cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Salem 2.0 extended data
Creators: name: Aussenac, Raphaël
name: Pérot, Thomas
name: Fortin, Mathieu
name: de Coligny, Francois
name: Monnet, Jean-Matthieu
name: Vallet, Patrick
Publisher: name: Zenodo
Year: 2021

description: Extended data of "The Salem simulator version 2.0: a tool for predicting the productivity of pure and mixed stands and simulating management operations".
description: This work was supported by the French National Forest Office (ONF) and 3 projects funded by the French Agency for ecological transition (ADEME): the SATAN project (n°1660C0008, REACCTIF program), the PROTEST project (n°1703C0069, GRAINE program) and the I-MAESTRO project (n°1903C0009). Project I-Maestro is supported under the umbrella of ERA-NET Cofund ForestValue by ADEME (FR), FNR (DE), MIZS (SI), NCN (PL). ForestValue has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement n°773324. The volume models and bark ratio models were carried out under the EMERGE project (ANR 2008-BIOE-003). The authors also wish to thank the IGN for providing freely the National Forest Inventory data.
On the spectrum of Farey and Gauss maps
Creators: name: Isola, Stefano
Publisher: name: arXiv
Year: 2003
Subjects: subject: Dynamical Systems (math.DS)
subject: Spectral Theory (math.SP)
subject: FOS: Mathematics
subject: 58F20, 58F25, 11F72, 11M26

description: In this paper we introduce Hilbert spaces of holomorphic functions given by generalized Borel and Laplace transforms which are left invariant by the transfer operators of the Farey map and its induced version, the Gauss map, respectively. By means of a suitable operator-valued power series we are able to study simultaneously the spectrum of both these operators along with the analytic properties of the associated dynamical zeta functions.
description: 23 pages
MOESM1 of Quantification of malaria antigens PfHRP2 and pLDH by quantitative suspension array technology in whole blood, dried blood spot and plasma
Creators: name: Martiáñez-Vendrell, Xavier
name: Jiménez, Alfons
name: Vásquez, Ana
name: Campillo, Ana
name: Incardona, Sandra
name: González, Raquel
name: Dionicia Gamboa
name: Torres, Katherine
name: Wellington Oyibo
name: Babacar Faye
name: Macete, Eusebio
name: Menéndez, Clara
name: Ding, Xavier
name: Mayor, Alfredo
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Plasma Physics
subject: Plant Biology

description: Additional file 1: Text S1. Biotinylation of detection mAbs. Text S2. Bead suspension array procedure. Text S3. Singleplex versus Multiplex testing. Text S4. Preparation and extraction of proteins from dried blood spots.
Hyperon-nucleon three-body forces and strangeness in neutron stars
Creators: name: Gerstung, Dominik
name: Kaiser, Norbert
name: Weise, Wolfram
Publisher: name: arXiv
Year: 2020
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Three-body forces acting on a $Λ$ hyperon in a nuclear medium are investigated, with special focus on the so-called hyperon puzzle in neutron stars. The hyperon-nucleon two-body interaction deduced from SU(3) chiral effective field theory is employed at next-to-leading order. Hyperon-nucleon three-body forces are approximated using saturation by decuplet baryons and are transcribed to density-dependent effective two-body interactions. These together are taken as input in a Brueckner-Bethe-Goldstone equation with explicit treatment of the $ΛN\leftrightarrowΣN$ and $ΛNN\leftrightarrowΣNN$ coupled channels. Single-particle potentials of a $Λ$ hyperon in symmetric nuclear matter and neutron matter are calculated. With parameters of the $ΛNN$ three-body force constrained by hypernuclear phenomenology, extrapolations to high baryon density are performed. By comparison of the $Λ$ and neutron chemical potentials at densities characteristic of the core of neutron stars it is found that the combined repulsive effects of two- and three-body correlations makes the appearance of $Λ$ hyperons in neutron stars energetically unfavourable, thus offering a possible solution to a longstanding question.
Spatio-Temporal Analysis of Car Distance, Greenhouse Gases and the Effect of Built Environment: a Latent Class Regression Analysis
Creators: name: Zahabi, Seyed Amir H.
name: Miranda-Moreno, Luis
name: Patterson, Zachary
name: Barla, Philippe
name: Zahabi, Seyed Amir H.
