cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Light emission from silicon with tin-containing nanocrystals
Creators: name: Roesgaard, Søren
name: Chevallier, Jacques
name: Gaiduk, Peter I.
name: Hansen, John Lundsgaard
name: Jensen, Pia Bomholt
name: Larsen, Arne Nylandsted
name: Svane, Axel
name: Balling, Peter
name: Julsgaard, Brian
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Tin-containing nanocrystals, embedded in silicon, have been fabricated by growing an epitaxial layer of Si_{1-x-y}Sn_{x}C_{y}, where x = 1.6 % and y = 0.04 %, followed by annealing at various temperatures ranging from 650 to 900 degrees C. The nanocrystal density and average diameters are determined by scanning transmission-electron microscopy to ~ 10^{17} cm^{-3} and ~ 5 nm, respectively. Photoluminescence spectroscopy demonstrates that the light emission is very pronounced for samples annealed at 725 degrees C, and Rutherford back-scattering spectrometry shows that the nanocrystals are predominantly in the diamond-structured phase at this particular annealing temperature. The origin of the light emission is discussed.
description: 5 pages, 3 figures, submitted to AIP Advances
Self Noise Reduction and Aerodynamics of Airfoils with Porous Trailing Edges
Creators: name: Geyer, Thomas Fritz
name: Sarradj, Ennes
Publisher: name: Technische Universität Berlin
Year: 2019
Subjects: subject: 530 Physik
subject: porous airfoils
subject: trailing edge
subject: noise reduction
subject: aerodynamics
subject: wind tunnel
subject: microphone array

description: The application of open-porous materials is a possible method to effectively reduce the aerodynamic noise of an airfoil. However, the porous consistency may have a negative effect on the aerodynamic performance of the airfoil, since very often the lift is decreased while the drag increases. In a recent investigation, the generation of trailing edge noise of a set of airfoil models made from different porous materials was examined experimentally. The materials were characterized mainly by their airflow resistivity. Besides the material, the chordwise extent of the porous material was varied, which was done by covering the front part of the porous airfoil with a thin, impermeable adhesive foil. Acoustic measurements were performed in an open jet wind tunnel using microphone array technology, while the aerodynamic performance was measured simultaneously using a six-component balance. In general, both the airflow resistivity and the extent of the porous material have an influence on the trailing edge noise. However, if a suitable material is chosen, the results show that a noticeable reduction of trailing edge noise is possible even with only a small chordwise extent of the porous material.
title: Intelligent Traffic Management: From Practical Stochastic Path Planning to Reinforcement Learning Based City-Wide Traffic Optimization
Creators: name: Ahmadi, Kamilia
Publisher: name: Utah State University
Year: 2021

description: This research focuses on intelligent traffic management including stochastic path planning and city scale traffic optimization. Stochastic path planning focuses on finding paths when edge weights are not fixed and change depending on the time of day/week. Then we focus on minimizing the running time of the overall procedure at query time utilizing precomputation and approximation. The city graph is partitioned into smaller groups of nodes and represented by its exemplar. In query time, source and destination pairs are connected to their respective exemplars and the path between those exemplars is found. After this, we move toward minimizing the city wide traffic congestion by making structural changes include changing the number of lanes, using ramp metering, varying speed limit, and modifying signal timing is possible. We propose a multi agent reinforcement learning (RL) framework for improving traffic flow in city networks. Our framework utilizes two level learning: a) each single agent learns the initial policy and b) multiple agents (changing the environment at the same time) update their policy based on the interaction with the dynamic environment and in agreement with other agents. The goal of RL agents is to interact with the environment to learn the optimal modification for each road segment through maximizing the cumulative reward over the set of possible actions in state space.
identification of agrophenotypes from NDVI data and derivation of leaf area index: r script and sample dataset
Creators: name: Simone Bregaglio
name: Sofia Bajocco
name: Fabrizio Ginaldi
Publisher: name: Zenodo
Year: 2022
Subjects: agrophenotype; principal component analysis; NDVI; cluster analysis

description: this script reproduces the methodology presented in the paper 'Improving the accuracy of sub-regional yield predictions by embedding local agrophenotypes into crop model parameter sets', currently submitted to Agricultural Systems. 
description: the research paper to which this script refers is currently submitted, a preprint version is available at https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4024161.

This work was conducted by the Council for Agricultural Research and Economics in collaboration with the Italian National Institute of Statistics (ISTAT) and supported by the Italian Ministry of Agricultural, Food and Forestry Policies (AgriDigit-Agromodelli, DM n. 36502 of 20/12/2018).
Microbial Communities of Hydrothermal Guaymas Basin Surficial Sediment Profiled at 2 Millimeter-Scale Resolution
Creators: name: Kalenborn, S.
name: Heyerhoff, B.
name: Nguyen, T.
name: Peterson, R.N.
name: Teske, A.
name: Wegener, G.
name: Tabai, H.
name: Sydow, K.
name: Engelen, B.
Publisher: name: Frontiers Media S.A.
Year: 2021

