cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Trait dynamics of Mediterranean xerophytic shrub communities growing on stabilised inland dunes respond to nutrient and aridity gradients
Creators: name: Chozas, Sergio
name: Correia, Otília
name: Santos, Ana M.C.
name: Hortal, Joaquín
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified

description: Background: Understanding the processes that determine community assembly and their dynamics is a central issue in ecology. The analysis of functional diversity can improve our understanding of these dynamics by identifying community assembly processes. Aims: We studied the effect of environment–community covariations on both functional diversity and functional structure of xerophytic shrub communities for inferring the community assembly processes shaping this vegetation type. Methods: Functional diversity was quantified using (1) community-weighted mean of the studied traits, (2) functional groups, defined using Ward’s hierarchical agglomerative clustering method and (3) Rao’s quadratic entropy. Relationships between functional diversity and environmental gradients were identified by Spearman correlations and modelled using generalised additive models. Results: Variations in community composition and functional diversity correlated with soil nutrient availability and aridity. Increasing nutrient availability resulted in both greater average plant height and higher abundance of plants with green photosynthetic organ colour, whereas the abundance of nanophanerophytes increases with aridity. Conclusions: The species composition and trait structure of the studied Mediterranean xerophytic shrub communities varies along nutrient and aridity gradients. This supports the importance of environmental filters for the local assembly and dynamics of these inland dune communities.
Rotating quantum turbulence in the unitary Fermi gas
Creators: name: Hossain, Khalid
name: Kobuszewski, Konrad
name: Forbes, Michael McNeil
name: Magierski, Piotr
name: Sekizawa, Kazuyuki
name: Wlazłowski, Gabriel
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Nuclear Theory (nucl-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantized vortices carry the angular momentum in rotating superfluids, and are key to the phenomenon of quantum turbulence. Advances in ultra-cold atom technology enable quantum turbulence to be studied in regimes with both experimental and theoretical control, unlike the original contexts of superfluid helium experiments. While much work has been performed with bosonic systems, detailed studies of fermionic quantum turbulence are nascent, despite wide applicability to other contexts such as rotating neutron stars. In this paper, we present the first large-scale study of quantum turbulence in rotating fermionic superfluids using an accurate orbital based time-dependent density functional theory (DFT) called the superfluid local density approximation (SLDA). We identify two different modes of turbulent decay in the dynamical equilibration of a rotating fermionic superfluid, and contrast these results with a computationally simpler orbital-free DFT, which we find can qualitatively reproduce these decay mechanisms if dissipation is explicitly included. These results demonstrate that one-body dissipation mechanisms intrinsic to fermionic superfluids play a key role differentiating fermionic from bosonic turbulence, but also suggest that simpler orbital-free theories may be corrected so that these more efficient techniques can be used to model extended physical systems such as neutron superfluids in neutron stars.
description: 13 pages, 8 figures. Accompanying movies can be found at http://wlazlowski.fizyka.pw.edu.pl/supplement/sm-rotating-turbulence/
title: 02_1152
Creators: name: Wesley Baldwin, John
name: Baldwin, John W.
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2018
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: L'ensemble de ces notes ont été crée par John Baldwin lors d'une de ses premières périodes de résidence à Paris. Ces documents comprennent tous les magistri qu’il avait pu rencontrer dans ses sources. Aux XIIème et XIIIème siècles, les universités n'existant pas encore, le titre de magister s'il évoque certainement une compétence n'est pas rattaché de façon systématique au passage par les écoles. De surcroît, les magistris sont le plus souvent désignés par leur seul prénom. La lecture de ces données est donc difficile et suppose un long travail pour tenter d'identifier un individu auquel on pourrait rattacher plusieurs mentions. John Baldwin avait donc renoncé à utiliser ces données pour donner un prolongement à sa magnifique étude sur les gradués d'université et leur emploi par les Capétiens et les Plantagenêts. Néanmoins, il a conservé ces données et elles sont potentiellement très utile dans le cadre de Studium, comme le sont toutes les mentions dans les volumes des Fasti Ecclesiae Gallicanae de chanoines portant ce titre de magister sans autres précisions. L'ampleur des dépouillements rend ces données très utiles et nous devons une grande reconnaissance à John Baldwin pour avoir pris la peine de faire photocopier ses fiches et de nous les avoir transmises amicalement.
Les données ainsi que les images des fiches sont accessibles sur le site Internet à l'adresse suivante : http://studium-baldwin.lamop.fr/.
Les transcriptions des fiches ont été effectuées par des étudiants de Paris 1 Panthéon - Sorbonne mais elles n'ont pas été corrigées par la suite.
description: Relation: https://lamop.hypotheses.org/
Additional file 1 of circCDYL2 promotes trastuzumab resistance via sustaining HER2 downstream signaling in breast cancer
Creators: name: Ling, Yun
name: Liang, Gehao
name: Lin, Qun
name: Fang, Xiaolin
name: Luo, Qing
name: Cen, Yinghuan
name: Mehrpour, Maryam
name: Hamai, Ahmed
name: Liu, Zihao
name: Shi, Yu
name: Li, Juanmei
name: Lin, Wanyi
name: Jia, Shijie
name: Yang, Wenqian
name: Liu, Qiang
name: Song, Erwei
name: Li, Jun
name: Gong, Chang
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Space Science
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Virology

