cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Introduction to JupyterLab
Creators: name: Girgin, S.
Publisher: name: Zenodo
Year: 2021
Subjects: jupyter
jupyterlab
training
interactive notebook
data science

description: Data analysis and computation by using interactive notebooks is becoming the new norm of data science for exploratory research, rapid prototyping, and education activities, especially for applications such as data mining, machine learning, and spatial analysis. Project Jupyter is one of the most common open-source software ecosystem for this purpose and JupyterLab is its new generation web-based interactive development environment for Jupyter notebooks, code, and data. This short training workshop organized by the Center of Expertise in Big Geodata Science (CRIB) aims to provide in-depth information and hands-on practice on JupyterLab including the following topics: User interface File management Viewers and editors Notebooks, code consoles, and terminals Editing notebooks Kernel management Extensions Remote desktop connection At the end of the training, you will have a better understanding on how to use JupyterLab and how to use it efficiently by following best practices.
description: For more information about the training please visit https://itc.nl/facillities/centres-of-expertise/big-geodata/training/introduction-to-jupyterlab/
Universal solvent restructuring induced by colloidal nanoparticles
Creators: name: Zobel, Mirijam
name: Neder, Reinhard B.
name: Kimber, Simon A. J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Colloidal nanoparticles, used for applications from catalysis and energy applications to cosmetics, are typically embedded in matrixes or dispersed in solutions. The entire particle surface, which is where reactions are expected to occur, is thus exposed. Here we show with x-ray pair distribution function analysis that polar and non-polar solvents universally restructure around nanoparticles. Layers of enhanced order exist with a thickness influenced by the molecule size and up to 2 nanometers beyond the nanoparticle surface. These results show that the enhanced reactivity of solvated nanoparticles includes a contribution from a solvation shell of the size of the particle itself.
description: Submitted version, published version has minor changes
Finding common ground: CSR and media responsibility
Creators: name: Bachmann, Philipp
name: Ingenhoff, Diana
Publisher: name: Zenodo
Year: 2017
Subjects: Corporate Social Responsibility
Media Ethics
Business Ethics

description: Media companies have a ‘dual responsibility’. For one, they produce and distribute media products intended to inform and entertain the population. This entails a set of duties that may be termed Media Responsibility (MR). On the other hand media companies, just like any other company, have to be profitable, as well as living up to social and ecological standards. These related duties may be designated Corporate Social Responsibility (CSR).
description: + ID der Publikation: hslu_75974 + Art des Beitrages: Buchkapitel/Beitrag in Sammelband + Herausgeberschaft: K.-D. Altmeppen; C. A. Hollifield; J. van Loon + Seiten: 147 - 157 + Sprache: Deutsch + Letzte Aktualisierung: 2020-06-25 11:28:37
Simple Derivation of the Lifetime and the Distribution of Faces for a Binary Subdivision Model
Creators: name: Hayashi, Yukio
Publisher: name: arXiv
Year: 2015
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Graphics (cs.GR)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: The iterative random subdivision of rectangles is used as a generation model of networks in physics, computer science, and urban planning. However, these researches were independent. We consider some relations in them, and derive fundamental properties for the average lifetime depending on birth-time and the balanced distribution of rectangle faces.
description: 2 figures
Valdivia, Gabriela, Matthew Himley, and Elizabeth Havice. Forthcoming. “Critical Resource Geography: An Introduction.” In The Routledge Handbook of Critical Resource Geography, edited by Matthew Himley, Elizabeth Havice, and Gabriela Valdivia. New York: Routledge.
Creators: name: Havice, Elizabeth
name: Valdivia, Gabriela
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2021

description: The Routledge Handbook of Critical Resource Geography offers a toolkit of critical, reflexive, and speculative approaches for studying resources and the socioecological systems with which they are co-constitutively entangled. This chapter introduces two fundamental ideas about critical resource geography that emerge from the Handbook’s contents: first, that the critical analysis of resource systems and their historical and contemporary geographies is integral for understanding the state of the world; second, that doing critical resource geography involves ongoing reflection on how, why, and for whom academic knowledge production about resources matters. To advance these propositions, this chapter situates the descriptor “critical” in critical resource geography and outlines key trajectories of intellectual-political analysis within this body of scholarship, organized around two thematic areas: “(Un)knowing the World of Resources” and “Unbounding the World of Resources.” Together, these sections outline a heuristic device, “resource-making/world-making,” that builds from and further develops relational forms of thinking central to resource geography. Then, the chapter provides an overview of the objectives and contents of the Handbook’s four main sections. Finally, the concluding section elaborates on the motivations that prompted this volume and invites readers to engage with the world of critical resource geography and the possibilities it presents.
Robustness of genuine tripartite entanglement under collective dephasing
Creators: name: Ali, Mazhar
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study robustness of genuine multipartite entanglement for a system of three qubits under collective dephasing. Using a computable entanglement monotone for multipartite systems, we found that almost every state is quite robust under this type of decoherence. We analyze random states and weighted graph states at infinity and found all of them to be genuinely entangled.
description: 4 pages, 5 figures
Havice, Elizabeth, Gabriela Valdivia, and Matthew Himley. Forthcoming. “Preface: Handbook-Making.” In The Routledge Handbook of Critical Resource Geography, edited by Matthew Himley, Elizabeth Havice, and Gabriela Valdivia. New York: Routledge.
Creators: name: Valdivia, Gabriela
name: Havice, Elizabeth
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2021

