cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Optimal control of plate shape with incompatible strain fields
Creators: name: Jones, Gareth Wyn
name: Mahadevan, L.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Optimization and Control (math.OC)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: A flat plate can bend into a curved surface if it experiences an inhomogeneous growth field. In this article a method is described that numerically determines the optimal growth field giving rise to an arbitrary target shape, optimizing for closeness to the target shape and for growth field smoothness. Numerical solutions are presented, for the full non-symmetric case as well as for simplified one-dimensional and axisymmetric geometries. This system can also be solved semi-analytically by positing an ansatz for the deformation and growth fields in a circular disk with given thickness profile. Paraboloidal, cylindrical and saddle-shaped target shapes are presented as examples, of which the last two exemplify a soft mode arising from a non-axisymmetric deformation of a structure with axisymmetric material properties.
description: 21 pages, 6 figures
Super-operator structures and no-go theorems for dissipative quantum phase transitions
Creators: name: Barthel, Thomas
name: Zhang, Yikang
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Physics (quant-ph)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: In the thermodynamic limit, the steady states of open quantum many-body systems can undergo nonequilibrium phase transitions due to a competition between coherent and driven-dissipative dynamics. Here, we consider Markovian systems and elucidate structures of the Liouville super-operator that generates the time evolution. In many cases of interest, an operator-basis transformation can bring the Liouvillian into a block-triangular form, making it possible to assess its spectrum. The spectral gap sets the asymptotic decay rate. The super-operator structure can be used to bound gaps from below, showing that, in a large class of systems, dissipative phase transitions are actually impossible and that the convergence to steady states follows an exponential temporal decay. Furthermore, when the blocks on the diagonal are Hermitian, the Liouvillian spectra obey Weyl ordering relations. The results apply, for example, to Davies generators and quadratic systems, and are also demonstrated for various spin models.
description: 8 pages; added discussion of block-triangular representations for quadratic fermionic and bosonic systems (see arXiv:2112.08344 and arXiv:2204.05346), further minor improvements; published version
Canons of Ancient Authors in the Age of Linked Open Data:
Creators: name: , Berti
Publisher: name: Zenodo
Year: 2023
Subjects: digital philology
digital classics

description: Slides of the Kolloquium "Phänomenologie der Digital Humanities" (Wintersemester 2022/2023), Freie Universität Berlin, February 22, 2023
description: DFG Projektnummer 434173983
The Near-InfraRed Planet Searcher: A new ESO spectrograph in La Silla
Creators: name: Vaulato, Valentina
name: Ehrenreich, David
Publisher: name: Zenodo
Year: 2023
Subjects: NIRPS
High-resolution spectroscopy
Exoplanets

description: The Near-InfraRed Planet Searcher (NIRPS) is a new ultra-stable infrared (YJH) spectrograph installed at the ESO 3.6 meters telescope in La Silla. NIRPS is designed to search for rocky planets orbiting M-dwarf stars and it operates in synergy with HARPS spectrograph. It is built with the goal of reaching a precision of 1 m/s, the typical radial velocity signal expected by an Earth analogue around a cool M-dwarf. The main goals of the mission are to perform an high-precision RV survey of M-dwarfs, to measure mass and density of known transiting planetary candidates around M stars and to characterise planetary atmospheres via transmission spectroscopy.
Quantumness of Gaussian Discord: Experimental Evidence and Role of System-Environment Correlations
Creators: name: Chille, Vanessa
name: Quinn, Niall
name: Peuntinger, Christian
name: Croal, Callum
name: Mista, Ladislav
name: Marquardt, Christoph
name: Leuchs, Gerd
name: Korolkova, Natalia
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We provide experimental evidence of quantum features in bi-partite states classified as entirely classical according to a conventional criterion based on the Glauber P-function but possessing non-zero Gaussian quantum discord. Their quantum nature is experimentally revealed by acting locally on one part of the discordant state. Adding an environmental system purifying the state, we unveil the flow of quantum correlations within a global pure system using the Koashi-Winter inequality. We experimentally verify and investigate the counterintuitive effect of discord increase under the action of local loss and link it to the entanglement with the environment. For a discordant state generated by splitting a state in which the initial squeezing is destroyed by random displacements, we demonstrate the recovery of entanglement highlighting the role of system-environment correlations.
description: 9 pages, 5 figures
D6.4 - Comparative study on CR data
Creators: name: Jacques Marteau
name: Theodore Avgitas
Publisher: name: Zenodo
Year: 2022

description: This report presents the data-analysis results for the Cosmic Muon Images demonstrator. It examines classification data provided by citizen scientists via workflows available in the project on the Zooniverse platform, concentrating on both the classification timelines - providing insights on the results of both workflows - and the machine-learning-algorithm results. The document concludes with a summary of the findings and with an outlook for the future of the demonstrator.
High-spin spectroscopy of 124,125,126Xe
Creators: name: Chowdhury, P.
name: Hagemann, G.B.
name: Engelhardt, C.
name: Herskind, B.
name: Amro, H.
name: Sletten, G.
name: Camera, F.
name: Clark, R.M.
name: Janssens, R.V.F.
name: Bracco, A.
name: Fallon, P.
name: Neusser-Neffgen, A.
name: Hübel, H.
name: Benzoni, G.
name: Al-Khatib, A.
name: Bringel, P.
name: Carpenter, M.P.
name: Khoo, T.L.
name: Hansen, C.R.
Publisher: name: Jagiellonian University
Year: 2007