description: Additional file 1.
Identification of drought-induced genes from the leaves of Rangpur lime (Citrus limon (L) Osbeck)
Creators: name: Şahin-Çevik, Mehtap
name: Çevik, Bayram
name: Topkaya-Kütük, Bengi
name: Yazıcı, Keziban
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biophysics
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Physiology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology
subject: Plant Biology

description: Water stress is one of the limiting factors for citrus production and Citrus species show great variation in their response to drought stress. Although the majority of Citrus rootstocks are sensitive to water stress, Rangpur lime (Citrus limon (L) Osbeck) (RL) shows a high degree of drought tolerance. Therefore, it has been used as a rootstock in drought-prone environments, but mechanisms of drought tolerance are not yet known. In this study, to explore the mechanisms of drought adaptation and tolerance, a subtractive cDNA library was constructed from the leaves of 14-day drought-stressed and non-stressed RL for identification of drought-induced genes. 285 cDNA sequences were obtained from randomly selected clones from the subtracted library containing the drought-induced genes. The expression analyses of 200 cDNAs in 14-day drought treated and untreated RL by macroarray hybridisation revealed that the expression of 56 cDNAs increased two to 11-fold. 30 non-redundant drought-induced genes were identified from these cDNAs and drought induction of eight selected genes was confirmed by a real-time RT-PCR assay suggesting that expressions of these genes were regulated by drought-stress. Genes identified in this study were mostly related with cell rescue and defense pathways involved in drought adaptation and tolerance of RL.
Implications of inertial subrange scaling for stably stratified mixing
Creators: name: Portwood, G. D.
name: Kops, S. M. de Bruyn
name: Caulfield, C. P.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: The effects of turbulent dynamic range on scalar mixing in stably stratified turbulence are investigated by an adaptation of the theoretical passive scalar modelling arguments of Beguier et al. (1978) and demonstrated statistically using direct numerical simulations of statistically stationary homogeneous stratified and sheared turbulence (SHSST). By analysis of inertial and inertial-convective subrange scaling, we show that the relationship between active scalar and turbulence time scales is predicted by the ratio of the Kolmogorov and Oboukhov-Corrsin constants provided there is sufficient scale separation for inertial and inertial-convective subrange scalings to be valid. With this analysis, we show that the turbulent mixing coefficient, $Γ\equiv χ/ε$, that is, within this context defined to be the ratio of available potential energy ($E_p$) and turbulent kinetic energy ($E_k$) dissipation rates, can be estimated by $E_p,E_k$ and a universal constant provided a Reynolds number is sufficiently high, observed here at $Re_b \equiv ε/ νN^2 \gtrapprox 300$ where $ν$ is the kinematic viscosity and $N$ is the characteristic buoyancy frequency. We propose a model for diapycnal mixing with robust theoretical parametrisation and asymptotic behaviour in this high-$Re_b$ limit.
Multipolar exchange interaction and complex order in insulating lanthanides
Creators: name: Iwahara, Naoya
name: Huang, Zhishuo
name: Neefjes, Ivo
name: Chibotaru, Liviu F.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: In insulating lanthanides, unquenched orbital momentum and weak crystal-field (CF) splitting of the atomic $J$ multiplet at lanthanide ions result in a highly ranked (multipolar) exchange interaction between them and a complex low-temperature magnetic order not fully uncovered by experiment. Explicitly correlated {\it ab initio } methods proved to be highly efficient for an accurate description of CF multiplets and magnetism of individual lanthanide ions in such materials. Here we extend this {\it ab initio } methodology and develop a first-principles microscopic theory of multipolar exchange interaction between $J$-multiplets in $f$ metal compounds. The key point of the approach is a complete account of Goodenough's exchange mechanism along with traditional Anderson's superexchange and other contributions, the former being dominant in many lanthanide materials. Application of this methodology to the description of the ground-state order in the neodymium nitride with rocksalt structure reveals the multipolar nature of its ferromagnetic order. We found that the primary and secondary order parameters (of $T_{1u}$ and $E_g$ symmetry, respectively) contain non-negligible $J$-tensorial contributions up to the ninth order. The calculated spin-wave dispersion and magnetic and thermodynamic properties show that they cannot be simulated quantitatively by confining to the ground CF multiplet on the Nd sites. Our results demonstrate that the {\it ab initio } approach to the low-energy Hamiltonian represents a powerful tool for the study of materials with complex magnetic order.
description: Main text (20 pages) + Supplementla Materials (76 pages)
Aqueous single step synthesis and structural characterization of allylated, propargylated, and benzylated 3-substituted 3-aminooxindoles
Creators: name: Karpe, Sameer A.
name: Singh, Man
name: L. Raju Chowhan
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 60506 Virology

