cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Applications of Crystal Collimation to the CERN Large Hadron Collider (LHC) and its High Luminosity Upgrade Project (HL-LHC)
Creators: name: D'Andrea, Marco
Publisher: name: Zenodo
Year: 2022
Subjects: crystal collimation
bent crystals
crystal channeling
LHC
HL-LHC
ion beams
proton beams
SixTrack simulations

description: Bent crystals can be used to efficiently steer charged particles by trapping impacting particles in the potential well generated by adjacent crystalline planes, resulting in a deflection equivalent to the effect of a magnetic field of hundreds of Tesla. This impressive property stimulates accelerator physicists to make use of crystals for advanced beam manipulations. In this Ph.D. work, the main results gathered with the use of bent crystals at the high-energy frontier in the CERN accelerator complex are reported, with particular focus on crystal collimation tests carried out at the LHC in 2018 with Pb ion beams. These activities allowed to demonstrate the cleaning improvement provided by this collimation scheme, and were a key ingredient in the decision to include crystal collimation in the HL-LHC baseline for the run starting in 2022. The code development effort aimed at improving the available simulation tools for crystal collimation with proton beams is also described, using as case studies two important applications beyond ion beam collimation that were explored at CERN: the double-crystal setup at the SPS and the deployment of crystals for the reduction of background on forward physics detectors.
Targeting melanoma metastasis and immunosuppression with a new mode of melanoma inhibitory activity (MIA) protein inhibition
Creators: name: Schmidt, Jennifer
name: Riechers, Alexander
name: Stoll, Raphael
name: Amann, Thomas
name: Fink, Florian
name: Spruss, Thilo
name: Gronwald, Wolfram
name: König, Burkhard
name: Hellerbrand, Claus
name: Bosserhoff, Anja Katrin
Publisher: name: Universität Regensburg
Year: 2012
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Amino Acid Sequence
subject: Animals
subject: Antineoplastic Agents/therapeutic use
subject: Cell Line, Tumor
subject: Extracellular Matrix Proteins/metabolism
subject: Humans
subject: Immune Tolerance/drug effects
subject: Melanoma/pathology
subject: Melanoma, Experimental/pathology
subject: Mice
subject: Models, Molecular
subject: Molecular Sequence Data
subject: Molecular Targeted Therapy/methods
subject: Neoplasm Metastasis
subject: Neoplasm Proteins/metabolism
subject: Oligopeptides/therapeutic use
subject: Protein Multimerization/drug effects
subject: Protein Structure, Quaternary

description: Melanoma is the most aggressive form of skin cancer, with fast progression and early dissemination mediated by the melanoma inhibitory activity (MIA) protein. Here, we discovered that dimerization of MIA is required for functional activity through mutagenesis of MIA which showed the correlation between dimerization and functional activity. We subsequently identified the dodecapeptide AR71, which prevents MIA dimerization and thereby acts as a MIA inhibitor. Two-dimensional nuclear magnetic resonance (NMR) spectroscopy demonstrated the binding of AR71 to the MIA dimerization domain, in agreement with in vitro and in vivo data revealing reduced cell migration, reduced formation of metastases and increased immune response after AR71 treatment. We believe AR71 is a lead structure for MIA inhibitors. More generally, inhibiting MIA dimerization is a novel therapeutic concept in melanoma therapy.
Detection of Strong Millimeter Emission from the Circumstellar Dust Disk Around V1094 Sco: Cold and Massive Disk around a T Tauri Star in a Quiescent Accretion Phase?
Creators: name: Tsukagoshi, Takashi
name: Saito, Masao
name: Kitamura, Yoshimi
name: Momose, Munetake
name: Shimajiri, Yoshito
name: Hiramatsu, Masaaki
name: Ikeda, Norio
name: Kamegai, Kazuhisa
name: Wilson, Grant
name: Yun, Min S.
name: Scott, Kimberly
name: Austermann, Jay
name: Perera, Thushara
name: Hughes, David
name: Aretxaga, Itziar
name: Mauskopf, Philip
name: Ezawa, Hajime
name: Kohno, Kotaro
name: Kawabe, Ryohei
Publisher: name: arXiv
Year: 2010
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present the discovery of a cold massive dust disk around the T Tauri star V1094 Sco in the Lupus molecular cloud from the 1.1 millimeter continuum observations with AzTEC on ASTE. A compact ($r\lesssim$320 AU) continuum emission coincides with the stellar position having a flux density of 272 mJy which is largest among T Tauri stars in Lupus. We also present the detection of molecular gas associated with the star in the five-point observations in $^{12}$CO J=3--2 and $^{13}$CO J=3--2. Since our $^{12}$CO and $^{13}$CO observations did not show any signature of a large-scale outflow or a massive envelope, the compact dust emission is likely to come from a disk around the star. The observed SED of V1094 Sco shows no distinct turnover from near infrared to millimeter wavelengths, which can be well described by a flattened disk for the dust component, and no clear dip feature around 10 $\micron$ suggestive of absence of an inner hole in the disk. We fit a simple power-law disk model to the observed SED. The estimated disk mass ranges from 0.03 to $\gtrsim$0.12 $M_\sun$, which is one or two orders of magnitude larger than the median disk mass of T Tauri stars in Taurus.
description: 18 pages, 4 figures, accepted for publication in ApJ
Confinement, Vacuum Structure: from QCD to Quantum Gravity
Creators: name: Pak, D. G.
Publisher: name: arXiv
Year: 2010
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: A minimal Lorentz gauge gravity model with R^2-type Lagrangian is proposed. In the absence of torsion the model admits a topological phase with unfixed metric. The model possesses a minimal set of dynamical degrees of freedom for the torsion. Remarkably, the torsion has the same number of dynamical of-shell degrees of freedom as the metric tensor. We trace an analogy between the structure of the quantum chromodynamics and the structure of possible theory of quantum gravity.
description: 7 pages; reduced version of talk given at IV International Symposium on Symmetries in Subatomic Physics (SSP 2009), plenary session in Honor of Yongmin Cho's 65th Birthday, Taipei, Taiwan, 2-5 June 2009; to appear in "Symmetries in Subatomic Physics", ed. P. Hwang.
A simple path to asymptotics for the frontier of a branching Brownian motion
Creators: name: Roberts, Matthew I.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: We give short proofs of two classical results about the position of the extremal particle in a branching Brownian motion, one concerning the median position and another the almost sure behaviour.
description: Published in at http://dx.doi.org/10.1214/12-AOP753 the Annals of Probability (http://www.imstat.org/aop/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations
Creators: name: Förster, Frank
name: Beisser, Daniela
name: Grohme, Markus A.
name: Liang, Chunguang
name: Mali, Brahim
name: Siegl, Alexander Matthias
name: Engelmann, Julia C.
name: Shkumatov, Alexander V.
name: Schokraie, Elham
name: Müller, Tobias
name: Schnölzer, Martina
name: Schill, Ralph O.
name: Frohme, Marcus
name: Dandekar, Thomas
Publisher: name: Universität Regensburg
Year: 2012
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin

description: Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant.
Deep sequencing of MYC DNA-binding sites in Burkitt lymphoma
Creators: name: Seitz, Volkhard
name: Butzhammer, Peter
name: Hirsch, Burkhard
name: Hecht, Jochen
name: Gütgemann, Ines
name: Ehlers, Anke
name: Lenze, Dido
name: Oker, Elisabeth
name: Sommerfeld, Anke
name: von der Wall, Edda
name: König, Christoph
name: Zinser, Christian
name: Spang, Rainer
name: Hummel, Michael
Publisher: name: Universität Regensburg
Year: 2011
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Binding Sites
subject: Burkitt Lymphoma/metabolism
subject: Chromatin Immunoprecipitation
subject: DNA, Neoplasm/genetics
subject: Gene Expression Profiling
subject: Gene Expression Regulation, Neoplastic
subject: Genome, Human
subject: High-Throughput Nucleotide Sequencing
subject: Humans
subject: Oligonucleotide Array Sequence Analysis
subject: Proto-Oncogene Proteins c-myc/metabolism
subject: RNA, Small Interfering/genetics
subject: Tumor Cells, Cultured
subject: Tumor Markers, Biological/genetics

description: BACKGROUND: MYC is a key transcription factor involved in central cellular processes such as regulation of the cell cycle, histone acetylation and ribosomal biogenesis. It is overexpressed in the majority of human tumors including aggressive B-cell lymphoma. Especially Burkitt lymphoma (BL) is a highlight example for MYC overexpression due to a chromosomal translocation involving the c-MYC gene. However, no genome-wide analysis of MYC-binding sites by chromatin immunoprecipitation (ChIP) followed by next generation sequencing (ChIP-Seq) has been conducted in BL so far. METHODOLOGY/PRINCIPAL FINDINGS: ChIP-Seq was performed on 5 BL cell lines with a MYC-specific antibody giving rise to 7,054 MYC-binding sites after bioinformatics analysis of a total of approx. 19 million sequence reads. In line with previous findings, binding sites accumulate in gene sets known to be involved in the cell cycle, ribosomal biogenesis, histone acetyltransferase and methyltransferase complexes demonstrating a regulatory role of MYC in these processes. Unexpectedly, MYC-binding sites also accumulate in many B-cell relevant genes. To assess the functional consequences of MYC binding, the ChIP-Seq data were supplemented with siRNA- mediated knock-downs of MYC in BL cell lines followed by gene expression profiling. Interestingly, amongst others, genes involved in the B-cell function were up-regulated in response to MYC silencing. CONCLUSION/SIGNIFICANCE: The 7,054 MYC-binding sites identified by our ChIP-Seq approach greatly extend the knowledge regarding MYC binding in BL and shed further light on the enormous complexity of the MYC regulatory network. Especially our observations that (i) many B-cell relevant genes are targeted by MYC and (ii) that MYC down-regulation leads to an up-regulation of B-cell genes highlight an interesting aspect of BL biology.
Jet deflection by very weak guide fields during magnetic reconnection
Creators: name: Goldman, Martin
name: Lapenta, Giovanni
name: Newman, David
name: Markidis, Stefan
name: Che, Haihong
Publisher: name: arXiv
Year: 2010
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: Simulations of antiparallel reconnection have shown collimated electron jets outflowing from the x-point, and associated highly elongated "outer electron diffusion regions." New PIC simulations with ion/electron mass ratios as large as 1836 show that jets are deflected towards the magnetic separatrix by out-of-plane guide fields, Bg, as small as 0.05 times the asymptotic reconnecting field, B0. The outer electron diffusion region is distorted and broken up, but the diffusion rate is unchanged. These results are interpreted in terms of electron dynamics and are compared to recent measurements of reconnection jets in the magnetosheath.
The most luminous galaxies in the Universe
Creators: name: Hill, Ryley
Publisher: name: University of British Columbia
Year: 2017