description: Handbooks are products of the careful curation of a diverse collection of contributions, but we rarely hear about how these collections come together — that is, about the processes of selecting, organizing, and looking after the items that end up in a collection. This Preface represents our effort to raise the curtain on our editorial process and the conditions under which the Handbook was created, which we see as part of our commitment to ongoing reflection on the question of how, why, and for whom the academic production of knowledge about resources matters (see Valdivia, Himley, and Havice, Chapter 1 this volume). It offers an overview of the intellectual-political method that unfolded incrementally and collaboratively during the production of the Handbook.
Existence and bifurcation of solutions for a double coupled system of Schrodinger equations
Creators: name: Tian, Rushun
name: Zhang, Zhitao
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 35B32, 35B38, 35J50, 58C40, 58E07

description: Consider the following system of double coupled Schrödinger equations arising from Bose-Einstein condensates etc., \begin{equation*} \left\{\begin{array}{l} -Δu + u =μ_1 u^3 + βuv^2- κv, -Δv + v =μ_2 v^3 + βu^2v- κu, u\neq0, v\neq0\ \hbox{and}\ u, v\in H^1(\R^N), \end{array} \right. \end{equation*}where $μ_1, μ_2$ are positive and fixed, $κ$ and $β$ are linear and nonlinear coupling parameters respectively. We first use critical point theory and Liouville type theorem to prove some existence and nonexistence results on the positive solutions of this system. Then using the positive and non-degenerate solution of the scalar equation $-Δω+ω=ω^3$, $ω\in H_r^1(\R^N)$, we construct a synchronized solution branch to prove that for $β$ in certain range and fixed, there exist a series of bifurcations in product space $\R\times H^1_r(\R^N)\times H^1_r(\R^N)$ with parameter $κ$.
description: Science China Mathematics,2015
Rapid and predictable evolution of admixed populations between two Drosophila species pairs
Creators: name: Earley, E.
name: Comeault, A.A.
name: Matute, D.R.
name: Jones, C.D.
name: Huang, W.
name: Mackay, T.F.C.
name: Serrato-Capuchina, A.
name: Monroy-Eklund, A.
name: Peede, D.
name: Coyne, J.A.
Publisher: name: Genetics Society of America
Year: 2020

description: The consequences of hybridization are varied, ranging from the origin of new lineages, introgression of some genes between species, to the extinction of one of the hybridizing species. We generated replicate admixed populations between two pairs of sister species of Drosophila: D. simulans and D. mauritiana; and D. yakuba and D. santomea. Each pair consisted of a continental species and an island endemic. The admixed populations were maintained by random mating in discrete generations for over 20 generations. We assessed morphological, behavioral, and fitness-related traits from each replicate population periodically, and sequenced genomic DNA from the populations at generation 20. For both pairs of species, species-specific traits and their genomes regressed to those of the continental species. A few alleles from the island species persisted, but they tended to be proportionally rare among all sites in the genome and were rarely fixed within the populations. This paucity of alleles from the island species was particularly pronounced on the X-chromosome. These results indicate that nearly all foreign genes were quickly eliminated after hybridization and that selection against the minor species genome might be similar across experimental replicates.
Multilocus evidence provides insight into the demographic history and asymmetrical gene flow between Ostrinia furnacalis and Ostrinia nubilalis (Lepidoptera: Crambidae) in the Yili area, Xinjiang, China
Creators: name: Li, Bing
Publisher: name: Zenodo
Year: 2022
Subjects: Sequencing
DNA extraction
molecular phylogenetic analyses
Gene flow analyses