name: Miranda-Moreno, Luis
name: Patterson, Zachary
name: Barla, Philippe
Publisher: name: Unknown
Year: 2013
Subjects: subject: Environmental Economics and Policy
subject: Greenhouse gas emissions
subject: spatio-temporal variations
subject: built environment
subject: latent class regression
subject: household clusters

description: This work examines the temporal-spatial variations of daily automobile distance traveled and greenhouse gas emissions (GHGs) and their association with built environment attributes and household socio-demographics. A GHGs household inventory is determined using link-level average speeds for a large and representative sample of households in three origin-destination surveys (1998, 2003 and 2008) in Montreal, Canada. For the emission inventories, different sources of data are combined including link-level average speeds in the network, vehicle occupancy levels and fuel consumption characteristics of the vehicle fleet. Built environment indicators over time such as population density, land use mix and transit accessibility are generated for each household in each of the three waves. A latent class (LC) regression modeling framework is then implemented to investigate the association of built environment and socio-demographics with GHGs and automobile distance traveled. Among other results, it is found that population density, transit accessibility and land-use mix have small but statistically significant negative impact on GHGs and car usage. Despite that this is in accordance with past studies, the estimated elasticities are greater than those reported in the literature for North American cities. Moreover, different household subpopulations are identified in which the effect of built environment varies significantly. Also, a reduction of the average GHGs at the household level is observed over time. According to our estimates, households produced 15% and 10% more GHGs in 1998 and 2003 respectively, compared to 2008. This reduction is associated to the improvement of the fuel economy of vehicle fleet and the decrease of motor-vehicle usage. A strong link is also observed between socio-demographics and the two travel outcomes. While number of workers is positively associated with car distance and GHGs, low and medium income households pollute less than high-income households.
Jigsaw-based Security in Data Transfer in Computer Networks
Creators: name: Vasudevan, Rangarajan
name: Abraham, Ajith
name: Sanyal, Sugata
name: Agrawal, Dharma P.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences
subject: E.3

description: In this paper, we present a novel encryption-less algorithm to enhance security in transmission of data in networks. The algorithm uses an intuitively simple idea of a 'jigsaw puzzle' to break the transformed data into multiple parts where these parts form the pieces of the puzzle. Then these parts are packaged into packets and sent to the receiver. A secure and efficient mechanism is provided to convey the information that is necessary for obtaining the original data at the receiver-end from its parts in the packets, that is, for solving the 'jigsaw puzzle'. The algorithm is designed to provide information-theoretic (that is, unconditional) security by the use of a one-time pad like scheme so that no intermediate or unintended node can obtain the entire data. An authentication code is also used to ensure authenticity of every packet.
Observations of the Ultra-compact X-ray Binary 4U 1543-624 in Outburst with NICER, INTEGRAL, Swift, and ATCA
Creators: name: Ludlam, R. M.
name: Shishkovsky, L.
name: Bult, P. M.
name: Miller, J. M.
name: Zoghbi, A.
name: Strohmayer, T. E.
name: Reynolds, M.
name: Natalucci, L.
name: Miller-Jones, J. C. A.
name: Jaisawal, G. K.
name: Guillot, S.
name: Gendreau, K. C.
name: García, J. A.
name: Fiocchi, M.
name: Fabian, A. C.
name: Chakrabarty, D.
name: Cackett, E. M.
name: Bahramian, A.
name: Arzoumanian, Z.
name: Altamirano, D.
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We report on X-ray and radio observations of the ultra-compact X-ray binary 4U 1543-624 taken in August 2017 during an enhanced accretion episode. We obtained NICER monitoring of the source over a $\sim10$ day period during which target-of-opportunity observations were also conducted with Swift, INTEGRAL, and ATCA. Emission lines were measured in the NICER X-ray spectrum at $\sim0.64$ keV and $\sim6.4$ keV that correspond to O and Fe, respectively. By modeling these line components, we are able to track changes in the accretion disk throughout this period. The innermost accretion flow appears to move inwards from hundreds of gravitational radii ($R_{g}=GM/c^{2}$) at the beginning of the outburst to $<8.7$ $R_{g}$ at peak intensity. We do not detect the source in radio, but are able to place a $3σ$ upper limit on the flux density at $27$ $μ$Jy beam$^{-1}$. Comparing the radio and X-ray luminosities, we find that the source lies significantly away from the range typical of black holes in the ${L}_{r}$-${L}_{x}$ plane, suggesting a neutron star (NS) primary. This adds to the evidence that NSs do not follow a single track in the ${L}_{r}$-${L}_{x}$ plane, limiting its use in distinguishing between different classes of NSs based on radio and X-ray observations alone.
description: 13 pages, 9 figures, 2 tables, accepted for publication in ApJ
CYGNO: Triple-GEM Optical Readout for Directional Dark Matter Search
Creators: name: Costa, I. Abritta
name: Baracchini, E.
name: Bedogni, R.
name: Bellini, F.
name: Benussi, L.
name: Bianco, S.
name: Caponero, M.
name: Cavoto, G.
name: Di Marco, E.
name: D'Imperio, G.
name: Maccarrone, G.
name: Marafini, M.
name: Mazzitelli, G.
name: Messina, A.
name: Petrucci, F.
name: Piccolo, D.
name: Pinci, D.
name: Renga, F.
name: Saviano, G.