description: High-spin states in 124,125,126Xe have been populated in the reaction 82Se(48Ca, xn) 130-xXe and γ-ray coincidences were measured with the GAMMASPHERE spectrometer. Twelve new bands extending into the spin 50-60 ℏ region are identified in 125Xe and 126Xe and previously known rotational bands at low spins arc confirmed and extended. Earlier known structures in 124Xe are confirmed and a new band is observed. Irregular structures are identified at the top of the yrast and a side band in this nucleus. Configuration assignments for the different structures are suggested.
Additional file 9 of The nuclear and mitochondrial genome assemblies of Tetragonisca angustula (Apidae: Meliponini), a tiny yet remarkable pollinator in the Neotropics
Creators: name: Ferrari, Rafael Rodrigues
name: Ricardo, Paulo Cseri
name: Dias, Felipe Cordeiro
name: de Souza Araujo, Natalia
name: Soares, Dalliane Oliveira
name: Zhou, Qing-Song
name: Zhu, Chao-Dong
name: Coutinho, Luiz Lehmann
name: Arias, Maria Cristina
name: Batista, Thiago Mafra
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Table S9. Contaminants (bacteria) found among the raw genome sequencing data of Tetragonisca angustula
Regular parallelisms on PG(3,R) admitting a 2-torus action
Creators: name: Löwen, Rainer
name: Steinke, Günter F.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: 51H10, 51A15, 51M30

description: A regular parallelism of real projective 3-space PG(3,R) is an equivalence relation on the line space such that every class is equivalent to the set of 1-dimensional complex subspaces of a 2-dimensional complex vector space. We shall assume that the set of classes is compact, and characterize those regular parallelisms that admit an action of a 2-dimensional torus group. We prove that there is a one-dimensional subtorus fixing every parallel class. From this property alone we deduce that the parallelism is a 2- or 3-dimensional regular parallelism in the sense of Betten and Riesinger. If a 2-torus acts, then the parallelism can be described using a so-called generalized line star which admits a 1-torus action. We also study examples of such parallelisms by constructing generalized line stars. In particular, we prove a claim which was presented by Betten and Riesinger with an incorrect proof. The present article continues a series of papers by the first author on parallelisms with large groups.
description: 2 figures
Rotating and Orbiting Strings in Dp-brane background
Creators: name: Biswas, Sagar
name: Panigrahi, Kamal L.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We probe the open fundamental strings in Dp-brane (p=1, 3, 5) backgrounds and find new classes of rotating and orbiting string solutions. We show that for various worldsheet embedding ansatz we get solutions of the string equations of motion that correspond to the well known giant magnon and single spikes, in addition to few new solutions corresponding to the orbiting strings. We make a systematic study of both rigidly rotating and orbiting strings in D1, D3 and D5-brane backgrounds.
description: 27 pages
Additional file 10 of The nuclear and mitochondrial genome assemblies of Tetragonisca angustula (Apidae: Meliponini), a tiny yet remarkable pollinator in the Neotropics
Creators: name: Ferrari, Rafael Rodrigues
name: Ricardo, Paulo Cseri
name: Dias, Felipe Cordeiro
name: de Souza Araujo, Natalia
name: Soares, Dalliane Oliveira
name: Zhou, Qing-Song
name: Zhu, Chao-Dong
name: Coutinho, Luiz Lehmann
name: Arias, Maria Cristina
name: Batista, Thiago Mafra
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Table S10. Orthogroup identification overview. 2nd column, number of orthologs identified by Orthofinder; 3rd column, number (and percentage) of identified orthologs that were assigned to orthogroups; 4th column, number (and percentage) of the identified orthologs that could not be assigned to any orthogroup; 5th column, number (and percentage) of orthogroups that were found in the genome of the corresponding species; 6th column, number of orthogroups that were found exclusively in the genome of the corresponding species; 7th column, number (and percentage) of the identified orthologs that were assigned to the orthogroups found exclusively in the genome of the corresponding species
Additional file 1: of Modeling the quantitative nature of neurodevelopmental disorders using Collaborative Cross mice
Creators: name: Molenhuis, Remco
name: Hilgo Bruining
name: Brandt, Myrna
name: Soldt, Petra
name: Atamni, Hanifa Abu-Toamih
name: J. Burbach
name: Iraqi, Fuad
name: Mott, Richard
name: Kas, Martien
Publisher: name: Figshare
Year: 2018
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Plant Biology

