cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Optical Nanoscopy of High-Tc Cuprate Nano-Constriction Devices Patterned by Helium Ion Beams
Creators: name: Gozar, Adrian
name: Litombe, Nicholas E.
name: Hoffman, Jennifer E.
name: Bozovic, Ivan
Publisher: name: arXiv
Year: 2017
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Helium-ion beams (HIB) focused to sub-nanometer scales have emerged as powerful tools for high-resolution imaging as well as nano-scale lithography, ion milling or deposition. Quantifying irradiation effects is essential for reliable device fabrication but most of the depth profiling information is provided by computer simulations rather than experiment. Here, we use atomic force microscopy (AFM) combined with scanning near-field optical microscopy (SNOM) to provide three-dimensional (3D) dielectric characterization of high-temperature superconductor devices fabricated by HIB. By imaging the infrared dielectric response we find that amorphization caused by the nominally 0.5 nm HIB extends throughout the entire 26.5 nm thickness of the cuprate film and by about 500 nm laterally. This unexpectedly widespread structural and electronic damage can be attributed to a Helium depth distribution substantially modified by internal device interfaces. Our study introduces AFM-SNOM as a quantitative nano-scale tomographic technique for non-invasive 3D characterization of irradiation damage in a wide variety of devices.
description: 9 pages, 5 figures
Asymptotically flat black holes in Horndeski theory and beyond
Creators: name: Babichev, Eugeny
name: Charmousis, Christos
name: Lehébel, Antoine
Publisher: name: arXiv
Year: 2017
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We find spherically symmetric and static black holes in shift-symmetric Horndeski and beyond Horndeski theories. They are asymptotically flat and sourced by a non trivial static scalar field. The first class of solutions is constructed in such a way that the Noether current associated with shift symmetry vanishes, while the scalar field cannot be trivial. This in certain cases leads to hairy black hole solutions (for the quartic Horndeski Lagrangian), and in others to singular solutions (for a Gauss-Bonnet term). Additionally, we find the general spherically symmetric and static solutions for a pure quartic Lagrangian, the metric of which is Schwarzschild. We show that under two requirements on the theory in question, any vacuum GR solution is also solution to the quartic theory. As an example, we show that a Kerr black hole with a non-trivial scalar field is an exact solution to these theories.
description: 21 pages, 2 figures
An extension of model selection curves framework to accelerated failure time models
Creators: name: Karami, Md Jamil Hasan
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: In most existing model selection criteria, a constant penalty multiplier is usually paired with a penalty function. A model selection criterion based on a single value of penalty multiplier, such as Akaike information criterion (AIC) and Bayesian information criterion (BIC), can be "unstable" as a different model may be selected if the penalty multiplier changes even by a small arbitrary amount. This thesis extends a recently developed model selection approach for (generalised) linear models, known as model selection curves (MSC), to accelerated failure time (AFT) models for survival data. In this approach, penalty multiplier in a predetermined range, instead of a single value, is considered. Model selection criteria based on this approach are thus considered more stable as the selected model is the least likely not to be selected even when the penalty multiplier changes. In addition to the two recently introduced longest cathetus criterion and longest hypotenuse criterion, a new criterion, called the triangle area criterion, is proposed in this thesis. Under some conditions, these three criteria are consistent in selecting a specified AFT model, similar to BIC. It is shown that the consistency result seems to hold even when sample size is only reasonably large using simulations. A model selection framework including these three MSC based criteria, as well as BIC and AIC, is proposed for AFT models of survival data. The framework was investigated through simulations considering survival data of various sizes and censoring proportions from different specified models. Moreover, the performance of those model selection criteria based on the MSC was examined in comparison to AIC and BIC. The results indicate that those criteria have the potential to outperform AIC and BIC in selecting the correct model. The model selection framework has also been applied to several real world survival data. A tool in R program is developed to visualise the results from applying the framework.
Searching for distant galaxy clusters in the XMM-XXL southern field using deep Z-band images from DECam
Creators: name: Gardner, David Brinson
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: We present a high-redshift galaxy cluster candidate catalogue created using two galaxy based detection methods: z' and 3.6 μm red sequence method and the Stellar Bump Sequence method. This utilises new z' band observations from the dark energy camera on the 8 m Blanco telescope in CTIO, Chile, in addition to mid-infrared Spitzer observations from the SSDF survey. These observations have 5σ sensitivity limits of 24.4, 21.8 and 21.5 ABmagnitude in z', 3.6 μm and 4.5 μm bands respectively. We create an aperture corrected z' band catalogue which is cross-referenced with an existing aperture corrected Spitzer 3.6 μm and 4.5 μm catalogue, to produce a catalogue containing 2,137,515 unique objects in the XXL-S field. We then use custom redshifted BC03 stellar population models to simulate the galactic red sequence, that we use to match observed colours created from the three bands used. By assigning redshifts based on colours to objects in our catalogue, we are able to create a spatial density map which we then analyse to look for overdensities of galaxies. Finally, we present a catalogue that contains 802 candidate galaxy clusters in the redshiftrange 0:4 < z < 2:1, of which 721 are new detections. We also detect 32 spectroscopically confirmed X-ray selected galaxy clusters at redshifts up to z = 0:87.