name: Tomassini, S.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: CYGNO is a project realising a cubic meter demonstrator to study the scalability of the performance of the optical approach for the readout of large-volume, GEM-equipped TPC. This is part of the CYGNUS proto-collaboration which aims at constructing a network of underground observatories for directional Dark Matter search. The combined use of high-granularity sCMOS and fast sensors for reading out the light produced in GEM channels during the multiplication processes was shown to allow on one hand to reconstruct 3D direction of the tracks, offering accurate energy measurements and sensitivity to the source directionality and, on the other hand, a high particle identification capability very useful to distinguish nuclear recoils. Results of the performed R&D and future steps toward a 30-100 cubic meter experiment will be presented.
description: 6th International Conference on Micro Pattern Gaseous Detectors, MPGD19
First Result for Dark Matter Search by WINERED
Creators: name: Yin, Wen
name: Bessho, Taiki
name: Ikeda, Yuji
name: Kobayashi, Hitomi
name: Taniguchi, Daisuke
name: Sameshima, Hiroaki
name: Matsunaga, Noriyuki
name: Otsubo, Shogo
name: Sarugaku, Yuki
name: Takeuchi, Tomomi
name: Kato, Haruki
name: Hamano, Satoshi
name: Kawakita, Hideyo
Publisher: name: arXiv
Year: 2024
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The identity of dark matter has been a mystery in astronomy, cosmology, and particle theory for about a century. Bessho, Ikeda, and Yin (2022), three of the current authors, proposed using the state-of-the-art infrared spectrographs, including WINERED at $6.5$m Magellan Clay telescope and NIRSpec at James Webb Space Telescope, as efficient detectors for the indirect detection of dark matter with the mass around eV by measuring the line photons from the dark matter two body decays. Applying this concept, we have performed spectrographic observations of dwarf spheroidal galaxies (dSphs) Leo V and Tucana II using WINERED by utilizing an object-sky-object nodding observation technique for background subtraction. We present the first result from this dark matter search. Employing zero consistent flux data after the sky subtraction, we have established one of the most stringent limits to date on dark matter decaying into line photons in the mass range of $1.8-2.7\,$eV. Our data can also be applied to constrain other spectra of photons from the dSphs.
description: 10 pages, 10 figures, 1 table, 6 data files attached, limits assuming NFW profile included, the effects from Earth rotation and revolution included in the Doppler shift analysis, conclusions unchanged, version appeared in PRL
Hypolepis Bernhardi 1806
Creators: name: Arana, Marcelo D.
name: Yañez, Agustina
name: Schwartsburd, Pedro B.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Polypodiales
Dennstaedtiaceae
Hypolepis

description: Key to the taxa of Hypolepis in Argentina
1. Laminae deltoid to triangular, basal pinnae equilateral, pseudoindusia absent or, if present, not ciliate......................................... 2
- Laminae rhombic, basal pinnae strongly inequilateral, pseudoindusia ciliate................................................................................. 3
 2. Rachises, costa and costules with capitate, glandular catenate hairs, pinnules with rounded lobes at the margin......................................................................................................................................................................................................... Hypolepis poeppigii
 - Rachises, costae and costules with acicular (non capitate) and glandular catenate hairs, pinnules with acute lobes at the margin................................................................................................................................................ Hypolepis rugosula subsp. poeppigiana
 3. Fronds 0.2–0.8 m long. Last pinnules narrowly lanceolate to linear, 2–5 × 8–15 mm, those of the distal pinnae sometimes falcate, usually with acute lobes at the margin and apex. Laminar tissue abaxially with abundant catenate-acicular hairs.............................................................................................................................................................................. Hypolepis stolonifera var. delasotae
 - Fronds 1.2–2 m long. Last pinnules oblong to broadly ovate, 8–15 × 25–30 mm, usually with rounded lobes at the margin and apex. Laminar tissue abaxially glabrous................................................................................ Hypolepis stolonifera var. stolonifera
description: Published as part of Arana, Marcelo D., Yañez, Agustina & Schwartsburd, Pedro B., 2014, An updated synopsis of Hypolepis Bernh. (Dennstaedtiaceae) from Argentina, pp. 91-102 in Phytotaxa 188 (2) on page 93, DOI: 10.11646/phytotaxa.188.2.3, http://zenodo.org/record/5147189
Perception of experience influences altruism and perception of agency influences trust in human–machine interactions
Creators: name: Rahwan, Talal
name: Battu, Balaraju
name: Oudah, Mayada
name: Gray, Kurt
name: Makovi, Kinga
Publisher: name: Springer Nature
Year: 2024

description: As robots become increasingly integrated into social economic interactions, it becomes crucial to understand how people perceive a robot’s mind. It has been argued that minds are perceived along two dimensions: experience, i.e., the ability to feel, and agency, i.e., the ability to act and take responsibility for one’s actions. However, the influence of these perceived dimensions on human–machine interactions, particularly those involving altruism and trust, remains unknown. We hypothesize that the perception of experience influences altruism, while the perception of agency influences trust. To test these hypotheses, we pair participants with bot partners in a dictator game (to measure altruism) and a trust game (to measure trust) while varying the bots’ perceived experience and agency, either by manipulating the degree to which the bot resembles humans, or by manipulating the description of the bots’ ability to feel and exercise self-control. The results demonstrate that the money transferred in the dictator game is influenced by the perceived experience, while the money transferred in the trust game is influenced by the perceived agency, thereby confirming our hypotheses. More broadly, our findings support the specificity of the mind hypothesis: Perceptions of different dimensions of the mind lead to different kinds of social behavior.
