cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
OFSSRank Experiment Results on Rosetta DecoySet 2024-03
Creators: name: Kadyan, Sachin
Publisher: name: Zenodo
Year: 2024

description: Introduction:

This release contains the results from the decoy-based inference experiments conducted on the OpenFold Single-Sequence model, (dubbed OpenFold-SoloSeq). using the Rosetta decoys set. The experiments were carried out on a cluster of A100 GPUs during March, 2024.

Contents:

`OFSSRank_Experiments_Rosetta_DecoySet_2024-03.csv`: A single CSV containing the inference results of all of the decoys. Each entry is one decoy, and contains:

it's OpenFold Single Sequence model (OpenFold-SoloSeq) inference results like pLDDT, pTM, output TM score, output RMSD value, the TM score between the output and the decoy(`tm_diff`), and 

the decoy's inherent properties like RMSD, RosettaScore, GDT_TS, danscore.

`test_templates_openfold.py`: The Python script used to run the decoy-injection experiments. Derives mainly from the AF2Rank script, but completely adapted for OpenFold, as well as many additional features.

`sh_test_templates_openfold.sh`: A shell script containing the command used to run the experiments. The parameters and configuration used for the experiment are specified therein.
Unsupervised machine learning in atomistic simulations, between predictions and understanding
Creators: name: Ceriotti, Michele
Publisher: name: arXiv
Year: 2019
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Automated analyses of the outcome of a simulation have been an important part of atomistic modeling since the early days, addressing the need of linking the behavior of individual atoms and the collective properties that are usually the final quantity of interest. Methods such as clustering and dimensionality reduction have been used to provide a simplified, coarse-grained representation of the structure and dynamics of complex systems, from proteins to nanoparticles. In recent years, the rise of machine learning has led to an even more widespread use of these algorithms in atomistic modeling, and to consider different classification and inference techniques as part of a coherent toolbox of data-driven approaches. This perspective briefly reviews some of the unsupervised machine-learning methods -- that are geared towards classification and coarse-graining of molecular simulations -- seen in relation to the fundamental mathematical concepts that underlie all machine-learning techniques. It discusses the importance of using concise yet complete representations of atomic structures as the starting point of the analyses, and highlights the risk of introducing preconceived biases when using machine learning to rationalize and understand structure-property relations. Supervised machine-learning techniques, that explicitly attempt to predict the properties of a material given its structure, are less susceptible to such biases. Current developments in the field suggest that using these two classes of approaches side-by-side and in a fully integrated mode, while keeping in mind the relations between the data analysis framework and the fundamental physical principles, will be key for realizing the full potential of machine learning to help understanding the behavior of complex molecules and materials.
The GALAH Survey: Lithium-strong KM dwarfs
Creators: name: Žerjal, M.
name: Ireland, M. J.
name: Nordlander, T.
name: Lin, J.
name: Casagrande, L.
name: Horner, J.
name: De Silva, G.
name: Martell, S.
name: Čotar, K.
name: Traven, G.
name: Zwitter, T.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Identifying and characterizing young stars in the Solar neighbourhood is essential to find and describe planets in the early stages of their evolution. This work seeks to identify nearby young stars showing a Lithium 6707.78$\,Å$ absorption line in the GALAH survey. A robust, data-driven approach is used to search for corresponding templates in the pool of 434,215 measured dwarf spectra in the survey. It enables a model-free search for best-matching spectral templates for all stars, including M dwarfs with strong molecular absorption bands. 3147 stars have been found to have measurable Lithium: 1408 G and 892 K0-K5 dwarfs (EW(Li)$>$0.1$\,$Å), 335 K5-K9 ($>$0.07$\,$Å) and 512 M0$\sim$M4 dwarfs ($>$0.05$\,$Å). Stars with such Lithium features are used to investigate the possibility of searching for young stars above the main sequence based merely on their parallaxes and broad-band photometry. Selection of young stars above the main sequence is highly effective for M dwarfs, moderately effective for K dwarfs and ineffective for G dwarfs. Using a combination of the Lithium information and the complete 6D kinematics from Gaia and GALAH, 305 new candidate moving group members have been found, 123 of which belong to the Scorpius-Centaurus association, 36 to the Pleiades and 25 to the Hyades clusters.
description: Submitted to MNRAS. 12 pages, 8 figures, 3 tables
Testing self-organized criticality by induced seismicity
Creators: name: Grasso, J. -R.
name: Sornette, D.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We examine the hypothesis proposed in recent years by several authors that the crust is in a self-organized critical (SOC) state by exploring how the SOC concept can help in understanding the observed earthquake clustering on relatively narrow fault domains and the phenomenon of induced seismicity. We review the major reported cases of induced seismicity in various parts of the world and find that both pore pressure changes (+/-p) and mass transfers (+/-m) leading to incremental deviatoric stresses of <<1 MPa are sufficient to trigger seismic instabilities in the uppermost crust with magnitude ranging up to 7.0 in otherwise historically aseismic areas. Once triggered, stress variations of at least 1 order of magnitude less but still larger than the ~0.01 MPa tidal stress are enough to sustain seismic activity. We argue that these observations are in accord with the SOC hypothesis as they show that a significant fraction of the crust is not far from instability and can thus be made unstable by minute perturbations. Not all perturbations, however, trigger seismic activity; this is also compatible with the SOC hypothesis which embodies naturally the existence of large heterogeneities in the stress field. In conclusion, the properties of induced seismicity and their rationalization in terms of the SOC concept provide further evidence that potential seismic hazards extend over a much larger area than that where earthquakes are frequent.
description: 15 pages, 3 tables, 14 figures (in press in Journal of Geophysical Research)
Assessing the hierarchy of long-term environmental controls on diatom communities of Yellowstone National Park using lacustrine sediment records
Creators: name: Chraïbi, Victoria L. Shaw
name: Fritz, Sherilyn C.
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Chraïbi VLS, Fritz SC. 2020. Assessing the hierarchy of long-term environmental controls on diatom communities of Yellowstone National Park using lacustrine sediment records. Lake Reserv Manage. 36:278–296. An ecosystem’s ability to maintain structure and function following disturbance, defined as resilience, is influenced by a hierarchy of environmental controls, including climate, surface cover, and ecological relationships that shape biological community composition and productivity. This study examined lacustrine sediment records of naturally fishless lakes in Yellowstone National Park to reconstruct the response of aquatic communities to climate and trophic cascades from fish stocking. Sediment records of diatom algae did not exhibit a distinct response to fish stocking in terms of assemblage or algal productivity. Instead, 3 of 4 lakes underwent a shift to dominance by benthic diatom species from 1935 to 1950, which suggests lower lake levels resulting from warmer, drier climatic conditions. The lake that did not undergo such a shift is fed by groundwater rather than snowmelt, suggesting a buffering effect by water source. Dissimilarity analysis shows that the diatom assemblages in all 4 lakes have become increasingly dissimilar since circa 1955, suggesting that communities have not yet stabilized from the first-order influence of climate. Thus, climate likely had a more prominent influence on diatom community structure than did manipulation of the fish community. Understanding the relative importance and interplay among abiotic and biotic stressors and the resultant resilience of an ecosystem provides implications for the adaptive management of lakes.
Electron energy loss spectroscopy of wall charges in plasma-facing dielectrics
Creators: name: Thiessen, E.
name: Bronold, F. X.
name: Fehske, H.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: We propose a setup enabling electron energy loss spectroscopy to determine the density of the electrons accumulated by an electro-positive dielectric in contact with a plasma. It is based on a two-layer structure inserted into a recess of the wall. Consisting of a plasma-facing film made out of the dielectric of interest and a substrate layer the structure is designed to confine the plasma-induced surplus electrons to the region of the film. The charge fluctuations they give rise to can then be read out from the backside of the substrate by near specular electron reflection. To obtain in this scattering geometry a strong charge-sensitive reflection maximum due to the surplus electrons the film has to be most probably pre-n-doped and sufficiently thin with the mechanical stability maintained by the substrate. We demonstrate the feasibility of the proposal by calculating the loss spectrum for an sapphire film on top of a CaO layer. We find a reflection maximum strongly shifting with the density of the surplus electrons and suggest to use it for its diagnostics.
description: 10 pages, 6 figures
Anapausis floricola Chandler 1999
Creators: name: Bächli, Gerhard
name: Merz, Bernhard
name: Haenni, Jean-Paul
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Scatopsidae
Anapausis
Anapausis floricola

