cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Variant analysis of the sporozoite surface antigen gene reveals that asymptomatic cattle from wildlife-livestock interface areas in northern Tanzania harbour buffalo-derived T. parva
Creators: name: Mwamuye, Micky M.
name: Odongo, David
name: Kazungu, Yvette
name: Kindoro, Fatuma
name: Gwakisa, Paul
name: Bishop, Richard P.
name: Nijhof, Ard M.
name: Obara, Isaiah
Publisher: name: Freie Universität Berlin
Year: 2020
Subjects: subject: Theileria parva
subject: p67
subject: Tp2
subject: Antigen diversity
subject: Cape Buffalo
subject: Live vaccine
subject: 600 Technik, Medizin, angewandte Wissenschaften::630 Landwirtschaft::630 Landwirtschaft und verwandte Bereiche

description: Buffalo-derived Theileria parva can ‘break through’ the immunity induced by the infection and treatment vaccination method (ITM) in cattle. However, no such ‘breakthroughs’ have been reported in northern Tanzania where there has been long and widespread ITM use in pastoralist cattle, and the Cape buffalo (Syncerus caffer) is also present. We studied the exposure of vaccinated and unvaccinated cattle in northern Tanzania to buffalo-derived T. parva using p67 gene polymorphisms and compared this to its distribution in vaccinated cattle exposed to buffalo-derived T. parva in central Kenya, where vaccine ‘breakthroughs’ have been reported. Additionally, we analysed the CD8+ T cell target antigen Tp2 for positive selection. Our results showed that 10% of the p67 sequences from Tanzanian cattle (n = 39) had a buffalo type p67 (allele 4), an allele that is rare among East African isolates studied so far. The percentage of buffalo-derived p67 alleles observed in Kenyan cattle comprised 19% of the parasites (n = 36), with two different p67 alleles (2 and 3) of presumptive buffalo origin. The Tp2 protein was generally conserved with only three Tp2 variants from Tanzania (n = 33) and five from Kenya (n = 40). Two Tanzanian Tp2 variants and two Kenyan Tp2 variants were identical to variants present in the trivalent Muguga vaccine. Tp2 evolutionary analysis did not show evidence for positive selection within previously mapped epitope coding sites. The p67 data indicates that some ITM-vaccinated cattle are protected against disease induced by a buffalo-derived T. parva challenge in northern Tanzania and suggests that the parasite genotype may represent one factor explaining this.
Soft X-Ray Single-Photon Detection With Superconducting Tantalum Nitride and Niobium Nanowires
Creators: name: Inderbitzin, Kevin
name: Engel, Andreas
name: Schilling, Andreas
Publisher: name: arXiv
Year: 2012
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: We have fabricated ultrafast dark count-free soft X-ray single-photon detectors (X-SNSPDs) from TaN with various conduction path widths, and we compare their properties with corresponding data from a Nb X-SNSPD. The TaN X-SNSPDs offer an improved detector performance regarding device detection efficiency, latching and pulse amplitudes. Wide conduction paths allow for a certain energy-resolving capability in contrast to narrow TaN conduction paths. However, wide paths also limit the detection efficiency at low temperatures, which can be explained within a hot-spot model.
description: 5 pages, 4 figures, 1 table
Antimicrobial Peptide Induced-Stress Renders Staphylococcus aureus Susceptible to Toxic Nucleoside Analogs
Creators: name: Rodriguez-Rojas, Alexandro
name: Nath, Arpita
name: El Shazely, Baydaa
name: Santi, Greta
name: Kim, Joshua Jay
name: Weise, Christoph
name: Kuropka, Benno
name: Rolff, Jens
Publisher: name: Freie Universität Berlin
Year: 2020
Subjects: subject: pexiganan
subject: antibiotic resistance
subject: antimetabolites
subject: antimicrobial peptides
subject: antibiotics
subject: nuceloside analogs
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Cationic antimicrobial peptides (AMPs) are active immune effectors of multicellular organisms and are also considered as new antimicrobial drug candidates. One of the problems encountered when developing AMPs as drugs is the difficulty of reaching sufficient killing concentrations under physiological conditions. Here, using pexiganan, a cationic peptide derived from a host defense peptide of the African clawed frog and the first AMP developed into an antibacterial drug, we studied whether sub-lethal effects of AMPs can be harnessed to devise treatment combinations. We studied the pexiganan stress response ofStaphylococcus aureusat sub-lethal concentrations using quantitative proteomics. Several proteins involved in nucleotide metabolism were elevated, suggesting a metabolic demand. We then show thatStaphylococcus aureusis highly susceptible to antimetabolite nucleoside analogs when exposed to pexiganan, even at sub-inhibitory concentrations. These findings could be used to enhance pexiganan potency while decreasing the risk of resistance emergence, and our findings can likely be extended to other antimicrobial peptides.
Molecular mechanism of inhibiting the SARS-CoV-2 cell entry facilitator TMPRSS2 with camostat and nafamostat
Creators: name: Hempel, Tim
name: Raich, Lluís
name: Olsson, Simon
name: Azouz, Nurit P.
name: Klingler, Andrea M.
name: Hoffmann, Markus
name: Pohlmann, Stefan
name: Rothenberg, Marc E.
name: Noé, Frank
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: SARS-CoV-2
subject: TMPRSS2
subject: camostat
subject: nafamostat
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: The entry of the coronavirus SARS-CoV-2 into human lung cells can be inhibited by the approved drugs camostat and nafamostat. Here we elucidate the molecular mechanism of these drugs by combining experiments and simulations. In vitro assays confirm that both drugs inhibit the human protein TMPRSS2, a SARS-Cov-2 spike protein activator. As no experimental structure is available, we provide a model of the TMPRSS2 equilibrium structure and its fluctuations by relaxing an initial homology structure with extensive 330 microseconds of all-atom molecular dynamics (MD) and Markov modeling. Through Markov modeling, we describe the binding process of both drugs and a metabolic product of camostat (GBPA) to TMPRSS2, reaching a Michaelis complex (MC) state, which precedes the formation of a long-lived covalent inhibitory state. We find that nafamostat has a higher MC population than camostat and GBPA, suggesting that nafamostat is more readily available to form the stable covalent enzyme-substrate intermediate, effectively explaining its high potency. This model is backed by our in vitro experiments and consistent with previous virus cell entry assays. Our TMPRSS2-drug structures are made public to guide the design of more potent and specific inhibitors.
Tricarbonylrhenium(I) and ‐technetium(I) Complexes with Tris(1,2,3‐triazolyl)phosphine Oxides
Creators: name: Li, Bo
name: Hildebrandt, Sarah
name: Hagenbach, Adelheid
name: Abram, Ulrich
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: tris(azolyl)phosphine oxides
subject: tricarbonylrhenium(I)
subject: tricarbonyltechnetium(I)
subject: tripod ligands
subject: 500 Naturwissenschaften und Mathematik::540 Chemie::540 Chemie und zugeordnete Wissenschaften