description: Figure S1. Haplotype-based and broad-sense heritability estimates in CC mice. Figure S2. Phenotypic correlations in CC mice. Figure S3. Quantification of stereotyped exploratory patterns in C57BL/6J and BTBR mice. Figure S4. Characterization of genes in QTL by predicted ASD implication. Table S1. Quantitative trait loci (QTLs) for neurobehavioral traits in CC mice. Table S2. Human homologous genes in QTLs derived from CC mice. (DOCX 8310Â kb)
Identification of a high-spin isomer in Mo99
Creators: name: Liu, Z.
name: Podolyák, Zs.
name: Carpenter, M.P.
name: Walker, P.M.
name: Jones, G.A.
name: Lane, G.J.
name: Chowdhury, P.
name: Carroll, J.J.
name: Kondev, F.G.
name: Williams, S.J.
name: Zhu, S.
name: Regan, P.H.
name: Janssens, R.V.F.
name: Chakrawarthy, R.S.
name: Thompson, N.J.
name: Khoo, T.L.
name: Stevenson, P.D.
name: Seweryniak, D.
name: Garnsworthy, A.B.
Publisher: name: American Physical Society
Year: 2007

description: A previously unreported isomer has been identified in Mo99 at an excitation energy of Ex=3010 keV, decaying with a half-life of T1/2=8(2) ns. The nucleus of interest was produced following fusion-fission reactions between a thick Al27 target frame and a Hf178 beam at a laboratory energy of 1150 MeV. This isomeric state is interpreted as an energetically favored, maximally aligned configuration of νh112 π(g92)2.
Misfolded protein oligomers induce an increase of intracellular Ca 2+ causing an escalation of reactive oxidative species
Creators: name: Fani, Giulia
name: La Torre, Chiara Ester
name: Cascella, Roberta
name: Cecchi, Cristina
name: Vendruscolo, Michele
name: Chiti, Fabrizio
Publisher: name: Apollo - University of Cambridge Repository
Year: 2022
Subjects: Original Article
NMDA receptors
AMPA receptors
Membrane destabilization
Calcium homeostasis
Oxidative stress
Protein misfolding
Neurodegenerative diseases

description: Funder: Università degli Studi di Firenze
description: Abstract: Alzheimer's disease is characterized by the accumulation in the brain of the amyloid β (Aβ) peptide in the form of senile plaques. According to the amyloid hypothesis, the aggregation process of Aβ also generates smaller soluble misfolded oligomers that contribute to disease progression. One of the mechanisms of Aβ oligomer cytotoxicity is the aberrant interaction of these species with the phospholipid bilayer of cell membranes, with a consequent increase in cytosolic Ca2+ levels, flowing from the extracellular space, and production of reactive oxygen species (ROS). Here we investigated the relationship between the increase in Ca2+ and ROS levels immediately after the exposure to misfolded protein oligomers, asking whether they are simultaneous or instead one precedes the other. Using Aβ42-derived diffusible ligands (ADDLs) and type A HypF-N model oligomers (OAs), we followed the kinetics of ROS production and Ca2+ influx in human neuroblastoma SH-SY5Y cells and rat primary cortical neurons in a variety of conditions. In all cases we found a faster increase of intracellular Ca2+ than ROS levels, and a lag phase in the latter process. A Ca2+-deprived cell medium prevented the increase of intracellular Ca2+ ions and abolished ROS production. By contrast, treatment with antioxidant agents prevented ROS formation, did not prevent the initial Ca2+ flux, but allowed the cells to react to the initial calcium dyshomeostasis, restoring later the normal levels of the ions. These results reveal a mechanism in which the entry of Ca2+ causes the production of ROS in cells challenged by aberrant protein oligomers.
Additional file 1: of Modeling the quantitative nature of neurodevelopmental disorders using Collaborative Cross mice
Creators: name: Molenhuis, Remco
name: Hilgo Bruining
name: Brandt, Myrna
name: Soldt, Petra
name: Atamni, Hanifa Abu-Toamih
name: J. Burbach
name: Iraqi, Fuad
name: Mott, Richard
name: Kas, Martien
Publisher: name: Figshare
Year: 2018
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Plant Biology

description: Figure S1. Haplotype-based and broad-sense heritability estimates in CC mice. Figure S2. Phenotypic correlations in CC mice. Figure S3. Quantification of stereotyped exploratory patterns in C57BL/6J and BTBR mice. Figure S4. Characterization of genes in QTL by predicted ASD implication. Table S1. Quantitative trait loci (QTLs) for neurobehavioral traits in CC mice. Table S2. Human homologous genes in QTLs derived from CC mice. (DOCX 8519Â kb)
A new bound for the Real Waring rank of monomials
Creators: name: Han, Kangjin
name: Moon, Hyunsuk
Publisher: name: arXiv
Year: 2021
Subjects: subject: Algebraic Geometry (math.AG)
subject: Commutative Algebra (math.AC)
subject: FOS: Mathematics
subject: 14P99, 12D05, 13P10, 14A25, 15A21, 14N15