description: Efficient zinc-mediated allylation, propargylation, and benzylation of isatin-derived imines were undertaken for the synthesis of 3-substituted 3-aminooxindoles with ≈80% yield. Such alternative approach has efficiently avoided the use of catalysts, severe reaction conditions, multistep procedures, and reaction additives. For exploring and materializing the synthetic utility, different allyl, propargyl, and benzyl bromides were used for generalizing the synthetic route. The structure of the synthesized compounds was established and confirmed by 1H NMR, 13C NMR, FTIR, and mass spectroscopic techniques.
Edge Exchangeable Models for Interaction Networks
Creators: name: Crane, Harry
name: Dempsey, Walter
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Neuroscience
subject: Biotechnology
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: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Computational Biology

description: Many modern network datasets arise from processes of interactions in a population, such as phone calls, email exchanges, co-authorships, and professional collaborations. In such interaction networks, the edges comprise the fundamental statistical units, making a framework for edge-labeled networks more appropriate for statistical analysis. In this context, we initiate the study of edge exchangeable network models and explore its basic statistical properties. Several theoretical and practical features make edge exchangeable models better suited to many applications in network analysis than more common vertex-centric approaches. In particular, edge exchangeable models allow for sparse structure and power law degree distributions, both of which are widely observed empirical properties that cannot be handled naturally by more conventional approaches. Our discussion culminates in the Hollywood model, which we identify here as the canonical family of edge exchangeable distributions. The Hollywood model is computationally tractable, admits a clear interpretation, exhibits good theoretical properties, and performs reasonably well in estimation and prediction as we demonstrate on real network datasets. As a generalization of the Hollywood model, we further identify the vertex components model as a nonparametric subclass of models with a convenient stick breaking construction.
Removal of hydrogen sulfide from methane using PEO-segmented copolymer-based multilayer composite membrane
Creators: name: Gholizadeh, Hoda
name: A. Aref Azar
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
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: 69999 Biological Sciences not elsewhere classified

description: The thermoplastic poly(urethane-urea) (PUU) was synthesized using polyethylene-glycol, 4,4ʹ-methylenediphenyl diisocyanate (MDI), and 1,2-ethandiamine (EDA) as a chain extender. A novel multilayer composite membrane consisting of the synthesized PUU, as a selective layer, a silicon rubber, as an interlayer, and the polyacrylonitrile (PAN) microporous support was prepared for the removal of acid gas. Moreover, the physical properties of the synthesized PEG-based polyurethane were investigated. Based on Differential Scanning Calorimeter (DSC) and ANDFourier Transform Infra-red Spectroscopy (FTIR) analyses, a higher microphase separation of hard and soft segments was observed for PUU. The permeabilities of pure CO2, pure CH4, and a ternary mixture of CH4, CO2, and H2S through the multilayer composite membrane were measured at different temperatures and pressures. The maximum values of selectivity, i.e., 52 and 15 for H2S/CH4 and CO2/CH4, respectively, were found at 25°C and 5 bar. The permeances of H2S and CO2 in the ternary mixture decreased on increasing the feed pressure because of membrane compression. The higher the temperature, the higher was the permeability of the gases due to the more molecular movement of the polymer chains. Therefore, the gas selectivity in the synthesized composite membrane decreased by increasing the temperature. The experiments showed that replacing the pure-gas measurements with the gas mixture measurements can substantially produce more relevant results.
Additional file 16 of Characterization and fine mapping of a new dwarf mutant in Brassica napus
Creators: name: Li, Xin
name: Xiang, Fujiang
name: Zhang, Wei
name: Yan, Jindong
name: Li, Xinmei
name: Zhong, Ming
name: Yang, Piao
name: Chen, Caiyan
name: Liu, Xuanming
name: Mao, Donghai
name: Zhao, Xiaoying
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 16: Figure S14. Phenotypes of L329 (left), bnd2 (right) and their hybrid (F1, middle) at the maturation stage.
6S RNA in Rhodobacter sphaeroides: 6S RNA and pRNA transcript levels peak in late exponential phase and gene deletion causes a high salt stress phenotype
Creators: name: Elkina, Daria
name: Weber, Lennart
name: Lechner, Marcus
name: Burenina, Olga
name: Weisert, Andrea
name: Kubareva, Elena
name: Hartmann, Roland K.
name: Klug, Gabriele
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Plant Biology
subject: Computational Biology

