cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Dolichogenidea turkmena
Creators: name: Fernandez-Triana, Jose
name: Sakagami, Kota
name: Shimizu, So
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Braconidae
Dolichogenidea
Dolichogenidea turkmena

description: D. turkmena (Telenga, 1955): Legs reddish; antenna moniliform, shorter than body; propodeum smooth; pterostigma yellow to transparent.
description: Published as part of Fernandez-Triana, Jose, Sakagami, Kota & Shimizu, So, 2018, Dolichogenidea maetoi sp. nov. (Hymenoptera: Braconidae) from Japan, the first parasitoid wasp recorded from Hyblaea fortissima (Lepidoptera), pp. 167-175 in Acta Entomologica Musei Nationalis Pragae 58 (1) on page 174, DOI: 10.2478/aemnp-2018-0014, http://zenodo.org/record/3699178
Elicitation on have-constructions and raising
Creators: name: Rudolph, Johnny (Soni)
name: Drummond, Emily
Publisher: name: California Language Archive, University of California, Berkeley
Year: 2022
Subjects: subject: nkr

description: Elicitation on have-constructions, which potentially involve copy raising, whether those pre-verbal subjects are topics, further questions about raising in general. No corresponding audio, which was lost due to technical issues.
Metabonomics study of the effects of single copy mutant KRAS in the presence or absence of WT allele using human HCT116 isogenic cell lines.
Creators: name: Varshavi, Dorna
name: Varshavi, Dorsa
name: McCarthy, Nicola
name: Veselkov, Kirill
name: Keun, Hector C
name: Everett, Jeremy R
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Original Article
KRAS
Mutations
HCT116
Cells
Colorectal cancer
Metabonomics
Metabolomics
Metabolic profiling
NMR

description: INTRODUCTION: KRAS was one of the earliest human oncogenes to be described and is one of the most commonly mutated genes in different human cancers, including colorectal cancer. Despite KRAS mutants being known driver mutations, KRAS has proved difficult to target therapeutically, necessitating a comprehensive understanding of the molecular mechanisms underlying KRAS-driven cellular transformation. OBJECTIVES: To investigate the metabolic signatures associated with single copy mutant KRAS in isogenic human colorectal cancer cells and to determine what metabolic pathways are affected. METHODS: Using NMR-based metabonomics, we compared wildtype (WT)-KRAS and mutant KRAS effects on cancer cell metabolism using metabolic profiling of the parental KRAS G13D/+ HCT116 cell line and its isogenic, derivative cell lines KRAS +/- and KRAS G13D/-. RESULTS: Mutation in the KRAS oncogene leads to a general metabolic remodelling to sustain growth and counter stress, including alterations in the metabolism of amino acids and enhanced glutathione biosynthesis. Additionally, we show that KRASG13D/+ and KRASG13D/- cells have a distinct metabolic profile characterized by dysregulation of TCA cycle, up-regulation of glycolysis and glutathione metabolism pathway as well as increased glutamine uptake and acetate utilization. CONCLUSIONS: Our study showed the effect of a single point mutation in one KRAS allele and KRAS allele loss in an isogenic genetic background, hence avoiding confounding genetic factors. Metabolic differences among different KRAS mutations might play a role in their different responses to anticancer treatments and hence could be exploited as novel metabolic vulnerabilities to develop more effective therapies against oncogenic KRAS.
Effect of hyperon-hyperon interaction on bulk viscosity and r-mode instability in neutron stars
Creators: name: Chatterjee, Debarati
name: Bandyopadhyay, Debades
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We investigate the effect of hyperon matter including hyperon-hyperon interaction on bulk viscosity. Equations of state are constructed within the framework of a relativistic field theoretical model where baryon-baryon interaction is mediated by the exchange of scalar and vector mesons. Hyperon-hyperon interaction is also taken into account by the exchange of two strange mesons. This interaction results in a smaller maximum mass neutron star compared with the case without the interaction. The coefficient of bulk viscosity due to the non-leptonic weak process is determined by these equations of state. The interacting hyperon matter reduces the bulk viscosity coefficient in a neutron star interior compared with the no interaction case. The r-mode instability is more effectively suppressed in hyperon-hyperon interaction case than that without the interaction.
description: 25 pages, 10 figures; two new figures added and results and discussion section revised; final version to appear in PRD
Perturbative structure of two- and four-point functions of color charge in a non-Gaussian small-$x$ action
Creators: name: Giannini, Andre V.
name: Nara, Yasushi
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We compute the perturbative expansion of the two- and four-point functions of color charges in the Color Glass Condensate framework considering the quartic correction to the McLerran-Venugopalan (MV) model of Gaussian color charge fluctuations. Expressions for these correlators in the perturbative expansion for small and large non-Gaussian color charge fluctuations are derived for arbitrary orders in perturbation theory. We explicitly show that the perturbative series does not converge at higher orders as expected. We apply the Borel-Padé resummation method to our problem to construct a convergent series. It is shown that the fully non-perturbative solution can be described by the Borel-Padé approximants constructed from the first few terms of the perturbative series for small non-Gaussian fluctuations.
description: 17 pages, 6 figures
Dolichogenidea turionellae
Creators: name: Fernandez-Triana, Jose
name: Sakagami, Kota
name: Shimizu, So
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Braconidae
Dolichogenidea
Dolichogenidea turionellae