description: The surficial hydrothermal sediments of Guaymas Basin harbor complex microbial communities where oxidative and reductive nitrogen, sulfur, and carbon-cycling populations and processes overlap and coexist. Here, we resolve microbial community profiles in hydrothermal sediment cores of Guaymas Basin on a scale of 2 millimeters, using Denaturing Gradient Gel Electrophoresis (DGGE) to visualize the rapid downcore changes among dominant bacteria and archaea. DGGE analysis of bacterial 16S rRNA gene amplicons identified free-living and syntrophic deltaproteobacterial sulfate-reducing bacteria, fermentative Cytophagales, members of the Chloroflexi (Thermoflexia), Aminicenantes, and uncultured sediment clades. The DGGE pattern indicates a gradually changing downcore community structure where small changes on a 2-millimeter scale accumulate to significantly changing populations within the top 4 cm sediment layer. Functional gene DGGE analyses identified anaerobic methane-oxidizing archaea (ANME) based on methyl-coenzyme M reductase genes, and members of the Betaproteobacteria and Thaumarchaeota based on bacterial and archaeal ammonia monooxygenase genes, respectively. The co-existence and overlapping habitat range of aerobic, nitrifying, sulfate-reducing and fermentative bacteria and archaea, including thermophiles, in the surficial sediments is consistent with dynamic redox and thermal gradients that sustain highly complex microbial communities in the hydrothermal sediments of Guaymas Basin.
Searching for quantum speedup in quasistatic quantum annealers
Creators: name: Amin, Mohammad
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We argue that a quantum annealer at very long annealing times is likely to experience a quasistatic evolution, returning a final population that is close to a Boltzmann distribution of the Hamiltonian at a single (freeze-out) point during the annealing. Such a system is expected to correlate well with a proper quantum Monte Carlo simulation. It may also correlate with simulated annealing if at the freeze-out point the quantum energy eigenvalues are close to the classical ones. These correlations are just signatures of equilibration and do not mean that the evolution of the quantum annealer is classical or can be simulated by quantum Monte Carlo. The computation time extracted from such a distribution reflects the equilibrium behavior and therefore provides no information about the underlying quantum dynamics. This makes the search for quantum speedup in suboptimal quantum annealers problematic. We use an open quantum master equation with realistic parameters to illustrate quasistatic evolution in a 16 qubit quantum annealer and discuss its implication for quantum speedup.
description: 5 pages, 4 figures, Last version to appear in PRA
Ex Vivo and In Vivo Analysis of a Novel Porcine Aortic Patch for Vascular Reconstruction
Creators: name: Stöwe, Ignacio
name: Pissarek, Jens
name: Moosmann, Pia
name: Pröhl, Annica
name: Pantermehl, Sven
name: Bielenstein, James
name: Radenkovic, Milena
name: Jung, Ole
name: Najman, Stevo
name: Alkildani, Said
name: Barbeck, Mike
Publisher: name: Technische Universität Berlin
Year: 2021
Subjects: subject: 540 Chemie und zugeordnete Wissenschaften
subject: vascular reconstruction
subject: vascular grafts
subject: xenografts
subject: porcine aorta
subject: bovine pericardium
subject: macrophages
subject: inflammation

description: (1) Background: The aim of the present study was the biocompatibility analysis of a novel xenogeneic vascular graft material (PAP) based on native collagen won from porcine aorta using the subcutaneous implantation model up to 120 days post implantationem. As a control, an already commercially available collagen-based vessel graft (XenoSure®) based on bovine pericardium was used. Another focus was to analyze the (ultra-) structure and the purification effort. (2) Methods: Established methodologies such as the histological material analysis and the conduct of the subcutaneous implantation model in Wistar rats were applied. Moreover, established methods combining histological, immunohistochemical, and histomorphometrical procedures were applied to analyze the tissue reactions to the vessel graft materials, including the induction of pro- and anti-inflammatory macrophages to test the immune response. (3) Results: The results showed that the PAP implants induced a special cellular infiltration and host tissue integration based on its three different parts based on the different layers of the donor tissue. Thereby, these material parts induced a vascularization pattern that branches to all parts of the graft and altogether a balanced immune tissue reaction in contrast to the control material. (4) Conclusions: PAP implants seemed to be advantageous in many aspects: (i) cellular infiltration and host tissue integration, (ii) vascularization pattern that branches to all parts of the graft, and (iii) balanced immune tissue reaction that can result in less scar tissue and enhanced integrative healing patterns. Moreover, the unique trans-implant vascularization can provide unprecedented anti-infection properties that can avoid material-related bacterial infections.
Zinc Deficiency Disturbs Mucin Expression, O-Glycosylation and Secretion by Intestinal Goblet Cells
Creators: name: Maares, Maria
name: Keil, Claudia
name: Straubing, Sophia
name: Robbe-Masselot, Catherine
name: Haase, Hajo
Publisher: name: Technische Universität Berlin
Year: 2020
Subjects: subject: 540 Chemie und zugeordnete Wissenschaften
subject: zinc deficiency
subject: intestinal mucins
subject: O-glycosylation
subject: goblet cells
subject: MUC2
subject: MUC5AC
subject: zinc homeostasis
subject: glycosyltransferases
subject: C1GALT1
subject: B3GNT6