description: The function of 6S RNA, a global regulator of transcription, was studied in the photosynthetic α-proteobacterium Rhodobacter sphaeroides. The cellular levels of R. sphaeroides 6S RNA peak toward the transition to stationary phase and strongly decrease during extended stationary phase. The synthesis of so-called product RNA transcripts (mainly 12–16-mers) on 6S RNA as template by RNA polymerase was found to be highest in late exponential phase. Product RNA ≥ 13-mers are expected to trigger the dissociation of 6S RNA:RNA polymerase complexes. A 6S RNA deletion in R. sphaeroides had no impact on growth under various metabolic and oxidative stress conditions (with the possible exception of tert-butyl hydroperoxide stress). However, the 6S RNA knockout resulted in a robust growth defect under high salt stress (0.25 M NaCl). Remarkably, the sspA gene encoding the putative salt stress-induced membrane protein SspA and located immediately downstream of the 6S RNA (ssrS) gene on the antisense strand was expressed at elevated levels in the ΔssrS strain when grown in the presence of 250 mM NaCl.
Weyl-Invariant Gravity and the Nature of Dark Matter
Creators: name: Shimon, Meir
Publisher: name: arXiv
Year: 2020
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The apparent missing mass in galaxies and galaxy clusters, commonly viewed as evidence for dark matter, could possibly originate from gradients in the gravitational coupling parameter, $G$, and active gravitational mass, $M_{act}$, rather than hypothetical beyond-the-standard-model particles. We argue that in (the weak field limit of) a Weyl-invariant extension of General Relativity, one can simply affect the change $Φ_{b}(x)\rightarrowΦ_{b}(x) + Φ_{DM}(x)$, where $Φ_{b}$ is the baryon-sourced potential and $Φ_{DM}$ is the `excess' potential. This is compensated by gradients of $GM_{act}$ and a fractional increase of $O(-4Φ_{DM}(x))$ in the baryon density, well below current detection thresholds on all relevant scales.
description: Matches published version
Research question and existing evidence: What are the most effective methods of ensuring health care facilities in California comply with SB 1138 requiring availability of plant-based foods in licensed health care facilities, and of using this opportunity to encourage overall increased use of plant-based foods in facilities?
Creators: name: Bishop, Tarun Edward
Publisher: name: OSF Registries
Year: 2019