Animacy effects on the processing of intransitive verbs: an eye-tracking study
Creators: name: Vernice, Mirta
name: Sorace, Antonella
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: This paper tested an assumption of the gradient model of split intransitivity put forward by Sorace (“Split Intransitivity Hierarchy” (SIH), 2000, 2004), namely that agentivity is a fundamental feature for unergatives but not for unaccusatives. According to this hypothesis, the animacy of the verb’s argument should affect the processing of unergative verbs to a greater extent than unaccusative verbs. By using eye-tracking methodology we monitored the online processing and integration costs of the animacy of the verb’s argument in intransitive verbs. We observed that inanimate subjects caused longer reading times only for unergative verbs, whereas the animacy of the verb’s argument did not influence the pattern of results for unaccusatives. In addition, the unergative verb data directly support the existence of gradient effects on the processing of the subject argument.
Additional file 4 of Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut
Creators: name: Yuan, Cuiling
name: Li, Chunjuan
name: Lu, Xiaodong
name: Zhao, Xiaobo
name: Yan, Caixia
name: Wang, Juan
name: Sun, Quanxi
name: Shan, Shihua
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 4. mRNA sequence of NAC genes from cultivated peanut.
Hierarchical Fully Convolutional Network for Joint Atrophy Localization and Alzheimer's Disease Diagnosis Using Structural MRI
Creators: name: Liu, Mingxia
name: Zhang, Jun
name: Shen, Dinggang
name: Lian, Chunfeng
Publisher: name: Institute of Electrical and Electronics Engineers (IEEE)
Year: 2018

description: Structural magnetic resonance imaging (sMRI) has been widely used for computer-aided diagnosis of neurodegenerative disorders, e.g., Alzheimer's disease (AD), due to its sensitivity to morphological changes caused by brain atrophy. Recently, a few deep learning methods (e.g., convolutional neural networks, CNNs) have been proposed to learn task-oriented features from sMRI for AD diagnosis, and achieved superior performance than the conventional learning-based methods using hand-crafted features. However, these existing CNN-based methods still require the pre-determination of informative locations in sMRI. That is, the stage of discriminative atrophy localization is isolated to the latter stages of feature extraction and classifier construction. In this paper, we propose a hierarchical fully convolutional network (H-FCN) to automatically identify discriminative local patches and regions in the whole brain sMRI, upon which multi-scale feature representations are then jointly learned and fused to construct hierarchical classification models for AD diagnosis. Our proposed H-FCN method was evaluated on a large cohort of subjects from two independent datasets (i.e., ADNI-1 and ADNI-2), demonstrating good performance on joint discriminative atrophy localization and brain disease diagnosis.
Nature and enactment of tasks for early English as a foreign language teaching (EFLT): a collaborative research project with teachers in Germany
Creators: name: Dreßler, Constanze R.
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: The ethnographic PhD case study is set within a collaborative research project in which teachers and researchers investigate early English as a foreign language (eEFL) tasks. Seven eEFL teachers from five project primary schools (PS) with students aged 6-10 years, in central urban Germany have been followed over a period of five years teaching eEFL in Grades 1-4 with a majority of Grade 4 classes. The research foci lie on: (i) the nature of eEFL tasks based on the academic conceptualisations of tasks and on the teachers' concepts of tasks to meaningfully integrate the theoretical and practical perspective; (ii) and on the teachers' task enactments that have been analysed with a multimodal and Mediated Discourse Analysis approach. The conceptualisation of the research focus poses the investigation of eEFL tasks at the centre of texts, accounts and discursive practices. This draws on the idea that social realities are constructed, insight is context-bound and views discourse as social action in which meaning is produced in interaction. Such an interdiscursive conceptualisation asks for an interdiscursive approach drawing on different data types (e.g., interviews, video recordings, observation protocols) being analysed with different methods. Results show that for eEFL tasks a strong emphasis on the students' personal interests may be beneficial to allow the young learners to experience English as a means of communication. It was found that the teachers used basic and elaborate task formats with a focus on role-plays, interviews, poster presentations or story reconstructions.Moreover, the results suggest that the often described difference between a task-as-workplan and task-as-action is also true for the eEFL classroom. Further, it can be assumed that eEFL tasks can emerge within a certain interplay of four key teaching practices of teachers:'doing school', 'providing space for learners to communicate', 'building a vocabulary' and 'teaching the spoken language'.