description: Approximately 1 billion people worldwide suffer from zinc deficiency, with severe consequences for their well-being, such as critically impaired intestinal health. In addition to an extreme degeneration of the intestinal epithelium, the intestinal mucus is seriously disturbed in zinc-deficient (ZD) animals. The underlying cellular processes as well as the relevance of zinc for the mucin-producing goblet cells, however, remain unknown. To this end, this study examines the impact of zinc deficiency on the synthesis, production, and secretion of intestinal mucins as well as on the zinc homeostasis of goblet cells using the in vitro goblet cell model HT-29-MTX. Zinc deprivation reduced their cellular zinc content, changed expression of the intestinal zinc transporters ZIP-4, ZIP-5, and ZnT1 and increased their zinc absorption ability, outlining the regulatory mechanisms of zinc homeostasis in goblet cells. Synthesis and secretion of mucins were severely disturbed during zinc deficiency, affecting both MUC2 and MUC5AC mRNA expression with ongoing cell differentiation. A lack of zinc perturbed mucin synthesis predominantly on the post-translational level, as ZD cells produced shorter O-glycans and the main O-glycan pattern was shifted in favor of core-3-based mucins. The expression of glycosyltransferases that determine the formation of core 1-4 O-glycans was altered in zinc deficiency. In particular, B3GNT6 mRNA catalyzing core 3 formation was elevated and C2GNT1 and C2GNT3 elongating core 1 were downregulated in ZD cells. These novel insights into the molecular mechanisms impairing intestinal mucus stability during zinc deficiency demonstrate the essentiality of zinc for the formation and maintenance of this physical barrier.
On the interpretation of dark matter self-interactions in Abell 3827
Creators: name: Kahlhoefer, Felix
name: Schmidt-Hoberg, Kai
name: Kummer, Janis
name: Sarkar, Subir
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Self-interactions of dark matter particles can potentially lead to an observable separation between the dark matter halo and the stars of a galaxy moving through a region of large dark matter density. Such a separation has recently been observed in a galaxy falling into the core of the galaxy cluster Abell 3827. We estimated the DM self-interaction cross section needed to reproduce the observed effects and find that the sensitivity of Abell 3827 has been significantly overestimated in a previous study. Our corrected estimate is $\tildeσ/m_\text{DM} \sim 3\:\text{cm}^2\:\text{g}^{-1}$ when self-interactions result in an effective drag force and $σ/m_\text{DM} \sim 1.5\:\text{cm}^2\:\text{g}^{-1}$ for the case of contact interactions, in some tension with previous upper bounds.
description: 5 pages, 3 figures; v2: matches published version
Additional file 1 of A patient-derived cell model for malignant transformation in IDH-mutant glioma
Creators: name: Kim, Olga
name: Sergi, Zach
name: Yu, Guangyang
name: Yamamoto, Kazutoshi
name: Quezado, Martha
name: Abdullaev, Zied
name: Crooks, Danel R.
name: Kishimoto, Shun
name: Li, Qi
name: Lu, Peng
name: Blackman, Burchelle
name: Andresson, Thorkell
name: Wu, Xiaolin
name: Tran, Bao
name: Wei, Jun S.
name: Zhang, Wei
name: Zhang, Meili
name: Song, Hua
name: Khan, Javed
name: Krishna, Murali C.
name: Brender, Jeffrey R.
name: Wu, Jing
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Supplementary Material 1.
Deep-sea hydrothermal vent sediments reveal diverse fungi with antibacterial activities
Creators: name: Beaudoin, D.
name: Burgaud, G.
name: Edgcomb, V.
name: Dayras, M.
name: Teske, A.
name: Mehiri, M.
name: Keeler, E.
name: Cassand, J.
Publisher: name: Oxford University Press
Year: 2021

description: Relatively little is known about the diversity of fungi in deep-sea, hydrothermal sediments. Less thoroughly explored environments are likely untapped reservoirs of unique biodiversity with the potential to augment our current arsenal of microbial compounds with biomedical and/or industrial applications. In this study, we applied traditional culture-based methods to examine a subset of the morphological and phylogenetic diversity of filamentous fungi and yeasts present in 11 hydrothermally influenced sediment samples collected from eight sites on the seafloor of Guaymas Basin, Mexico. A total of 12 unique isolates affiliating with Ascomycota and Basidiomycota were obtained and taxonomically identified on the basis of morphological features and analyses of marker genes including actin, β-tubulin, small subunit ribosomal DNA (18S rRNA), internal transcribed spacer (ITS) and large subunit ribosomal DNA (26S rRNA) D1/D2 domain sequences (depending on taxon). A total of 11 isolates possess congeners previously detected in, or recovered from, deep-sea environments. A total of seven isolates exhibited antibacterial activity against human bacterial pathogens Staphylococcus aureus ATCC-35556 and/or Escherichia coli ATCC-25922. This first investigation suggests that hydrothermal environments may serve as promising reservoirs of much greater fungal diversity, some of which may produce biomedically useful metabolites.
Effects of Airport Runoff Pollution on Water Quality in Bay Area Sites Surrounding San Francisco and Oakland Airports
Creators: name: Walters, Elisabeth
name: Spuller, Kerri
Publisher: name: QUBES Educational Resources
Year: 2023