description: Tianshan Mountain provides a model for studying biological evolution and speciation. Here we assess the evolutionary history of the Ostrinia furnacalis and Ostrinia nubilalis, which are sympatric in the Yili River Valley in Xinjiang, China. Our study is based on the historical gene flow analyses of two species by using three mitochondrial DNA (mtDNA, COI & COII & Cytb) and four nuclear DNA (nuDNA, EF-1α & Wingless & RPS5 & CAD) markers obtained from representatives of HC (Huocheng), YN (Yining), XY (Xinyuan) and MNS (Manasi). Our results reveal that there is a strong asymmetrical gene flow pattern between the four populations. The population migratory pathways between these different populations show inflow into HC and YN, outflow from XY, and that MNS maintained a flow balance. Bayesian divergence time dating based on the COI gene suggest the genetic divergence between the two species in this area may have occurred in the late-Pleistocene (0.003–0.0127 Mya). Neutrality tests (Tajima's D, Fu's Fs) and mismatch distribution test results suggest that population expansion events may not have occurred in the recent past, which may follow the 'mountain isolation' hypothesis. The ML and BI trees of the mtDNA haplotype dataset show that ECB haplotypes are clustered together in a distinct clade and are clearly separate from ACB haplotypes. However, the geographical pattern of haplotype distribution is less clear and there is no strong correspondence between haplotypes and their geographical pattern for both ACB and ECB, implying that there has been frequent gene flow among the geographic populations in the Tianshan Mountains. These findings confirm that geological factors play an important role in driving genetic patterns.
description: Funding provided by: National Natural Science Foundation of China
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809
Award Number: 31772508
description: To evaluate the variation in genetic diversity among four geographical populations, we calculated the number of haplotypes (Nh), haplotype diversity (Hd), and nucleotide diversity (π) for each population using DnaSP v 6.12.03 (Rozas & Librado, 2017) based on the combined three mitochondrial genes dataset (MTD) and combined four nuclear genes dataset (NUD), respectively. Genetic distances within and between populations were calculated in MEGA v 11. 0. 8 (Tamura et al., 2021) employing the Kimura 2-parameter (K2P) model (Kimura, 1980; Kumar et al., 2016). In order to infer the historical gene flow and the direction of gene flow, we used Bayesian stochastic search variable selection (BSSVS) analyses (Su et al., 2015) based on the MTD.
A Thesis Submitted in Partial Fulfillment of the Requirements for Award of Master of Arts Degree in Logistics and Supply Chain Management.
Creators: name: Leelt Desta
Publisher: name: Zenodo
Year: 2016

description: Retail activities turn out to be one of the significant themes playing the role in supply chain management and logistics. The major goal of the retail industry or retail merchandising system is to influence possible consumers to purchase a particular products assortment at a particular retail store (Risch, 1991).

The main purpose of this study is to assess the current status of logistics management practice in the food stuff retail stores with the aim of identifying gaps, potentials and constraints for development of effective and efficient logistics management. The outcome of this research will help the retail stores to understand the strength and weakness of their activity, it will help them to realize the gaps, which needs further improvement and it will provide good information for further researchers
Time and its categories in Classical Greek: language and thought
Creators: name: FAURE, Richard
name: GOLFIN, Emmanuel
name: GRASSO, Elsa
Publisher: name: Journal of Interdisciplinary Methodologies and Issues in Science - JIMIS-CNRS-Episciences - ESPACE - Agorantic
Year: 2019
Subjects: time
history
philosophy
linguistics
tense
aspect
mood

description: The conceptions of time are manifold (cyclic, linear, subjective/objective etc.). This is also true of Ancient Greece (Lloyd 1976). However, in Classical Greece certain human sciences arise and evolve at the same time, including History (Herodotus, Thucydides) and Philosophy (Plato, Aristotle), which may share a common notion of time. We explore the idea that these developments are related to what we observe in the language in the same period, namely that the marking of aspect and mood steps back and gives way to a more precise marking of time in the verbal system. This may be due to mutual influences of the categories of language and thought, as already observed in Benveniste (1958).
Root microbiome modulates plant growth promotion induced by low doses of glyphosate
Creators: name: Jones, C.D.
name: Leon-Reyesa, A.
name: Finkel, O.M.
name: Salas-González, I.
name: Fitzpatrick, C.R.
name: Ramirez-Villacis, D.X.
name: Dangl, J.L.
Publisher: name: American Society for Microbiology
Year: 2020