description: Anapausis floricola Chandler, 1999.
 1 ♂, Morgins (VS), Les Têtes, 28.07.2004, leg. G. Bächli (MHNN). Neufund.
description: Published as part of Bächli, Gerhard, Merz, Bernhard & Haenni, Jean-Paul, 2014, Dritter Nachtrag zur Checkliste der Diptera der Schweiz, pp. 119-140 in Entomo Helvetica 7 on page 123, DOI: 10.5169/seals-985967, http://zenodo.org/record/8096745
Recycling probability and dynamical properties of germinal center reactions
Creators: name: Meyer-Hermann, Michael
name: Deutsch, Andreas
name: Or-Guil, Michal
Publisher: name: arXiv
Year: 2001
Subjects: subject: Biological Physics (physics.bio-ph)
subject: Cell Behavior (q-bio.CB)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: We introduce a new model for the dynamics of centroblasts and centrocytes in a germinal center. The model reduces the germinal center reaction to the elements considered as essential and embeds proliferation of centroblasts, point mutations of the corresponding antibody types represented in a shape space, differentiation to centrocytes, selection with respect to initial antigens, differentiation of positively selected centrocytes to plasma or memory cells and recycling of centrocytes to centroblasts. We use exclusively parameters with a direct biological interpretation such that, once determined by experimental data, the model gains predictive power. Based on the experiment of Han et al. (1995b) we predict that a high rate of recycling of centrocytes to centroblasts is necessary for the germinal center reaction to work reliably. Furthermore, we find a delayed start of the production of plasma and memory cells with respect to the start of point mutations, which turns out to be necessary for the optimization process during the germinal center reaction. The dependence of the germinal center reaction on the recycling probability is analyzed.
description: 30 pages, 8 figures
title: Expanded Aurality: Doing Sonic Feminism in the White Cube
Creators: name: Kazlauskaite, Sandra
Publisher: name: Goldsmiths, University of London
Year: 2020