description: In this paper we consider the Waring rank of monomials over the real and the rational numbers. We give a new upper bound for it by establishing a way in which one can take a structured apolar set for any given monomial $X_0^{a_0}X_1^{a_1}\cdots X_n^{a_n}$ ($a_i>0$). This bound coincides with the real Waring rank in the case $n=1$ and in the case $\min(a_i)=1$, which are all the known cases for the real rank of monomials. Our bound is also lower than any other known general bounds for the real Waring rank. Since all of the constructions are still valid over the rational numbers, this provides a new result for the rational Waring rank of any monomial as well. Some examples and computational implementation for potential use are presented in the end.
description: 21 pages, 1 Table included, accepted for publication in SIAGA
Additional file 11 of The nuclear and mitochondrial genome assemblies of Tetragonisca angustula (Apidae: Meliponini), a tiny yet remarkable pollinator in the Neotropics
Creators: name: Ferrari, Rafael Rodrigues
name: Ricardo, Paulo Cseri
name: Dias, Felipe Cordeiro
name: de Souza Araujo, Natalia
name: Soares, Dalliane Oliveira
name: Zhou, Qing-Song
name: Zhu, Chao-Dong
name: Coutinho, Luiz Lehmann
name: Arias, Maria Cristina
name: Batista, Thiago Mafra
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Table S11. Overview of the predicted orthogroup changes,, expansions (2nd to 4th columns) and contractions (5th to 7th columns), for the genome of each insect species analyzed. Numbers between parenthesis in the 2nd and 5th columns indicate the number of orthogroups found to be rapidly expanding and contracting, respectively. Positive or negative numbers in the 9th column indicate an overall expansion or contraction, respectively
Hydrodynamic responses of a thin floating disk to regular waves
Creators: name: Yiew, Lucas
name: Bennetts, Luke
name: Meylan, Michael
name: French, Ben
name: Thomas, Giles
Publisher: name: arXiv
Year: 2015
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Atmospheric and Oceanic Physics (physics.ao-ph)
subject: FOS: Physical sciences

description: Laboratory wave basin measurements of the surge, heave and pitch of a floating plastic disk caused by regular incident waves are presented. The measurements are used to validate two theoretical models: one based on slope-sliding theory and the other on combined potential-flow and thin-plate theories.
description: 20 pages, 16 figures, 1 table
Quantized enveloping superalgebra of type $P$
Creators: name: Ahmed, Saber
name: Grantcharov, Dimitar
name: Guay, Nicolas
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Algebra (math.QA)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics

description: We introduce a new quantized enveloping superalgebra $\mathfrak{U}_q{\mathfrak{p}}_n$ attached to the Lie superalgebra ${\mathfrak{p}}_n$ of type $P$. The superalgebra $\mathfrak{U}_q{\mathfrak{p}}_n$ is a quantization of a Lie bisuperalgebra structure on ${\mathfrak{p}}_n$ and we study some of its basic properties. We also introduce the periplectic $q$-Brauer algebra and prove that it is the centralizer of the $\mathfrak{U}_q {\mathfrak{p}}_n$-module structure on ${\mathbb C}(n|n)^{\otimes l}$. We end by proposing a definition for a new periplectic $q$-Schur superalgebra.
description: 14 pages, minor corrections to the earlier version
Interpretable Sensitivity Analysis for Balancing Weights
Creators: name: Soriano, Dan
name: Ben-Michael, Eli
name: Bickel, Peter J.
name: Feller, Avi
name: Pimentel, Samuel D.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: Assessing sensitivity to unmeasured confounding is an important step in observational studies, which typically estimate effects under the assumption that all confounders are measured. In this paper, we develop a sensitivity analysis framework for balancing weights estimators, an increasingly popular approach that solves an optimization problem to obtain weights that directly minimizes covariate imbalance. In particular, we adapt a sensitivity analysis framework using the percentile bootstrap for a broad class of balancing weights estimators. We prove that the percentile bootstrap procedure can, with only minor modifications, yield valid confidence intervals for causal effects under restrictions on the level of unmeasured confounding. We also propose an amplification to allow for interpretable sensitivity parameters in the balancing weights framework. We illustrate our method through extensive real data examples.
Additional file 12 of The nuclear and mitochondrial genome assemblies of Tetragonisca angustula (Apidae: Meliponini), a tiny yet remarkable pollinator in the Neotropics
Creators: name: Ferrari, Rafael Rodrigues
name: Ricardo, Paulo Cseri
name: Dias, Felipe Cordeiro
name: de Souza Araujo, Natalia
name: Soares, Dalliane Oliveira
name: Zhou, Qing-Song
name: Zhu, Chao-Dong
name: Coutinho, Luiz Lehmann
name: Arias, Maria Cristina
name: Batista, Thiago Mafra
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Table S12. Expansions (+) and contractions (-) in rapidly evolving odorant receptor orthogroups within Meliponini. “0” indicates that the orthogroup did not change in size for the corresponding species or node. <3>, ancestor of Meliponini; <5>, ancestor of Tetragonisca angustula plus Frieseomelitta varia; <1>, ancestor of Melipona
EFFECT OF CLASSROOM ENVIRONMENT ON STUDENTS' ACADEMIC ACHIEVEMENT IN ENGLISH AT SECONDARY SCHOOL LEVEL
Creators: name: SHAZIA SALEEM
name: Dr. KIFAYAT KHAN
name: MARIA BIBI
name: RABIYA MUNSIF
Publisher: name: Zenodo
Year: 2023
Subjects: Effect, Conducive Classroom Environment, Traditional Classroom, Environment, Academic Achievement, Active Participation.