description: Glyphosate is a commonly used herbicide with a broad action spectrum. However, at sublethal doses, glyphosate can induce plant growth, a phenomenon known as hormesis. Most glyphosate hormesis studies have been performed under microbe-free or reduced-microbial-diversity conditions; only a few were performed in open systems or agricultural fields, which include a higher diversity of soil microorganisms. Here, we investigated how microbes affect the8 hormesis induced by low doses of glyphosate. To this end, we used Arabidopsis thaliana and a well-characterized synthetic bacterial community of 185 strains (SynCom) that mimics the root-associated microbiome of Arabidopsis. We found that a dose of 3.6 x 10-6 g acid equivalent/liter (low dose of glyphosate, or LDG) produced an ~14% increase in the shoot dry weight (i.e., hormesis) of uninoculated plants. Unexpectedly, in plants inoculated with the SynCom, LDG reduced shoot dry weight by 17%. We found that LDG enriched two Firmicutes and two Burkholderia strains in the roots. These specific strains are known to act as root growth inhibitors (RGI) in monoassociation assays. We tested the link between RGI and shoot dry weight reduction in LDG by assembling a new synthetic community lacking RGI strains. Dropping RGI strains out of the community restored growth induction by LDG. Finally, we showed that individual RGI strains from a few specific phyla were sufficient to switch the response to LDG from growth promotion to growth inhibition. Our results indicate that glyphosate hormesis was completely dependent on the root microbiome composition, specifically on the presence of root growth inhibitor strains.
Coupling models of cattle and farms with models of badgers for predicting the dynamics of bovine tuberculosis (TB)
Creators: name: Moustakas, Aristides
name: Evans, Matthew R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Computational Engineering, Finance, and Science (cs.CE)
subject: Dynamical Systems (math.DS)
subject: Applications (stat.AP)
subject: Computation (stat.CO)
subject: FOS: Biological sciences
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Bovine TB is a major problem for the agricultural industry in several countries. TB can be contracted and spread by species other than cattle and this can cause a problem for disease control. In the UK and Ireland, badgers are a recognised reservoir of infection and there has been substantial discussion about potential control strategies. We present a coupling of individual based models of bovine TB in badgers and cattle, which aims to capture the key details of the natural history of the disease and of both species at approximately county scale. The model is spatially explicit it follows a very large number of cattle and badgers on a different grid size for each species and includes also winter housing. We show that the model can replicate the reported dynamics of both cattle and badger populations as well as the increasing prevalence of the disease in cattle. Parameter space used as input in simulations was swept out using Latin hypercube sampling and sensitivity analysis to model outputs was conducted using mixed effect models. By exploring a large and computationally intensive parameter space we show that of the available control strategies it is the frequency of TB testing and whether or not winter housing is practised that have the most significant effects on the number of infected cattle, with the effect of winter housing becoming stronger as farm size increases. Whether badgers were culled or not explained about 5%, while the accuracy of the test employed to detect infected cattle explained less than 3% of the variance in the number of infected cattle.
Extreme Thouless effect in a minimal model of dynamic social networks
Creators: name: Bassler, K. E.
name: Liu, Wenjia
name: Schmittmann, B.
name: Zia, R. K. P.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: In common descriptions of phase transitions, first order transitions are characterized by discontinuous jumps in the order parameter and normal fluctuations, while second order transitions are associated with no jumps and anomalous fluctuations. Outside this paradigm are systems exhibiting `mixed order transitions' displaying a mixture of these characteristics. When the jump is maximal and the fluctuations range over the entire range of allowed values, the behavior has been coined an `extreme Thouless effect'. Here, we report findings of such a phenomenon, in the context of dynamic, social networks. Defined by minimal rules of evolution, it describes a population of extreme introverts and extroverts, who prefer to have contacts with, respectively, no one or everyone. From the dynamics, we derive an exact distribution of microstates in the stationary state. With only two control parameters, $N_{I,E}$ (the number of each subgroup), we study collective variables of interest, e.g., $X$, the total number of $I$-$E $ links and the degree distributions. Using simulations and mean-field theory, we provide evidence that this system displays an extreme Thouless effect. Specifically, the fraction $X/\left( N_{I}N_{E}\right) $ jumps from $0$ to $1$ (in the thermodynamic limit) when $N_{I}$ crosses $N_{E}$, while all values appear with equal probability at $N_{I}=N_{E}$.
description: arXiv admin note: substantial text overlap with arXiv:1408.5421
Challenges and solutions for analysing dual RNA-seq data for non-model host–pathogen systems
Creators: name: Jones, C.D.
name: O'Keeffe, K.R.
Publisher: name: British Ecological Society
Year: 2019

description: Dual RNA-seq simultaneously profiles the transcriptomes of a host and of a pathogen during infection and may reveal the mechanisms underlying host–pathogen interactions. Dual RNA-seq is inherently a mixture of transcripts from at least two species (host and pathogen), so this mixture must be computationally sorted into host and pathogen components. Sorting relies on aligning reads to respective reference genomes, which may be unavailable for both species in non-model host–pathogen pairs. This lack of genomic resources may present challenges to applying dual RNA-seq to non-model systems. We assessed the accuracy of alignments of dual RNA-seq when using the genomic resources of a closely related species to the species of interest by simulating datasets of mixed transcripts from a host and pathogen. Specifically, we compared how different aligners performed across different proportions of pathogen-to-host transcripts and across variation in the genetic distance between the pathogen genome and reference genome. We performed extensive analyses for a host plant with a fungal pathogen, and then, we extended the plant–fungus results by repeating key analyses in vertebrate (human)–fungus and vertebrate–bacterium systems. Aligners that were able to map pathogen transcripts to the reference genome of a species closely related to the pathogen (a ‘related reference genome’) also mismapped transcripts originating from the host to the pathogen's related reference genome. This resulted in regions where this occurred being quantified as overexpressed. If a host reference genome was available, we show that, to minimize host transcript mismapping and retain the ability to map pathogen transcripts, one could concatenate the host genome with the pathogen's related reference genome, then map transcripts to the concatenated genomes. If a host genome was unavailable, assembling reads de novo prior to aligning substantially decreased host read mismapping, while retaining the ability to map pathogen transcripts to a related reference genome. The application of dual RNA-seq to organisms without reference genomes is currently limited. We propose an analytical workflow that leverages the genomic resources of species closely related to species of interest to facilitate the application of dual RNA-seq to reveal the mechanisms of host–pathogen interactions across a wider array of systems.
An Extension of Nori Fundamental Group
Creators: name: Otabe, Shusuke
Publisher: name: arXiv
Year: 2015
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics

description: In this paper, we study a certain extension of Nori's fundamental group in the case where a base field is of characteristic 0 and give structure theorems about it. As a result, for a smooth projective curve with genus $g$>1, we prove that Nori's fundamental group acts faithfully on the category of unipotent bundles on the universal covering. In the case when $g=1$, we give a more finer result.
description: 30 pages, to appear in Comm Alg, Remark 1.6 is included, dropped the smoothness assumption from the most part, changed to use a word "unipotent bundle" instead of "nilpotent bundle", at a suggestion of the referee, Section 5.2 is included
Quantum state space-dimension as a quantum resource
Creators: name: Plastino, Angelo
name: Bellomo, Guido
name: Plastino, Angel R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We argue that the dimensionality of the space of quantum systems' states should be considered as a legitimate resource for quantum information tasks. The assertion is supported by the fact that quantum states with discord-like capacities can be obtained from classically correlated states in spaces of dimension large enough. We illustrate things with some simple examples that justify our claim.
description: 4 pages, 1 figure; submitted to Int. J. Quantum Info; v2: minor changes
Micro-meteoroid seismic uplift and regolith concentration on kilometric scale asteroids
Creators: name: Garcia, Raphael F.
name: Murdoch, Naomi
name: Mimoun, David
Publisher: name: arXiv
Year: 2015
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: Seismic shaking is an attractive mechanism to explain the destabilisation of regolith slopes and the regolith migration found on the surfaces of asteroids (Richardson et al. 2004; Miyamoto et al. 2007). Here, we use a continuum mechanics method to simulate the seismic wave propagation in an asteroid. Assuming that asteroids can be described by a cohesive core surrounded by a thin non-cohesive regolith layer, our numerical simulations of vibrations induced by micro-meteoroids suggest that the surface peak ground accelerations induced by micro-meteoroid impacts may have been previously under-estimated. Our lower bound estimate of vertical accelerations induced by seismic waves is about 50 times larger than previous estimates. It suggests that impact events triggering seismic activity are more frequent than previously assumed for asteroids in the kilometric and sub-kilometric size range. The regolith lofting is also estimated by a first order ballistic approximation. Vertical displacements are small, but lofting times are long compared to the duration of the seismic signals. The regolith movement has a non-linear dependence on the distance to the impact source which is induced by the type of seismic wave generating the first movement. The implications of regolith concentration in lows of surface acceleration potential are also discussed. We suggest that the resulting surface thermal inertia variations of small fast rotators may induce an increased sensitivity of these objects to the Yarkovsky effect.
description: Accepted for publication in Icarus
Variation in hybrid gene expression: Implications for the evolution of genetic incompatibilities in interbreeding species
Creators: name: Monroy-Eklund, A.
name: Pfennig, K.S.
name: Seidl, F.
name: Levis, N.A.
name: Jones, C.D.
name: Ehrenreich, I.M.
Publisher: name: Blackwell Publishing Ltd
Year: 2019

description: Interbreeding species often produce low-fitness hybrids due to genetic incompatibilities between parental genomes. Whether these incompatibilities reflect fixed allelic differences between hybridizing species, or, alternatively, standing variants that segregate within them, remains unknown for many natural systems. Yet, evaluating these alternatives is important for understanding the origins and nature of species boundaries. We examined these alternatives using spadefoot toads (genus Spea), which naturally hybridize. Specifically, we contrasted patterns of gene expression in hybrids relative to pure-species types in experimentally produced tadpoles from allopatric parents versus those from sympatric parents. We evaluated the prediction that segregating variation should result in gene expression differences between hybrids derived from sympatric parents versus hybrids derived from allopatric parents, and found that 24% of the transcriptome showed such differences. Our results further suggest that gene expression in hybrids has evolved in sympatry owing to evolutionary pressures associated with ongoing hybridization. Although we did not measure hybrid incompatibilities directly, we discuss the implications of our findings for understanding the nature of hybrid incompatibilities, how they might vary across populations over time, and the resulting effects on the evolutionary maintenance - or breakdown - of reproductive barriers between species.
Supplementary document for Development of a Multimodal Mobile Colposcope for Real-Time Cervical Cancer Detection - 6011008.pdf
Creators: name: Coole, Jackson
name: Brenes, David
name: Possati-Resende, Julio
name: Antoniazzi, Márcio
name: Fonseca, Bruno
name: Maker, Yajur
name: Kortum, Alex
name: Vohra, Imran
name: Schwarz, Richard
name: Carns, Jennifer
Publisher: name: Optica Publishing Group
Year: 2022
Subjects: subject: 90399 Biomedical Engineering not elsewhere classified
subject: FOS: Medical engineering

description: Revised supplemental
The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response
Creators: name: Castrillo, G.
name: Teixeira, P.J.P.L.
name: Spaepen, S.
name: Dangl, J.L.
name: Salas-González, I.
name: Jones, C.D.
name: Finkel, O.M.
name: Law, T.F.
Publisher: name: Public Library of Science
Year: 2019