title: ADCO, Cinquième cartulaire de Saint-Étienne de Dijon (1664), Cart. 28 (G 132), 258 folios, f. 00180
Creators: name: de la Côte d'Or, Archives départementales
name: Petot, Frédéric
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2012
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: cartulaire
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: Cinquième cartulaire de Saint-Étienne de Dijon (1664), Archives départementales de la Côte-d'Or, Cart. 28 (G 132), 258 folios, f. 00180, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cinquième cartulaire de Saint-Étienne de Dijon (1664), Archives départementales de la Côte-d'Or, Cart. 28 (G 132), 258 folios, f. 00180, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https://manuscrits.cbma-project.eu/
description: Provenance: abbaye Saint-Étienne de Dijon
description: Provenance: http://www.wikidata.org/entity/Q15945019
Complete elimination of nonlinear light-matter interactions with broadband ultrafast laser pulses
Creators: name: Shu, Chuan-Cun
name: Dong, Daoyi
name: Petersen, Ian R.
name: Henriksen, Niels E.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: Atomic Physics (physics.atom-ph)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: The absorption of a single photon that excites a quantum system from a low to a high energy level is an elementary process of light-matter interaction, and a route towards realizing pure single-photon absorption has both fundamental and practical implications in quantum technology. Due to nonlinear optical effects, however, the probability of pure single-photon absorption is usually very low, which is particularly pertinent in the case of strong ultrafast laser pulses with broad bandwidth. Here we demonstrate theoretically a counterintuitive coherent single-photon absorption scheme by eliminating nonlinear interactions of ultrafast laser pulses with quantum systems. That is, a completely linear response of the system with respect to the spectral energy density of the incident light at the transition frequency can be obtained for all transition probabilities between 0 and 100% in a multi-level quantum systems. To that end, a new multi-objective optimization algorithm is developed to find an optimal spectral phase of an ultrafast laser pulse, which is capable of eliminating all possible nonlinear optical responses while maximizing the probability of single-photon absorption between quantum states. This work not only deepens our understanding of light-matter interactions, but also offers a new way to study photophysical and photochemical processes in the "absence" of nonlinear optical effects.
description: 11 pages, 5 figures
The children's acquisition of shenme in Mandarin Chinese
Creators: name: Liao, Min
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Mandarin Chinese is known as an in-situ language. In Mandarin, wh-questions are not formed by displacing wh-phrases, as in English. Rather, Mandarin wh-phrases remain in their argument positions in the surface syntax. Attesting to this characterization of Mandarin is the fact that wh-words can be used both to ask questions and to make statements. In statements, the wh-word shenme ‘what’ is similar in meaning to the existential expression renhe (English ‘any’), and it is semantically related to the disjunction word huozhe (English ‘or’). This thesis explores Mandarin-speaking children’s interpretations of the wh-word shenme ‘what’ by comparing its interpretation to that of renhe ‘any’ and huozhe ‘or’ in three formally distinct linguistic contexts. The distributional and interpretive patterns of these expressions are used in a series of experimental investigations to assess children’s knowledge of the semantic properties of these contexts. In one set of (upward entailing) contexts, shenme ‘what’ is a question marker, renhe ‘any’ is prohibited, and the disjunction word huozhe ‘or’ has disjunctive truth conditions. In the second set of contexts (downward entailing, but not antiadditive), shenme remains a question marker, and huozhe continues to be assigned disjunctive truth conditions; however, renhe is permitted in these contexts. The third set of (downward entailing, anti-additive) contexts includes the Mandarin adverbial quantifier dou ‘all.’ In such contexts, shenme, renhe, and huozhe are all licensed, but they yield a ‘conjunctive’ meaning that is different in character from the meanings of these expressions in the other linguistic contexts. Despite this intricate pattern, the findings from the experimental studies demonstrated Mandarin-speaking children’s mastery of the semantics of shenme, renhe and huozhe. The findings are interpreted as evidence of the linguistic competence by young children to compose the complex meanings of sentences with multiple logical expressions. This study offers new data on the acquisition of logical expressions, and reveals the importance of the principles of linguistic theory, and logic, in explaining the course of child language development. The study also sheds new light on the special linguistic properties of Mandarin.
Hierarchical High-Order Functional Connectivity Networks and Selective Feature Fusion for MCI Classification
Creators: name: Zhang, Han
name: Shen, Dinggang
name: the Alzheimer's Disease Neuroimaging Initiative
name: Chen, Xiaobo
name: Lee, Seong-Whan
Publisher: name: Springer Nature
Year: 2017

description: Conventional Functional connectivity (FC) analysis focuses on characterizing the correlation between two brain regions, whereas the high-order FC can model the correlation between two brain region pairs. To reduce the number of brain region pairs, clustering is applied to group all the brain region pairs into a small number of clusters. Then, a high-order FC network can be constructed based on the clustering result. By varying the number of clusters, multiple high-order FC networks can be generated and the one with the best overall performance can be finally selected. However, the important information contained in other networks may be simply discarded. To address this issue, in this paper, we propose to make full use of the information contained in all high-order FC networks. First, an agglomerative hierarchical clustering technique is applied such that the clustering result in one layer always depends on the previous layer, thus making the high-order FC networks in the two consecutive layers highly correlated. As a result, the features extracted from high-order FC network in each layer can be decomposed into two parts (blocks), i.e., one is redundant while the other might be informative or complementary, with respect to its previous layer. Then, a selective feature fusion method, which combines sequential forward selection and sparse regression, is developed to select a feature set from those informative feature blocks for classification. Experimental results confirm that our novel method outperforms the best single high-order FC network in diagnosis of mild cognitive impairment (MCI) subjects.