description: This thesis is a practice-led quest to expand aurality in white cube gallery spaces. Using video art installation practice, feminist phenomenology and spatial theory, it explores the soundscape of whitened contemporary exhibition spaces and questions how women-produced sounding video artworks, the experiencing bodies and background noise affect the production of the gallery in perceptual and socio-political terms. This project proposes that the archetypal white cube, as a product of modernism, has served as an architectural and institutional construct since the start ofthe twentieth century. Built on ocularcentric, patriarchal and capitalist ideology, it has continued to condition our way of displaying and experiencing art. The white cube has primarily accommodated rational, individualised and decontextualised white heteronormative middle-class male subjects, whilst quieting and excluding stereotypically ‘irrational’, ‘subjective’ and ‘feminised’ bodies and their sound from the gallery walls. The white cube, in this sense, has operated as a site of policed silencing and gendered control. This thesis makes an intervention into the field of contemporary art and museum studies by proposing the need to readdress the legacy of the whitecube’s gendered and autonomous ideology by bringing video art, sound and genderstudies into the white cube debate through theory and practice. This project introduces a methodology of sonic feminism: the acts of speaking the mother tongue and listening to all-sound when exhibiting and experiencing video art inside the gallery walls. Whilst reflecting on my video art projects, I propose that once we allow our bodies to engage in the totality of sound and speak in a language that aims to offer rather than claimwhen being with art, we might begin to dismantle the white cube’s gendered and spatio-temporal limitations. We might then discover a more expanded white cube – anaesthetic site that exceeds gender binaries, empowers social connectedness andoffers a whole-bodied engagement with art, a white cube that is home for all-bodies rather than some.
Additional file 1 of HOXC6 impacts epithelial-mesenchymal transition and the immune microenvironment through gene transcription in gliomas
Creators: name: Huang, Hui
name: Huo, Zhengyuan
name: Jiao, Jiantong
name: Ji, Wei
name: Huang, Jin
name: Bian, Zheng
name: Xu, Bin
name: Shao, Junfei
name: Sun, Jun
Publisher: name: figshare
Year: 2022
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology

description: Additional file 1: Figure S1 A flow chart to  better reflect the design of our bioinformatics investigation.
Quasiparticle spectrum in the vortex state of d-wave superconductors
Creators: name: Won, H.
name: Maki, K.
Publisher: name: arXiv
Year: 2000
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Quasiparticle spectrum associated with the nodal structure in d-wave superconductors is of great interest. We study theoretically the quasi-particle spectrum in a planar magnetic field, where the effect of the magnetic field is treated in terms of the Doppler shift. We obtain the angular dependent specific heat in the presence of a planar magnetic field and impurities, both in the superclean limit (Gamma/Delta << H/H_{c2}<< 1) and in the clean limit (H/H_{c2} << Gamma/Delta <<1). Also a similar analysis is used for the thermal conductivity tensor within the a-b plane. In particular, in contrast to the earlier works, we find a fourfold symmetry term in κ_{\parallel} and κ_{\perp} \sim -H \sin(2θ) where kappa_{perp} are the diagonal- and the off-diagonal components of the thermal conductivity tensor and θis the angle between the heat current and the magnetic field.
description: RevTex, 5 pages, 5 postscript figures
Dicrostolis falcinervis
Creators: name: Bächli, Gerhard
name: Merz, Bernhard
name: Haenni, Jean-Paul
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Scatopsidae
Dicrostolis
Dicrostolis falcinervis