description: D. turionellae (Nixon, 1971): Ovipositor sheath longer than metatibia (1.5 times); T2 with posterior margin sinuate.
description: Published as part of Fernandez-Triana, Jose, Sakagami, Kota & Shimizu, So, 2018, Dolichogenidea maetoi sp. nov. (Hymenoptera: Braconidae) from Japan, the first parasitoid wasp recorded from Hyblaea fortissima (Lepidoptera), pp. 167-175 in Acta Entomologica Musei Nationalis Pragae 58 (1) on page 174, DOI: 10.2478/aemnp-2018-0014, http://zenodo.org/record/3699178
Dolichogenidea turcmenica
Creators: name: Fernandez-Triana, Jose
name: Sakagami, Kota
name: Shimizu, So
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Braconidae
Dolichogenidea
Dolichogenidea turcmenica

description: D. turcmenica (Tobias, 1967): Vein R1 much shorter than pterostigma; pterostigma pale with thin brown margins; most veins transparent; propodeum mostly polished and without areola (only small rugae above nucha); T2 transverse and smooth.
description: Published as part of Fernandez-Triana, Jose, Sakagami, Kota & Shimizu, So, 2018, Dolichogenidea maetoi sp. nov. (Hymenoptera: Braconidae) from Japan, the first parasitoid wasp recorded from Hyblaea fortissima (Lepidoptera), pp. 167-175 in Acta Entomologica Musei Nationalis Pragae 58 (1) on page 174, DOI: 10.2478/aemnp-2018-0014, http://zenodo.org/record/3699178
Systematic study of the PDC speckle structure for quantum imaging applications
Creators: name: Brida, G.
name: Genovese, M.
name: Meda, A.
name: Predazzi, E.
name: Ruo-Berchera, I.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Sub shot noise imaging of weak object by exploiting Parametric Down Converted light represents a very interesting technological development. A precise characterization of PDC speckle structure in dependence of pump beam parameters is a fundamental tool for this application. In this paper we present a first set of data addressed to this purpose.
Conditions for direct black hole seed collapse near a radio-loud quasar 1 Gyr after the Big Bang
Creators: name: Overzier, Roderik A.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Observations of luminous quasars and their supermassive black holes at z~6 suggest that they formed at dense matter peaks in the early universe. However, few studies have found definitive evidence that the quasars lie at cosmic density peaks, in clear contrast with theory predictions. Here we present new evidence that the radio-loud quasar SDSS J0836+0054 at z=5.8 could be part of a surprisingly rich structure of galaxies. This conclusion is reached by combining a number of findings previously reported in the literature: Bosman et al. (2020) obtained the redshifts of three companion galaxies, confirming an overdensity of i-dropouts found by Zheng et al. (2006). By comparing this structure with those found near other quasars and large overdense regions in the field at z~6-7, we show that the SDSS J0836+0054 field is among the densest structures known at these redshifts. One of the spectroscopic companions is a very massive star-forming galaxy (log M_*/M_sun ~ 10.3) based on its unambiguous detection in a Spitzer 3.6 um image. This suggests that the quasar field hosts not one, but at least two rare, massive dark matter halos (log M_halo/M_sun > 12), corresponding to a galaxy overdensity of at least 20. We discuss the properties of the young radio source. We conclude that the environment of SDSS J0836+0054 resembles, at least qualitatively, the type of conditions that may have spurred the direct collapse of a massive black hole seed according to recent theory.
description: Accepted by ApJ
SARS-CoV-2 transmission across age groups in France and implications for control.
Creators: name: Tran Kiem, Cécile
name: Bosetti, Paolo
name: Paireau, Juliette
name: Crépey, Pascal
name: Salje, Henrik
name: Lefrancq, Noemie
name: Fontanet, Arnaud
name: Benamouzig, Daniel
name: Boëlle, Pierre-Yves
name: Desenclos, Jean-Claude
name: Opatowski, Lulla
name: Cauchemez, Simon
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Article
/631/114/2397
/631/114/2415
/631/326/596/4130
/692/308/174
/141
/129
article