Additional file 9 of Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut
Creators: name: Yuan, Cuiling
name: Li, Chunjuan
name: Lu, Xiaodong
name: Zhao, Xiaobo
name: Yan, Caixia
name: Wang, Juan
name: Sun, Quanxi
name: Shan, Shihua
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 9. Exon-intron structure comparison between AdNAC59, AdNAC80, AdNAC81 and their orthologues AiNAC59, AiNAC9, AiNAC29.
Lipidomics reveal aryl hydrocarbon receptor (Ahr)-regulated lipid metabolic pathway in alpha-naphthyl isothiocyanate (ANIT)-induced intrahepatic cholestasis
Creators: name: Wang, Bao-Long
name: Zhang, Chang-Wen
name: Wang, Liang
name: Tang, Kun-Long
name: Tanaka, Naoki
name: Gonzalez, Frank J.
name: Xu, Yong
name: Fang, Zhong-Ze
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Biotechnology
subject: Evolutionary Biology
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Mental Health
subject: Computational Biology

description: 1. Ultra-performance liquid chromatography coupled with electrospray ionization quadrupole mass spectrometry (UPLC-ESI-QTOF MS)-based lipidomics was employed to elucidate new mechanism of alpha-naphthyl isothiocyanate (ANIT)-induced intrahepatic cholestasis in mice. 2. Multiple lipid components significantly increased in ANIT-induced intrahepatic cholestasis, including PC 16:0, 20:4, PC 16:0, 22:6, PC 16:0, 18:2, LPC 18:2, PC 18:2, LPC 18:1, PC 18:1, 14:0, SM 18:1, 16:0, oleoylcarnitine and palmitoylcarnitine. This alteration of lipid profile was induced by the changed expression of genes choline kinase (Chk) a, sphingomyelin phosphodiesterase (SMPD) and stearoyl-coenzyme A desaturase 1 (SCD1). 3. Knockout of aryl hydrocarbon receptor (Ahr) in mice can significantly reverse ANIT-induced intrahepatic cholestasis, as indicated by lowered ALT, AST and ALP activity, and liver histology. Aryl hydrocarbon receptor knockout significantly reversed ANIT-induced lipid metabolism alteration through regulating the expression of Chka. 4. In conclusion, this study demonstrated ANIT-induced lipid metabolism disruption might be the potential pathogenesis of ANIT-induced intrahepatic cholestasis in mice.
A dynamical model for FR II type radio sources with terminated jet activity
Creators: name: Kuligowska, Elżbieta
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The extension of the KDA analytical model of FR II-type source evolution originally assuming a continuum injection process in the jet-IGM (intergalactic medium) interaction towards a case of the jet's termination is presented and briefly discussed. The dynamical evolution of FR II-type sources predicted with this extended model, hereafter referred to as KDA EXT, and its application to the chosen radio sources. Following the classical approach based on the source's continuous injection and self-similarity, I propose the effective formulae describing the length and luminosity evolution of the lobes during an absence of the jet flow, and present the resulting diagrams for the characteristics mentioned. Using an algorithm based on the numerical integration of a modified formula for jet power, the KDA EXT model is fitted to three radio galaxies. Their predicted spectra are then compared to the observed spectra, proving that these fits are better than the best spectral fit provided by the original KDA model of the FR II-type sources dynamical evolution.
title: Funérailles du duc Philippe le Bon - Archives départementales de la Côte-d'Or, B 310
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2022
Subjects: subject: LaMOP
subject: Laboratoire de médiévistique occidentale de Paris

description: Relation du déroulement des funérailles du duc Philippe Le Bon (juin 1467)
Archives départementales de la Côte-d’Or, B 310
Document transcrit dans le cadre des ateliers de paléographie du Chancelier Rolin des Archives départements des Côtes d’Or
description: Source: https://archives.cotedor.fr/v2/site/AD21/web/media/04_apprendre/02_ateliers_chancelier_rolin/paleographie/debutants/2013_2014/document_03.pdf
description: Source: https://www.nakala.fr/10.34847/nkl.3efd78ft
description: Funérailles du duc Philippe le Bon - Archives départementales de la Côte-d'Or, B 310
How do the properties of training scenarios influence the robustness of reservoir operating policies to climate uncertainty?
Creators: name: Zeff, Harrison B.
name: Cohen, Jonathan S.
name: Herman, Jonathan D.