description: Two potentially tripodal ligands, tris(1-phenyl-1H-1,2,3-triazol-4-yl)phosphine oxide (OP((1,2,3)Tz(1-Ph))(3)) and tris(1-benzyl-1H-1,2,3-triazol-4-yl)phosphine oxide (OP((1,2,3)Tz(1-benz))(3)), were used in reactions with [Re(CO)(5)Br] and (NEt4)(2)[Tc(CO)(3)Cl-3]. While the formation of rhenium complexes with bidentate and tridentate coordinated phosphine oxides was observed, for technetium only cationic complexes with tripodal coordinated OP((1,2,3)Tz(1-R)) ligands were isolated. The products have been characterized spectroscopically and by single crystal X-ray diffraction.
Symmetries of Three Harmonically-Trapped Particles in One Dimension
Creators: name: Harshman, N. L.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Quantum Physics (quant-ph)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We present a method for solving trapped few-body problems and apply it to three equal-mass particles in a one-dimensional harmonic trap, interacting via a contact potential. By expressing the relative Hamiltonian in Jacobi cylindrical coordinates, i.e. the two-dimensional version of three-body hyperspherical coordinates, we discover an underlying ${\rm C}_{6v}$ symmetry. This symmetry simplifies the calculation of energy eigenstates of the full Hamiltonian in a truncated Hilbert space constructed from the trap Hamiltonian eigenstates. Particle superselection rules are implemented by choosing the relevant representations of ${\rm C}_{6v}$. We find that the one-dimensional system shows nearly the full richness of the three-dimensional system, and can be used to understand separability and reducibility in this system and in standard few-body approximation techniques.
description: 27 pages, 5 figures, 6 tables, 37 references, 4 footnotes, 1 article; v2 has revised introduction and results sections as well as typos corrected
The relative contributions of infectious and mitotic spread to HTLV-1 persistence
Creators: name: Laydon, Daniel J.
name: Sunkara, Vikram
name: Boelen, Lies
name: Bangham, Charles R. M.
name: Asquith, Becca
Publisher: name: Freie Universität Berlin
Year: 2020
Subjects: subject: Leukemia-virus type-1
subject: T-cell Leukemia/Lymphoma
subject: proviral load
subject: asymptomatic carriers
subject: clonal expansion
subject: species richness
subject: estimators
subject: dynamics
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Human T-lymphotropic virus type-1 (HTLV-1) persists within hosts via infectious spread (de novoinfection) and mitotic spread (infected cell proliferation), creating a population structure of multiple clones (infected cell populations with identical genomic proviral integration sites). The relative contributions of infectious and mitotic spread to HTLV-1 persistence are unknown, and will determine the efficacy of different approaches to treatment. The prevailing view is that infectious spread is negligible in HTLV-1 persistence beyond early infection. However, in light of recent high-throughput data on the abundance of HTLV-1 clones, and recent estimates of HTLV-1 clonal diversity that are substantially higher than previously thought (typically between 10(4)and 10(5)HTLV-1(+)T cell clones in the body of an asymptomatic carrier or patient with HTLV-1-associated myelopathy/tropical spastic paraparesis), ongoing infectious spread during chronic infection remains possible. We estimate the ratio of infectious to mitotic spread using a hybrid model of deterministic and stochastic processes, fitted to previously published HTLV-1 clonal diversity estimates. We investigate the robustness of our estimates using three alternative estimators. We find that, contrary to previous belief, infectious spread persists during chronic infection, even after HTLV-1 proviral load has reached its set point, and we estimate that between 100 and 200 new HTLV-1 clones are created and killed every day. We find broad agreement between all estimators. The risk of HTLV-1-associated malignancy and inflammatory disease is strongly correlated with proviral load, which in turn is correlated with the number of HTLV-1-infected clones, which are created by de novo infection. Our results therefore imply that suppression of de novo infection may reduce the risk of malignant transformation.
P. Tucoo-Chala, Quand l'Islam était aux portes des Pyrénées. De Gaston IV le Croisé à la croisade des Albigeois (XIe–XIIIe siècles), 1994
Creators: name: Vones, L.
Publisher: name: Francia
Year: 2019