description: Phosphate starvation response (PSR) in nonmycorrhizal plants comprises transcriptional reprogramming resulting in severe physiological changes to the roots and shoots and repression of plant immunity. Thus, plant-colonizing microorganisms-the plant microbiota -are exposed to direct influence by the soil's phosphorus (P) content itself as well as to the indirect effects of soil P on the microbial niches shaped by the plant. The individual contribution of these factors to plant microbiota assembly remains unknown. To disentangle these direct and indirect effects, we planted PSR-deficient Arabidopsis mutants in a long-term managed soil P gradient and compared the composition of their shoot and root microbiota to wild-type plants across different P concentrations. PSR-deficiency had a larger effect on the composition of both bacterial and fungal plant-associated microbiota than soil P concentrations in both roots and shoots. To dissect plant-microbe interactions under variable P conditions, we conducted a microbiota reconstitution experiment. Using a 185-member bacterial synthetic community (SynCom) across a wide P concentration gradient in an agar matrix, we demonstrated a shift in the effect of bacteria on the plant from a neutral or positive interaction to a negative one, as measured by rosette size. This phenotypic shift was accompanied by changes in microbiota composition: the genus Burkholderia was specifically enriched in plant tissue under P starvation. Through a community drop-out experiment, we demonstrated that in the absence of Burkholderia from the SynCom, plant shoots accumulated higher ortophosphate (Pi) levels than shoots colonized with the full SynCom but only under Pi starvation conditions. Therefore, Pi-stressed plants are susceptible to colonization by latent opportunistic competitors found within their microbiome, thus exacerbating the plant's Pi starvation.
L'espace d'un instant
Creators: name: VEZINA, Jean-François
Publisher: name: Journal of Interdisciplinary Methodologies and Issues in Science - JIMIS-CNRS-Episciences - ESPACE - Agorantic
Year: 2020
Subjects: Synchronicité
Archétypes
Aléa du quantique
Intrication du désir
Individuation

description: Au cours des dernières années, le concept de synchronicité a connu un regain d’intérêt dans la population et les rayons de livres de développement personnel. Malheureusement diffusé avec une méconnaissance des subtilités de la pensée de Jung, comment remettre de la rigueur dans ce concept tout en gardant une certaine ouverture ? Dans cet article, nous mettons en relation le principe de l’aléa du quantique établi comme propriété fondamentale du temps par le mathématicien Alain Connes avec les notions de synchronicité, d’archétypes et d’individuation développées par Jung en collaboration avec le prix Nobel de physique Wolfgang Pauli.
Tachyon-Warm Intermediate and Logamediate Inflation in the Brane-World Model in the Light of Planck Data
Creators: name: Kamali, Vahid
name: Setare, Mohammad Reza
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Tachyon inflationary universe model on the brane in the context of warm inflation is studied. In slow-roll approximation and in longitudinal gauge, we find the primoradial perturbation spectrums for this scenario. We also present the general expressions of the tensor-scalar ratio, scalar spectral index and its running. We develop our model by using exponential potential, the characteristics of this model are calculated in great details. We also study our model in the context of intermediate (where scale factor expands as: $a=a_0\exp(At^f)$) and logamediate (where the scale factor expands as: $a=a_0\exp(A[\ln t]^ν)$) models of inflation. In these two sectors, dissipative parameter is considered as a constant parameter and a function of tachyon field. Our model is compatible with observational data. The parameters of the model are restricted by recent observational data from the nine-year Wilkinson microwave anisotropy probe (WMAP9) and Planck data.
description: arXiv admin note: substantial text overlap with arXiv:1302.0493, arXiv:1408.6516, arXiv:1407.2604, arXiv:1312.2832
Natural variation in sugar tolerance associates with changes in signaling and mitochondrial ribosome biogenesis
Creators: name: Soeder, C.
name: Kokki, K.
name: Havula, E.
name: Hietakangas, V.
name: Jones, C.D.
name: Lamichane, N.
name: Melvin, R.G.
Publisher: name: eLife Sciences Publications Ltd
Year: 2018

description: How dietary selection affects genome evolution to define the optimal range of nutrient intake is a poorly understood question with medical relevance. We have addressed this question by analyzing Drosophila simulans and sechellia, recently diverged species with differential diet choice. D. sechellia larvae, specialized to a nutrient scarce diet, did not survive on sugar-rich conditions, while the generalist species D. simulans was sugar tolerant. Sugar tolerance in D. simulans was a tradeoff for performance on low-energy diet and was associated with global reprogramming of metabolic gene expression. Hybridization and phenotype-based introgression revealed the genomic regions of D. simulans that were sufficient for sugar tolerance. These regions included genes that are involved in mitochondrial ribosome biogenesis and intracellular signaling, such as PPP1R15/Gadd34 and SERCA, which contributed to sugar tolerance. In conclusion, genomic variation affecting genes involved in global metabolic control defines the optimal range for dietary macronutrient composition.
Design of synthetic bacterial communities for predictable plant phenotypes
Creators: name: Castrillo, G.
name: Jones, C.D.
name: Jojic, V.
name: Mucyn, T.
name: Finkel, O.M.
name: Gao, T.
name: Shank, E.A.
name: Law, T.F.
name: Salas González, I.
name: Feltcher, M.E.
name: Dangl, J.L.
name: Herrera Paredes, S.
name: Teixeira, P.J.P.L.
name: Powers, M.J.
Publisher: name: Public Library of Science
Year: 2018