description: Dicrostolis falcinervis (Duda, 1928). (Haenni 2008).
description: Published as part of Bächli, Gerhard, Merz, Bernhard & Haenni, Jean-Paul, 2014, Dritter Nachtrag zur Checkliste der Diptera der Schweiz, pp. 119-140 in Entomo Helvetica 7 on page 123, DOI: 10.5169/seals-985967, http://zenodo.org/record/8096745
Electron--electron Interactions in Disordered Metals: Keldysh Formalism
Creators: name: Kamenev, Alex
name: Andreev, Anton
Publisher: name: arXiv
Year: 1998
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: We develop a field theory formalism for the disordered interacting electron liquid in the dynamical Keldysh formulation. This formalism is an alternative to the previously used replica technique. In addition it naturally allows for the treatment of non-equilibrium effects. Employing the gauge invariance of the theory and carefully choosing the saddle point in the $Q$-matrix manifold, we separate purely phase effects of the fluctuating potential from the ones that change quasi-particle dynamics. As a result, the cancellation of super-divergent diagrams (double logarithms in d=2) is automatically build in the formalism. As a byproduct we derive a non--perturbative expression for the single particle density of states. The remaining low-energy sigma--model describes the quantum fluctuations of the electron distribution function. Its saddle point equation appears to be the quantum kinetic equation with an appropriate collision integral along with collisionless terms. Altshuler-Aronov corrections to conductivity are shown to arise from the one-loop quantum fluctuation effects.
description: RevTeX, 22 pages with 6 figures
A particle system approach to aggregation phenomena
Creators: name: Flandoli, Franco
name: Leocata, Marta
Publisher: name: arXiv
Year: 2019
Subjects: subject: Probability (math.PR)
subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: Inspired by a PDE-ODE system of aggregation developed in the biomathematical literature, an interacting particle system representing aggregation at the level of individuals is investigated. It is proved that the empirical density of the individual converges to solution of the PDE-ODE system.
Charge ordering in the TMTTF family of molecular conductors
Creators: name: Chow, D. S.
name: Zamborszky, F.
name: Alavi, B.
name: Tantillo, D. J.
name: Baur, A.
name: Merlic, C. A.
name: Brown, S. E.
Publisher: name: arXiv
Year: 2000
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Using one- and two-dimensional NMR spectroscopy applied to $^{13}$C spin-labeled (TMTTF)$_2$AsF$_6$ and (TMTTF)$_2$PF$_6$, we demonstrate the existence of an intermediate charge-ordered phase in the TMTTF family of charge-transfer salts. At ambient temperature, the spectra are characteristic of nuclei in equivalent environments, or molecules. Below a continuous charge-ordering transition temperature T$_{co}$, the spectra are explained by assuming there are two inequivalent molecules with unequal electron densities. The absence of an associated magnetic anomaly indicates only the charge degrees of freedom are involved and the lack of evidence for a structural anomaly suggests that charge/lattice coupling is too weak to drive the transition.
description: 4 pages, 4 eps figures
MPEC 2024-G35 : 2024 GF
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2024
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469
subject: 2024 GF

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
Non-crossing run-and-tumble particles on a line
Creators: name: Doussal, Pierre Le
name: Majumdar, Satya N.
name: Schehr, Gregory
Publisher: name: arXiv
Year: 2019
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We study active particles performing independent run and tumble motion on an infinite line with velocities $v_0 σ(t)$, where $σ(t) = \pm 1$ is a dichotomous telegraphic noise with constant flipping rate $γ$. We first consider one particle in the presence of an absorbing wall at $x=0$ and calculate the probability that it has survived up to time $t$ and is at position $x$ at time $t$. We then consider two particles with independent telegraphic noises and compute exactly the probability that they do not cross up to time $t$. Contrarily to the case of passive (Brownian) particles this two-RTP problem can not be reduced to a single RTP with an absorbing wall. Nevertheless, we are able to compute exactly the probability of no-crossing of two independent RTP's up to time $t$ and find that it decays at large time as $t^{-1/2}$ with an amplitude that depends on the initial condition. The latter allows to define an effective length scale, analogous to the so called `` Milne extrapolation length'' in neutron scattering, which we demonstrate to be a fingerprint of the active dynamics.
description: 19 pages, 3 figures; revised version, Refs. added
Additional file 2 of Genome sequencing and comparative genomic analysis of highly and weakly aggressive strains of Sclerotium rolfsii, the causal agent of peanut stem rot
Creators: name: Yan, Liying
name: Wang, Zhihui
name: Song, Wanduo
name: Fan, Pengmin
name: Kang, Yanping
name: Lei, Yong
name: Wan, Liyun
name: Huai, Dongxin
name: Chen, Yuning
name: Wang, Xin
name: Sudini, Hari
name: Liao, Boshou
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 2: Figure S2. Genome annotation statistics of S. rolfsii GP3 and ZY by blasting against five databases including GO, KOG, KEGG, NR and Swiss_pro
Paleolimnological assessment of long-term changes in a boreal recreational lake of the Fermont mining region (subarctic Quebec, Canada)
Creators: name: Jacques, Olivier
name: Pienitz, Reinhard
name: Ghassen Ibrahim
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Cell Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry

description: Jacques O, Pienitz R, Ibrahim G. 2020. Paleolimnological assessment of long-term changes in a boreal recreational lake of the Fermont mining region (subarctic Quebec, Canada). Lake Reserv Manage. XX:XXX–XXX. Lac Carheil is a boreal recreational lake located near Fermont, a remote town of subarctic Quebec built in the 1970s to support iron ore mining activities. Harmful cyanobacterial blooms were recently observed at its surface, suggesting that it suffered from eutrophication. However, long-term water quality data were lacking to properly understand its current condition. We therefore undertook a paleolimnological study to investigate past limnological changes in the lake based on the multiproxy analysis of sediment cores. The cores retrieved from Lac Carheil were marked by numerous distinct laminae representing past episodes of high-energy events in the lake catchment. Furthermore, diatom assemblages of the sediments revealed that the limnological conditions of the lake had been relatively stable for more than a thousand years before beginning to change around 1840 AD. This was mainly evidenced by the emergence of species indicative of nutrient enrichment (e.g., Aulacoseira subarctica, Fragilaria crotonensis), which suggested an early eutrophication potentially attributable to climate change. The period of modern settlement (1971–2015) was characterized by a decrease in the carbon to nitrogen ratio (C/N) of the sediments, and marked increases in their organic matter content, diatom total abundance, and diatom-inferred total phosphorus concentrations, which indicated an enhanced primary production. Nevertheless, our results suggested that the disturbance level of the lake was weak and that its prospect for recovery is good. Our study provides valuable reference data to assist the management of Lac Carheil, and reveals first insights into the sedimentological and limnological history of the Fermont mining region.
Atrichops crassipes
Creators: name: Bächli, Gerhard
name: Merz, Bernhard
name: Haenni, Jean-Paul
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Athericidae
Atrichops
Atrichops crassipes