description: Submillimetre galaxies have become essential tools in studying the high redshift Universe. Reaching luminosities well over 10¹³ L⊙, they constitute the vast majority of star formation during this early epoch. Their combined infrared and submillimetre emission output is comparable in energy density to all of the optical and ultraviolet light emitted by all of the galaxies in the observable Universe. We have used the Submillimeter Array at 860 μm to observe the brightest submillimetre sources in 4 deg² of the Cosmology Legacy Survey. Previous interferometric studies have found a significant amount of multiplicity at the bright end of the single-dish number counts, suggesting a steepening in the drop-off brighter than 10 mJy, but these studies suffered from small-number statistics. We have targeted 75 of the brightest flux density-ordered single-dish SCUBA-2 sources down to approximately 10 mJy, achieving an average synthesized beam size of 2.4 arcsec and an average depth of 1.5 mJy in our primary beam-corrected maps, corresponding to 4σ detections of about 6 mJy. Our data is sufficient to distinguish between intrinsically bright galaxies and systems that break up into two ≳6 mJy galaxies with flux ratios less than 2 and separated by about 2 arcsec or more, corresponding to a physical distance of around 20 kpc at z=2. We include in our study 28 archival observations of similar nature, bringing our sample size to 103. We statistically deboost our flux density measurements and use these to compute the cumulative and differential number counts of our sample, finding them to be consistent with previous single-dish survey number counts within the uncertainties but with a systematic offset between 2 and 20 per cent. We compute the probability that a >10 mJy single-dish submm source resolves into two or more galaxies with a brightest to second-brightest flux density ratio less than 2 to be about 15 per cent. Assuming the remaining 85 per cent of the targets are ultra-luminous galaxies between redshifts 2 and 3, we find the surface density of >500 M⊙ yr-¹ sources to be 8^{+2}_{-1} deg-² and a likely volume density of 660^{+140}_{-120} Gpc-³.
H2rs: Deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments
Creators: name: Janda, Jan-Oliver
name: Popal, Ajmal
name: Bauer, Jochen
name: Busch, Markus
name: Klocke, Michael
name: Spitzer, Wolfgang
name: Keller, Jörg
name: Merkl, Rainer
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: 570 Biowissenschaften, Biologie

