 14% success rate, our proposed method is 100% successful in detecting the trajectory within the GS's close proximity (success: angular error < 10°). The proposed method is especially suitable for barely-visible needles, for which appearance-based enhancement methods fail.
Arabidopsis nanodomain-delimited ABA signaling pathway regulates the anion channel SLAH3
Creators: name: Demir, Fatih
name: Horntrich, Claudia
name: Blachutzik, Jörg O.
name: Scherzer, Sönke
name: Reinders, Yvonne
name: Kierszniowska, Sylwia
name: Schulze, Waltraud X.
name: Harms, Gregory S.
name: Hedrich, Rainer
name: Geiger, Dietmar
name: Kreuzer, Ines
Publisher: name: Universität Regensburg
Year: 2013
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Abscisic Acid/metabolism
subject: Animals
subject: Anions/metabolism
subject: Arabidopsis/metabolism
subject: Arabidopsis Proteins/metabolism
subject: Detergents/pharmacology
subject: Fluorescence Resonance Energy Transfer
subject: Green Fluorescent Proteins/metabolism
subject: Ion Channels/metabolism
subject: Lipid Metabolism
subject: Mass Spectrometry
subject: Microscopy, Confocal
subject: Microscopy, Fluorescence
subject: Oocytes/metabolism
subject: Protein Structure, Tertiary
subject: RNA, Complementary/metabolism
subject: Signal Transduction
subject: Sterols/metabolism
subject: Xenopus/metabolism

description: The phytohormone abscisic acid (ABA) plays a key role in the plant response to drought stress. Hence, ABA-dependent gene transcription and ion transport is regulated by a variety of protein kinases and phosphatases. However, the nature of the membrane-delimited ABA signal transduction steps remains largely unknown. To gain insight into plasma membrane-bound ABA signaling, we identified sterol-dependent proteins associated with detergent resistant membranes from Arabidopsis thaliana mesophyll cells. Among those, we detected the central ABA signaling phosphatase ABI1 (abscisic-acid insensitive 1) and the calcium-dependent protein kinase 21 (CPK21). Using fluorescence microscopy, we found these proteins to localize in membrane nanodomains, as observed by colocalization with the nanodomain marker remorin Arabidopsis thaliana remorin 1.3 (AtRem 1.3). After transient coexpression, CPK21 interacted with SLAH3 [slow anion channel 1 (SLAC1) homolog 3] and activated this anion channel. Upon CPK21 stimulation, SLAH3 exhibited the hallmark properties of S-type anion channels. Coexpression of SLAH3/CPK21 with ABI1, however, prevented proper nanodomain localization of the SLAH3/CPK21 protein complex, and as a result anion channel activation failed. FRET studies revealed enhanced interaction of SLAH3 and CPK21 within the plasma membrane in response to ABA and thus confirmed our initial observations. Interestingly, the ABA-induced SLAH3/CPK21 interaction was modulated by ABI1 and the ABA receptor RCAR1/PYL9 [regulatory components of ABA receptor 1/PYR1 (pyrabactin resistance 1)-like protein 9]. We therefore propose that ABA signaling via inhibition of ABI1 modulates the apparent association of a signaling and transport complex within membrane domains that is necessary for phosphorylation and activation of the S-type anion channel SLAH3 by CPK21.
Role of Symmetry in the Transport Properties of Graphene Nanoribbons under Bias
Creators: name: Li, Zuanyi
name: Qian, Haiyun
name: Wu, Jian
name: Gu, Bing-Lin
name: Duan, Wenhui
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: The intrinsic transport properties of zigzag graphene nanoribbons (ZGNRs) are investigated using first principles calculations. It is found that although all ZGNRs have similar metallic band structure, they show distinctly different transport behaviors under bias voltages, depending on whether they are mirror symmetric with respect to the midplane between two edges. Asymmetric ZGNRs behave as conventional conductors with linear current-voltage dependence, while symmetric ZGNRs exhibit unexpected very small currents with the presence of a conductance gap around the Fermi level. This difference is revealed to arise from different coupling between the conducting subbands around the Fermi level, which is dependent on the symmetry of the systems.
description: 4 pages, 4 figures
Structural and functional analysis of plant Oil-body Lipase  EgLIP1 from Elaeis guineensis
Creators: name: TEY, JIA RONG
Publisher: name: Zenodo
Year: 2025