description: Atrichops crassipes (Meigen, 1820). (Oertli 1995, Sartori et al. 2011).
description: Published as part of Bächli, Gerhard, Merz, Bernhard & Haenni, Jean-Paul, 2014, Dritter Nachtrag zur Checkliste der Diptera der Schweiz, pp. 119-140 in Entomo Helvetica 7 on page 123, DOI: 10.5169/seals-985967, http://zenodo.org/record/8096745
Graphene oxide upregulates the homeostatic functions of primary astrocytes and modulates astrocyte-to-neuron communication
Creators: name: Chiacchiaretta, Martina
name: Bramini, Mattia
name: Rocchi, Anna
name: Armirotti, Andrea
name: Giordano, Emanuele
name: Vázquez, Ester
name: Bandiera, Tiziano
name: Ferroni, Stefano
name: Cesca, Fabrizia
name: Benfenati, Fabio
Publisher: name: arXiv
Year: 2018
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: Cell Behavior (q-bio.CB)
subject: FOS: Biological sciences

description: Graphene-based materials are the focus of intense research efforts to devise novel theranostic strategies for targeting the central nervous system. In this work, we have investigated the consequences of long-term exposure of primary rat astrocytes to pristine graphene (GR) and graphene oxide (GO) flakes. We demonstrate that GR/GO interfere with a variety of intracellular processes as a result of their internalization through the endo-lysosomal pathway. Graphene-exposed astrocytes acquire a more differentiated morphological phenotype associated with extensive cytoskeletal rearrangements. Profound functional alterations are induced by GO internalization, including the upregulation of inward-rectifying K+ channels and of Na+-dependent glutamate uptake, which are linked to the astrocyte capacity to control the extracellular homeostasis. Interestingly, GO-pretreated astrocytes promote the functional maturation of co-cultured primary neurons by inducing an increase in intrinsic excitability and in the density of GABAergic synapses. The results indicate that graphene nanomaterials profoundly affect astrocyte physiology in vitro, with consequences for neuronal network activity. This work supports the view that GO-based materials could be of great interest to address pathologies of the central nervous system associated to astrocyte dysfunctions.
description: This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in Nano Letters. To access the final edited and published work see https://pubs.acs.org/articlesonrequest/AOR-wvjrggcBp7kC8NwEImXr
Stratiomyinae Latreille 1802
Creators: name: Bächli, Gerhard
name: Merz, Bernhard
name: Haenni, Jean-Paul
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Stratiomyidae

description: Stratiomyinae
 Stratiomys cenisia Meigen, 1822. (Merz 2012a). (schon von Schoch (1890) aus der Schweiz erwähnt, aber kein Material vorhanden und wegen Artenverwechslungmöglichkeiten nicht in die Checkliste aufgenommen (Haenni & Merz 1998: 161)).
 Stratiomys ruficornis (Macquart, 1838). (Merz 2012a).
description: Published as part of Bächli, Gerhard, Merz, Bernhard & Haenni, Jean-Paul, 2014, Dritter Nachtrag zur Checkliste der Diptera der Schweiz, pp. 119-140 in Entomo Helvetica 7 on page 123, DOI: 10.5169/seals-985967, http://zenodo.org/record/8096745
Coupling of intrinsic Josephson oscillations in layered superconductors by charge fluctuations
Creators: name: Preis, Ch.
name: Helm, Ch.
name: Keller, J.
name: Sergeev, A.
name: Kleiner, R.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: The coupling of Josephson oscillations in layered superconductors is studied with help of a tunneling Hamiltonian formalism. The general form of the current density across the barriers between the superconducting layers is derived. The induced charge fluctuations on the superconducting layers lead to a coupling of the Josephson oscillations in different junctions. A simplified set of equations is then used to study the non-linear dynamics of the system. In particular the influence of the coupling on the current-voltage characteristics is investigated and upper limits for the coupling strength are estimated from a comparison with experiments on cuprate superconductors.
description: To be published in proceedings of SPIE conference San Diego 1998
Coherence length of neutrino oscillations in quantum field-theoretical approach
Creators: name: Egorov, Vadim O.
name: Volobuev, Igor P.
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We consider a novel quantum field-theoretical approach to the description of processes passing at finite space-time intervals based on the Feynman diagram technique in the coordinate representation. The most known processes of this type are neutrino and neutral kaon oscillations. The experimental setting of these processes requires one to adjust the rules of passing to the momentum representation in the Feynman diagram technique in accordance with it, which leads to a modification of the Feynman propagator in the momentum representation. The approach does not make use of wave packets, both initial and final particle states are described by plane waves, which simplifies the calculations considerably. We consider neutrino oscillation processes, where the neutrinos are produced in three-particle weak decays of nuclei and detected in the charged-current interaction with nuclei or in the charged- and neutral-current interactions with electrons. Particular examples are considered and it is shown that the momentum spread of the produced neutrinos and the energy dependence of the differential cross section of the detection process result in the suppression of neutrino oscillation, which is characterized by a coherence length specific for a pair of production and detection processes. This coherence length turns out to be much less than the coherence length in the standard quantum-mechanical approach defined by the quantum uncertainty of neutrino momentum.
description: LaTex, 18 pages, 15 figures. Multiple adjustments
Tabaninae Latreille 1802
Creators: name: Bächli, Gerhard
name: Merz, Bernhard
name: Haenni, Jean-Paul
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Tabanidae