Low Energy Neutrino Physics after SNO and KamLAND
Creators: name: Oberauer, Lothar
Publisher: name: arXiv
Year: 2004
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: In the recent years important discoveries in the field of low energy neutrino physics (E$_ν$ in the $\approx$ MeV range) have been achieved. Results of the solar neutrino experiment SNO show clearly flavor transitions from $ν_e$ to $ν_{μ,τ}$. In addition, the long standing solar neutrino problem is basically solved. With KamLAND, an experiment measuring neutrinos emitted from nuclear reactors at large distances, evidence for neutrino oscillations has been found. The values for the oscillation parameters, amplitude and phase, have been restricted. In this paper the potential of future projects in low energy neutrino physics is discussed. This encompasses future solar and reactor experiments as well as the direct search for neutrino masses. Finally the potential of a large liquid scintillator detector in an underground laboratory for supernova neutrino detection, solar neutrino detection, and the search for proton decay $p \to K^+ ν$ is discussed.
description: Invited brief review, World Scientific Publishing Company
MPRAD: A Monte Carlo and ray-tracing code for the proton radiography in high-energy-density plasma experiments
Creators: name: Lu, Yingchao
name: Li, Hui
name: Flippo, Kirk A.
name: Kelso, Kwyntero
name: Liao, Andy
name: Li, Shengtai
name: Liang, Edison
Publisher: name: arXiv
Year: 2019
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: Proton radiography is used in various high-energy-density (HED) plasma experiments. In this paper, we describe a Monte Carlo and ray-tracing simulation tool called MPRAD that can be used for modeling the deflection of proton beams in arbitrary three dimensional electromagnetic fields, as well as the diffusion of the proton beams by Coulomb scattering and stopping power. The Coulomb scattering and stopping power models in cold matter and fully ionized plasma are combined using interpolation. We discuss the application of MPRAD in a few setups relevant to HED plasma experiments where the plasma density can play a role in diffusing the proton beams and affecting the prediction and interpretation of the proton images. It is shown how the diffusion due to plasma density can affect the resolution and dynamical range of the proton radiography.
description: 11 pages, 4 figures
MARS: Meaning-Aware Response Scoring for Uncertainty Estimation in Generative LLMs
Creators: name: Bakman, Yavuz Faruk
name: Yaldiz, Duygu Nur
name: Buyukates, Baturalp
name: Tao, Chenyang
name: Dimitriadis, Dimitrios
name: Avestimehr, Salman
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computation and Language (cs.CL)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Generative Large Language Models (LLMs) are widely utilized for their excellence in various tasks. However, their tendency to produce inaccurate or misleading outputs poses a potential risk, particularly in high-stakes environments. Therefore, estimating the correctness of generative LLM outputs is an important task for enhanced reliability. Uncertainty Estimation (UE) in generative LLMs is an evolving domain, where SOTA probability-based methods commonly employ length-normalized scoring. In this work, we propose Meaning-Aware Response Scoring (MARS) as an alternative to length-normalized scoring for UE methods. MARS is a novel scoring function that considers the semantic contribution of each token in the generated sequence in the context of the question. We demonstrate that integrating MARS into UE methods results in a universal and significant improvement in UE performance. We conduct experiments using three distinct closed-book question-answering datasets across five popular pre-trained LLMs. Lastly, we validate the efficacy of MARS on a Medical QA dataset. Code can be found https://github.com/Ybakman/LLM_Uncertainity.