description: We know of no direct evidence published on this issue since SB 1138 was enacted in September, 2018, and took effect January 1, 2019. Studies and articles on related issues will direct our research and inform our report. Space limitations prevent us from citing and describing all our research here, but some examples follow.
 There is a need for dietitian expertise for nutritional assessment and care planning to meet special food needs.i Therapeutic diets currently served in institutions are often unpalatable and lessen quality of life. ii Patients need a clinical advocate for dietary needs, there is inadequate nutrition needs screening, hospitals don’t adequately monitor patient intake, and there is diffusion of responsibilities and lack of communication between staff. iii
  Sustainable food advocates are studying challenges to provision of sustainable healthy food in healthcare facilities.  For example, advocates found health benefits and patient satisfaction from making sustainable food more attractive to patients by providing 6-7 smaller meals per day, and plan to extend research to implementing plant-based diets in health facilities.iv   
 How food service staff communicate and interact with patients when presenting food options and serving food is also a primary factor in patient satisfaction with hospital food. v  It will be helpful to learn whether financial cost of providing quality plant-based food is perceived as a barrier, as that is a question that has been addressed by research. vi
 Research on effective animal advocacy in other contexts will also inform this project. For example, project staff will use Animal Charity Evaluators (ACE”) reports on the effects of diet choice to quantify results of changing diets in health care institutions.vii   To identify future legal interventions and ways to analyze ex post the effectiveness of SB 1138, project staff will review studies such as the study of the effectiveness of California’s battery cage ban.viii
Machine Learning for Cataract Classification and Grading on Ophthalmic Imaging Modalities: A Survey
Creators: name: Zhang, Xiaoqing
name: Hu, Yan
name: Xiao, Zunjie
name: Fang, Jiansheng
name: Higashita, Risa
name: Liu, Jiang
Publisher: name: arXiv
Year: 2020
Subjects: subject: Image and Video Processing (eess.IV)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Machine Learning (cs.LG)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: Cataracts are the leading cause of visual impairment and blindness globally. Over the years, researchers have achieved significant progress in developing state-of-the-art machine learning techniques for automatic cataract classification and grading, aiming to prevent cataracts early and improve clinicians' diagnosis efficiency. This survey provides a comprehensive survey of recent advances in machine learning techniques for cataract classification/grading based on ophthalmic images. We summarize existing literature from two research directions: conventional machine learning methods and deep learning methods. This survey also provides insights into existing works of both merits and limitations. In addition, we discuss several challenges of automatic cataract classification/grading based on machine learning techniques and present possible solutions to these challenges for future research.
description: 26 pages, 13 figures
Demonstrating the Tapered Gridded Estimator (TGE) for the Cosmological HI 21-cm Power Spectrum using $150 \, {\rm MHz}$ GMRT observations
Creators: name: Pal, Srijita
name: Bharadwaj, Somnath
name: Ghosh, Abhik
name: Choudhuri, Samir
Publisher: name: arXiv
Year: 2020
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We apply the Tapered Gridded Estimator (TGE) for estimating the cosmological 21-cm power spectrum from $150 \, {\rm MHz}$ GMRT observations which corresponds to the neutral hydrogen (HI) at redshift $z = 8.28$. Here TGE is used to measure the Multi-frequency Angular Power Spectrum (MAPS) $C_{\ell}(Δν)$ first, from which we estimate the 21-cm power spectrum $P(k_{\perp},k_{\parallel})$. The data here are much too small for a detection, and the aim is to demonstrate the capabilities of the estimator. We find that the estimated power spectrum is consistent with the expected foreground and noise behaviour. This demonstrates that this estimator correctly estimates the noise bias and subtracts this out to yield an unbiased estimate of the power spectrum. More than $47\%$ of the frequency channels had to be discarded from the data owing to radio-frequency interference, however the estimated power spectrum does not show any artifacts due to missing channels. Finally, we show that it is possible to suppress the foreground contribution by tapering the sky response at large angular separations from the phase center. We combine the k modes within a rectangular region in the `EoR window' to obtain the spherically binned averaged dimensionless power spectra $Δ^{2}(k)$ along with the statistical error $σ$ associated with the measured $Δ^{2}(k)$. The lowest $k$-bin yields $Δ^{2}(k)=(61.47)^{2}\,{\rm K}^{2}$ at $k=1.59\,\textrm{Mpc}^{-1}$, with $σ=(27.40)^{2} \, {\rm K}^{2}$. We obtain a $2 \, σ$ upper limit of $(72.66)^{2}\,\textrm{K}^{2}$ on the mean squared HI 21-cm brightness temperature fluctuations at $k=1.59\,\textrm{Mpc}^{-1}$.
description: 15 pages, 12 figures, Accepted for publication in MNRAS
title: Circadian Alterations Increase with Progression in a Patient-Derived Cell Culture Model of Breast Cancer
Creators: name: Lin, Hui-Hsien
name: Taylor, Stephanie R.
name: Farkas, Michelle E.
Publisher: name: University of Massachusetts Amherst
Year: 2021
Subjects: subject: breast cancer
subject: cancer progression
subject: circadian rhythm
subject: metastatic cells
subject: rhythmicity