description: -
description: Francia, Bd. 26 Nr. 1 (1999)
Gauge theories and gravity
Creators: name: Sobreiro, R. F.
name: Tomaz, A. A.
name: Otoya, V. J. Vasquez
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Pure gauge theories for de Sitter, anti de Sitter and orthogonal groups, in four-dimensional Euclidean spacetime, are studied. It is shown that, if the theory is asymptotically free and a dynamical mass is generated, then an effective geometry may be induced and a gravity theory emerges.
description: 6pp. No figues. Seminar presented at the 7th International Conference on Mathematical Methods in Physics - Joint Conference: CBPF-IMPA-ICTP-SISSA-TWAS, CBPF, Rio de Janeiro, April 16-20 2012
N. Boskovska Leimgruber (Hg.), Die Frühe Neuzeit in der Geschichtswissenschaft. Forschungstendenzen und Forschungsergebnisse, 1997
Creators: name: Amalvi, C.
Publisher: name: Francia
Year: 2019

description: -
description: Francia, Bd. 26 Nr. 2 (1999)
Rapid evolution of trait correlation networks during bacterial adaptation to the rhizosphere
Creators: name: Li, Erqin
name: Ryo, Masahiro
name: Kowalchuk, George A.
name: Bakker, Peter A. H. M.
name: Jousset, Alexandre
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: Bacteria
subject: experimental evolution
subject: rhizosphere
subject: trait correlation network
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: There is a growing awareness that traits do not evolve individually but rather are organized as modular networks of covarying traits. Although the importance of multi-trait correlation has been linked to the ability to evolve in response to new environmental conditions, the evolvability of the network itself has to date rarely been assessed experimentally. By following the evolutionary dynamics of a model bacterium adapting to plant roots, we demonstrate that the whole structure of the trait correlation network is highly dynamic. We experimentally evolved Pseudomonas protegens, a common rhizosphere dweller, on the roots of Arabidopsis thaliana. We collected bacteria at regular intervals and determined a range of traits linked to growth, stress resistance, and biotic interactions. We observed a rapid disintegration of the original trait correlation network. Ancestral populations showed a modular network, with the traits linked to resource use and stress resistance forming two largely independent modules. This network rapidly was restructured during adaptation, with a loss of the stress resistance module and the appearance of new modules out of previously disconnected traits. These results show that evolutionary dynamics can involve a deep restructuring of phenotypic trait organization, pointing to the emergence of novel life history strategies not represented in the ancestral phenotype.
Coupling spectral imaging and laboratory analyses to digitally map sediment parameters and stratigraphic layers in Yeha, Ethiopia
Creators: name: Haburaj, Vincent
name: Japp, Sarah
name: Gerlach, Iris
name: Hoelzmann, Philipp
name: Schütt, Brigitte
Publisher: name: Freie Universität Berlin
Year: 2020
Subjects: subject: soil
subject: spectroscopy
subject: reassessment
subject: combination
subject: iron
subject: 500 Naturwissenschaften und Mathematik::550 Geowissenschaften, Geologie::550 Geowissenschaften

description: Quantitative analyses of soil and sediment samples are often used to complement stratigraphic interpretations in archaeological and geoscientific research. The outcome of such analyses often is confined to small parts of the examined profiles as only a limited number of samples can be extracted and processed. Recent laboratory studies show that such selectively measured soil and sediment characteristics can be spatially extrapolated using spectral image data, resulting in reliable maps of a variety of parameters. However, on-site usage of this method has not been examined. We therefore explore, whether image data (RGB data and visible and near infrared hyperspectral data), acquired under regular fieldwork conditions during an archaeological excavation, in combination with a sampling strategy that is close to common practice, can be used to produce maps of soil organic matter, hematite, calcite, several weathering indices and grain size characteristics throughout complex archaeological profiles. We examine two profiles from an archaeological trench in Yeha (Tigray, Ethiopia). Our findings show a promising performance of RGB data and its derivative CIELAB as well as hyperspectral data for the prediction of parameters via random forest regression. By including two individual profiles we are able to assess the accuracy and reproducibility of our results, and illustrate the advantages and drawbacks of a higher spectral resolution and the necessary additional effort during fieldwork. The produced maps of the parameters examined allow us to critically reflect on the stratigraphic interpretation and offer a more objective basis for layer delineation in general. Our study therefore promotes more transparent and reproducible documentation for often destructive archaeological fieldwork.
T. Meyer, »Endlich eine Tat, eine befreiende Tat...« Alfred von Kiderlen-Wächters »Panthersprung nach Agadir« unter dem Druck der öffentlichen Meinung, 1997
Creators: name: Elzer, H.
Publisher: name: Francia
Year: 2019