description: Airports contribute to pollution through point source and non point source pollution, which can have a negative effect on water quality and aquatic life. The purpose of the study was to determine if runoff pollution from SFO and OAK airports impacts water quality in the Bay Area. We tested water quality at 12 sites surrounding two airports in the Bay Area. We tested for pH and the presence of specific metals and nitrates. As a result of the analysis, we found that the presence of zinc, copper, chromium and nitrate increases as we get closer to the airport. The pH remained constant throughout the sites. We concluded that airport pollution is a likely source of elevated concentrations of some heavy metals and nitrates in the San Francisco Bay.
Heirarchical Self Assembly: Self Organized nano-structures in a nematically ordered matrix of self assembled polymeric chains
Creators: name: Mubeena, Shaikh
name: Chatterji, Apratim
Publisher: name: arXiv
Year: 2014
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We report many different nano-structures which are formed when model nano-particles of different sizes (diameter σ n ) are allowed to aggregate in a background matrix of semi-flexible self assembled polymeric worm like micellar chains. The different nano-structures are formed by the dynamical arrest of phase-separating mixtures of micellar monomers and nano-particles. The different mor- phologies obtained are the result of an interplay of the available free volume, the elastic energy of deformation of polymers, the density (chemical potential) of the nano-particles in the polymer ma- trix and, of course, the ratio of the size of self assembling nano-particles and self avoidance diameter of polymeric chains. We have used a hybrid semi-grand canonical Monte Carlo simulation scheme to obtain the (non-equilibrium) phase diagram of the self-assembled nano-structures. We observe rod-like structures of nano-particles which get self assembled in the gaps between the nematically ordered chains as well as percolating gel-like network of conjoined nanotubes. We also find a totally unexpected interlocked crystalline phase of nano-particles and monomers, in which each crytal plane of nanoparticles is separated by planes of perfectly organized polymer chains. We identified the con- dition which leads to such interlocked crystal structure. We suggest experimental possibilities of how the results presented in this paper could be used to obtain different nano-structures in the lab.
Washability of E-Textiles: Failure Modes and Influences on Washing Reliability
Creators: name: Rotzler, Sigrid
name: Schneider-Ramelow, Martin
Publisher: name: Technische Universität Berlin
Year: 2021
Subjects: subject: 670 Industrielle Fertigung
subject: electronic textiles
subject: e-textiles
subject: smart textiles
subject: wash testing
subject: washability
subject: reliability
subject: failure modes

description: E-textiles, hybrid products that incorporate electronic functionality into textiles, often need to withstand washing procedures to ensure textile typical usability. Yet, the washability—which is essential for many e-textile applications like medical or sports due to hygiene requirements—is often still insufficient. The influence factors for washing damage in textile integrated electronics as well as common weak points are not extensively researched, which makes a targeted approach to improve washability in e-textiles difficult. As a step towards reliably washable e-textiles, this review bundles existing information and findings on the topic: a summary of common failure modes in e-textiles brought about by washing as well as influencing parameters that affect the washability of e-textiles. The findings of this paper can be utilized in the development of e-textile systems with an improved washability.
Derivation of Lighthill’s Eighth Power Law of an Aeroacoustic Quadrupole in Acoustic Spacetime
Creators: name: Masovic, Drasko
name: Sarradj, Ennes
Publisher: name: Technische Universität Berlin
Year: 2020
Subjects: subject: 530 Physik
subject: acoustic spacetime
subject: Lighthill’s aeroacoustic analogy
subject: quadrupole radiation

description: Acoustic spacetime is a four-dimensional manifold analogue to the relativistic spacetime with the reference speed of light replaced by the speed of sound. It has been established primarily for the indirect studies of relativistic phenomena by means of their better understood acoustic analogues. More recently, it has also been used for the analytical treatment of sound propagation in various uniform and non-uniform flows of the background fluid. In this paper the analogy is extended and utilized to derive Lighthill’s eight power law for sound generation of an aeroacoustic quadrupole. Adding to the existing analogue theory, propagating sound waves are described in terms of a weak perturbation of the background acoustic spacetime metric. The obtained result proves that the acoustic analogy can be extended to cover both weak perturbation of the fluid due to the sound waves and certain sound generation mechanisms, at least in incompressible low Mach number flows.
Access to Public Parks, Drinking Fountains, and Clean Public Drinking Water Across Income Brackets in the Bay Area
Creators: name: Zaroff, Eliza
name: Holmquist, Anna
Publisher: name: QUBES Educational Resources
Year: 2023