Strong Coupling Expansion for the Pairing Hamiltonian
Creators: name: Yuzbashyan, Emil A.
name: Baytin, Alexander A.
name: Altshuler, Boris L.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The paper is devoted to the effects of superconducting pairing in small metallic grains. It turns out that at strong superconducting coupling and in the limit of large Thouless conductance one can explicitly determine the low energy spectrum of the problem. We start with the strong coupling limit and develop a systematic expansion in powers of the inverse coupling constant for the many-particle spectrum of the system. The strong coupling expansion is based on the formal exact solution of the Richardson model and converges for realistic values of the coupling constant. We use this expansion to study the low energy excitations of the system, in particular energy and spin gaps in the many-body spectrum.
description: 16 pages, 3 figures
A comprehensive review on the influence of light on signaling cross-talk and molecular communication against phyto-microbiome interactions
Creators: name: Anshuman Shah
name: Shaily Tyagi
name: Saratale, Ganesh Dattatraya
name: Guzik, Urszula
name: Anyi Hu
name: Sreevathsa, Rohini
name: Vaddi Damodara Reddy
name: Rai, Vandna
name: Sikandar I. Mulla
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: Generally, plant growth, development, and their productivity are mainly affected by their growth rate and also depend on environmental factors such as temperature, pH, humidity, and light. The interaction between plants and pathogens are highly specific. Such specificity is well characterized by plants and pathogenic microbes in the form of a molecular signature such as pattern-recognition receptors (PRRs) and microbes-associated molecular patterns (MAMPs), which in turn trigger systemic acquired immunity in plants. A number of Arabidopsis mutant collections are available to investigate molecular and physiological changes in plants under the presence of different light conditions. Over the past decade(s), several studies have been performed by selecting Arabidopsis thaliana under the influence of red, green, blue, far/far-red, and white light. However, only few phenotypic and molecular based studies represent the modulatory effects in plants under the influence of green and blue lights. Apart from this, red light (RL) actively participates in defense mechanisms against several pathogenic infections. This evolutionary pattern of light sensitizes the pathologist to analyze a series of events in plants during various stress conditions of the natural and/or the artificial environment. This review scrutinizes the literature where red, blue, white, and green light (GL) act as sensory systems that affects physiological parameters in plants. Generally, white and RL are responsible for regulating various defense mechanisms, but, GL also participates in this process with a robust impact! In addition to this, we also focus on the activation of signaling pathways (salicylic acid and jasmonic acid) and their influence on plant immune systems against phytopathogen(s).
Analysing The Impact of Sequence Composition on Language Model Pre-Training
Creators: name: Zhao, Yu
name: Qu, Yuanbin
name: Staniszewski, Konrad
name: Tworkowski, Szymon
name: Liu, Wei
name: Miłoś, Piotr
name: Wu, Yuxiang
name: Minervini, Pasquale
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: Most language model pre-training frameworks concatenate multiple documents into fixed-length sequences and use causal masking to compute the likelihood of each token given its context; this strategy is widely adopted due to its simplicity and efficiency. However, to this day, the influence of the pre-training sequence composition strategy on the generalisation properties of the model remains under-explored. In this work, we find that applying causal masking can lead to the inclusion of distracting information from previous documents during pre-training, which negatively impacts the performance of the models on language modelling and downstream tasks. In intra-document causal masking, the likelihood of each token is only conditioned on the previous tokens in the same document, eliminating potential distracting information from previous documents and significantly improving performance. Furthermore, we find that concatenating related documents can reduce some potential distractions during pre-training, and our proposed efficient retrieval-based sequence construction method, BM25Chunk, can improve in-context learning (+11.6\%), knowledge memorisation (+9.8\%), and context utilisation (+7.2\%) abilities of language models without sacrificing efficiency.
MOESM2 of Engineering of Streptomyces lividans for heterologous expression of secondary metabolite gene clusters
Creators: name: Ahmed, Yousra
name: Rebets, Yuriy
name: Estévez, Marta
name: Zapp, Josef
name: Myronovskyi, Maksym
name: Luzhetskyy, Andriy
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Additional file 2: Fig. S1. BPC chromatogram extract of S. lividans TK24.
Stochastic ISTA/FISTA Adaptive Step Search Algorithms for Convex Composite Optimization
Creators: name: Nguyen, Lam M.
name: Scheinberg, Katya
name: Tran, Trang H.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: We develop and analyze stochastic variants of ISTA and a full backtracking FISTA algorithms [Beck and Teboulle, 2009, Scheinberg et al., 2014] for composite optimization without the assumption that stochastic gradient is an unbiased estimator. This work extends analysis of inexact fixed step ISTA/FISTA in [Schmidt et al., 2011] to the case of stochastic gradient estimates and adaptive step-size parameter chosen by backtracking. It also extends the framework for analyzing stochastic line-search method in [Cartis and Scheinberg, 2018] to the proximal gradient framework as well as to the accelerated first order methods.
description: To appear at the Journal of Optimization Theory and Applications
MOESM3 of Engineering of Streptomyces lividans for heterologous expression of secondary metabolite gene clusters
Creators: name: Ahmed, Yousra
name: Rebets, Yuriy
name: Estévez, Marta
name: Zapp, Josef
name: Myronovskyi, Maksym
name: Luzhetskyy, Andriy
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Space Science
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Computational Biology

description: Additional file 3: Fig. S2. Proposed structures for 4a–d.