description: -
description: Francia, Bd. 26 Nr. 3 (1999)
The combination of quillaja and yucca saponins in broilers: effects on performance, nutrient digestibility and ileal morphometrics
Creators: name: Bafundo, K. W.
name: Männer, Klaus
name: Duerr, I.
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: Quillaja and yucca saponins
subject: nutrient digestibility
subject: ileal morphology
subject: performance
subject: productivity
subject: 600 Technik, Medizin, angewandte Wissenschaften::630 Landwirtschaft::630 Landwirtschaft und verwandte Bereiche

description: 1. Two series of studies were conducted to determine the effects of a combination of ground plant material derived from Quillaja saponaria trees and Yucca schidigera plants (QY) as sources of saponin, on performance, productivity, nutrient digestibility and ileal morphology of growing broilers. In each trial, 480 Cobb male birds were allocated equally to 24 pens at one-day-of-age according to body weight 2. The studies consisted of two identical floor pen trials in which performance and nutrient digestibility were assessed and two trials where performance and ileal morphology were determined. In each trial, 0, 250 or 500 ppm QY were included in feed given to the broilers from 1-35 or 1-42 d of age, respectively. Eight (digestibility) or 12 (morphology) randomised replicate pens were used. 3. In the digestibility trials, two birds per pen were moved to metabolism cages at d 21. Excreta was collected for a five-day period (d 21 to 25) for the determination of apparent total tract digestibility of dry and organic matter, fat and ash and nitrogen retention. For intestinal morphology, ileal segments were collected from four birds/pen on d 21 to determine villus height and crypt depth. Performance data were collected in each trial series. 4. Results showed that feeding graded levels of QY produced significant linear improvements in performance and productivity at d 35, and similar linear effects were observed for N retention and all apparent digestibility measurements. Morphology data showed that birds receiving 250 and 500 ppm QY had significantly increased villus height 5. These results indicated that QY exerted a positive influence on the intestinal tract by increasing the absorptive surface and improving nutrient digestibility. These effects were considered to be associated with the performance improvements recorded in both experiments.
Finding Characters Satisfying a Maximal Condition for Their Unipotent Support
Creators: name: Taylor, Jay
Publisher: name: arXiv
Year: 2012
Subjects: subject: Representation Theory (math.RT)
subject: FOS: Mathematics

description: In this article we extend independent results of Lusztig and Hézard concerning the existence of irreducible characters of finite reductive groups, (defined in good characteristic and arising from simple algebraic groups), satisfying a strong numerical relationship with their unipotent support. Along the way we obtain some results concerning quasi-isolated semisimple elements.
description: 35 pages; changes from (v2): added an index of notation and added a new part to the main theorem (Theorem 2.11)
Cerebellar Morphology and Behavioral Profiles in Mice Lacking Heparan Sulfate Ndst Gene Function
Creators: name: Lewejohann, Lars
name: Pallerla, Srinivas R.
name: Schreiber, Rebecca S.
name: Gerula, Joanna
name: Grobe, Kay
Publisher: name: Freie Universität Berlin
Year: 2020
Subjects: subject: Purkinje cell
subject: heparan sulfate
subject: extracellular matrix
subject: knockout mouse
subject: Ndst
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Disruption of the Heparan sulfate (HS)-biosynthetic gene N-acetylglucosamine N-Deacetylase/N-sulfotransferase 1 (Ndst1) during nervous system development causes malformations that are composites of those caused by mutations of multiple HS binding growth factors and morphogens. However, the role of Ndst function in adult brain physiology is less explored. Therefore, we generated mice bearing a Purkinje-cell-specific deletion in Ndst1 gene function by using Cre/loxP technology under the control of the Purkinje cell protein 2 (Pcp2/L7) promotor, which results in HS undersulfation. We observed that mutant mice did not show overt changes in the density or organization of Purkinje cells in the adult cerebellum, and behavioral tests also demonstrated normal cerebellar function. This suggested that postnatal Purkinje cell development and homeostasis are independent of Ndst1 function, or that impaired HS sulfation upon deletion of Ndst1 function may be compensated for by other Purkinje cell-expressed Ndst isoforms. To test the latter possibility, we additionally deleted the second Purkinje-cell expressed Ndst family member, Ndst2. This selectively abolished reproductive capacity of compound mutant female, but not male, mice, suggesting that ovulation, gestation, or female reproductive behavior specifically depends on Ndst-dependent HS sulfation in cells types that express Cre under Pcp2/L7 promotor control.
On the noise-induced passage through an unstable periodic orbit II: General case
Creators: name: Berglund, Nils
name: Gentz, Barbara
Publisher: name: arXiv
Year: 2012
Subjects: subject: Probability (math.PR)
subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics
subject: 60H10, 34F05 (Primary) 60J05, 60F10 (Secondary)