description: Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant–bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation–responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. Finally, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communities.
A family of lowered isothermal models
Creators: name: Gieles, Mark
name: Zocchi, Alice
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present a family of self-consistent, spherical, lowered isothermal models, consisting of one or more mass components, with parameterised prescriptions for the energy truncation and for the amount of radially biased pressure anisotropy. The models are particularly suited to describe the phase-space density of stars in tidally limited, mass-segregated star clusters in all stages of their life-cycle. The models extend a family of isotropic, single-mass models by Gomez-Leyton and Velazquez, of which the well-known Woolley, King and Wilson (in the non-rotating and isotropic limit) models are members. We derive analytic expressions for the density and velocity dispersion components in terms of potential and radius, and introduce a fast model solver in PYTHON (LIMEPY), that can be used for data fitting or for generating discrete samples.
description: 17 pages, 10 figures, 4 appendices, MNRAS, updated to match final journal style
Finding Influential Bloggers
Creators: name: Gliwa, Bogdan
name: Zygmunt, Anna
Publisher: name: arXiv
Year: 2015
Subjects: subject: Social and Information Networks (cs.SI)
subject: FOS: Computer and information sciences

description: Blogging is a popular way of expressing opinions and discussing topics. Bloggers demonstrate different levels of commitment and most interesting are influential bloggers. Around such bloggers, the groups are forming, which concentrate users sharing similar interests. Finding such bloggers is an important task and has many applications e.g. marketing, business, politics. Influential ones affect others which is related to the process of diffusion. However, there is no objective way to telling which blogger is more influential. Therefore, researchers take into consideration different criteria to assess bloggers (e.g. SNA centrality measures). In this paper we propose new, efficient method for influential bloggers discovery which is based on relation of commenting in blogger's thread and is defined on bloggers level. Next, we compare results with other, comparative method proposed by Agarwal et al. called iFinder which is based on links between posts.
An aberrant NOTCH2-BCR signaling axis in B cells from patients with chronic GVHD
Creators: name: Jones, C.D.
name: Tata, P.V.
name: Siebel, C.W.
name: Owzar, K.
name: Su, H.
name: Anand, S.
name: Suthers, A.N.
name: Zhang, D.
name: Kuan, P.F.
name: Jia, W.
name: Blazar, B.R.
name: Serody, J.S.
name: Maillard, I.
name: Poe, J.C.
name: Rose, J.J.
name: Chao, N.J.
name: Horwitz, M.E.
name: Hakim, F.T.
name: Sarantopoulos, S.
name: Ho, V.T.
name: Pavletic, S.Z.
name: Vincent, B.G.
Publisher: name: American Society of Hematology
Year: 2017

description: B-cell receptor (BCR)-activated B cells contribute to pathogenesis in chronic graft-versus-host disease (cGVHD), a condition manifested by both B-cell autoreactivity and immune deficiency. We hypothesized that constitutive BCR activation precluded functional B-cell maturation in cGVHD. To address this, we examined BCR-NOTCH2 synergy because NOTCH has been shown to increase BCR responsiveness in normal mouse B cells. We conducted ex vivo activation and signaling assays of 30 primary samples from hematopoietic stem cell transplantation patients with and without cGVHD. Consistent with a molecular link between pathways, we found that BCR-NOTCH activation significantly increased the proximal BCR adapter protein BLNK. BCR-NOTCH activation also enabled persistent NOTCH2 surface expression, suggesting a positive feedback loop. Specific NOTCH2 blockade eliminated NOTCH-BCR activation and significantly altered NOTCH downstream targets and B-cell maturation/effector molecules. Examination of the molecular underpinnings of this “NOTCH2-BCR axis” in cGVHD revealed imbalanced expression of the transcription factors IRF4 and IRF8, each critical to B-cell differentiation and fate. All-trans retinoic acid (ATRA) increased IRF4 expression, restored the IRF4-to-IRF8 ratio, abrogated BCR-NOTCH hyperactivation, and reduced NOTCH2 expression in cGVHD B cells without compromising viability. ATRA-treated cGVHD B cells had elevated TLR9 and PAX5, but not BLIMP1 (a gene-expression pattern associated with mature follicular B cells) and also attained increased cytosine guanine dinucleotide responsiveness. Together, we reveal a mechanistic link between NOTCH2 activation and robust BCR responses to otherwise suboptimal amounts of surrogate antigen. Our findings suggest that peripheral B cells in cGVHD patients can be pharmacologically directed from hyperactivation toward maturity.
Plastic potential: how the phenotypes and adaptations of pathogens are influenced by microbial interactions within plants
Creators: name: Mitchell, C.E.
name: Carbone, I.
name: Jones, C.D.
name: O'Keeffe, K.R.
Publisher: name: Elsevier Ltd
Year: 2017