description: Circadian rhythm disruption can elicit the development of various diseases, including breast cancer. While studies have used cell lines to study correlations between altered circadian rhythms and cancer, these models have different genetic backgrounds and do not mirror the changes that occur with disease development. Isogenic cell models can recapitulate changes across cancer progression. Hence, in this study, a patient-derived breast cancer model, the 21T series, was used to evaluate changes to circadian oscillations of core clock protein transcription as cells progress from normal to malignant states. Three cell lines were used: H16N2 (normal breast epithelium), 21PT (atypical ductal hyperplasia), and 21MT-1 (invasive metastatic carcinoma). The cancerous cells are both HER2+. We assessed the transcriptional profiles of two core clock proteins, BMAL1 and PER2, which represent a positive and negative component of the molecular oscillator. In the normal H16N2 cells, both genes possessed rhythmic mRNA oscillations with close to standard periods and phases. However, in the cancerous cells, consistent changes were observed: both genes had periods that deviated farther from normal and did not have an anti-phase relationship. In the future, mechanistic studies should be undertaken to determine the oncogenic changes responsible for the circadian alterations found.
Fast Moment Estimation for Generalized Latent Dirichlet Models
Creators: name: Shiwen Zhao
name: Engelhardt, Barbara E.
name: Sayan Mukherjee
name: Dunson, David B.
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: We develop a generalized method of moments (GMM) approach for fast parameter estimation in a new class of Dirichlet latent variable models with mixed data types. Parameter estimation via GMM has computational and statistical advantages over alternative methods, such as expectation maximization, variational inference, and Markov chain Monte Carlo. A key computational advantage of our method, Moment Estimation for latent Dirichlet models (MELD), is that parameter estimation does not require instantiation of the latent variables. Moreover, performance is agnostic to distributional assumptions of the observations. We derive population moment conditions after marginalizing out the sample-specific Dirichlet latent variables. The moment conditions only depend on component mean parameters. We illustrate the utility of our approach on simulated data, comparing results from MELD to alternative methods, and we show the promise of our approach through the application to several datasets. Supplementary materials for this article are available online.
Additional file 8: of New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics
Creators: name: Hu, Weichang
name: Hua, Xiuting
name: Zhang, Qing
name: Wang, Jianping
name: Shen, Qiaochu
name: Zhang, Xingtan
name: Wang, Kai
name: Yu, Qingyi
name: Lin, Yann-Rong
name: Ming, Ray
name: Zhang, Jisen
Publisher: name: figshare
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Marine Biology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: The primers for PCR verification of SWEET4e and SWEET16b in two Saccharum species. (DOCX 17 kb)
Dissolved oxygen in Lake Santo Parmense (1991)
Creators: name: [Unknown]
Publisher: name: FZ-Juelich B2SHARE
Year: 2020

description: Dataset provides dissolved oxygen measured in Lake Santo Parmense in 1991. Dissolved oxygen was measured by means of an oxygen probe at different depths over the whole water column at the point of maximum depth of the lake. On three dates water samples were collected with a Ruttner bottle and dissolved oxygen was measured by means of the Winkler method.
MOESM2 of Small extracellular vesicles derived from embryonic stem cells restore ovarian function of premature ovarian failure through PI3K/AKT signaling pathway
Creators: name: Liu, Mengyu
name: Qiu, Yu
name: Xue, Zhuowei
name: Wu, Ruoyu
name: Li, Jie
name: Niu, Xin
name: Yuan, Ji
name: Wang, Yang
name: Wu, Qingkai
Publisher: name: figshare
Year: 2020
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Developmental Biology
subject: Cancer
subject: Mental Health
subject: Computational Biology

description: Additional file 2. ESCs-sEVs restored ovarian function in a naturally aging mouse model. A-a E2 was significantly increased compared to the Aging-control group. A-b FSH was significantly decreased compared to the Aging-control group. A-c AMH was significantly increased compared to the Aging-control group. B H&E staining for ovaries. B-a Aging mice after ESCs-sEVs treatment. B-b Aging mice without ESCs-sEVs treatment. B-c Eight-week old normal mice. Scale bar = 300 μm. ***P < 0.001, control versus ESCs-sEVs group.
Exceptional points and scattering of discrete mechanical metamaterials
Creators: name: Wang, Weidi
name: Amirkhizi, Alireza V.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: Exceptional points (EPs) are complex singularities of parametric linear operators where two or more eigenvalues and eigenvectors coalesce. EPs are attracting increasing interest in mechanical metamaterials due to their strong potentials for wave filtering, cloaking, and sensing applications. This work studies the band topology and scattering behaviors near EPs, using discrete models of metamaterial (MM) systems. The questions of existence of EPs and their physical manifestations will be addressed with particular focus on symmetry considerations and scattering behavior. Discrete mass-spring models with adjustable parameters are used here to elucidate the EP-related phenomena in a fundamental form. The transfer and scattering matrices are analyzed to provide practical insights on the restrictions associated with reciprocity and fundamental symmetries. By including complex stiffness in frequency domain as a representation of non-conservative mechanical loss or gain, the MM arrays can be tuned to achieve bi-directional transparency or one-way reflection when operating at the EPs. This analytical study will contribute to the understandings of EPs in mechanical context and the design of micro-structured media for novel applications.
description: The Version of Record of this article is published in The European Physical Journal Plus, and is available online at https://doi.org/10.1140/epjp/s13360-022-02626-6
Aqueous Single Step Synthesis and Structural Characterization of Allylated, Propargylated, and Benzylated 3-Substituted 3-Aminooxindoles
Creators: name: Karpe, Sameer A.
name: Singh, Man
name: L. Raju Chowhan
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 60506 Virology