description: Consider a dynamical system given by a planar differential equation, which exhibits an unstable periodic orbit surrounding a stable periodic orbit. It is known that under random perturbations, the distribution of locations where the system's first exit from the interior of the unstable orbit occurs, typically displays the phenomenon of cycling: The distribution of first-exit locations is translated along the unstable periodic orbit proportionally to the logarithm of the noise intensity as the noise intensity goes to zero. We show that for a large class of such systems, the cycling profile is given, up to a model-dependent change of coordinates, by a universal function given by a periodicised Gumbel distribution. Our techniques combine action-functional or large-deviation results with properties of random Poincaré maps described by continuous-space discrete-time Markov chains.
description: 44 pages, 4 figures
Tidying-up the plant nuclear space: domains, functions, and dynamics
Creators: name: Santos, Ana Paula
name: Gaudin, Valérie
name: Mozgová, Iva
name: Pontvianne, Frédéric
name: Schubert, Daniel
name: Tek, Ahmet L.
name: Dvořáčková, Martina
name: Liu, Chang
name: Fransz, Paul
name: Rosa, Stefanie
Publisher: name: Freie Universität Berlin
Year: 2020
Subjects: subject: 3D Chromatin organization
subject: chromocentres
subject: gene expression
subject: liquid-liquid phase separation (LLPS)
subject: nuclear domains
subject: nuclear bodies
subject: nucleolus
subject: nuclear periphery
subject: 500 Naturwissenschaften und Mathematik::580 Pflanzen (Botanik)::580 Pflanzen (Botanik)

description: Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.
Halo-to-Halo Similarity and Scatter in the Velocity Distribution of Dark Matter
Creators: name: Mao, Yao-Yuan
name: Strigari, Louis E.
name: Wechsler, Risa H.
name: Wu, Hao-Yi
name: Hahn, Oliver
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We examine the Velocity Distribution Function (VDF) in dark matter halos from Milky Way to cluster mass scales. We identify an empirical model for the VDF with a wider peak and a steeper tail than a Maxwell--Boltzmann distribution, and discuss physical explanations. We quantify sources of scatter in the VDF of cosmological halos and their implication for direct detection of dark matter. Given modern simulations and observations, we find that the most significant uncertainty in the VDF of the Milky Way arises from the unknown radial position of the solar system relative to the dark matter halo scale radius.
description: Accepted to ApJ. Figure 3 and 5 and Section 4 newly added. 6 pages, 6 figures, typeset using emulateapj
Site-selective protonation of the one-electron reduced cofactor in [FeFe]-hydrogenase
Creators: name: Laun, Konstantin
name: Baranova, Iuliia
name: Duan, Jifu
name: Kertess, Leonie
name: Wittkamp, Florian
name: Apfel, Ulf-Peter
name: Happe, Thomas
name: Senger, Moritz
name: Stripp, Sven T.
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: [FeFe]-hydrogenases
subject: H-2 oxidation
subject: H-2 evolution
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Hydrogenases are bidirectional redox enzymes that catalyze hydrogen turnover in archaea, bacteria, and algae. While all types of hydrogenase show H-2 oxidation activity, [FeFe]-hydrogenases are excellent H-2 evolution catalysts as well. Their active site cofactor comprises a [4Fe-4S] cluster covalently linked to a diiron site equipped with carbon monoxide and cyanide ligands. The active site niche is connected with the solvent by two distinct proton transfer pathways. To analyze the catalytic mechanism of [FeFe]-hydrogenase, we employ operando infrared spectroscopy and infrared spectro-electrochemistry. Titrating the pH under H-2 oxidation or H-2 evolution conditions reveals the influence of site-selective protonation on the equilibrium of reduced cofactor states. Governed by pK(a) differences across the active site niche and proton transfer pathways, we find that individual electrons are stabilized either at the [4Fe-4S] cluster (alkaline pH values) or at the diiron site (acidic pH values). This observation is discussed in the context of the complex interdependence of hydrogen turnover and bulk pH.
Synthesis of Homogeneous Manganese-Doped Titanium Oxide Nanotubes from Titanate Precursors
Creators: name: Szirmai, Péter
name: Horváth, Endre
name: Náfrádi, Bálint
name: Micković, Zlatko
name: Smajda, Rita
name: Djokić, Dejan M.
name: Schenk, Kurt
name: Forró, László
name: Magrez, Arnaud
Publisher: name: arXiv
Year: 2012
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report a novel synthesis route of homogeneously manganese-doped titanium dioxide nanotubes in a broad concentration range. The scroll-type trititanate (H(2)Ti(3)O(7)) nanotubes prepared by hydrothermal synthesis were used as precursors. Mn2+ ions were introduced by an ion exchange method resulting Mn(x)H(2-x)Ti(3)O(7). In a subsequent heat-treatment they were transformed into Mn(y)Ti(1-y)O(2) where y=x/(3+x). The state and the local environment of the Mn2+ ions in the precursor and final products were studied by Electron Spin Resonance (ESR) technique. It was found that the Mn2+ ions occupy two positions: the first having an almost perfect cubic symmetry while the other is in a strongly distorted octahedral site. The ratio of the two Mn2+ sites is independent of the doping level and amounts to 15:85 in Mn(x)H(2-x)Ti(3)O(7) and to 5:95 in Mn(y)Ti(1-y)O(2). SQUID magnetometry does not show long-range magnetic order in the homogeneously Mn2+-doped nanotubes.
description: 7 pages, 6 figures
A. Terroine (†), L. Fossier, avec le concours d'Y. de Montenon (†), Chartes et documents de l'abbaye de Saint-Magloire. T. I: fin du Xe siècle-1280, 1998
Creators: name: Lohrmann, D.
Publisher: name: Francia
Year: 2019