A global test of factorization for nucleon-nucleon, gamma p and gamma gamma scattering
Creators: name: Block, M. M.
name: Kang, K.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The purpose of this note is to show that the cross section factorization relation $σ_{nn}(s)/σ_{γp}(s) = σ_{γp}(s)/ σ_{γγ}(s)$ is satisfied experimentally in the energy domain $8\le\sqrt s\le 2000$ GeV, where the $σ$'s are total cross sections and $nn$ denotes the even portion of the $pp$ and $\pbar p$ total cross section. A convenient phenomenological paramaterization for a global simultaneous fit to the $pp$, $\pbar p$, $γp$ and $γγ$ total cross section data together with the $ρ$-value data for $pp$ and $\pbar p$ is provided by using real analytic amplitudes. Within experimental errors, we show that factorization is satisfied when we unfold the published $γγ$ data which had averaged the cross sections obtained by using the two different PHOJET and PYTHIA Monte Carlo results. Our analysis clearly favors the PHOJET results and suggests that the additive quark model, together with vector meson dominance, allows one to compute $σ_{γp}(s)$ and $σ_{γγ}(s)$ from $σ_{nn}(s)$ with essentially no free parameters. The universal $ρ$-value predicted by our fit, {\em i.e.,} $ρ_{nn} = ρ_{γp} = ρ_{γγ}$, is compared to the $ρ$-value obtained by a QCD-inspired analysis of $\pbar p$ and $pp$ data, including the p-air cross sections from cosmic rays. The $ρ$-values obtained from the two techniques are essentially indistinguishable in the energy region $8\le\sqrt s\le 2000$ GeV, giving us increased confidence in our parameterization of the cross sections needed for the factorization relation.
description: Latex2e, 13 pages, 7 postscript figures placed with epsfig.sty. Minor corrections and clarifications
Histidine-rich glycoprotein possesses antioxidant activity through self-oxidation and inhibition of hydroxyl radical production via chelating divalent metal ions in Fenton’s reaction
Creators: name: Wake, Hidenori
name: Takahashi, Yohei
name: Yoshii, Yukinori
name: Shangze Gao
name: Mori, Shuji
name: Dengli Wang
name: Teshigawara, Kiyoshi
name: Nishibori, Masahiro
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Sepsis is caused by infections associated with life-threatening multiple organ failure (MOF). Septic MOF appears to be closely related to circulatory failure due to immunothrombosis. This process involves the production of reactive oxygen spices (ROS) in inflammatory sites. Therefore, the detoxification of the systemic excess ROS is important for the improvement of the process in septic pathogenesis. Histidine-rich glycoprotein (HRG), a plasma glycoprotein, ameliorates a septic condition through the suppression of both excess ROS production from neutrophils and immunothrombosis. Hydroxyl radical is known as the most important species among ROS in pathogenesis; however, the direct influence of HRG on hydroxyl radical formation and ROS activity is poorly understood. In this study, we showed that HRG, in a concentration-dependent manner, efficiently inhibited the production of hydroxyl radical induced by the Fenton’s reaction through chelation of the divalent iron. HRG also exhibited antioxidant activity against peroxyl radical by oxidation of HRG itself as a substrate; however, it did not show superoxide dismutase and catalase-like activities. Additionally, HRG enhanced glutathione peroxidase, a well-known antioxidant enzyme, activity. These results suggest that HRG may play a unique role in suppression of the production of hydroxyl radicals and subsequent tissue damage at inflammatory sites. Marked reduction in plasma HRG in sepsis might lose such an important protective mechanism. Thus, the present study provides evidence that inhibition of ROS and ROS-production systems by HRG may contribute to antiseptic effects in vivo and that HRG could be potential therapy for ROS-related diseases.
Study of the controversial resveratrol that interact with the endogenous glutathione thiyl radical in cancer cells
Creators: name: Yin, Bo
name: Liu, Rui Rui
name: Meng, Ya Jie
name: Zhai, Hong Lin
name: Li, Sha Sha
name: Muhire, Jules
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
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: Developmental Biology
subject: Cancer
subject: Science Policy

description: Found in various natural food products, many in vitro evidence indicated that resveratrol (RES) has been linked to neuroprotective and cardioprotective effects and prevent cancer development. However, human clinical trials have been conducted with varying results, making the usage of RES controversial. In this paper, we demonstrated that the drug RES could be conjugated with the high levels of endogenous GS• in cancer cells. 5,5-Dimethyl-1-Pyrroline-N-Oxide (DMPO) was employed to capture the GS•. The molecular mechanism of the reaction between RES and GS• was further studied by UV-Vis spectrometry, mass spectrometry and Density Functional Theory (DFT) calculations. Besides, the formation of the adduct GS-RES in cancer cell was obtained when RES was added during incubation. Further study indicated that over 77.6% of the RES was consumed in cancer cells. This study suggested that endogenous GS• may be one of the important factors to cause the depletion of anti-tumour drugs during chemotherapy, which should be paid special attention in clinical therapeutics and drug development.