description: Tabaninae
 Haematopota ocelligera Kröber, 1922. (Aistleitner 2008).
description: Published as part of Bächli, Gerhard, Merz, Bernhard & Haenni, Jean-Paul, 2014, Dritter Nachtrag zur Checkliste der Diptera der Schweiz, pp. 119-140 in Entomo Helvetica 7 on page 123, DOI: 10.5169/seals-985967, http://zenodo.org/record/8096745
The Source Regions of Whistlers
Creators: name: Koronczay, Dávid
name: Lichtenberger, János
name: Clilverd, Mark A.
name: Rodger, Craig J.
name: Lotz, Stefan I.
name: Sannikov, Dmitry V.
name: Cherneva, Nina V.
name: Raita, Tero
name: Darrouzet, Fabien
name: Moore, Robert C.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: We present a new method for identifying the source regions of lightning generated whistlers observed at a fixed location. In addition to the spatial distribution of causative lightning discharges, we calculate the transmission ratio of lightning discharges into ground detectable whistlers as a function of location. Our method relies on the time of the whistlers and the time and source location of spherics from a global lightning database. We apply this method to whistlers recorded at fifteen ground based stations in the AWDANet (Automatic Whistler Detector and Analyzer Network) operating between 2007-2018 and to located lightning strokes from the WWLLN (World Wide Lightning Location Network) database. We present the obtained maps of causative lightning and transmission ratios. Our results show that the source region of whistlers corresponding to each ground station is around the magnetic conjugate point of the respective station. The size of the source region is typically less than 2000 km in radius with a small fraction of sources extending to up to 3500 km. The transmission ratio is maximal at the conjugate point and decreases with increasing distance from it. This conforms to the theory that whistlers detected on the ground propagated in a ducted mode through the plasmasphere and thus the lightning strokes of their causative spherics must cluster around the footprint of the ducts in the other hemisphere. Our method applied resolves the whistler excitation region mystery that resulted from correlation-based analysis methods, concerning the source region of whistlers detected in Dunedin, New Zealand.
description: 22 pages, 10 figures, submitted to Journal of Geophysical Research, Space Physics
A STRIPAK complex mediates axonal transport of autophagosomes and dense core vesicles through PP2A regulation.
Creators: name: Neisch, Amanda
name: Neufeld, Thomas P.
name: Hays, Thomas S
Publisher: name: Health Research Alliance
Year: 2019
Subjects: subject: Cell Biology
subject: 60410 Neurogenetics
subject: FOS: Biological sciences

description: Here we show that the STRIPAK complex regulates the transport of a subset of organelles, autophagosomes and dense core vesicles. We have found that the dynein motor complex is linked to one of its cargo, autophagosomes through the STRIPAK complex. The STRIPAK complex contains the phosphatase PP2A, and the activity of the phosphatase is essential to regulate the transport of both autophagosomes and dense core vesicles.
Visualizing biogeochemical heterogeneity in soils and sediments: A review of advanced micro-scale sampling and imaging methods
Creators: name: Li, Cai
name: Ding, Shiming
name: Chen, Musong
name: Zhong, Zhilin
name: Sun, Qin
name: Wang, Yan
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Medicine
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified

description: For soils and sediments, which are complex and heterogeneous, root-triggered processes, bioturbation of benthic communities, and local decomposition of reactive organic materials can greatly increase their biogeochemical heterogeneity. In practice, common monitoring methods can only be used to determine the centimeter- to millimeter-scale heterogeneity from vertical or horizontal one-dimensional profiles. However, significant heterogeneity exists in both soils and sediments on the millimeter to sub-millimeter scales. Therefore, in-situ and high-resolution sampling and imaging methods are essential to capture the spatial and temporal heterogeneity of soils and sediments. This article reviews micro-scale sampling methods in soil and sediments, including diffusive equilibration in thin films (DET), diffusive gradient in thin films (DGT), planar optodes (PO), nanoparticle- and microparticle-based luminescence imaging, and soil zymography. Besides, we introduce their imaging principles and approaches in detail, and discuss some problems and solutions during imaging. Micro-scale sampling and imaging methods have given us many insights into the biogeochemical processes in soils and sediments, but the full potential of these methods has not been exhausted yet. Finally, the potential directions for the development of micro-scale sampling methods in the study of complex biogeochemical processes in heterogeneous soils and sediments are prospected.
Hopping Transport in SrTiO3/Nd1-xTiO3/SrTiO3 Heterostructures
Creators: name: Thoutam, Laxman Raju
name: Yue, Jin
name: Xu, Peng
name: Jalan, Bharat
Publisher: name: arXiv
Year: 2018
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Electronic transport near the insulator-metal transition is investigated in the molecular beam epitaxy-grown SrTiO3/Nd1-xTiO3/SrTiO3 heterostructures using temperature dependent magnetotransport measurements. It was found that Nd-vacancies introduce localized electronic states resulting in the variable range hopping transport at low temperatures. At a fixed Nd-vacancies concentration, a crossover from Mott to Efros-Shklovskii (ES) variable range hopping transport was observed with decreasing temperature. With increasing disorder, a sign reversal of magnetoresistance from positive to negative was observed revealing interplay between intra-state interaction and the energy dependence of the localization length as a function of disorder. These findings highlight the important role of stoichiometry when exploring intrinsic effect using heterostructure and interfaces in addition to offering broad opportunity to tailor low temperature transport using non-stoichiometry defects.
Salgado et al (2021). Habitat heterogeneity enables spatial and temporal coexistence of native and invasive macrophytes in shallow lake landscapes. River Research and Applications.
Creators: name: Salgado, Jorge
name: Sayer, Carl
name: Willby, Nigel
name: Baker, Ambroise G.
name: Goldsmith, Ben
name: McGowan, Suzanne
name: Davidson, Thomas A.
name: Bexell, Patrik
name: Patmore, Ian R.
name: Okamura, Beth
Publisher: name: figshare
Year: 2021
Subjects: subject: 50202 Conservation and Biodiversity
subject: FOS: Biological sciences
subject: Ecology
subject: 50102 Ecosystem Function
subject: FOS: Earth and related environmental sciences
subject: 50206 Environmental Monitoring
subject: Botany
subject: 60299 Ecology not elsewhere classified
subject: 60204 Freshwater Ecology
subject: 69902 Global Change Biology

description: These data supports the manuscript of Salgado et al. Habitat heterogeneity enables spatial and temporal coexistence of native and invasive macrophytes in shallow lake landscapes. River Research and Applications.
Abstract: Macrophyte invasive alien species (IAS) fitness is often hypothesised to be associated with beneficial environmental conditions (environmental matching) or species-poor communities. However, positive correlations between macrophyte IAS abundance and native plant richness can also arise, due to habitat heterogeneity (defined here as variation in abiotic and native biotic conditions over space and time). We analysed survey and palaeoecological data for macrophytes in satellite lakes along the Upper Lough Erne (ULE) system (Northern Ireland, UK), covering a gradient of eutrophication and connectivity to partition how environmental conditions, macrophyte diversity and habitat heterogeneity explained the abundance of Elodea canadensis, a widely distributed non-native macrophyte in Europe. E. canadensis abundance positively correlated with macrophyte richness at both the within- and between-lake scales indicating coexistence of native and invasive species over time. E. canadensis was also more prolific in highly connected and macrophyte-rich lakes, but sparser in the more eutrophic-isolated ones. Partial boosted regression trees revealed that in eutrophic-isolated lakes, E. canadensis abundances correlated with water clarity (negatively), plant diversity (positively), and plant cover (negatively) whereas in diverse-connected lakes, beta diversity (both positively and negatively) related to most greatly E. canadensis abundance. Dense macrophyte cover and unfavourable environmental conditions thus appear to confer invasibility resistance and sufficient habitat heterogeneity to mask any single effect of native biodiversity or environmental matching in controlling E. canadensis abundance. Therefore, in shallow lake landscapes, habitat heterogeneity variously enables the coexistence of native macrophytes and E. canadensis, reducing the often-described homogenisation effects of invasive macrophytes.
Thereva ziegleri Holston 2008
Creators: name: Bächli, Gerhard
name: Merz, Bernhard
name: Haenni, Jean-Paul
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Therevidae
Thereva
Thereva ziegleri