Publisher: name: Elsevier
Year: 2021

description: Reservoir control policies provide a flexible option to adapt to the uncertain hydrologic impacts of climate change. This challenge requires robust policies capable of navigating scenarios that are wetter, drier, or more variable than anticipated. While a number of prior studies have trained robust policies using large scenario ensembles, there remains a need to understand how the properties of training scenarios impact policy robustness. Specifically, this study investigates scenario properties including annual runoff, snowpack, and baseline regret - the difference between baseline policy and perfect foresight performance in an individual scenario. Results indicate that policies trained to scenario subsets with high baseline regret outperform those generated with other training sets in both wetter and drier futures, largely by adopting an intra-annual hedging strategy. The approach highlights the potential to improve the efficiency and robustness of policy training by considering both the hydrologic properties and baseline regret of the training ensemble.
Waves and ﬂuid-solid interaction in stented blood vessels - Supplementary material from Waves and fluid–solid interaction in stented blood vessels
Creators: name: S. Frecentese
name: L. P. Argani
name: A. B. Movchan
name: N. V. Movchan
name: G. Carta
name: M. L. Wall
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Mechanics
subject: 90399 Biomedical Engineering not elsewhere classified
subject: FOS: Medical engineering
subject: 10299 Applied Mathematics not elsewhere classified
subject: FOS: Mathematics

description: In the Supplementary material the dispersion curves for different types of stents and deformation modes are presented.
Bayesian equilibria of axisymmetric plasmas
Creators: name: Kwak, Sehyun
name: Svensson, J.
name: Ford, O.
name: Appel, L.
name: Ghim, Y. -c.
name: Contributors, JET
Publisher: name: arXiv
Year: 2021
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: We present a Bayesian method for inferring axisymmetric plasma equilibria from the magnetic field and plasma pressure measurements. The method calculates all possible solutions for plasma current and pressure distributions consistent with the measurements and magnetohydrodynamic (MHD) force balance. Toroidal plasma current and magnetic field coils are modelled as a set of axisymmetric current-carrying solid beams. The other parameters such as plasma pressure and poloidal current flux are given as a function of poloidal magnetic flux, which is determined given a 2D current distribution. Plasma pressure and poloidal current flux profiles are modelled as Gaussian processes whose smoothness is optimally chosen based on the principle of Occam's razor. To find equilibrium solutions, we introduce an MHD force balance constraint at every plasma current beam as a part of the prior knowledge. Given all these physical quantities, predictions calculated by the predictive (forward) models for diagnostics are compared to the observations. The high dimensional complex posterior probability distribution is explored by a new algorithm based on the Gibbs sampling scheme.
Human CD22 Inhibits Murine B Cell Receptor Activation in a Human CD22 Transgenic Mouse Model
Creators: name: Fung-Leung, Wai-Ping
name: Connors, Edward P
name: Ballet, Romain
name: Butcher, Eugene C
name: Kulis, Michael D
name: Macauley, Matthew S
name: Shanina, Elena
name: Paulson, James C
name: Bednar, Kyle J
name: Arlian, Britni M
name: Juan, Joana
name: Duan, Shiteng
name: Rao, Tadimeti S
Publisher: name: The American Association of Immunologists
Year: 2017

description: CD22, a sialic acid-binding Ig-type lectin (Siglec) family member, is an inhibitory coreceptor of the BCR with established roles in health and disease. The restricted expression pattern of CD22 on B cells and most B cell lymphomas has made CD22 a therapeutic target for B cell-mediated diseases. Models to better understand how in vivo targeting of CD22 translates to human disease are needed. In this article, we report the development of a transgenic mouse expressing human CD22 (hCD22) in B cells and assess its ability to functionally substitute for murine CD22 (mCD22) for regulation of BCR signaling, Ab responses, homing, and tolerance. Expression of hCD22 on transgenic murine B cells is comparable to expression on human primary B cells, and it colocalizes with mCD22 on the cell surface. Murine B cells expressing only hCD22 have identical calcium (Ca2+) flux responses to anti-IgM as mCD22-expressing wild-type B cells. Furthermore, hCD22 transgenic mice on an mCD22-/- background have restored levels of marginal zone B cells and Ab responses compared with deficiencies observed in CD22-/- mice. Consistent with these observations, hCD22 transgenic mice develop normal humoral responses in a peanut allergy oral sensitization model. Homing of B cells to Peyer's patches was partially rescued by expression of hCD22 compared with CD22-/- B cells, although not to wild-type levels. Notably, Siglec-engaging antigenic liposomes formulated with an hCD22 ligand were shown to prevent B cell activation, increase cell death, and induce tolerance in vivo. This hCD22 transgenic mouse will be a valuable model for investigating the function of hCD22 and preclinical studies targeting hCD22.