description: Francia, Bd. 27 Nr. 1 (2000)
Unification and limitations of error suppression techniques for adiabatic quantum computing
Creators: name: Young, Kevin C.
name: Sarovar, Mohan
Publisher: name: arXiv
Year: 2012
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: While adiabatic quantum computation (AQC) possesses some intrinsic robustness to noise, it is expected that a form of error control will be necessary for large scale computations. Error control ideas developed for circuit-model quantum computation do not transfer easily to the AQC model and to date there have been two main proposals to suppress errors during an AQC implementation: energy gap protection and dynamical decoupling. Here we show that these two methods are fundamentally related and may be analyzed within the same formalism. We analyze the effectiveness of such error suppression techniques and identify critical constraints on the performance of error suppression in AQC, suggesting that error suppression by itself is insufficient for fault-tolerant, large-scale AQC and that a form of error correction is needed. This manuscript has been superseded by the articles, "Error suppression and error correction in adiabatic quantum computation I: techniques and challenges," arXiv:1307.5893, and "Error suppression and error correction in adiabatic quantum computation II: non-equilibrium dynamics," arXiv:1307.5892.
description: 9 pages. Update replaces "Equivalence" with "Unification." This manuscript has been superseded by the two-article series: arXiv:1307.5892 and arXiv:1307.5893
Temporal Evolution of the Scattering Polarization of the CaII IR Triplet in Hydrodynamical Models of the Solar Chromosphere
Creators: name: Carlin, E. S.
name: Ramos, A. Asensio
name: Bueno, J. Trujillo
Publisher: name: arXiv
Year: 2012
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Velocity gradients in a stellar atmospheric plasma have an impact on the anisotropy of the radiation field that illuminates each point within the medium, and this may in principle influence the scattering line polarization that results from the induced atomic level polarization. Here we analyze the emergent linear polarization profiles of the Ca II infrared triplet after solving the radiative transfer problem of scattering polarization in time-dependent hydrodynamical models of the solar chromosphere, taking into account the impact of the plasma macroscopic velocity on the atomic level polarization. We discuss the influence that the velocity and temperature shocks in the considered chromospheric models have on the temporal evolution of the scattering polarization signals of the Ca II infrared lines, as well as on the temporally averaged profiles. Our results indicate that the increase of the linear polarization amplitudes caused by macroscopic velocity gradients may be significant in realistic situations. We also study the effect of the integration time, the microturbulent velocity and the photospheric dynamical conditions, and discuss the feasibility of observing with large-aperture telescopes the temporal variation of the scattering polarization profiles. Finally, we explore the possibility of using the differential Hanle effect in the IR triplet of Ca II with the intention of avoiding the characterization of the zero-field polarization to infer magnetic fields in dynamic situations.
description: 12 pages, 9 figures. Accepted for publication in ApJ. New figure added, typos corrected
Systematic functional analysis of rab GTPases reveals limits of neuronal robustness to environmental challenges in flies
Creators: name: Kohrs, Friederike E.
name: Daumann, Ilsa-Maria
name: Pavlovic, Bojana
name: Jin, Eugene Jennifer
name: Kiral, F. Ridvan
name: Lin, Shih-Ching
name: Wolfenberg, Heike
name: Mathejczyk, Thomas F.
name: Linneweber, Gerit A.
name: Hiesinger, P. Robin
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: rab GTPases
subject: neuronal robustness
subject: flies
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Rab GTPases are molecular switches that regulate membrane trafficking in all cells. Neurons have particular demands on membrane trafficking and express numerous Rab GTPases of unknown function. Here, we report the generation and characterization of molecularly defined null mutants for all 26 rab genes in Drosophila. In flies, all rab genes are expressed in the nervous system where at least half exhibit particularly high levels compared to other tissues. Surprisingly, loss of any of these 13 nervous system-enriched Rabs yielded viable and fertile flies without obvious morphological defects. However, all 13 mutants differentially affected development when challenged with different temperatures, or neuronal function when challenged with continuous stimulation. We identified a synaptic maintenance defect following continuous stimulation for six mutants, including an autophagy-independent role of rab26. The complete mutant collection generated in this study provides a basis for further comprehensive studies of Rab GTPases during development and function in vivo.
Investigation of CTA 1 with Suzaku Observation
Creators: name: Lin, Lupin C. C.
name: Takata, Jumpei
name: Kong, Albert K. H.
name: Hui, C. Y.
name: Enoto, Teruaki
name: Chang, H. K.
name: Huang, Regina H. H.
name: Liang, J. S.
name: Shibata, Shinpei
name: Hwang, C. Y.
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We report on an 105 ks Suzaku observation of the supernova remnant CTA 1 (G119.5+10.2). The Suzaku soft X-ray observation was carried out with both timing mode and imaging mode. A ~ 10' extended feature, which is interpreted as a bow-shock component of the pulsar wind nebula (PWN), is revealed in this deep observation for the first time. The nebular spectrum can be modelled by a power-law with a photon index of ~ 1.8 which suggests a slow synchrotron cooling scenario. The photon index is approximately constant across this extended feature. We compare and discuss our observations of this complex nebula with previous X-ray investigations. We do not obtain any significant pulsation from the central pulsar in the soft (0.2-12 keV) and hard (10-60 keV) X-ray data. The non-detection is mainly due to the loss of the precise imaging ability to accurately determine the source contribution. The spectra of XIS and HXD can be directly connected without a significant spectral break according to our analysis. Future observations of NuSTAR and Astro-H would be able to resolve the contamination and provide an accurate hard X-ray measurement of CTA 1.
description: 9 pages, 7 figures, accepted by MNRAS
Quantum Square Well Bound States Described by Equations with Non-locality
Creators: name: Ohira, Toru
Publisher: name: arXiv
Year: 2012
Subjects: subject: General Physics (physics.gen-ph)
subject: FOS: Physical sciences