description: Access to green space and clean drinking water can be unequally distributed in urban spaces, often associated with income inequality. Little is known about public drinking water and green space inequities in the Bay Area. For our study, we asked, “How do public park access, drinking fountain access, and the quality of public drinking water differ across income brackets in the Bay Area?” and hypothesized that there would be a significant positive correlation between income and the number of drinking fountains, the number of parks, and drinking fountain water quality. For each Bay Area sub-region, water samples from four drinking fountains from four different ZIP codes were analyzed, and the number of parks and fountains was recorded in relation to income for eight different ZIP codes, resulting in 20 analyzed fountains and 40 analyzed ZIP...
Dynamics of multi-stage infections on networks
Creators: name: Sherborne, N.
name: Blyuss, K. B.
name: Kiss, I. Z.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: Populations and Evolution (q-bio.PE)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: This paper investigates the dynamics of infectious diseases with a non-exponentially distributed infectious period. This is achieved by considering a multi-stage infection model on networks. Using pairwise approximation with a standard closure, a number of important characteristics of disease dynamics are derived analytically, including the final size of an epidemic and a threshold for epidemic outbreaks, and it is shown how these quantities depend on disease characteristics, as well as the number of disease stages. Stochastic simulations of dynamics on networks are performed and compared to the results of pairwise models for several realistic examples of infectious diseases to illustrate the role played by the number of stages in the disease dynamics. These results show that a higher number of disease stages results in faster epidemic outbreaks with a higher peak prevalence and a larger final size of the epidemic. The agreement between the pairwise and simulation methods is excellent in the cases we consider.
description: 23 pages, 8 figures
Night Matters—Why the Interdisciplinary Field of “Night Studies” Is Needed
Creators: name: Kyba, Christopher C.M.
name: Pritchard, Sara B.
name: Ekirch, A. Roger
name: Eldridge, Adam
name: Jechow, Andreas
name: Preiser, Christine
name: Kunz, Dieter
name: Henckel, Dietrich
name: Hölker, Franz
name: Barentine, John
name: Berge, Jørgen
name: Meier, Josiane
name: Gwiazdzinski, Luc
name: Spitschan, Manuel
name: Milan, Mirik
name: Bach, Susanne
name: Schroer, Sibylle
name: Straw, Will
Publisher: name: Technische Universität Berlin
Year: 2020
Subjects: subject: 300 Sozialwissenschaften
subject: night
subject: night science
subject: night studies
subject: nyctology
subject: interdisciplinary studies

description: The night has historically been neglected in both disciplinary and interdisciplinary research. To some extent, this is not surprising, given the diurnal bias of human researchers and the difficulty of performing work at night. The night is, however, a critical element of biological, chemical, physical, and social systems on Earth. Moreover, research into social issues such as inequality, demographic changes, and the transition to a sustainable economy will be compromised if the night is not considered. Recent years, however, have seen a surge in research into the night. We argue that “night studies” is on the cusp of coming into its own as an interdisciplinary field, and that when it does, the field will consider questions that disciplinary researchers have not yet thought to ask.
10 Years of Extreme Microbiology: An Interim Reflection and Future Prospects
Creators: name: Teske, A.
Publisher: name: Frontiers Media S.A.
Year: 2020

description: Gazing into the crystal ball and predicting the future for the next 10 years for Extreme Microbiology can lead to equal shares of amusement and bewilderment down the road, best encapsulated in the exclamation “What were we thinking?” Keeping this caveat in mind while not worrying not too much about it will help coming up with a useful idea or two. Also, looking into what the Extreme Microbiology Section has become should be helpful; realitymay contradict even themost elaborate prognosticating efforts, and point into new directions that even the very wise may not foresee.
rAAV Engineering for Capsid-Protein Enzyme Insertions and Mosaicism Reveals Resilience to Mutational, Structural and Thermal Perturbations
Creators: name: Feiner, Rebecca C.
name: Teschner, Julian
name: Teschner, Kathrin E.
name: Radukic, Marco T.
name: Baumann, Tobias
name: Hagen, Sven
name: Hannappel, Yvonne
name: Biere, Niklas
name: Anselmetti, Dario
name: Arndt, Katja M.
name: Müller, Kristian M.
Publisher: name: Technische Universität Berlin
Year: 2019
Subjects: subject: 540 Chemie und zugeordnete Wissenschaften
subject: adeno-associated-virus
subject: β-lactamase
subject: inverted terminal repeat
subject: loop modification
subject: capsid stability