description: Efficient zinc-mediated allylation, propargylation, and benzylation of isatin derived imines were undertaken for the synthesis of 3-substituted 3-aminooxindoles with ≈ 80% yield. Such alternative approach has efficiently avoided the use of catalysts, severe reaction conditions, multistep procedures, and reaction additives. For exploring and materializing the synthetic utility, different allyl, propargyl, and benzyl bromides were used for generalizing the synthetic route. The structure of the synthesized compounds was established and confirmed by 1H NMR, 13C NMR, FTIR, and mass spectroscopic techniques.
Conversion of the stacking orientation of bilayer graphene due to \break the interaction of BN-dopants
Creators: name: Abdullah, Nzar Rauf
name: Rashid, Hunar Omar
name: Tang, Chi-Shung
name: Manolescu, Andrei
name: Gudmundsson, Vidar
Publisher: name: arXiv
Year: 2021
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: A conversion of AA- to AB-stacking bilayer graphene (BLG) due to interlayer interaction is demonstrated. Two types of interlayer interactions, an attractive and a repulsive, between the Boron and Nitrogen dopant atoms in BLG are found. In the presence of the attractive interaction, an AA-stacking of BN-codoped BLG is formed with a less stable structure leading to weak mechanical properties of the system. Low values of the Young modulus, the ultimate strength and stress, and the fracture strength are observed comparing to a pure BLG. In addition, the attractive interaction induces a small bandgap that deteriorates the thermal and optical properties of the system. In contrast, in the presence of a repulsive interaction between the B and N atoms, the AA-stacking is converted to a AB-stacking with a more stable structure. Improved mechanical properties such as higher Young modulus, the ultimate strength and stress, fracture strength are obtained comparing to the AA-stacked BN-codoped BLG. Furthermore, a larger bandgap of the AB-stacked bilayer enhances the thermal and the optical characteristics of the system.
description: RevTeX, 10 pages with 8 included figures
Oracle Estimation of a Change Point in High-Dimensional Quantile Regression
Creators: name: Sokbae Lee
name: Liao, Yuan
name: Seo, Myung Hwan
name: Youngki Shin
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: Cancer

description: In this article, we consider a high-dimensional quantile regression model where the sparsity structure may differ between two sub-populations. We develop ℓ1-penalized estimators of both regression coefficients and the threshold parameter. Our penalized estimators not only select covariates but also discriminate between a model with homogenous sparsity and a model with a change point. As a result, it is not necessary to know or pretest whether the change point is present, or where it occurs. Our estimator of the change point achieves an oracle property in the sense that its asymptotic distribution is the same as if the unknown active sets of regression coefficients were known. Importantly, we establish this oracle property without a perfect covariate selection, thereby avoiding the need for the minimum level condition on the signals of active covariates. Dealing with high-dimensional quantile regression with an unknown change point calls for a new proof technique since the quantile loss function is nonsmooth and furthermore the corresponding objective function is nonconvex with respect to the change point. The technique developed in this article is applicable to a general M-estimation framework with a change point, which may be of independent interest. The proposed methods are then illustrated via Monte Carlo experiments and an application to tipping in the dynamics of racial segregation. Supplementary materials for this article are available online.
More Tolerant Reconstructed Networks by Self-Healing against Attacks in Saving Resource
Creators: name: Hayashi, Yukio
name: Tanaka, Atsushi
name: Matsukubo, Jun
Publisher: name: arXiv
Year: 2021
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Social and Information Networks (cs.SI)
subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Complex network infrastructure systems for power-supply, communication, and transportation support our economical and social activities, however they are extremely vulnerable against the frequently increasing large disasters or attacks. Thus, a reconstructing from damaged network is rather advisable than empirically performed recovering to the original vulnerable one. In order to reconstruct a sustainable network, we focus on enhancing loops so as not to be trees as possible by node removals. Although this optimization is corresponded to an intractable combinatorial problem, we propose self-healing methods based on enhancing loops in applying an approximate calculation inspired from a statistical physics approach. We show that both higher robustness and efficiency are obtained in our proposed methods with saving the resource of links and ports than ones in the conventional healing methods. Moreover, the reconstructed network by healing can become more tolerant than the original one before attacks, when some extent of damaged links are reusable or compensated as investment of resource. These results will be open up the potential of network reconstruction by self-healing with adaptive capacity in the meaning of resilience.
description: 23 pages, 6 figures. arXiv admin note: text overlap with arXiv:2008.00651
Edge exchangeable models for interaction networks
Creators: name: Crane, Harry
name: Dempsey, Walter
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Neuroscience
subject: Biotechnology
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: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Computational Biology