description: Abstract
The aim of the study was to examine the effect of classroom environment on students' academic achievement in English at secondary school level. It was hypothesised that there is no significant difference between the experimental and control group in terms of academic achievement in English after intervention. To carry out this research, true experimental research design was employed. Secondary school students of district Haripur were considered as the population of the study. Seventy (70) students at Government Girls High School Bhera (GGHSB) district Haripur were selected as a sample of the study. A self-constructed English Academic Achievement Test (EAAT) of reliability coefficient 0.829 was used to collect data. The students were divided into experimental and control groups each consisted of thirty-five (35) students through the pertest EAAT scores. The experimental and control groups were taught English in Conducive Classroom Environment (CCE), and Traditional Classroom Environment (TCE) respectively. Both these groups were post-tested through utilizing the same EAAT. The analysed data revealed that experimental group performed very well in the test as compared to the control group. So, students taught English in CCE took active participation in activities that led them towards higher achievement in English. It was suggested that classrooms may be well-organized, well equipped, and facilitated to create an effective learning environment that motivate the students for higher learning.
High autophagic vesicle content marks facultative stem cells of the gut
Creators: name: Parham, Louis R.
name: Johnson, Nicolette M.
name: Lengner, Christopher J.
name: Hamilton, Kathryn E.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Understanding how macroautophagy/autophagy contributes to tissue homeostasis is essential for understanding organismal health. The intestinal epithelium is an ideal model to define mechanisms that regulate tissue homeostasis because it houses well-defined populations of intestinal stem cells. Active intestinal stem cells (a-ISCs) are defined by their active cycling and self-renewal during homeostasis, which supports continual tissue turnover in vivo. In vitro, this is observed as long-term organoid formation capacity. A second population of stem cells, called “facultative intestinal stem cells” (f-ISCs), are defined by their ability to 1) survive tissue damage that depletes the injury-sensitive a-ISCs and 2) reenter the cell cycle to repopulate the a-ISC compartment and regenerate the epithelium. The prospective identification of f-ISCs has been challenging, as cells expressing markers of multiple differentiated lineages, particularly secretory lineages, appear to function as f-ISCs in diverse injury contexts. We evaluated cell age (defined as time elapsed after cell cycle exit) and autophagic state (marked by autophagic vesicle content) as molecular features that may be related to f-ISC capacity. We found that autophagic state, but not cell age, prospectively identifies f-ISCs within multiple lineages. As such, we describe autophagy as a lineage-agnostic marker of f-ISC capacity in the mammalian intestine.
Comparing the sensitivity of social networks, web graphs, and random graphs with respect to vertex removal
Creators: name: Martin, Christoph
name: Niemeyer, Peter
Publisher: name: arXiv
Year: 2014
Subjects: subject: Social and Information Networks (cs.SI)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: The sensitivity of networks regarding the removal of vertices has been studied extensively within the last 15 years. A common approach to measure this sensitivity is (i) removing successively vertices by following a specific removal strategy and (ii) comparing the original and the modified network using a specific comparison method. In this paper we apply a wide range of removal strategies and comparison methods in order to study the sensitivity of medium-sized networks from real world and randomly generated networks. In the first part of our study we observe that social networks and web graphs differ in sensitivity. When removing vertices, social networks are robust, web graphs are not. This effect is conclusive with the work of Boldi et al. who analyzed very large networks. For similarly generated random graphs we find that the sensitivity highly depends on the comparison method. The choice of the removal strategy has surprisingly marginal impact on the sensitivity as long as we consider removal strategies implied by common centrality measures. However, it has a strong effect when removing the vertices in random order.
description: 11 pages, 4 figures
Personal Data in Research
Creators: name: van der Burgt, Henry
name: de Laat, Stijn
name: Jansen, Daphne
name: Lamers, Didi
name: Marcoux, Katherine
name: Slouwerhof, Inge
Publisher: name: Zenodo
Year: 2023
Subjects: General Data Protection Regulation
personal data
privacy
research data management
RDM
research data
data management
data organisation

description: A presentation on the topic of personal data and how this can be applied to scientific research in the context of the General Data Protection Regulation (GDPR). The presentation seeks answers to the question how one can best handle personal data in each phase of a research project, by introducing the basics of the GDPR and the various key concepts which are important when doing research that involves identifiable personal data.

The presentation introduces the research cycle and provides pragmatic ways in which researchers can include good privacy practices during the phases of research planning, data collection, data analysis, publishing and archiving of the research data.

The presentation provides researchers with a basic understanding of the GDRP, an awareness for the role of personal data in each phase of the research cycle and knowledge on when to reach out for assistance and who to contact in the support infrastructure of the Radboud University in Nijmegen.

Topics include:

What is the GDPR? When, where and how does it apply to academic research?

What exceptions are there for special categories or sensitive personal data?

How does personal data affect your storage and security practices?

How to best handle personal data during each phase of your research?

What are the privacy rights of your participants?