description: This repository contains the AlphaFold 2 predicted models for Elaeis guineensis Lipase 1 (EgLIP1) and N-terminus truncated EgLIP1. Molecular dynamics with and without ligand 1-palmitoyl-glycerol was performed, and the clustered trajectories deposited can be found in this repository. The Python and shell codes used in conformation clustering and hydrogen bond analysis can also be accessed.
Hard Row to Hoe: Perspectives on Sustainable Agricultural Policy in Illinois
Creators: name: Pape, Laura
Publisher: name: University of Chicago
Year: 2022

description: The dramatic transformation of agriculture during the 20th and early 21st centuries has resulted in perceived competition regarding the future of agriculture between conventional and sustainable views. In reality, many farmers engage in both types of agriculture. Through an investigation of farmer perceptions of agricultural practices and policy, this study seeks to understand the state of sustainable agriculture in Illinois. In this study, I strive to answer two questions. What motivates Illinois farmers to engage in sustainable agricultural practices, and what barriers exist to implementing said practices? Secondly, how can the Illinois government support farmers' use of sustainable agricultural practices? By researching these questions, I seek to inform future sustainable agricultural policy in Illinois. Through the analysis of eleven interviews with Illinois farmers and agricultural experts, I find a wide range of motivations and constraints to implementing or expanding the use of sustainable practices. Considering these factors, I suggest the following policies to facilitate the transition and expansion of sustainable agriculture in Illinois: (1) direct extension service research toward local research on sustainable practices, (2) expand and simplify governmental outreach regarding sustainable agricultural programs, (3) revise crop insurance “good farming practices” to include sustainable methods, and (4) stabilize the agricultural labor force with increased pathways to residency and citizenship for undocumented farmworkers.
Cs5Sn9(OH)x4 NH3
Creators: name: Friedrich, Ute
name: Korber, Nikolaus
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: 540 Chemie

description: The title compound, penta­caesium nona­stannide hydroxide tetra­ammonia, crystallized from a solution of CsSnBi in liquid ammonia. The Sn94- unit forms a monocapped quadratic anti­prism. The hydroxide ion is surrounded by five caesium cations, which form a distorted quadratic pyramidal polyhedron. A three-dimensional network is formed by Cs-Sn [3.8881 (7) Å to 4.5284 (7) Å] and Cs-NH3 [3.276 (7)-3.636 (7) Å] contacts.
Precision control of charge coherence in parallel double dot systems through spin-orbit interaction
Creators: name: Jin, Jinshuang
name: Zhang, Wei-Min
name: Tu, Matisse Wei-Yuan
name: Wang, Nien-En
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: In terms of the exact quantum master equation solution for open electronic systems, the coherent dynamics of two charge states described by two parallel quantum dots with one fully polarized electron on either dot is investigated in the presence of spin-orbit interaction. We demonstrate that the double dot system can stay in a dynamically decoherence free space. The coherence between two double dot charge states can be precisely manipulated through a spin-orbit coupling. The effects of the temperature, the finite bandwidth of lead, and the energy deviations during the coherence manipulation are also explored.
description: 6 pagges, 4 figures
Structural and functional analysis of plant Oil-body Lipase  EgLIP1 from Elaeis guineensis
Creators: name: TEY, JIA RONG
Publisher: name: Zenodo
Year: 2025

description: This repository contains the AlphaFold 2 predicted models for Elaeis guineensis Lipase 1 (EgLIP1) and N-terminus truncated EgLIP1. Molecular dynamics with ligand 1-palmitoyl-glycerol was performed, and the clustered trajectories deposited can be found in this repository. The Python and shell codes used in conformation clustering and hydrogen bond analysis can also be accessed.