description: Background The identification of functionally important residue positions is an important task of computational biology. Methods of correlation analysis allow for the identification of pairs of residue positions, whose occupancy is mutually dependent due to constraints imposed by protein structure or function. A common measure assessing these dependencies is the mutual information, which is based on Shannon’s information theory that utilizes probabilities only. Consequently, such approaches do not consider the similarity of residue pairs, which may degrade the algorithm’s performance. One typical algorithm is H2r, which characterizes each individual residue position k by the conn(k)-value, which is the number of significantly correlated pairs it belongs to. Results To improve specificity of H2r, we developed a revised algorithm, named H2rs, which is based on the von Neumann entropy (vNE). To compute the corresponding mutual information, a matrix A is required, which assesses the similarity of residue pairs. We determined A by deducing substitution frequencies from contacting residue pairs observed in the homologs of 35 809 proteins, whose structure is known. In analogy to H2r, the enhanced algorithm computes a normalized conn(k)-value. Within the framework of H2rs, only statistically significant vNE values were considered. To decide on significance, the algorithm calculates a p-value by performing a randomization test for each individual pair of residue positions. The analysis of a large in silico testbed demonstrated that specificity and precision were higher for H2rs than for H2r and two other methods of correlation analysis. The gain in prediction quality is further confirmed by a detailed assessment of five well-studied enzymes. The outcome of H2rs and of a method that predicts contacting residue positions (PSICOV) overlapped only marginally. H2rs can be downloaded from http://www-bioinf.uni-regensburg.de webcite. Conclusions Considering substitution frequencies for residue pairs by means of the von Neumann entropy and a p-value improved the success rate in identifying important residue positions. The integration of proven statistical concepts and normalization allows for an easier comparison of results obtained with different proteins. Comparing the outcome of the local method H2rs and of the global method PSICOV indicates that such methods supplement each other and have different scopes of application.
Preparation of Highly Crystalline TiO2 Nanostructures by Acid-assisted Hydrothermal Treatment of Hexagonal-structured Nanocrystalline Titania/Cetyltrimethyammonium Bromide Nanoskeleton
Creators: name: Dai, Shuxi
name: Wu, Yanqiang
name: Sakai, Toshio
name: Du, Zuliang
name: Sakai, Hideki
name: Abe, Masahiko
Publisher: name: arXiv
Year: 2010
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Highly crystalline TiO2 nanostructures were prepared through a facile inorganic acid-assisted hydrothermal treatment of hexagonal-structured assemblies of nanocrystalline titiania templated by cetyltrimethylammonium bromide (Hex-ncTiO2/CTAB Nanoskeleton) as starting materials. All samples were characterized by X-ray diffraction (XRD) and transmission electron microscopy (TEM). The influence of hydrochloric acid concentration on the morphology, crystalline and the formation of the nanostructures were investigated. We found that the morphology and crystalline phase strongly depended on the hydrochloric acid concentrations. More importantly, crystalline phase was closely related to the morphology of TiO2 nanostructure. Nanoparticles were polycrystalline anatase phase, and aligned nanorods were single crystalline rutile phase. Possible formation mechanisms of TiO2 nanostructures with various crystalline phases and morphologies were proposed.
description: Nanoscale Research Letters, 2010, DOI: 10.1007/s11671-010-9720-0
MAESTRO: An Adaptive Low Mach Number Hydrodynamics Algorithm for Stellar Flows
Creators: name: Nonaka, A.
name: Almgren, A. S.
name: Bell, J. B.
name: Lijewski, M. J.
name: Malone, C. M.
name: Zingale, M.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: Many astrophysical phenomena are highly subsonic, requiring specialized numerical methods suitable for long-time integration. In a series of earlier papers we described the development of MAESTRO, a low Mach number stellar hydrodynamics code that can be used to simulate long-time, low-speed flows that would be prohibitively expensive to model using traditional compressible codes. MAESTRO is based on an equation set derived using low Mach number asymptotics; this equation set does not explicitly track acoustic waves and thus allows a significant increase in the time step. MAESTRO is suitable for two- and three-dimensional local atmospheric flows as well as three-dimensional full-star flows. Here, we continue the development of MAESTRO by incorporating adaptive mesh refinement (AMR). The primary difference between MAESTRO and other structured grid AMR approaches for incompressible and low Mach number flows is the presence of the time-dependent base state, whose evolution is coupled to the evolution of the full solution. We also describe how to incorporate the expansion of the base state for full-star flows, which involves a novel mapping technique between the one-dimensional base state and the Cartesian grid, as well as a number of overall improvements to the algorithm. We examine the efficiency and accuracy of our adaptive code, and demonstrate that it is suitable for further study of our initial scientific application, the convective phase of Type Ia supernovae.
description: Accepted to Astrophysical Journal Suppliment (http://iop.org). 56 pages, 15 figures.
Expression and function of methylthioadenosine phosphorylase in chronic liver disease
Creators: name: Czech, Barbara
name: Dettmer, Katja
name: Valletta, Daniela
name: Saugspier, Michael Sebastian
name: Koch, Andreas
name: Stevens, Axel Peter
name: Thasler, Wolfgang E.
name: Müller, Martina
name: Oefner, Peter J.
name: Bosserhoff, Anja-Katrin
name: Hellerbrand, Claus
Publisher: name: Universität Regensburg
Year: 2013
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin

description: To study expression and function of methylthioadenosine phosphorylase (MTAP), the rate-limiting enzyme in the methionine and adenine salvage pathway, in chronic liver disease. DESIGN: MTAP expression was analyzed by qRT-PCR, Western blot and immunohistochemical analysis. Levels of MTA were determined by liquid chrmatography-tandem mass spectrometry. RESULTS: MTAP was downregulated in hepatocytes in murine fibrosis models and in patients with chronic liver disease, leading to a concomitant increase in MTA levels. In contrast, activated hepatic stellate cells (HSCs) showed strong MTAP expression in cirrhotic livers. However, also MTA levels in activated HSCs were significantly higher than in hepatocytes, and there was a significant correlation between MTA levels and collagen expression in diseased human liver tissue indicating that activated HSCs significantly contribute to elevated MTA in diseased livers. MTAP suppression by siRNA resulted in increased MTA levels, NFκB activation and apoptosis resistance, while overexpression of MTAP caused the opposite effects in HSCs. The anti-apoptotic effect of low MTAP expression and high MTA levels, respectively, was mediated by induced expression of survivin, while inhibition of survivin abolished the anti-apoptotic effect of MTA on HSCs. Treatment with a DNA demethylating agent induced MTAP and reduced survivin expression, while oxidative stress reduced MTAP levels but enhanced survivin expression in HSCs. CONCLUSION: MTAP mediated regulation of MTA links polyamine metabolism with NFκB activation and apoptosis in HSCs. MTAP and MTAP modulating mechanisms appear as promising prognostic markers and therapeutic targets for hepatic fibrosis.
Trihyperkahler reduction and instanton bundles on CP^3
Creators: name: Jardim, Marcos
name: Verbitsky, Misha
Publisher: name: arXiv
Year: 2011
Subjects: subject: Algebraic Geometry (math.AG)
subject: Differential Geometry (math.DG)
subject: Symplectic Geometry (math.SG)
subject: FOS: Mathematics