How does personal data affect your possibilities to archive, share and publish data?
Simulation comparisons between Bayesian and de-biased estimators in low-rank matrix completion
Creators: name: Mai, The Tien
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (stat.ML)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: In this paper, we study the low-rank matrix completion problem, a class of machine learning problems, that aims at the prediction of missing entries in a partially observed matrix. Such problems appear in several challenging applications such as collaborative filtering, image processing, and genotype imputation. We compare the Bayesian approaches and a recently introduced de-biased estimator which provides a useful way to build confidence intervals of interest. From a theoretical viewpoint, the de-biased estimator comes with a sharp minimax-optimal rate of estimation error whereas the Bayesian approach reaches this rate with an additional logarithmic factor. Our simulation studies show originally interesting results that the de-biased estimator is just as good as the Bayesian estimators. Moreover, Bayesian approaches are much more stable and can outperform the de-biased estimator in the case of small samples. In addition, we also find that the empirical coverage rate of the confidence intervals obtained by the de-biased estimator for an entry is absolutely lower than of the considered credible interval. These results suggest further theoretical studies on the estimation error and the concentration of Bayesian methods as they are quite limited up to present.
Mapping the periphery of deformation in the A∼80 region: A study of Nb83
Creators: name: Sun, Y.
name: Hammond, N.J.
name: Fischer, S.M.
name: Sinha, S.
name: Mukharjee, G.
name: Lister, C.J.
name: Moore, E.F.
name: Carpenter, M.P.
name: Balamuth, D.P.
name: Freeman, S.J.
name: Janssens, R.V.F.
name: Seweryniak, D.
name: Carney, J.
Publisher: name: American Physical Society
Year: 2007

description: Nb83 has been studied in order to locate the upper extent of large deformation in the N∼Z∼40 region and ascertain its sign and magnitude. The decay scheme has been considerably extended by studying gamma decay following the Ni58(Si28, p2n)Nb83 reaction at 204 and 215 MeV and using Gammasphere. Both signature partners of two rotational bands have been observed. The band properties support a Iπ=52+ ground state spin assignment. The in-band branching ratios and multipole mixing ratios were found to be consistent with significant prolate deformation, as found in other N=42 isotones. The bands are particularly similar to the isotone Y81. A projected shell model analysis has been performed which provides good reproduction of the features of both bands. The calculations indicate the nucleus to be nearly axially symmetric. Nb82,83 may be the heaviest nuclei in the A∼80 region with large deformation. The deformation is predicted to fall in heavier systems approaching Sn100. The conditions appear to be right for the occurrence of K isomers.
Effect of Cypermethrin and Oxyfluorfen on alimentary canal of earthworm, Eisenia foetida
Creators: name: D. S. PATIL 1, P. K. BAGUL2 P. A. SURYAWANSHI 3 AND B. C. MORE 4
Publisher: name: Zenodo
Year: 2022
Subjects: Eisenia foetida; Cypermethrin; Oxyfluorfen; histology; tissue; gut; etc.

description: Abstract Agriculture is the cornerstone of our Indian economy, and the usage of pesticides is an inseparable part of this trade. Pesticidal residues does not degrade in soil, it remains in the soil and indirectly enters the gut of earthworms through their feeding. Earthworms are soil engineers feed on soil and humus. These residues have negative impact on tissues of alimentary canal. In present piece of work lower and higher sublethal doses of Cypermethrin (Insecticide) and Oxyfluorfen (Herbicide) are administered to earthworm species E. foetida and kept for 90 days. At the end of the experiment the animals were kept on wet filter paper to remove the dust from the alimentary canal and cut into small pieces. Permanent histological slide preparation was done. Slides were selected and histological damages were recorded. Normally the wall of alimentary canal consists of four layers i.e. peritoneum, muscular, enteric epithelium and cuticle. In control worm all the histological structures of foregut, midgut and hindgut were normal but the worms treated with Cypermethrin shown breaks in foregut. While in midgut inner cuticle shown damages, eroded epidermis. Damages are also observed in peritoneum. Accumulation of foreign bodies are seen in chloragogen cells. In hindgut several damages are seen in peritoneum, vacuolization in coelom. In the worms treated with oxyfluorfen, foregut shown unfolded cuticle. Slight injury is observed in longitudinal muscles and detached peritoneum. Similarly, the midgut and hindgut is not much affected in the treatment of oxyfluorfen. It means cypermethrin is much toxic causes histological damages. It my effect on absorption while comparatively oxyfluorfen is less toxic. Histological endpoints are very important for eco-toxicological studies.
A remark on Fine's arithmetic functions
Creators: name: Patkowski, Alexander E.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics

description: In this note, we take another look at some arithmetic identities of N.J. Fine associated with divisor functions. We connect these functions with indefinite quadratic forms using a result due to Andrews. As a consequence, arithmetic theorems are extracted.
Atg1-dependent phosphorylation of Vps34 is required for dynamic regulation of the phagophore assembly site and autophagy in Saccharomyces cerevisiae
Creators: name: Lee, Yongook
name: Kim, Bongkeun
name: Jang, Hae-Soo
name: Huh, Won-Ki
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology

description: Macroautophagy/autophagy is a key catabolic pathway in which double-membrane autophagosomes sequester various substrates destined for degradation, enabling cells to maintain homeostasis and survive under stressful conditions. Several autophagy-related (Atg) proteins are recruited to the phagophore assembly site (PAS) and cooperatively function to generate autophagosomes. Vps34 is a class III phosphatidylinositol 3-kinase, and Atg14-containing Vps34 complex I plays essential roles in autophagosome formation. However, the regulatory mechanisms of yeast Vps34 complex I are still poorly understood. Here, we demonstrate that Atg1-dependent phosphorylation of Vps34 is required for robust autophagy activity in Saccharomyces cerevisiae. Following nitrogen starvation, Vps34 in complex I is selectively phosphorylated on multiple serine/threonine residues in its helical domain. This phosphorylation is important for full autophagy activation and cell survival. The absence of Atg1 or its kinase activity leads to complete loss of Vps34 phosphorylation in vivo, and Atg1 directly phosphorylates Vps34 in vitro, regardless of its complex association type. We also demonstrate that the localization of Vps34 complex I to the PAS provides a molecular basis for the complex I-specific phosphorylation of Vps34. This phosphorylation is required for the normal dynamics of Atg18 and Atg8 at the PAS. Together, our results reveal a novel regulatory mechanism of yeast Vps34 complex I and provide new insights into the Atg1-dependent dynamic regulation of the PAS. Abbreviations: ATG: autophagy-related; BARA: the repeated, autophagy-specific Co-IP: co-immunoprecipitation; GFP: green fluorescent protein; IP-MS: immunoprecipitation followed by tandem mass spectrometry; NTD: the N-terminal domain; PAS: phagophore assembly site; PtdIns3P: phosphatidylinositol-3-phosphate; PtdIns3K: phosphatidylinositol 3-kinase; SUR: structurally uncharacterized region; Vps34[KD]: Vps34D731N.
Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression based convolutional neural networks
Creators: name: Weitz, Philippe
name: Wang, Yinxi
name: Kartasalo, Kimmo
name: Egevad, Lars
name: Lindberg, Johan
name: Grönberg, Henrik
name: Eklund, Martin
name: Rantalainen, Mattias
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Molecular phenotyping by gene expression profiling is common in contemporary cancer research and in molecular diagnostics. However, molecular profiling remains costly and resource intense to implement, and is just starting to be introduced into clinical diagnostics. Molecular changes, including genetic alterations and gene expression changes, occuring in tumors cause morphological changes in tissue, which can be observed on the microscopic level. The relationship between morphological patterns and some of the molecular phenotypes can be exploited to predict molecular phenotypes directly from routine haematoxylin and eosin (H&E) stained whole slide images (WSIs) using deep convolutional neural networks (CNNs). In this study, we propose a new, computationally efficient approach for disease specific modelling of relationships between morphology and gene expression, and we conducted the first transcriptome-wide analysis in prostate cancer, using CNNs to predict bulk RNA-sequencing estimates from WSIs of H&E stained tissue. The work is based on the TCGA PRAD study and includes both WSIs and RNA-seq data for 370 patients. Out of 15586 protein coding and sufficiently frequently expressed transcripts, 6618 had predicted expression significantly associated with RNA-seq estimates (FDR-adjusted p-value < 1*10-4) in a cross-validation. 5419 (81.9%) of these were subsequently validated in a held-out test set. We also demonstrate the ability to predict a prostate cancer specific cell cycle progression score directly from WSIs. These findings suggest that contemporary computer vision models offer an inexpensive and scalable solution for prediction of gene expression phenotypes directly from WSIs, providing opportunity for cost-effective large-scale research studies and molecular diagnostics.
Lifetime measurements of triaxial strongly deformed bands in Tm163
Creators: name: Li, T.
name: Zhu, S.
name: Wang, X.
name: Ghugre, S.S.
name: Hammond, N.J.
name: Moore, E.F.
name: Mukherjee, G.
name: Carpenter, M.P.
name: Pattabiraman, N.S.
name: Seweryniak, D.
name: Janssens, R.V.F.
name: Garg, U.
name: Gu, Y.
name: Frauendorf, S.
name: Lauritsen, T.
Publisher: name: American Physical Society
Year: 2007