description: We present here a simple equation explicitly incorporating non-locality, which reproduces quantized energy levels of the bound states for the square well potentials. Introduction of this equation is motivated by studies of differential equation with time delayed feedback, which can be viewed as describing temporal non-locality.
description: 4 pages, 1 figure, submitted for a publication
Climate Variability Rather Than Livestock Grazing Dominates Changes in Alpine Grassland Productivity Across Tibet
Creators: name: Li, Meng
name: Wu, Jianshuang
name: Feng, Yunfei
name: Niu, Ben
name: He, Yongtao
name: Zhang, Xianzhou
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: climate change
subject: grassland degradation
subject: human activities
subject: NPP
subject: Tibetan Plateau
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Alpine grasslands on the Tibetan Plateau, being vulnerable to environmental and anthropogenic changes, have experienced dramatic climate change and intensive livestock grazing during the last half-century. Climate change, coupled with grazing activities, has profoundly altered alpine grassland function and structure and resulted in vast grassland degradation. To restore degraded grasslands, the Central Government of China has implemented the Ecological Security Barrier Protection and Construction Project since 2008 across the Tibetan Autonomous Region. However, the relative effect of climate change and grazing activities on the variation in alpine grassland productivity is still under debate. In this study, we quantified how aboveground net primary production (ANPP) varied before (2000-2008) and after (2009-2017) starting the project across different alpine grasslands and how much variance in ANPP could be attributed to climate change and grazing disturbance, in terms of temperature, precipitation, solar radiation, and grazing intensity. Our results revealed that Tibet's climate got warmer and wetter, and grazing intensity decreased after starting the project. Mean ANPP increased at approximately 81% of the sites, on average from 27.0 g C m(-2) during 2000-2008 to 28.4 g C m(-2) during 2009-2017. The ANPP positively correlated with annual temperature and precipitation, but negatively with grazing intensity for both periods. Random forest modeling indicated that grazing intensity (14.5%) had a much lower influence in controlling the dynamics of grassland ANPP than precipitation (29.0%), suggesting that precipitation variability was the key factor for alpine grassland ANPP increase across Tibet.
Types of single particle symmetry breaking in transition metal oxides due to electron correlation
Creators: name: Wagner, Lucas K.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Very accurate wave functions are calculated for small transition metal oxide molecules. These wave functions are decomposed using reduced density matrices to study the underlying correlation of electrons. The correlation is primarily of left-right type between the transition metals and the oxygen atoms, which is mediated by excitations from the nominal single Slater ground state into antibonding and d-type orbitals. In a localized representation, this correlation manifests itself in a 2-electron hopping term that is off-diagonal. This term is of similar magnitude to the commonly considered Hubbard-type on-site interaction.
Precision-cut bovine udder slices (PCBUS) as an in-vitro-model of an early phase of infection of bovine mastitis
Creators: name: Filor, Viviane
name: Petry, Monique
name: Meißner, Jessica
name: Kietzmann, Manfred
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: Bovine mastitis
subject: Cytokine profile
subject: In-vitro-model
subject: Precision-cut bovine udder slices
subject: 600 Technik, Medizin, angewandte Wissenschaften::630 Landwirtschaft::630 Landwirtschaft und verwandte Bereiche