Expanding FLew with a Boolean connective
Creators: name: Ertola-Biraben, Rodolfo C.
name: Esteva, Francesc
name: Godo, Lluís
Publisher: name: arXiv
Year: 2016
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics

description: We expand FLew with a unary connective whose algebraic counterpart is the operation that gives the greatest complemented element below a given argument. We prove that the expanded logic is conservative and has the Finite Model Property. We also prove that the corresponding expansion of the class of residuated lattices is an equational class.
description: 15 pages, 4 figures in Soft Computing, published online 23 July 2016
Additional file 1 of Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences
Creators: name: Jiang, Yuji
name: Luan, Lu
name: Hu, Kaijie
name: Liu, Manqiang
name: Chen, Ziyun
name: Geisen, Stefan
name: Chen, Xiaoyun
name: Li, Huixin
name: Xu, Qinsong
name: Bonkowski, Michael
name: Sun, Bo
Publisher: name: figshare
Year: 2020
Subjects: subject: Plant Biology
subject: FOS: Biological sciences

description: Additional file 1: Fig. S1. Soil characteristics in the rhizosphere under manure treatments. Fig. S2. The alkaline and acid phosphomonoesterase activity in the rhizosphere under manure treatments. Fig. S3. The structure of arbuscular mycorrhizal fungi, fungivorous protist and nematode communities by principal coordinate analysis. Fig. S4. The ratios of arbuscular mycorrhizal fungi to plant biomass and fungivorous nematodes to plant biomass. Fig. S5. Correlation coefficients between arbuscular mycorrhizal fungi (AMF) community (biomass, diversity, and composition), fungivorous protists and nematodes, ALP activity, AMF colonization and the expression of ZMPht1;6 gene. Fig. S6. Mean contribution of soil variables, arbuscular mycorrhizal fungi (AMF) community, protists, and nematodes to AMF colonization and expression of P transporter gene ZMPht1;6 based on random forest modelling. Table S1. The characteristics of fine roots under four manure treatments.
Human Immunodeficiency Virus Treatment and Prevention for Pregnant and Postpartum Women in Global Settings
Creators: name: Chi, Benjamin H
name: Saidi, Friday
Publisher: name: Elsevier
Year: 2022

description: Efforts to prevent mother-to-child transmission of human immunodeficiency virus (HIV) have led to dramatic reductions in pediatric HIV worldwide. New advances in HIV treatment and prevention, focused on pregnant and breastfeeding women living with HIV, have improved maternal health while decreasing vertical and horizontal HIV transmission. In this article, we describe how such interventions-including antiretroviral therapy and HIV pre-exposure prophylaxis-can be incorporated into antepartum and postpartum care in global settings.
Figure S1 from Overcoming hydrodynamic challenges in suspension feeding by juvenile Mya arenaria clams.
Creators: name: Clos, Kevin T. Du
name: Houshuo Jiang
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: 110601 Biomechanics
subject: FOS: Health sciences

description: Exhalant velocities plotted against distance from the center of the exhalant siphon outlet. Each line represents a single, manually-tracked particle. Results are from one video sequence (200 frames).
Additional file 1 of Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut
Creators: name: Yuan, Cuiling
name: Li, Chunjuan
name: Lu, Xiaodong
name: Zhao, Xiaobo
name: Yan, Caixia
name: Wang, Juan
name: Sun, Quanxi
name: Shan, Shihua
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. mRNA sequence of NAC genes from two wild peanuts.
Robust Estimation of Scattering in Pulsar Timing Analysis
Creators: name: Lentati, L.
name: Kerr, M.
name: Dai, S.
name: Shannon, R. M.
name: Hobbs, G.
name: Oslowski, S.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present a robust approach to incorporating models for the time-variable broadening of the pulse profile due to scattering in the ionized interstellar medium into profile-domain pulsar timing analysis. We use this approach to simultaneously estimate temporal variations in both the dispersion measure (DM) and scattering, together with a model for the pulse profile that includes smooth evolution as a function of frequency, and the pulsar's timing model. We show that fixing the scattering timescales when forming time-of-arrival estimates, as has been suggested in the context of traditional pulsar timing analysis, can significantly underestimate the uncertainties in both DM, and the arrival time of the pulse, leading to bias in the timing parameters. We apply our method using a new, publicly available, GPU accelerated code, both to simulations, and observations of the millisecond pulsar PSR J1643$-$1224. This pulsar is known to exhibit significant scattering variability compared to typical millisecond pulsars, and we find including low-frequency ($< 1$ GHz) data without a model for these scattering variations leads to significant periodic structure in the DM, and also biases the astrometric parameters at the $4σ$ level, for example, changing proper motion in right ascension by $0.50 \pm 0.12$. If low frequency observations are to be included when significant scattering variations are present, we conclude it is necessary to not just model those variations, but also to sample the parameters that describe the variations simultaneously with all other parameters in the model, a task for which profile domain pulsar timing is ideally suited.