description: Thereva ziegleri Holston, 2008. (Holston 2008).
description: Published as part of Bächli, Gerhard, Merz, Bernhard & Haenni, Jean-Paul, 2014, Dritter Nachtrag zur Checkliste der Diptera der Schweiz, pp. 119-140 in Entomo Helvetica 7 on page 123, DOI: 10.5169/seals-985967, http://zenodo.org/record/8096745
Additional file 3 of Severity distribution and treatment of chronic obstructive pulmonary disease in China: baseline results of an observational study
Creators: name: Yang, Ting
name: Cai, Baiqiang
name: Cao, Bin
name: Kang, Jian
name: Wen, Fuqiang
name: Chen, Yahong
name: Jian, Wenhua
name: Shang, Hongyan
name: Wang, Chen
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 3: Table S1. Distribution of prescribed mono- and combination maintenance therapies for COPD by severity group (GOLD 2016). Table S2. Distribution of medications prescribed in any form for COPD maintenance by severity group (GOLD 2016). Table S3. Distribution of prescribed stable COPD medications as drug class in mono- or combination therapies by baseline COPD airway limitation severity. Table S4. Distribution of prescribed mono- and combination maintenance therapies for COPD by severity group (GOLD 2017). Table S5. Distribution of medications prescribed in any form for COPD maintenance by severity group (GOLD 2017). Table S6. Distribution of prescribed mono- and combination maintenance therapies for COPD by geographical regions. Table S7. Distribution of medications prescribed in any form for COPD maintenance by geographical regions.
Strange Cepheids and RR Lyrae
Creators: name: Buchler, J. Robert
name: Kollath, Zoltan
Publisher: name: arXiv
Year: 2001
Subjects: subject: Astrophysics (astro-ph)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Strange modes can occur in radiative classical Cepheids and RR Lyrae models. These are vibrational modes that are trapped near the surface as a result of a 'potential barrier' caused by the sharp hydrogen partial ionization region. Typically the modal number of the strange mode falls between the 7th and 12th overtone, depending on the astrophysical parameters of the equilibrium stellar models (L, M, \Teff, X, Z). Interestingly these modes can be linearly unstable outside the usual instability strip, in which case they should be observable as new kinds of variable stars, 'strange Cepheids' or 'strange RR Lyrae' stars. The present paper reexamines the linear stability properties of the strange modes by taking into account the effects of an isothermal atmosphere, and of turbulent convection. It is found that the linear vibrational instability of the strange modes is resistant to both of these effects. Nonlinear hydrodynamic calculations indicate that the pulsation amplitude of these modes is likely to saturate at the millimagnitude level. These modes should therefore be detectable albeit not without effort.
description: 6 pages, 7 figures, submitted to ApJ
Calibrating star-formation rate prescriptions at different scales (10 pc to 1 kpc) in M31
Creators: name: Tomicic, Neven
name: Ho, I-Ting
name: Kreckel, Kathryn
name: Schinnerer, Eva
name: Leroy, Adam
name: Groves, Brent
name: Sandstrom, Karin
name: Blanc, Guillermo A.
name: Jarrett, Thomas
name: Thilker, David
name: Kapala, Maria
name: McElroy, Rebecca
Publisher: name: arXiv
Year: 2019
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We calibrate commonly used star formation rate (SFR) prescriptions using observations in five kpc-sized fields in the nearby galaxy Andromeda (M31) at 10\,pc spatial resolution. Our observations at different scales enable us to resolve the star-forming regions and to distinguish them from non star-forming components. We use extinction corrected H$α$ from optical integral field spectroscopy as our reference tracer and have verified its reliability via tests. It is used to calibrate monochromatic and hybrid (H$α$+a$\times$IR and FUV+b$\times$IR) SFR prescriptions, which use FUV (GALEX), 22\,$μ$m (WISE) and 24\,$μ$m (MIPS). Additionally, we evaluate other multi-wavelength infra-red tracers. Our results indicate that the SFR prescriptions do not change (in M31) with spatial scales or with subtraction of the diffuse component. For the calibration factors in the hybrid SFR prescriptions, we find a$\approx$0.2 and b$\approx$22 in M31, which are a factor of 5 higher than in the literature. As the fields in M31 exhibit high attenuation and low dust temperatures, lie at large galacto-centric distances, and suffer from high galactic inclination compared to measurements in other galaxies, we propose that the fields probe a dust layer extended along the line of sight that is not directly spatially associated with star-forming regions. This (vertically) extended dust component increases the attenuation and alters the SFR prescriptions in M31 compared to literature measurements. We recommend that SFR prescriptions should be applied with caution at large galacto-centric distances and in highly inclined galaxies, due to variations in the relative (vertical) distribution of dust and gas.
description: 17 pages of the main text, 28 pages in total, 19 figures (13 figures in the main text), 5 tables (3 tables in the main text)
Piezoelectric mechanism of orientation of stripe structures in two-dimensional electron systems
Creators: name: Fil, D. V.
Publisher: name: arXiv
Year: 2000
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: A piezoelectric mechanism of orientation of stripes in two-dimensional quantum Hall systems in GaAs heterostructures is considered. The anisotropy of the elastic moduli and the boundary of the sample are taken into account. It is found that in the average the stripes line up with the [110] axis. In double layer systems the wave vector of the stripe structure rotates from the [110] to [100] axis if the period of density modulation becomes large than the interlayer distance. From the experimental point of view it means that in double layer systems anisotropic part of resistivity changes its sign under variation of the external magnetic field.
description: 8 pages