description: A trisymplectic structure on a complex 2n-manifold is a triple of holomorphic symplectic forms such that any linear combination of these forms has constant rank 2n, n or 0, and degenerate forms in $Ω$ belong to a non-degenerate quadric hypersurface. We show that a trisymplectic manifold is equipped with a holomorphic 3-web and the Chern connection of this 3-web is holomorphic, torsion-free, and preserves the three symplectic forms. We construct a trisymplectic structure on the moduli of regular rational curves in the twistor space of a hyperkaehler manifold, and define a trisymplectic reduction of a trisymplectic manifold, which is a complexified form of a hyperkaehler reduction. We prove that the trisymplectic reduction in the space of regular rational curves on the twistor space of a hyperkaehler manifold M is compatible with the hyperkaehler reduction on M. As an application of these geometric ideas, we consider the ADHM construction of instantons and show that the moduli space of rank r, charge c framed instanton bundles on CP^3 is a smooth, connected, trisymplectic manifold of complex dimension 4rc. In particular, it follows that the moduli space of rank 2, charge c instanton bundles on CP^3 is a smooth complex manifold dimension 8c-3, thus settling a 30-year old conjecture.
description: 42 pages, v. 3.2, changes in section 3.1: the notion of trisymplectic structure stated differently, Clifford algebra action introduced
Biological characterization of adult MYC-translocation-positive mature B-cell lymphomas other than molecular Burkitt lymphoma
Creators: name: Aukema, Sietse M.
name: Kreuz, Markus
name: Kohler, Christian
name: Rosolowski, Maciej
name: Hasenclever, Dirk
name: Hummel, Michael
name: Küppers, Ralf
name: Lenze, Dido
name: Ott, German
name: Pott, Christiane
name: Richter, Julia
name: Rosenwald, Andreas
name: Szczepanowski, Monika
name: Schwaenen, Carsten
name: Stein, Harald
name: Trautmann, Heiko
name: Wessendorf, Swen
name: Trümper, Lorenz
name: Loeffler, Markus
name: Spang, Rainer
name: Kluin, Philip M.
name: Klapper, Wolfram
name: Siebert, Reiner
Publisher: name: Universität Regensburg
Year: 2013
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin

description: Chromosomal translocations affecting the MYC oncogene are the biological hallmark of Burkitt lymphomas but also occur in a subset of other mature B-cell lymphomas. If accompanied by a chromosomal break targeting the BCL2 and/or BCL6 oncogene these MYC translocation-positive (MYC(+)) lymphomas are called double-hit lymphomas, otherwise the term single-hit lymphomas is applied. In order to characterize the biological features of these MYC(+) lymphomas other than Burkitt lymphoma we explored, after exclusion of molecular Burkitt lymphoma as defined by gene expression profiling, the molecular, pathological and clinical aspects of 80 MYC-translocation-positive lymphomas (31 single-hit, 46 double-hit and 3 MYC(+)-lymphomas with unknown BCL6 status). Comparison of single-hit and double-hit lymphomas revealed no difference in MYC partner (IG/non-IG), genomic complexity, MYC expression or gene expression profile. Double-hit lymphomas more frequently showed a germinal center B-cell-like gene expression profile and had higher IGH and MYC mutation frequencies. Gene expression profiling revealed 130 differentially expressed genes between BCL6(+)/MYC(+) and BCL2(+)/MYC(+) double-hit lymphomas. BCL2(+)/MYC(+) double-hit lymphomas more frequently showed a germinal center B-like gene expression profile. Analysis of all lymphomas according to MYC partner (IG/non-IG) revealed no substantial differences. In this series of lymphomas, in which immunochemotherapy was administered in only a minority of cases, single-hit and double-hit lymphomas had a similar poor outcome in contrast to the outcome of molecular Burkitt lymphoma and lymphomas without the MYC break. Our data suggest that, after excluding molecular Burkitt lymphoma and pediatric cases, MYC(+) lymphomas are biologically quite homogeneous with single-hit and double-hit lymphomas as well as IG-MYC and non-IG-MYC(+) lymphomas sharing various molecular characteristics.
Mau Mau and masculinity : race, gender, and the body in colonial Kenya
Creators: name: Wilkinson, Conor Joseph Ward
Publisher: name: University of British Columbia
Year: 2017