description: Funder: AXA Research Fund (Le Fonds AXA pour la Recherche); doi: https://doi.org/10.13039/501100001961
description: Funder: We acknowledge financial support from the Investissement d'Avenir program, the Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases program (grant ANR-10-LABX-62-IBEID), Santé Publique France, the INCEPTION project (PIA/ANR-16-COV-0005), the European Union’s Horizon 2020 research and innovation program under grant 101003589 (RECOVER) and 874735 (VEO), AXA and Groupama.
description: The shielding of older individuals has been proposed to limit COVID-19 hospitalizations while relaxing general social distancing in the absence of vaccines. Evaluating such approaches requires a deep understanding of transmission dynamics across ages. Here, we use detailed age-specific case and hospitalization data to model the rebound in the French epidemic in summer 2020, characterize age-specific transmission dynamics and critically evaluate different age-targeted intervention measures in the absence of vaccines. We find that while the rebound started in young adults, it reached individuals aged ≥80 y.o. after 4 weeks, despite substantial contact reductions, indicating substantial transmission flows across ages. We derive the contribution of each age group to transmission. While shielding older individuals reduces mortality, it is insufficient to allow major relaxations of social distancing. When the epidemic remains manageable (R close to 1), targeting those most contributing to transmission is better than shielding at-risk individuals. Pandemic control requires an effort from all age groups.
New Insights into Uniformly Accelerated Detector in a Quantum Field
Creators: name: Lin, Shih-Yuin
name: Hu, B. L.
Publisher: name: arXiv
Year: 2006
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We obtained an exact solution for a uniformly accelerated Unruh-DeWitt detector interacting with a massless scalar field in (3+1) dimensions which enables us to study the entire evolution of the total system, from the initial transient to late-time steady state. We find that the Unruh effect as derived from time-dependent perturbation theory is valid only in the transient stage and is totally invalid for cases with proper acceleration smaller than the damping constant. We also found that, unlike in (1+1)D results, the (3+1)D uniformly accelerated Unruh-DeWitt detector in a steady state does emit a positive radiated power of quantum nature at late-times, but it is not connected to the thermal radiance experienced by the detector in the Unruh effect proper.
description: 6 pages, invited talk given by SYL at the conference of International Association for Relativistic Dynamics (IARD), June 2006, Storrs, Connecticut, USA
A fast semi-discrete optimal transport algorithm for a unique reconstruction of the early Universe
Creators: name: Lévy, Bruno
name: Mohayaee, Roya
name: von Hausegger, Sebastian
Publisher: name: arXiv
Year: 2020
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Numerical Analysis (math.NA)
subject: Analysis of PDEs (math.AP)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We leverage powerful mathematical tools stemming from optimal transport theory and transform them into an efficient algorithm to reconstruct the fluctuations of the primordial density field, built on solving the Monge-Ampère-Kantorovich equation. Our algorithm computes the optimal transport between an initial uniform continuous density field, partitioned into Laguerre cells, and a final input set of discrete point masses, linking the early to the late Universe. While existing early universe reconstruction algorithms based on fully discrete combinatorial methods are limited to a few hundred thousand points, our algorithm scales up well beyond this limit, since it takes the form of a well-posed smooth convex optimization problem, solved using a Newton method. We run our algorithm on cosmological $N$-body simulations, from the AbacusCosmos suite, and reconstruct the initial positions of $\mathcal{O}(10^7)$ particles within a few hours with an off-the-shelf personal computer. We show that our method allows a unique, fast and precise recovery of subtle features of the initial power spectrum, such as the baryonic acoustic oscillations.
description: 22 pages
Elicitation on focus and topic positions
Creators: name: Lekka, Mina
name: Drummond, Emily
Publisher: name: California Language Archive, University of California, Berkeley
Year: 2022
Subjects: subject: nkr

description: Elicitation on focus marking with go (question/answer pairs, corrections, association with focus); competition between se/ni and go marking; and aboutness topics and subject position, using an original storyboard archived in another bundle.
The Principle of Certainty
Creators: name: Yasin, Muhammad
Publisher: name: figshare
Year: 2021
Subjects: subject: 20202 Nuclear Physics
subject: FOS: Physical sciences
subject: 20203 Particle Physics
subject: 20603 Quantum Information, Computation and Communication
subject: Quantum Mechanics
subject: Atomic Physics
subject: 20201 Atomic and Molecular Physics
subject: 20299 Atomic, Molecular, Nuclear, Particle and Plasma Physics not elsewhere classified