description: Recombinant adeno-associated viruses (rAAV) provide outstanding options for customization and superior capabilities for gene therapy. To access their full potential, facile genetic manipulation is pivotal, including capsid loop modifications. Therefore, we assessed capsid tolerance to modifications of the structural VP proteins in terms of stability and plasticity. Flexible glycine-serine linkers of increasing sizes were, at the genetic level, introduced into the 587 loop region of the VP proteins of serotype 2, the best studied AAV representative. Analyses of biological function and thermal stability with respect to genome release of viral particles revealed structural plasticity. In addition, insertion of the 29 kDa enzyme β-lactamase into the loop region was tested with a complete or a mosaic modification setting. For the mosaic approach, investigation of VP2 trans expression revealed that a Kozak sequence was required to prevent leaky scanning. Surprisingly, even the full capsid modification with β-lactamase allowed for the assembly of capsids with a concomitant increase in size. Enzyme activity assays revealed lactamase functionality for both rAAV variants, which demonstrates the structural robustness of this platform technology.
K-mouflage gravity models that pass Solar System and cosmological constraints
Creators: name: Barreira, Alexandre
name: Brax, Philippe
name: Clesse, Sebastien
name: Li, Baojiu
name: Valageas, Patrick
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We show that Solar System tests can place very strong constraints on K-mouflage models of gravity, which are coupled scalar field models with nontrivial kinetic terms that screen the fifth force in regions of large gravitational acceleration. In particular, the bounds on the anomalous perihelion of the Moon imposes stringent restrictions on the K-mouflage Lagrangian density, which can be met when the contributions of higher-order operators in the static regime are sufficiently small. The bound on the rate of change of the gravitational strength in the Solar System constrains the coupling strength $β$ to be smaller than $0.1$. These two bounds impose tighter constraints than the results from the Cassini satellite and Big Bang Nucleosynthesis. Despite the Solar System restrictions, we show that it is possible to construct viable models with interesting cosmological predictions. In particular, relative to $Λ$-CDM, such models predict percent-level deviations for the clustering of matter and the number density of dark matter haloes. This makes these models predictive and testable by forthcoming observational missions.
description: 15 pages
A coefficient average approximation towards Gutzwiller wavefunction formalism
Creators: name: Liu, Jun
name: Yao, Yongxin
name: Wang, Cai-Zhuang
name: Ho, Kai-Ming
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Gutzwiller wavefunction is a physically well motivated trial wavefunction for describing correlated electron systems. In this work, a new approximation is introduced to facilitate evaluation of the expectation value of any operator within the Gutzwiller wavefunction formalism. The basic idea is to make use of a specially designed average over Gutzwiller wavefunction coefficients expanded in the many-body Fock space to approximate the ratio of expectation values between a Gutzwiller wavefunction and its underlying noninteracting wavefunction. To check with the standard Gutzwiller approximation (GA), we test its performance on single band systems and find quite interesting properties. On finite systems, we noticed that it gives superior performance than GA, while on infinite systems it asymptotically approaches GA. Analytic analysis together with numerical tests are provided to support this claimed asymptotic behavior. At the end, possible improvements on the approximation and its generalization towards multiband systems are illustrated and discussed.
description: 20 pages 4 figures, submitted to Journal of Physics: Condensed Matter
Working memory training in patients with schizophrenia
Creators: name: El-Mir, Mohammed
Publisher: name: figshare
Year: 2022
Subjects: Clinical Psychology

description: The current study dealt with training working memory in people with schizophrenia, it also aimed to verify whether the capacity of working memory capacity improves in people with schizophrenia through its training, and also aimed to verify the effectiveness of working memory training in improving the visual and auditory cognitive processes. 30 subjects suffering from schizophrenia, and whose ages ranged between 20 and 50 years, participated in this study. They were divided into two groups (15), one of which underwent training, while the second group (15) did not receive it. The researcher used a set of cognitive tests in evaluating working memory components according to the Baddley and Hitch (1974) model. The training was based on a working memory training program. The statistical analysis of the data of this study revealed that the capacity of the working memory components (the phonological loop, the execution center and the visual-spatial sketchpad) improves in people with schizophrenia due to the training of working memory. This improvement in the capacity of working memory, is reflected positively on the processes of visual and auditory perception among people with schizophrenia.
Emergent topological properties in interacting one-dimensional systems with spin-orbit coupling
Creators: name: Kainaris, Nikolaos
name: Carr, Sam T.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We present analysis of a single channel interacting quantum wire problem in the presence of spin-orbit interaction. The spin-orbit coupling breaks the spin-rotational symmetry from SU(2) to U(1) and breaks inversion symmetry. The low-energy theory is then a two band model with a difference of Fermi velocities $δv$. Using bosonization and a two-loop renormalization group procedure we show that electron-electron interactions can open a gap in the spin sector of the theory when the interaction strength $U$ is smaller than $δv$ in appropriate units. For repulsive interactions, the resulting strong coupling phase is of the spin-density-wave type. We show that this phase has peculiar emergent topological properties. The gapped spin sector behaves as a topological insulator, with zero-energy edge modes with fractional spin. On the other hand, the charge sector remains critical, meaning the entire system is metallic. However, this bulk electron liquid as a whole exhibits properties commonly associated with the one-dimensional edge states of two-dimensional spin-Hall insulators, in particular, the conduction of $2e^2/h$ is robust against nonmagnetic impurities.
description: 16 pages, 3 figures
Untitled ItemWorking memory training in patients with schizophrenia
Creators: name: El-Mir, Mohammed
Publisher: name: figshare
Year: 2022
Subjects: Clinical Psychology

description: The current study dealt with training working memory in people with schizophrenia, it also aimed to verify whether the capacity of working memory capacity improves in people with schizophrenia through its training, and also aimed to verify the effectiveness of working memory training in improving the visual and auditory cognitive processes. 30 subjects suffering from schizophrenia, and whose ages ranged between 20 and 50 years, participated in this study. They were divided into two groups (15), one of which underwent training, while the second group (15) did not receive it. The researcher used a set of cognitive tests in evaluating working memory components according to the Baddley and Hitch (1974) model. The training was based on a working memory training program. The statistical analysis of the data of this study revealed that the capacity of the working memory components (the phonological loop, the execution center and the visual-spatial sketchpad) improves in people with schizophrenia due to the training of working memory. This improvement in the capacity of working memory, is reflected positively on the processes of visual and auditory perception among people with schizophrenia.
Étude du paysage sonore du silence (Modèle)
Creators: name: Paquette-Bigras, Ève
Publisher: name: Zenodo
Year: 2020
Subjects: études de l'environnement sonore
Data Management Plan
Plan de gestion des données
Exemplar
Modèle
paysage sonore
fichier audio
fichier sonore