description: This thesis interrogates the role of British conceptions of race, gender, and the body in the detention camps that Britain established in Kenya during the Mau Mau Emergency (1952-1960). It aims to reframe the ways we consider the violence that occurred in these camps. To date, scholars have been largely uncritical about the ways in which masculinity operated during the Emergency. They have not reflected on the way British masculinity affected—and was affected by—the colonial sphere. Those that have considered gender have generally assumed that static, timeless notions of manhood were imported to Kenya, and that tropes about manliness were utilized unidirectionally by colonizers against colonized. In contrast, this thesis argues that Mau Mau detention camps amplified the hierarchy of racialized masculinity in Kenya to new extremes, resulting in physical and mental torture of tens of thousands of detained Africans. Importantly, British men’s attempts to define and control African detainees’ minds and bodies according to their preconceptions of race, gender, and the body ran jointly with colonial administrators’ efforts to police their own officer corps. Understanding how British men conceived the masculine body—particularly as it related to its racialization (or lack thereof)—is imperative if we are to make sense of the violence done against African men in the Mau Mau camps. This study accordingly begins by sketching the role of masculinity in the British Empire— particularly as it pertained to the surveillance of the Empire’s colonial troops—and then proceeds to examine the implications of masculinity in Kenya before and during the Emergency. Ultimately it argues that the British did not possess the cultural scripts necessary to sufficiently make sense of what they called Kenyan “primitivism.” In the Mau Mau oathing rituals the colonizers saw African behaviors that flouted the gender norms the British understood as necessary to their colonial endeavour. Many of these norms were informed by codes of racial and sexual purity. As a result, the British widely viewed Kenyan oath takers as culturally unintelligible, as “unreal” bodies governed by illegitimate expression. During the Emergency, violence became the overwhelming British response to this conundrum.
A least angle regression model for the prediction of canonical and non-canonical miRNA-mRNA interactions
Creators: name: Engelmann, Julia C.
name: Spang, Rainer
Publisher: name: Universität Regensburg
Year: 2012
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Base Sequence
subject: Gene Expression Profiling
subject: Gene Expression Regulation
subject: Gene Regulatory Networks/genetics
subject: Humans
subject: MicroRNAs/metabolism
subject: Models, Genetic
subject: Molecular Sequence Annotation
subject: Oncogenes
subject: RNA, Messenger/metabolism
subject: Regression Analysis
subject: Reproducibility of Results
subject: Transcription, Genetic

description: microRNAs (miRNAs) are short non-coding RNAs with regulatory functions in various biological processes including cell differentiation, development and oncogenic transformation. They can bind to mRNA transcripts of protein-coding genes and repress their translation or lead to mRNA degradation. Conversely, the transcription of miRNAs is regulated by proteins including transcription factors, co-factors, and messenger molecules in signaling pathways, yielding a bidirectional regulatory network of gene and miRNA expression. We describe here a least angle regression approach for uncovering the functional interplay of gene and miRNA regulation based on paired gene and miRNA expression profiles. First, we show that gene expression profiles can indeed be reconstructed from the expression profiles of miRNAs predicted to be regulating the specific gene. Second, we propose a two-step model where in the first step, sequence information is used to constrain the possible set of regulating miRNAs and in the second step, this constraint is relaxed to find regulating miRNAs that do not rely on perfect seed binding. Finally, a bidirectional network comprised of miRNAs regulating genes and genes regulating miRNAs is built from our previous regulatory predictions. After applying the method to a human cancer cell line data set, an analysis of the underlying network reveals miRNAs known to be associated with cancer when dysregulated are predictors of genes with functions in apoptosis. Among the predicted and newly identified targets that lack a classical miRNA seed binding site of a specific oncomir, miR-19b-1, we found an over-representation of genes with functions in apoptosis, which is in accordance with the previous finding that this miRNA is the key oncogenic factor in the mir-17-92 cluster. In addition, we found genes involved in DNA recombination and repair that underline its importance in maintaining the integrity of the cell.
Beryllium10: a free and simple tool for creating and managing group safety data sheets
Creators: name: Kochmann, Sven
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: Safety data sheet; Toxicological data; Globally Harmonised System (GHS); Laboratory hazards and risks; Laboratory safety
subject: 540 Chemie

description: Background Countless chemicals and mixtures are used in laboratories today, which all possess their own properties and dangers. Therefore, it is important to brief oneself about possible risks and hazards before doing any experiments. However, this task is laborious and time consuming. Summary Beryllium10 is a program, which supports users by carrying out a large part of the work such as collecting/importing data sets from different providers and compiling most of the information into a single group safety data sheet, which is suitable for having all necessary information at hand while an experiment is in progress. We present here the features of Beryllium10, their implementation, and their design and development criteria and ideas. Conclusion A program for creating and managing of group safety data sheets was developed and released as open source under GPL. The program provides a fast and clear user-interface, and well-conceived design for collecting and managing safety data. It is available for download from the web page http://beryllium.keksecks.de webcite.
Tannic acid label indicates abnormal cell development coinciding with regeneration of renal tubules
Creators: name: Minuth, Will W.
name: Denk, Lucia
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: 570 Biowissenschaften, Biologie

description: Background Stem/progenitor cells are in the focus of research as a future therapeutic option to stimulate regeneration in diseased renal parenchyma. However, current data indicate that successful seeding of implanted stem/progenitor cells is prevented by harmful interstitial fluid and altered extracellular matrix. To find out possible parameters for cell adaptation, the present investigation was performed. Methods Renal stem/progenitor cells were mounted in an artificial interstitium for perfusion culture. Exposure to chemically defined but CO2-independent culture media was tested during 13 days. Cell biological features were then analyzed by histochemistry, while structural details were investigated by transmission electron microscopy after conventional and improved fixation of specimens. Results Culture of renal stem/progenitor cells as well in Leibovitz’s L-15 Medium as CO2 Independent Medium shows in fluorescence microscopy spatial development of numerous tubules. Specimens of both media fixed by conventional glutaraldehyde exhibit in electron microscopy a homogeneous cell population in developed tubules. In contrast, fixation by glutaraldehyde including tannic acid illuminates that dispersed dark marked cells of unknown function are present. The screening further demonstrates that the dark cell type does not comply with cells found in embryonic, maturing or matured renal parenchyma. Conclusions The actual data show that development of abnormal cell features must be taken into account, when regeneration of renal tubules is simulated under in vitro conditions.
The Costs of Technology: An Analysis of the Community Concerns About the Use of ShotSpotter in Chicago
Creators: name: Preeya, Patel
Publisher: name: University of Chicago
Year: 2022