Biotechnological applications of mammalian odorant-binding proteins
Creators: name: Gonçalves, Filipa
name: Ribeiro, Artur
name: Silva, Carla
name: Cavaco-Paulo, Artur
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Plant Biology

description: The olfactory system of mammals allows the detection and discrimination of thousands of odors from the environment. In mammals, odorant-binding proteins (OBPs) are considered responsible to carry odorant molecules across the aqueous nasal mucus to the olfactory receptors (ORs). The three-dimensional structure of these proteins presents eight antiparallel β-sheets and a short α-helical segment close to the C terminus, typical of the lipocalins family. The great ability of OBPs to bind differentiated ligand molecules has driven the research to understand the mechanisms underlying the OBP function in nature and the development of advanced biotechnological applications. This review describes the role of mammalian OBPs in the olfactory perception, highlighting the influence of several key parameters (amino acids, temperature, ionic strength, and pH) in the formation of the OBP/ligand complex. The information from the literature regarding OBP structure, affinity, the strength of binding, and stability inspiring the development of several applications herein detailed.
Solid-Liquid Transition in a Skyrmion Matter
Creators: name: Garanin, Dmitry A.
name: Chudnovsky, Eugene M.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report Monte-Carlo studies of the orientational order and melting of a 2D skyrmion lattice containing more than one million spins. Two models have been investigated, a microscopic model of lattice spins with Dzyaloshinskii-Moryia interaction that possesses skyrmions, and the model in which skyrmions are treated as point particles with repulsive interaction derived from a spin model. They produce similar results. The skyrmion lattice exhibits a sharp one-step transition between solid and liquid phases on temperature and the magnetic field. This solid-liquid transition is characterized by the kink in the magnetization. The field-temperature phase diagram is computed. We show that the application of the field gradient to a 2D system of skyrmions produces a solid-liquid interface that must be possible to observe in experiments.
description: 11 pages, 14 figures
A review of the institutional landscape for dual-career hiring in higher education
Creators: name: Fisher, Jill A.
name: Parker, Amelia
name: Waltz, Margaret
name: Monahan, Torin
Publisher: name: Springer Nature
Year: 2024

description: Meeting the needs of dual-career academic couples has become an important part of university efforts to foster family-friendly workplaces. Many universities have developed formal or informal approaches to addressing dual-career issues, but variation across institutions has made it difficult to detect wider patterns or probe their implications. In this paper, we analyze the dual-career policies and materials (848 documents total) of all R1 institutions in the United States. As with studies from roughly two decades ago, we find deficiencies in institutional support and transparency. However, given reduced state revenues for institutions of higher education and a rise in precarious employment arrangements over the same time period, conditions for academic couples are arguably worse today. In order for universities to address these concerns and contribute meaningfully to broader forms of inclusion, we argue that there is a need for sustained funding commitments and infrastructural support for dual-career programs.
Manifestation of the bulk phase transition in the edge energy spectrum in a two dimensional bilayer electron system
Creators: name: Deviatov, E. V.
name: Wurtz, A.
name: Lorke, A.
name: Melnikov, M. Yu.
name: Dolgopolov, V. T.
name: Wixforth, A.
name: Campman, K. L.
name: Gossard, A. C.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We use a quasi-Corbino sample geometry with independent contacts to different edge states in the quantum Hall effect regime to investigate the edge energy spectrum of a bilayer electron system at total filling factor $ν=2$. By analyzing non-linear $I-V$ curves in normal and tilted magnetic fields we conclude that the edge energy spectrum is in a close connection with the bulk one. At the bulk phase transition spin-singlet - canted antiferromagnetic phase $I-V$ curve becomes to be linear, indicating the disappearance or strong narrowing of the $ν=1$ incompressible strip at the edge of the sample.
description: 5 pages, 5 figures
Mormon Polygamy and American Law in the 19th Century
Creators: name: May, Ashley
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2019

description:
The Church of Jesus Christ of Latter-day Saints is a religion founded in post-Revolution America. Back in the 19th century, some Saints, or commonly known as Mormons, would follow the religious law of plural marriage, where men would marry multiple women. However, the Mormon church in the present does not have this practice. What made the Mormons remove this law from their religion?