description: 12 pages, 6 figures, Accepted to MNRAS
Identifying Autism Spectrum Disorder With Multi-Site fMRI via Low-Rank Domain Adaptation
Creators: name: Huang, Jiashuang
name: Liu, Mingxia
name: Yap, Pew-Thian
name: Wang, Mingliang
name: Zhang, Daoqiang
name: Shen, Dinggang
Publisher: name: Institute of Electrical and Electronics Engineers (IEEE)
Year: 2019

description: Autism spectrum disorder (ASD) is a neurodevelopmental disorder that is characterized by a wide range of symptoms. Identifying biomarkers for accurate diagnosis is crucial for early intervention of ASD. While multi-site data increase sample size and statistical power, they suffer from inter-site heterogeneity. To address this issue, we propose a multi-site adaption framework via low-rank representation decomposition (maLRR) for ASD identification based on functional MRI (fMRI). The main idea is to determine a common low-rank representation for data from the multiple sites, aiming to reduce differences in data distributions. Treating one site as a target domain and the remaining sites as source domains, data from these domains are transformed (i.e., adapted) to a common space using low-rank representation. To reduce data heterogeneity between the target and source domains, data from the source domains are linearly represented in the common space by those from the target domain. We evaluated the proposed method on both synthetic and real multi-site fMRI data for ASD identification. The results suggest that our method yields superior performance over several state-of-the-art domain adaptation methods.
A strongly correlated metal built from Sachdev-Ye-Kitaev models
Creators: name: Song, Xue-Yang
name: Jian, Chao-Ming
name: Balents, Leon
Publisher: name: arXiv
Year: 2017
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Strongly correlated metals comprise an enduring puzzle at the heart of condensed matter physics. Commonly a highly renormalized heavy Fermi liquid occurs below a small coherence scale, while at higher temperatures a broad incoherent regime pertains in which quasi-particle description fails. Despite the ubiquity of this phenomenology, strong correlations and quantum fluctuations make it challenging to study. The Sachdev-Ye-Kitaev(SYK) model describes a $0+1$D quantum cluster with random all-to-all \emph{four}-fermion interactions among $N$ Fermion modes which becomes exactly solvable as $N\rightarrow \infty$, exhibiting a zero-dimensional non-Fermi liquid with emergent conformal symmetry and complete absence of quasi-particles. Here we study a lattice of complex-fermion SYK dots with random inter-site \emph{quadratic} hopping. Combining the imaginary time path integral with \emph{real} time path integral formulation, we obtain a heavy Fermi liquid to incoherent metal crossover in full detail, including thermodynamics, low temperature Landau quasiparticle interactions, and both electrical and thermal conductivity at all scales. We find linear in temperature resistivity in the incoherent regime, and a Lorentz ratio $L\equiv \frac{κρ}{T}$ varies between two universal values as a function of temperature. Our work exemplifies an analytically controlled study of a strongly correlated metal.
description: 17 pages, 6 figures
Cosmography and Data Visualization
Creators: name: Pomarede, Daniel
name: Courtois, Helene M.
name: Hoffman, Yehuda
name: Tully, R. Brent
Publisher: name: arXiv
Year: 2017
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Cosmography, the study and making of maps of the universe or cosmos, is a field where visual representation benefits from modern three-dimensional visualization techniques and media. At the extragalactic distance scales, visualization is contributing in understanding the complex structure of the local universe, in terms of spatial distribution and flows of galaxies and dark matter. In this paper, we report advances in the field of extragalactic cosmography obtained using the SDvision visualization software in the context of the Cosmicflows Project. Here, multiple visualization techniques are applied to a variety of data products: catalogs of galaxy positions and galaxy peculiar velocities, reconstructed velocity field, density field, gravitational potential field, velocity shear tensor viewed in terms of its eigenvalues and eigenvectors, envelope surfaces enclosing basins of attraction. These visualizations, implemented as high-resolution images, videos, and interactive viewers, have contributed to a number of studies: the cosmography of the local part of the universe, the nature of the Great Attractor, the discovery of the boundaries of our home supercluster of galaxies Laniakea, the mapping of the cosmic web, the study of attractors and repellers.
description: Accepted for publication in the PASP Special Focus Issue: Techniques and Methods for Astrophysical Data Visualization
Additional file 2 of Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut
Creators: name: Yuan, Cuiling
name: Li, Chunjuan
name: Lu, Xiaodong
name: Zhao, Xiaobo
name: Yan, Caixia
name: Wang, Juan
name: Sun, Quanxi
name: Shan, Shihua
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2. gDNA sequence of NAC genes from two wild peanuts
Bayesian modelling of multiple plasma diagnostics at Wendelstein 7-X
Creators: name: Kwak, Sehyun
name: Svensson, J.
name: Bozhenkov, S.
name: Mora, H. Trimino
name: Hoefel, U.
name: Pavone, A.
name: Krychowiak, M.
name: Langenberg, A.
name: Ghim, Y. -c.