description: While police agencies continue to rely heavily on technologies to perform the basic functions of law enforcement, research has largely ignored the community impacts of certain technologies. In Chicago, the gunshot detection tool ShotSpotter has raised concerns with community members that have gone unexamined and unrecognized by city officials. Through semi-structured interviews with Chicago community advocates, city officials, public defenders, and other stakeholders with knowledge about ShotSpotter, this paper explores the major concerns about the impacts of ShotSpotter and its use by CPD and law enforcement actors. In the absence of rigorous research about the effects of this technology, this paper relies on the findings of the 2021 Office of Inspector General report about ShotSpotter’s operational effectiveness to provide implications for how these concerns should direct the City’s actions with respect to their contract with ShotSpotter and future decisions about technology deployment. Analysis of these interviews revealed that community advocates were most concerned with ShotSpotter’s contribution to the hyper-policing of majority Black and Latinx neighborhoods on the South and West sides of Chicago and its wrongful use as prosecutorial evidence in courts. Ultimately, the concerns that community advocates and researchers expressed in this paper suggest that the City should cancel its contract with ShotSpotter and signal a shared desire for increased community investment, political representation, and government accountability.
Raf kinases mediate the phosphorylation of eukaryotic translation elongation factor 1A and regulate its stability in eukaryotic cells
Creators: name: Sanges, C.
name: Scheuermann, C.
name: Zahedi, R. P.
name: Sickmann, A.
name: Lamberti, A.
name: Migliaccio, N.
name: Baljuls, A.
name: Marra, M.
name: Zappavigna, S.
name: Reinders, Jörg
name: Rapp, U.
name: Abbruzzese, A.
name: Caraglia, M.
name: Arcari, P.
Publisher: name: Universität Regensburg
Year: 2012
Subjects: subject: EF-1A; Raf kinases; signal transduction; apoptosis; ubiquitin; mass spectrometry
subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Animals
subject: Apoptosis/genetics
subject: COS Cells
subject: Cercopithecus aethiops
subject: Gene Expression Regulation
subject: Humans
subject: Models, Molecular
subject: Mutation
subject: Peptide Elongation Factor 1/metabolism
subject: Phosphoproteins/metabolism
subject: Phosphorylation
subject: Protein Binding
subject: Protein Multimerization
subject: Protein Stability
subject: Protein Structure, Tertiary
subject: Proto-Oncogene Proteins B-raf/metabolism
subject: Proto-Oncogene Proteins c-raf/metabolism
subject: Recombinant Proteins/metabolism
subject: Signal Transduction
subject: Transfection

description: We identified eukaryotic translation elongation factor 1A (eEF1A) Raf-mediated phosphorylation sites and defined their role in the regulation of eEF1A half-life and of apoptosis of human cancer cells. Mass spectrometry identified in vitro S21 and T88 as phosphorylation sites mediated by B-Raf but not C-Raf on eEF1A1 whereas S21 was phosphorylated on eEF1A2 by both B- and C-Raf. Interestingly, S21 belongs to the first eEF1A GTP/GDP-binding consensus sequence. Phosphorylation of S21 was strongly enhanced when both eEF1A isoforms were preincubated prior the assay with C-Raf, suggesting that the eEF1A isoforms can heterodimerize thus increasing the accessibility of S21 to the phosphate. Overexpression of eEF1A1 in COS 7 cells confirmed the phosphorylation of T88 also in vivo. Compared with wt, in COS 7 cells overexpressed phosphodeficient (A) and phospho-mimicking (D) mutants of eEF1A1 (S21A/D and T88A/D) and of eEF1A2 (S21A/D), resulted less stable and more rapidly proteasome degraded. Transfection of S21 A/D eEF1A mutants in H1355 cells increased apoptosis in comparison with the wt isoforms. It indicates that the blockage of S21 interferes with or even supports C-Raf induced apoptosis rather than cell survival. Raf-mediated regulation of this site could be a crucial mechanism involved in the functional switching of eEF1A between its role in protein biosynthesis and its participation in other cellular processes.
Characterization of Talagrand's transport-entropy inequalities in metric spaces
Creators: name: Gozlan, Nathaël
name: Roberto, Cyril
name: Samson, Paul-Marie
Publisher: name: arXiv
Year: 2011
Subjects: subject: Probability (math.PR)
subject: Functional Analysis (math.FA)
subject: FOS: Mathematics