Deficiency of Grx1 leads to high sensitivity of HeLaS3 cells to oxidative stress via excessive accumulation of intracellular oxidants including ROS
Creators: name: Tingyi Zhao
name: Zhang-Akiyama, Qiu-Mei
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Oxidative stress is often initiated by excess reactive oxygen species (ROS) production, resulting in macromolecular damage, which is implicated in many disease states. Glutaredoxin 1 (Grx1) is an antioxidant enzyme that plays an important role in redox signaling and redox homeostasis. In the present study, we generated HeLaS3 cell lines deficient in Grx1 by the CRISPR/CAS9 system to clarify how Grx1 affects the physiological activities of HeLaS3 cells to respond to oxidative stress. First, the survival assay revealed that Grx1-deficient HeLaS3 cells were more sensitive to γ-ray irradiation, heat shock and H2O2 exposure than HeLaS3 wild-type cells. Next, the intracellular redox state was investigated using a fluorescent probe (2′-7′dichlorofluorescin diacetate), and the oxidized state of total proteins and a peroxidase Prx2 were measured by Western blot analysis. Exposure to γ-ray irradiation, heat shock and H2O2 significantly induced more accumulation of intracellular oxidants including ROS and higher levels of oxidized proteins in Grx1-deficient HeLaS3 cells. Furthermore, MitoSox Red staining demonstrated that Grx1 deficiency causes a higher level of oxidants production in mitochondria. Moreover, Grx1-deficient HeLaS3 cells had a higher cytochrome c level and higher apoptosis rate (Annexin-V/FITC and EthD-III staining assay) upon oxidative stress. These results suggested that Grx1 deficiency lead to mitochondrial redox homeostasis disruption and apoptotic cell death upon oxidative stress. In addition, the results of proliferation assay and MitoTracker staining assay (multinuclear cell formation rate) suggested that oxidative stress exposure inhibits cell proliferation maybe by affecting cytoplasmic division in Grx1-deficient HeLaS3 cells.
Higher Impurity AdS/CFT Correspondence in the Near-BMN Limit
Creators: name: Callan,, Curtis G.
name: McLoughlin, Tristan
name: Swanson, Ian
Publisher: name: arXiv
Year: 2004
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The pp-wave/BMN limit of the AdS/CFT correspondence has exposed the Maldacena conjecture to a new regimen of direct tests. In one line of pursuit, finite-radius curvature corrections to the Penrose limit (which appear in inverse powers of the string angular momentum J) have been found to induce a complicated system of interaction perturbations to string theory on the pp-wave; these have been successfully matched to corresponding corrections to the BMN dimensions of N=4 super Yang-Mills (SYM) operators to two loops in the 't Hooft coupling lambda. This result is tempered by a well-established breakdown in the correspondence at three loops. Notwithstanding the third-order mismatch, we proceed with this line of investigation by subjecting the string and gauge theories to new and significantly more rigorous tests. Specifically, we extend our earlier results at O(1/J) in the curvature expansion to include string states and SYM operators with three worldsheet or R-charge impurities. In accordance with the two-impurity problem, we find a perfect and intricate agreement between both sides of the correspondence to two-loop order in lambda and, once again, the string and gauge theory predictions fail to agree at third order.
description: 45 pages, LaTeX; notation and references corrected
Electron-hole asymmetry in electrical conductivity of low-fluorinated graphene: Numerical study
Creators: name: Kolesnikov, D. V.
name: Osipov, V. A.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: By using the real-space Green-Kubo formalism we study numerically the electron transport properties of low-fluorinated graphene. At low temperatures the diffuse transport regime is expected to be prevalent, and we found a pronounced electron-hole asymmetry in electrical conductivity as a result of quasi-resonant scattering on the localized states. For the finite temperatures in the variable-range hopping transport regime the interpretation of numerical results leads to the appearance of local minima and maxima of the resistance near the energies of the localized states. A comparison with the experimental measurements of the resistance in graphene samples with various fluorination degrees is discussed.
Structural Studies on Semiconducting Hydrogenated Amorphous Silicon Oxide Films
Creators: name: Iftiquar, S. M.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Condensed Matter (cond-mat)
subject: FOS: Physical sciences

description: In hydrogenated amorphous silicon oxide (a-SiO:H) films, incorporation of oxygen enhances optical gap due to a large number of St-O-Si bond formation, which lies deep into valence band states. An induction effect of this Si-O on other bonds within the network also takes place. At higher oxygen content micro-void forms and bonded hydrogen accumulates in di and/or polyhydride form. At this stage a phase separation of Si-rich and O-rich region taking place. A peak shift of absorption spectra within 1850 - 2250 cm-1, towards higher wave number is continuous. A gradual increase and broadening of 850 cm-1 absorption band on both sides of peak position indicate higher structural disorder in network formation. It may be considered that the stretching vibration of-OH bonded to Si gives rise to 780 cm-1 absorption band. This Si-OH formation is beneficial which prevents deterioration in photosensitivity due to reduction in bonded hydrogen content. Hydrogen content is found reducing as oxygen content increases from zero to ~15 at.%. A systematic study is carried out to correlate the optoelectronic property with local atomic arrangement.