name: Team, W7-X
Publisher: name: arXiv
Year: 2021
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Consistent inference of the electron density and temperature has been carried out with multiple heterogeneous plasma diagnostic data sets at Wendelstein 7-X. The predictive models of the interferometer, Thomson scattering and helium beam emission spectroscopy systems have been developed in the Minerva framework and combined to a single joint model. The electron density and temperature profiles are modelled by Gaussian processes with their hyperparameters. The model parameters such as the calibration factor of the Thomson scattering system and the model predictive uncertainties are regarded as additional unknown parameters. The joint posterior probability distribution of the electron density and temperature profiles, hyperparameters of the Gaussian processes and model parameters is explored by Markov chain Monte Carlo algorithms. The posterior samples drawn from the joint posterior distribution are numerically marginalised over the hyperparameters and model parameters to obtain the marginal posterior distributions of the electron density and temperature profiles. The inference of these profiles is performed with different combinations of the interferometer and Thomson scattering data as well as either the empirical electron density and temperature constraints at the limiter/divertor positions introduced by \textit{virtual observations} or the edge density and temperature from the helium beam emission data. Furthermore, the addition of the X-ray imaging crystal spectrometers to the joint model for the ion temperature profiles is demonstrated. All these profiles presented in this work are inferred with the optimal hyperparameters and model parameters by exploring the full joint posterior distribution which intrinsically embodies Bayesian Occam's razor.
Identifying robust adaptive irrigation operating policies to balance deeply uncertain economic food production and groundwater sustainability trade-offs
Creators: name: Reed, Patrick M
name: Zeff, Harrison B
name: Rodríguez-Flores, José M.
name: Medellín-Azuara, Josué
name: Gupta, Rohini S
Publisher: name: Elsevier
Year: 2023

description: Increasing irrigation demand has heavily relied on groundwater use, especially in places with highly variable water supplies that are vulnerable to drought. Groundwater management in agriculture is becoming increasingly challenging given the growing effects from overdraft and groundwater depletion worldwide. However, multiple challenges emerge when seeking to develop sustainable groundwater management in irrigated systems, such as trade-offs between the economic revenues from food production and groundwater resources, as well as the broad array of uncertainties in food-water systems. In this study we explore the applicability of Evolutionary Multi-Objective Direct Policy Search (EMODPS) to identify adaptive irrigation policies that water agencies and farmers can implement including operational decisions related to land use and groundwater use controls as well as groundwater pumping fees. The EMODPS framework yields state-aware, adaptive policies that respond dynamically as system state conditions change, for example with variable surface water (e.g., shifting management strategies across wet versus dry years). For this study, we focus on the Semitropic Water Storage district located in the San Joaquin Valley, California to provide broader insights relevant to ongoing efforts to improve groundwater sustainability in the state. Our findings demonstrate that adaptive irrigation policies can achieve sufficiently flexible groundwater management to acceptably balance revenue and sustainability goals across a wide range of uncertain future scenarios. Among the evaluated policy decisions, pumping restrictions and reductions in inflexible irrigation demands from tree crops are actions that can support dry-year pumping while maximizing groundwater storage recovery during wet years. Policies suggest that an adaptive pumping fee is the most flexible decision to control groundwater pumping and land use.
Supplementary Tables from The functional highly sensitive brain: a review of the brain circuits underlying sensory processing sensitivity and seemingly related disorders
Creators: name: Acevedo, Bianca
name: Aron, Elaine
name: Pospos, Sarah
name: Jessen, Dana
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Neuroscience
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 60801 Animal Behaviour
subject: FOS: Biological sciences
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: S1: Comparison of Major Regional Neural Activation Patterns Reported in fMRI studies of Sensory Processing Sensitivity, Autism Spectrum Disorder, Post-traumatic Stress Disorder and Schizophrenia; S2: fMRI studies of Sensory Processing Sensitivity and Autism Spectrum Disorder examining brain responsivity to emotional stimuli
Probing QCD perturbation theory at high energies with continuum extrapolated lattice data
Creators: name: Sint, Stefan
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Precision tests of QCD perturbation theory are not readily available from experimental data. The main reasons are systematic uncertainties due to the confinement of quarks and gluons, as well as kinematical constraints which limit the accessible energy scales. We here show how continuum extrapolated lattice data may overcome such problems and provide excellent probes of renormalized perturbation theory. This work corresponds to an essential step in the ALPHA collaboration's project to determine the $Λ$-parameter in 3-flavour QCD. I explain the basic techniques used in the high energy regime, namely the use of mass-independent renormalization schemes for the QCD coupling constant in a finite Euclidean space time volume. When combined with finite size techniques this allows one to iteratively step up the energy scale by factors of 2, thereby quickly covering two orders of magnitude in scale. We may then compare perturbation theory (with $β$-functions available up to 3-loop order) to our non-perturbative data for a 1-parameter family of running couplings. We conclude that a target precision of 3 percent for the $Λ$-parameter requires non-perturbative data up to scales where $α_s\approx 0.1$, whereas the apparent precision obtained from applying perturbation theory around $α_s \approx 0.2$ can be misleading. This should be taken as a general warning to practitioners of QCD perturbation theory.
description: 10 pages, 4 figures; contributed to XIIth Confinement and the Hadron Spectrum, Thessaloniki, 28 August - 4 September 2016, to appear in the proceedings