description: We give a characterization of transport-entropy inequalities in metric spaces. As an application we deduce that such inequalities are stable under bounded perturbation (Holley-Stroock perturbation Lemma).
Circulating dendritic cell precursors in chronic kidney disease: a cross-sectional study
Creators: name: Paul, Katharina
name: Kretzschmar, Daniel
name: Yilmaz, Atilla
name: Bärthlein, Barbara
name: Titze, Stephanie
name: Wolf, Gunter
name: Busch, Martin
Publisher: name: Universität Regensburg
Year: 2013
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Adult
subject: Aged
subject: Aged, 80 and over
subject: Blood Cell Count/statistics & numerical data
subject: Causality
subject: Comorbidity
subject: Coronary Artery Disease/pathology
subject: Cross-Sectional Studies
subject: Dendritic Cells/pathology
subject: Female
subject: Germany/epidemiology
subject: Hematopoietic Stem Cells/pathology
subject: Humans
subject: Male
subject: Middle Aged
subject: Prevalence
subject: Renal Insufficiency, Chronic/pathology
subject: Risk Factors
subject: Young Adult

description: BACKGROUND: Dendritic cells (DC) are professional antigen-presenting cells in the immune system. They patrol the blood as circulating dendritic cell precursors (DCP). Decreased blood DCP count has been shown to be related to atherosclerotic plaque burden. Since chronic kidney disease (CKD) is associated with chronic inflammation and increased cardiovascular risk, the aim of our study was to investigate a potential effect of CKD on circulating DCP numbers especially in patients with a history of cardiovascular disease. METHODS: The number of circulating myeloid (mDCP), plasmacytoid (pDCP), and total DCP (tDCP) was analysed by flow cytometry in 245 patients with CKD stage 3 (with and without known cardiovascular events) and 85 coronary healthy controls. In addition, data were compared with a historical group of 130 patients with known coronary artery disease (CAD). RESULTS: Compared to controls, patients with CKD 3 revealed a significant decrease in circulating mDCP (-29%), pDCP (-43%), and tDCP (-38%) (P < 0.001, respectively). Compared with CAD-patients, the decrease in circulating DCP in CKD was comparable or even more pronounced indicating a potential role for DCP in cardiovascular risk potentiation due to CKD. CONCLUSIONS: Based on previous findings in CAD, the marked decrease of DCP in CKD implicates a potential role for DCP as a mediator of cardiovascular disease. Whether DCP in CKD may act as new cardiovascular biomarkers needs to be established in future prospective trials.
description: authors on behalf of the GCKD-Study Investigators
Bandwidth selection in kernel density estimation: Oracle inequalities and adaptive minimax optimality
Creators: name: Goldenshluger, Alexander
name: Lepski, Oleg
Publisher: name: arXiv
Year: 2010
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics

description: We address the problem of density estimation with $\mathbb{L}_s$-loss by selection of kernel estimators. We develop a selection procedure and derive corresponding $\mathbb{L}_s$-risk oracle inequalities. It is shown that the proposed selection rule leads to the estimator being minimax adaptive over a scale of the anisotropic Nikol'skii classes. The main technical tools used in our derivations are uniform bounds on the $\mathbb{L}_s$-norms of empirical processes developed recently by Goldenshluger and Lepski [Ann. Probab. (2011), to appear].
description: Published in at http://dx.doi.org/10.1214/11-AOS883 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Spatially probed electron-electron scattering in a two-dimensional electron gas
Creators: name: Jura, M. P.
name: Grobis, M.
name: Topinka, M. A.
name: Pfeiffer, L. N.
name: West, K. W.
name: Goldhaber-Gordon, D.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Using scanning gate microscopy (SGM), we probe the scattering between a beam of electrons and a two-dimensional electron gas (2DEG) as a function of the beam's injection energy, and distance from the injection point. At low injection energies, we find electrons in the beam scatter by small-angles, as has been previously observed. At high injection energies, we find a surprising result: placing the SGM tip where it back-scatters electrons increases the differential conductance through the system. This effect is explained by a non-equilibrium distribution of electrons in a localized region of 2DEG near the injection point. Our data indicate that the spatial extent of this highly non-equilibrium distribution is within ~1 micrometer of the injection point. We approximate the non-equilibrium region as having an effective temperature that depends linearly upon injection energy.
description: 8 pages, 6 figures
Symptom shift in 200 patients with H63D syndrome associated with abnormal TCS findings in substantia nigra (2024)
Creators: name: Adams, Jacob
name: Kaufmann, Marianne
name: Honda, Riku
name: Smith, Lucas
name: Diamandis, Carolina
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 429999
subject: Other health sciences not elsewhere classified

description: In a study on the prevention of injury in patients with H63D syndrome and cataplexy, statistical analysis revealed an unexpected but clinically highly significant finding. Apparently, in this patient population, an inverse correlation exists between the severity of tic symptomatology on the one hand and narcolepsy with cataplexy on the other hand, as well as a parallel increase in the typical signs of degeneration observed in B-mode transcranial sonography of the substantia nigra (TCS). This finding has clinically far-reaching implications.Peer review completed by Dr. Müller and his team at Swabian Research. June, 2024