description: With the Doppler Shift Attenuation Method, quadrupole transition moments Qt were determined for the two recently proposed triaxial strongly deformed (TSD) bands in Tm163. The measured Qt values indicate that the deformation of these bands is larger than that of the yrast signature partners. However, the measured values are smaller than those predicted by theory. This observation appears to be valid for TSD bands in several nuclei of the region.
Building with Drones: Accurate 3D Facade Reconstruction using MAVs
Creators: name: Daftry, Shreyansh
name: Hoppe, Christof
name: Bischof, Horst
Publisher: name: arXiv
Year: 2015
Subjects: subject: Robotics (cs.RO)
subject: Artificial Intelligence (cs.AI)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Automatic reconstruction of 3D models from images using multi-view Structure-from-Motion methods has been one of the most fruitful outcomes of computer vision. These advances combined with the growing popularity of Micro Aerial Vehicles as an autonomous imaging platform, have made 3D vision tools ubiquitous for large number of Architecture, Engineering and Construction applications among audiences, mostly unskilled in computer vision. However, to obtain high-resolution and accurate reconstructions from a large-scale object using SfM, there are many critical constraints on the quality of image data, which often become sources of inaccuracy as the current 3D reconstruction pipelines do not facilitate the users to determine the fidelity of input data during the image acquisition. In this paper, we present and advocate a closed-loop interactive approach that performs incremental reconstruction in real-time and gives users an online feedback about the quality parameters like Ground Sampling Distance (GSD), image redundancy, etc on a surface mesh. We also propose a novel multi-scale camera network design to prevent scene drift caused by incremental map building, and release the first multi-scale image sequence dataset as a benchmark. Further, we evaluate our system on real outdoor scenes, and show that our interactive pipeline combined with a multi-scale camera network approach provides compelling accuracy in multi-view reconstruction tasks when compared against the state-of-the-art methods.
description: 8 Pages, 2015 IEEE International Conference on Robotics and Automation (ICRA '15), Seattle, WA, USA
Additional file 13 of The nuclear and mitochondrial genome assemblies of Tetragonisca angustula (Apidae: Meliponini), a tiny yet remarkable pollinator in the Neotropics
Creators: name: Ferrari, Rafael Rodrigues
name: Ricardo, Paulo Cseri
name: Dias, Felipe Cordeiro
name: de Souza Araujo, Natalia
name: Soares, Dalliane Oliveira
name: Zhou, Qing-Song
name: Zhu, Chao-Dong
name: Coutinho, Luiz Lehmann
name: Arias, Maria Cristina
name: Batista, Thiago Mafra
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Table S13. Predicted number of orthogroups in expansion (2nd column) and contraction (3rd column) in for the genome of each sampled stingless bee species based on OrthoVenn analysis
Defining and Detecting Toxicity on Social Media: Context and Knowledge are Key
Creators: name: Sheth, Amit
name: Shalin, Valerie L.
name: Kursuncu, Ugur
Publisher: name: arXiv
Year: 2021
Subjects: subject: Social and Information Networks (cs.SI)
subject: FOS: Computer and information sciences

description: Online platforms have become an increasingly prominent means of communication. Despite the obvious benefits to the expanded distribution of content, the last decade has resulted in disturbing toxic communication, such as cyberbullying and harassment. Nevertheless, detecting online toxicity is challenging due to its multi-dimensional, context sensitive nature. As exposure to online toxicity can have serious social consequences, reliable models and algorithms are required for detecting and analyzing such communication across the vast and growing space of social media. In this paper, we draw on psychological and social theory to define toxicity. Then, we provide an approach that identifies multiple dimensions of toxicity and incorporates explicit knowledge in a statistical learning algorithm to resolve ambiguity across such dimensions.
Level structure of Rh92: Implications for the two-proton decay of Ag94m
Creators: name: Janssens, R.V.F.
name: Andersson, L.-L.
name: Lauritsen, T.
name: Johansson, E.K.
name: Lister, C.J.
name: Rudolph, D.
name: Reviol, W.
name: Pechenaya, O.L.
name: Seweryniak, D.
name: Charity, R.J.
name: Chiara, C.J.
name: Carpenter, M.P.
name: Zhu, S.
name: Sarantites, D.G.
Publisher: name: American Physical Society
Year: 2007

description: The 21+ isomer in Ag94 has recently been reported to have a two-proton decay branch to Rh92. We have populated Rh92 through the Ca40(Ni58,αpn) reaction at 240 MeV, and have performed detailed spectroscopic measurements of the levels, finding new states and measuring angular distributions of γ rays. We find no evidence for the states reported to be populated by the two-proton decay of Ag94m. The calculated Q-value for the two-proton decay implies that this process directly feeds low-lying yrast, or near-yrast, states in Rh92, which is very difficult to reconcile with our observations. Several scenarios for the population of Rh92 are discussed, none of which appears to be satisfactory.
POLYHERBAL TABLET: FORMULATION, EVALUATION, AND ANTI-DIABETIC ACTIVITY OF ETHANOLIC EXTRACT OF LEAVES OF T. PORTULACASTRUM AND A. MARMELOS
Creators: name: Dr. Nihar Ranjan Kar
name: Sarath Babu V
name: Brijendra Singh
name: S. Varalaxmi
name: Kirti Kaushal
name: Sharang Bali
name: Dr. P. Dharani Prasad
Publisher: name: Zenodo
Year: 2023
Subjects: Polyherbal tablet, Anti-diabetic activity, Alloxan, Circulifer tenellus

description: Abstract 
Diabetes, which has been known about since ancient times, is one of the oldest diseases in the world. Given what we know now, it is pretty amazing how early this illness was understood, as may be deduced from the available ancient medical texts. To effectively cure hyperglycaemia and maintain normal blood sugar levels, ancient Indian medicine made considerable use of medicinal herbs. Numerous medicinal plants have been studied recently to discover their effects and determine whether they have any antihyperglycemic potential. An ethanolic extract of the leaves from Circulifer tenellus was used in the current experiment to make and evaluate a polyherbal tablet. The added anti-diabetic efficacy of the enhanced formulation was investigated in an alloxan-induced animal model. Results show that the improved batch demonstrated significant activity compared to standard medicine.
On summation formulas in probability theory
Creators: name: Patkowski, Alexander E.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics

description: We offer some summation formulas that appear to have great utility in probability theory. The proofs require some recent results from analysis that have thus far been applied to basic hypergeometric functions.