description: Plan de gestion de données pour une recherche fictive en études de l'environnement sonore. Les données sont des fichiers audio.
Additional file 2 of A patient-derived cell model for malignant transformation in IDH-mutant glioma
Creators: name: Kim, Olga
name: Sergi, Zach
name: Yu, Guangyang
name: Yamamoto, Kazutoshi
name: Quezado, Martha
name: Abdullaev, Zied
name: Crooks, Danel R.
name: Kishimoto, Shun
name: Li, Qi
name: Lu, Peng
name: Blackman, Burchelle
name: Andresson, Thorkell
name: Wu, Xiaolin
name: Tran, Bao
name: Wei, Jun S.
name: Zhang, Wei
name: Zhang, Meili
name: Song, Hua
name: Khan, Javed
name: Krishna, Murali C.
name: Brender, Jeffrey R.
name: Wu, Jing
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Supplementary Material 2.
Beal's Conjecture vs. "Positive Zero", Fight
Creators: name: Moore, Angela
Publisher: name: arXiv
Year: 2015
Subjects: subject: History and Overview (math.HO)
subject: FOS: Mathematics

description: This article seeks to encourage a mathematical dialog regarding a possible solution to Beals Conjecture. It breaks down one of the worlds most difficult math problems into laymans terms and encourages people to question some of the most fundamental rules of mathematics. More specifically; it reinforces basic algebra/critical thinking skills, makes use of properties attributed to the number one and reanalyzes the definition of a positive integer in order to provide a potential counterexample to Beals Conjecture.
description: Extended version
Search for a bound H-dibaryon using local six-quark interpolating operators
Creators: name: Green, Jeremy
name: Francis, Anthony
name: Junnarkar, Parikshit
name: Miao, Chuan
name: Rae, Thomas
name: Wittig, Hartmut
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: We present early results from a lattice QCD study seeking a bound $H$-dibaryon using $N_f=2$ flavors of $O(a)$ improved Wilson fermions and a quenched strange quark. We compute a matrix of two-point functions using operators consisting of the two independent local products of six positive-parity-projected quarks with the appropriate quantum numbers, which belong to the singlet and 27-plet irreducible representations of flavor SU(3). To expand this basis, we also independently vary the quark-field smearing, and apply a new scheme to reduce the noise caused by smearing. We then find the ground-state mass by solving the generalized eigenvalue problem. We show results from ensembles with pion masses 451 MeV and 1 GeV, and compare with other lattice calculations.
description: 7 pages, 3 figures. Talk presented at the 32nd International Symposium on Lattice Field Theory (Lattice 2014), 23-28 June, 2014, Columbia University, New York, NY, USA
PHENIX measurements of charm, bottom, and Drell-Yan via dimuons in p+p and p+Au collisions at √sNN=200GeV
Creators: name: Leung, Yue Hang
Publisher: name: Zenodo
Year: 2020
Subjects: rhic
phenix
drell-yan
charm
bottom
dimuon
hp18

description: PHENIX measurements of heavy flavor, used to probe nuclear matter.
Impedance Variation and Learning Strategies in Human-Robot Interaction
Creators: Mojtaba Sharifia, Amir Zakerimanesh, Javad K. Mehr, Ali Torabi, Vivian K. Mushahwar, Mahdi Tavakoli
Publisher: name: University of Alberta Library
Year: 2021

In this survey, various concepts and methodologies developed over the past two decades for varying and learning the impedance or admittance of robotic systems that physically interact with humans are explored. For this purpose, the assumptions and mathematical formulations for online adjustment of impedance models and controllers for physical humanrobot interaction (HRI) are categorized and compared. In this systematic review, studies on (a) variation and (b) learning of appropriate impedance elements are taken into account. These strategies are classified and described in terms of their objectives, points of view (approaches), signal requirements (including position, HRI force and EMG activity). Different