description: Background The aim of this study was to establish precision-cut bovine udder slices (PCBUS) as an in-vitro-model to investigate pathophysiological processes in the early phase of mastitis in order to have the possibility to investigate new therapeutic approaches for the treatment of such udder inflammation in later studies. Furthermore, this model should contribute to substitute in-vivo-experiments. Bovine mastitis is one of the most common and costly infectious diseases in the dairy industry, which is largely associated with the use of antimicrobial agents. Given this problem of antimicrobial resistance, it is essential to step up research into bacterial infectious diseases. Thus, the transfer of the in-vitro-model of precision-cut tissue slices to the bovine udder enables broad research into new therapeutic approaches in this area and can also be used to address issues in basic research or the characterisation of complex pathophysiological processes. Results A stimulation with LPS, PGN or the combination of both substances (LPS:PGN) demonstrates the ability of the PCBUS to react with a significant secretion of IL-1ß, TNF-α and PGE2. Conclusion The slices represent an instrument for investigating pharmacological interactions with udder tissue, which can be useful for studies on pharmacological questions and the understanding of complex pathophysiological processes of infection and inflammation.
Controlling pairing of π-conjugated electrons in 2D covalent organic radical frameworks via in-plane strain
Creators: name: Alcón, Isaac
name: Santiago, Raúl
name: Ribas-Arino, Jordi
name: Deumal, Mercè
name: Moreira, Ibério De P. R.
name: Bromley, Stefan T.
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: Electronic materials
subject: Electronic properties and materials
subject: Structure prediction
subject: Two-dimensional materials
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Controlling the electronic states of molecules is a fundamental challenge for future sub-nanoscale device technologies. -conjugated bi-radicals are very attractive systems in this respect as they possess two energetically close, but optically and magnetically distinct, electronic states: the open-shell antiferromagnetic/paramagnetic and the closed-shell quinoidal diamagnetic states. While it has been shown that it is possible to statically induce one electronic ground state or the other by chemical design, the external dynamical control of these states in a rapid and reproducible manner still awaits experimental realization. Here, via quantum chemical calculations, we demonstrate that in-plane uniaxial strain of 2D covalently linked arrays of radical units leads to smooth and reversible conformational changes at the molecular scale that, in turn, induce robust transitions between the two kinds of electronic distributions. Our results pave a general route towards the external control, and thus technological exploitation, of molecular-scale electronic states in organic 2D materials. Controlling the electronic states of molecules is a fundamental challenge for future sub-nanoscale device technologies but the external dynamical control of these states still awaits experimental realization. Here, via quantum chemical calculations, the authors demonstrate that in-plane uniaxial strain of 2D covalently linked arrays of radical units induces controlled pairing of pi -conjugated electrons in a reversible way.
A holomorphic characterization of operator algebras
Creators: name: Neal, Matthew
name: Russo, Bernard
Publisher: name: arXiv
Year: 2012
Subjects: subject: Operator Algebras (math.OA)
subject: FOS: Mathematics
subject: 47L25, 47L70, 17C65

description: A necessary and sufficient condition for an operator space to support a multiplication making it completely isometric and isomorphic to a unital operator algebra is proved. The condition involves only the holomorphic structure of the Banach spaces underlying the operator space.
description: 29 pages, submitted
Climbing Jacob's ladder: A density functional theory case study for Ag2ZnSnSe4 and Cu2ZnSnSe4
Creators: name: Fritsch, Daniel
name: Schorr, Susan
Publisher: name: Freie Universität Berlin
Year: 2020
Subjects: subject: density functional theory
subject: hybrid functional
subject: kesterite
subject: chalcogenide
subject: solar cell material
subject: band structure
subject: dielectric function
subject: 500 Naturwissenschaften und Mathematik::550 Geowissenschaften, Geologie::550 Geowissenschaften

description: Recent advances in the development of exchange and correlation functionals to be employed in density functional theory calculations combined with the availability of ever more powerful high-performance computing facilities, let predictive computational materials science become reality. In order to assess the quality of calculated material properties, Jacob's ladder provides an informal classification, where exchange and correlation functionals of similar capabilities are placed at the same rung of this ladder, while improved and more accurate ones are placed at higher rungs. Climbing Jacob's ladder, i.e. employing more accurate exchange and correlation functionals, increases the quality of the results and the computational demands, and provides some guidance as to what accuracies and computational costs to expect from specific calculations. This is particular important for materials whose electronic ground state properties are incorrectly described, e.g. small band gap semiconductors, and materials, where system sizes for subsequent investigations, like defect properties or band offsets in heterostructures, become prohibitively large for more accurate exchange and correlation functionals. Here, we provide a systematic density functional theory study on the ground state properties of Ag2ZnSnSe4 and Cu2ZnSnSe4 for the lowest four rungs of Jacob's ladder. Cu2ZnSnSe4, and in particular its alloys with Ag, is a promising candidate material for future thin-film solar cell absorber layers. In the present work, the obtained material properties are compared to available experimental data, allowing to benchmark the accuracy of the employed exchange and correlation functionals. We also provide a comparative study for subsequent quasiparticle calculations. Therein, the influence of differently obtained eigenvalues and orbitals as starting points are critically assessed with respect to available experimental data. Our results show that, structural properties based on the SCAN functional show overall best agreement with available experimental data, whereas additional hybrid functional calculations are necessary for satisfying results on electronic and optical properties.