description: Many modern network datasets arise from processes of interactions in a population, such as phone calls, email exchanges, co-authorships, and professional collaborations. In such interaction networks, the edges comprise the fundamental statistical units, making a framework for edge-labeled networks more appropriate for statistical analysis. In this context we initiate the study of edge exchangeable network models and explore its basic statistical properties. Several theoretical and practical features make edge exchangeable models better suited to many applications in network analysis than more common vertex-centric approaches. In particular, edge exchangeable models allow for sparse structure and power law degree distributions, both of which are widely observed empirical properties that cannot be handled naturally by more conventional approaches. Our discussion culminates in the Hollywood model, which we identify here as the canonical family of edge exchangeable distributions. The Hollywood model is computationally tractable, admits a clear interpretation, exhibits good theoretical properties, and performs reasonably well in estimation and prediction as we demonstrate on real network datasets. As a generalization of the Hollywood model, we further identify the vertex components model as a nonparametric subclass of models with a convenient stick breaking construction.
$C_2$-equivariant topological modular forms
Creators: name: Chua, Dexter
Publisher: name: arXiv
Year: 2021
Subjects: subject: Algebraic Topology (math.AT)
subject: FOS: Mathematics

description: We compute the homotopy groups of the $C_2$ fixed points of equivariant topological modular forms at the prime $2$ using the descent spectral sequence. We then show that as a $\mathrm{TMF}$-module, it is isomorphic to the tensor product of $\mathrm{TMF}$ with an explicit finite cell complex.
description: v3: Published in Journal of Homotopy and Related Structures v2: Added appendix on connective equivariant tmf. Minor adjustments
Lack of evidence for microplastic contamination in honey
Creators: name: Mühlschlegel, Peter
name: Hauk, Armin
name: Walter, Ulrich
name: Sieber, Robert
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular 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: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Honey samples from Switzerland were investigated with regard to their microplastic particle burden. Five representative honey samples of different origin were processed following a standardized protocol to separate plastic-based microparticles from particles of natural origin, such as pollen, propolis, wax, and bee-related debris. The procedure was optimized to minimize post-sampling microplastic cross-contamination in the laboratory. The isolated microplastic particles were characterized and grouped by means of light microscopy as well as chemically characterized by microscopically coupled Raman and Fourier transform infrared spectroscopy. Five particle classes with an abundance significantly above blank levels were identified: black particles (particle count between 1760/kg and 8680/kg), white transparent fibres (particle count between 132/kg and 728/kg), white transparent particles (particle count between 60/kg and 172/kg), coloured fibres (particle count between 32/kg and 108/kg), and coloured particles (particle count between 8/kg and 64/kg). The black particles, which represented the majority of particles, were identified as char or soot and most probably originated from the use of smokers, a widespread practice in beekeeping. The majority of fibres were identified as cellulose or polyethylene terephthalate and were most likely of textile origin. In addition to these particle and fibre groups lower numbers of fragments were detected that were related to glass, polysaccharides or chitin, and few bluish particles contained copper phthalocyanine pigment. We found no indications that the honey samples were significantly contaminated with microplastic particles.
MOESM1 of Patient-derived xenografts of different grade gliomas retain the heterogeneous histological and genetic features of human gliomas
Creators: name: Zeng, Wenxin
name: Tang, Zhaohua
name: Li, Yongguo
name: Yin, Guangnian
name: Liu, Zili
name: Gao, Jie
name: Chen, Yan
name: Chen, Feilan
Publisher: name: figshare
Year: 2020
Subjects: subject: Space Science
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Marine Biology
subject: Cancer

description: Additional file 1: Table S1. Semi-quantitative analysis of immunehistochemistry of primary tumors and xenograft tumors.