description: Predicting the effects of plant-associated microbes on emergence, spread, and evolution of plant pathogens demands an understanding of how pathogens respond to these microbes at two levels of biological organization: that of an individual pathogen and that of a pathogen population across multiple individual plants. We first examine the plastic responses of individual plant pathogens to microbes within a shared host, as seen through changes in pathogen growth and multiplication. We then explore the limited understanding of how within-plant microbial interactions affect pathogen populations and discuss the need to incorporate population-level observations with population genomic techniques. Finally, we suggest that integrating across levels will further our understanding of the ecological and evolutionary impacts of within-plant microbial interactions on pathogens.
title: Perceived Control of Academic Events in Turkish and English Adolescents: Comparing Classical Test Theory and Item Response Theory to Detect Item Biases Across Cultures
Creators: name: Ertubey, Candan
Publisher: name: Goldsmiths, University of London
Year: 1999

description: Perceived control was investigated in secondary school adolescents from secular Turkish and British schools. Five published questionnaires were used. Perceived control was measured mainly with the Control beliefs, Means-Ends beliefs, and Agency Scale (CAMI - Skinner, Baltes, Chapman, 1988) As supplementary measures, Nowicki and Strickland's (1973) Internal-External Locus of Control for Children Scale (CNSIE) and Palenzuela's (1988) Multiple Academic Specific Locus of Control Scale (MASLOC) were also used. Two other questionnaires, measuring social antecedents, were included in the study. These were the Religiosity in Youth Scale (Rothbough & Jessor, 1976) and the F-Scale (Adorno, 1950; Christie, 1991). In order to detect item biases within and between cultures, two procedures were followed: a) The questionnaires were translated from English to Turkish, and then both versions were completed by a bilingual Turkish sample. Translation fidelity was tested using three different approaches: Generalizability theory (Cronbach et al., 1972; Shavelson & Webb, 1991), Classical Item Analysis (Nunnally, 1978) and Item Response Theory (Lord, 1980; Hambleton et al., 1990). The results are discussed in terms of consistency and the cost of the procedure. b) The Turkish and English versions of the questionnaires were completed by unilingual Turkish and English samples in their own language. The purpose here was to detect similar (etic) and different (emic) functioning of the items across cultures using Classical and Modem item analysis. The questionnaires were found to be functioning similarly in the two cultures. But CNSIE was found to be a poor scale in both cultures and was not used in the next stage. In the final part of the thesis perceived control was investigated as a function of culture, religion, religiosity, authoritarianism, age and gender. The perceived control scale showed significant cultural differences on 3 out of 10 subscales of CAM!. Agency beliefs and MASLOC showed significant effects of religion, religiosity, authoritarianism and gender. Generally, the Turkish sample was more Internal, more religious, and authoritarian. The gender differences were more inconsistent in terms of the direction of the relationship, with boys more internal on attribute while girls were more internal on unknown factors and effort.
Comparative analysis of behavioral and transcriptional variation underlying CO2 sensory neuron function and development in Drosophila
Creators: name: McLaughlin, J.
name: Leo, C.
name: Okuwa, S.
name: Rambarat, P.
name: Volkan, P.C.
name: Jones, C.D.
name: Monroy-Eklund, A.
name: Pan, J.W.
name: Clark, S.
name: Yang, H.
Publisher: name: Taylor and Francis Inc.
Year: 2017

description: Carbon dioxide is an important environmental cue for many insects, regulating many behaviors including some that have direct human impacts. To further improve our understanding of how this system varies among closely related insect species, we examined both the behavioral response to CO2 as well as the transcriptional profile of key developmental regulators of CO2 sensory neurons in the olfactory system across the Drosophila genus. We found that CO2 generally evokes repulsive behavior across most of the Drosophilids we examined, but this behavior has been lost or reduced in several lineages. Comparisons of transcriptional profiles from the developing and adult antennae for subset these species suggest that behavioral differences in some species may be due to differences in the expression of the CO2 co-receptor Gr63a. Furthermore, these differences in Gr63a expression are correlated with changes in the expression of a few genes known to be involved in the development of the CO2 circuit, namely dac, an important regulator of sensilla fate for sensilla that house CO2 ORNs, and mip120, a member of the MMB/dREAM epigenetic regulatory complex that regulates CO2 receptor expression. In contrast, most of the other known structural, molecular, and developmental components of the peripheral Drosophila CO2 olfactory system seem to be well-conserved across all examined lineages. These findings suggest that certain components of CO2 sensory ORN development may be more evolutionarily labile, and may contribute to differences in CO2-evoked behavioral responses across species.