methods involving linear/nonlinear analyses (e.g., optimal control design and nonlinear Lyapunov-based stability guarantee) and Gaussian approximation algorithms (e.g., GMM-based and DMPbased strategies) are reviewed. Current challenges and research trends in physical HRI are finally discussed.
Additional file 5 of Potential impact of climatic factors on malaria in Rwanda between 2012 and 2021: a time-series analysis
Creators: name: Rubuga, Felix K.
name: Ahmed, Ayman
name: Siddig, Emmanuel
name: Sera, Francesco
name: Moirano, Giovenale
name: Aimable, Mbituyumuremyi
name: Albert, Tuyishime
name: Gallican, Nshogoza R.
name: Nebié, Eric I.
name: Kitema, Gatera F.
name: Vounatsou, Penelope
name: Utzinger, Jürg
name: Cissé, Guéladio
Publisher: name: figshare
Year: 2024
Subjects: subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Supplementary Material 5.
Protoplanetary disk lifetimes vs stellar mass and possible implications for giant planet populations
Creators: name: Ribas, Álvaro
name: Bouy, Hervé
name: Merín, Bruno
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We study the dependence of protoplanetary disk evolution on stellar mass using a large sample of young stellar objects in nearby young star-forming regions. We update the protoplanetary disk fractions presented in our recent work (paper I of this series) derived for 22 nearby (< 500 pc) associations between 1 and 100 Myr. We use a subsample of 1 428 spectroscopically confirmed members to study the impact of stellar mass on protoplanetary disk evolution. We divide this sample into two stellar mass bins (2 M$_{\odot}$ boundary) and two age bins (3 Myr boundary), and use infrared excesses over the photospheric emission to classify objects in three groups: protoplanetary disks, evolved disks, and diskless. The homogeneous analysis and bias corrections allow for a statistically significant inter-comparison of the obtained results. We find robust statistical evidence of disk evolution dependence with stellar mass. Our results, combined with previous studies on disk evolution, confirm that protoplanetary disks evolve faster and/or earlier around high-mass (> 2 M$_{\odot}$) stars. We also find a roughly constant level of evolved disks throughout the whole age and stellar mass spectra. We conclude that protoplanetary disk evolution depends on stellar mass. Such a dependence could have important implications for gas giant planet formation and migration, and could contribute to explaining the apparent paucity of hot Jupiters around high-mass stars.
description: Accepted for publication in A&A. 13 pages, 8 figures, 5 tables
Metabolic strategies of marine subseafloor Chloroflexi inferred from genome reconstructions
Creators: name: Huber, J.A.
name: Fincker, M.
name: Orphan, V.J.
name: Teske, A.
name: Rappé, M.S.
name: Spormann, A.M.
Publisher: name: Blackwell Publishing Ltd
Year: 2020

description: Uncultured members of the Chloroflexi phylum are highly enriched in numerous subseafloor environments. Their metabolic potential was evaluated by reconstructing 31 Chloroflexi genomes from six different subseafloor habitats. The near ubiquitous presence of enzymes of the Wood–Ljungdahl pathway, electron bifurcation, and ferredoxin-dependent transport-coupled phosphorylation indicated anaerobic acetogenesis was central to their catabolism. Most of the genomes simultaneously contained multiple degradation pathways for complex carbohydrates, detrital protein, aromatic compounds, and hydrogen, indicating the coupling of oxidation of chemically diverse organic substrates to ubiquitous CO2 reduction. Such pathway combinations may confer a fitness advantage in subseafloor environments by enabling these Chloroflexi to act as primary fermenters and acetogens in one microorganism without the need for syntrophic H2 consumption. While evidence for catabolic oxygen respiration was limited to two phylogenetic clusters, the presence of genes encoding putative reductive dehalogenases throughout the phylum expanded the phylogenetic boundary for potential organohalide respiration past the Dehalococcoidia class.
Additional file 1 of Genomic dissection of the correlation between milk yield and various health traits using functional and evolutionary information about imputed sequence variants of 34,497 German Holstein cows
Creators: name: Schneider, Helen
name: Krizanac, Ana-Marija
name: Falker-Gieske, Clemens
name: Heise, Johannes
name: Tetens, Jens
name: Thaller, Georg
name: Bennewitz, Jörn
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Supplementary Material 1.
A Letter of Concern Regarding Increased Risk of COVID-19 Among Users of Proton Pump Inhibitors by Almario, Chey, and Spiegel
Creators: name: Dahly, Darren
name: Elia, Mario
name: Johansen, Michael
Publisher: name: Zenodo
Year: 2020
Subjects: COVID-19
PPIs

description: We are writing to share our concerns about a recent paper entitled Increased Risk of COVID-19 Among Users of Proton Pump Inhibitors by Almario, Chey, and Spiegel (hereby the authors) which will soon be published in the American Journal of Gastroenterology. The research, taken at face value, suggests that the risk of COVID-19 is increased for adults taking Proton Pump Inhibitors (PPIs). However, there are multiple irregularities about the underlying data that give pause. Because the current version of the paper appears to have been peer reviewed but is not yet final, we wanted to raise these concerns prior to the paper’s final publication.
description: In response to: https://journals.lww.com/ajg/Documents/AJG-20-1811_R1(PUBLISH%20AS%20WEBPART).pdf
Large scale structure and ISW effect in decaying vacuum cosmology
Creators: name: Velten, H.
name: Borges, H. A.
name: Carneiro, S.
name: Fazolo, R.
name: Gomes, S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The concordance particle creation model - a class of $Λ(t)$CDM cosmologies - is studied using large scale structure (LSS) formation, with particular attention to the integrated Sachs-Wolfe (ISW) effect. The evolution of the gravitational potential and the amplitude of the cross-correlation of the cosmic microwave background (CMB) signal with LSS surveys are calculated in detail. We properly include in our analysis the peculiarities involving the baryonic dynamics of the $Λ(t)$CDM model which were not included in previous works. Although both the $Λ(t)$CDM and the standard cosmology are in agreement with available data for the CMB-LSS correlation, the former presents a slightly higher signal which can be identified with future data.
description: 5 pages, 4 figures