description: It is possible to prove the principle of certainty in a different way from the theory of relativity, de Broglie particle wave duality, the principle of uncertainty. The principle of certainty is the formula for measuring the position and momentum of a particle at the same time. If the theory of relativity, the principle of uncertainty is correct, then the principle of certainty must be considered correct. Because it is possible to prove the principle of certainty from the principle of uncertainty, it is also possible to prove the principle of certainty from the theory of special relativity. Again the idea of ​​the principle of certainty comes from the de Broglie particle wave duality principle. Max Planck's radiation formula can be proved from the principle of certainty.
Dolichogenidea ultima
Creators: name: Fernandez-Triana, Jose
name: Sakagami, Kota
name: Shimizu, So
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Braconidae
Dolichogenidea
Dolichogenidea ultima

description: D. ultima (Kotenko, 1986): Ovipositor sheath longer than metatibia (original description does not provide details but states that it is “noticeably longer”); propodeum areola open anteriorly but with transverse carinae; T1 less than 1.5 times as long as wide.
description: Published as part of Fernandez-Triana, Jose, Sakagami, Kota & Shimizu, So, 2018, Dolichogenidea maetoi sp. nov. (Hymenoptera: Braconidae) from Japan, the first parasitoid wasp recorded from Hyblaea fortissima (Lepidoptera), pp. 167-175 in Acta Entomologica Musei Nationalis Pragae 58 (1) on page 174, DOI: 10.2478/aemnp-2018-0014, http://zenodo.org/record/3699178
Classification of four qubit states and their stabilisers under SLOCC operations
Creators: name: Dietrich, Heiko
name: de Graaf, Willem A.
name: Marrani, Alessio
name: Origlia, Marcos
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: Representation Theory (math.RT)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We classify four qubit states under SLOCC operations, that is, we classify the orbits of the group $\mathrm{\mathop{SL}}(2,\mathbb{C})^4$ on the Hilbert space $\mathcal{H}_4 = (\mathbb{C}^2)^{\otimes 4}$. We approach the classification by realising this representation as a symmetric space of maximal rank. We first describe general methods for classifying the orbits of such a space. We then apply these methods to obtain the orbits in our special case, resulting in a complete and irredundant classification of $\mathrm{\mathop{SL}}(2,\mathbb{C})^4$-orbits on $\mathcal{H}_4$. It follows that an element of $(\mathbb{C}^2)^{\otimes 4}$ is conjugate to an element of precisely 87 classes of elements. Each of these classes either consists of one element or of a parametrised family of elements, and the elements in the same class all have equal stabiliser in $\mathrm{\mathop{SL}}(2,\mathbb{C})^4$. We also present a complete and irredundant classification of elements and stabilisers up to the action of ${\rm Sym}_4\ltimes\mathrm{\mathop{SL}}(2,\mathbb{C})^4$ where ${\rm Sym}_4$ permutes the four tensor factors of $(\mathbb{C}^2)^{\otimes 4}$.
Vaccine Confidence and Hesitancy at the Start of COVID-19 Vaccine Deployment in the UK: An Embedded Mixed-Methods Study.
Creators: name: Roberts, Chrissy H
name: Brindle, Hannah
name: Rogers, Nina T
name: Eggo, Rosalind M
name: Enria, Luisa
name: Lees, Shelley
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Public Health
COVID-19
vaccines
mixed-methods
anthropology
trust
misinformation

description: Background: Approval for the use of COVID-19 vaccines has been granted in a number of countries but there are concerns that vaccine uptake may be low amongst certain groups. Methods: This study used a mixed methods approach based on online survey and an embedded quantitative/qualitative design to explore perceptions and attitudes that were associated with intention to either accept or refuse offers of vaccination in different demographic groups during the early stages of the UK's mass COVID-19 vaccination programme (December 2020). Analysis used multivariate logistic regression, structural text modeling and anthropological assessments. Results: Of 4,535 respondents, 85% (n = 3,859) were willing to have a COVID-19 vaccine. The rapidity of vaccine development and uncertainties about safety were common reasons for COVID-19 vaccine hesitancy. There was no evidence for the widespread influence of mis-information, although broader vaccine hesitancy was associated with intentions to refuse COVID-19 vaccines (OR 20.60, 95% CI 14.20-30.30, p < 0.001). Low levels of trust in the decision-making (OR 1.63, 95% CI 1.08, 2.48, p = 0.021) and truthfulness (OR 8.76, 95% CI 4.15-19.90, p < 0.001) of the UK government were independently associated with higher odds of refusing COVID-19 vaccines. Compared to political centrists, conservatives and liberals were, respectively, more (OR 2.05, 95%CI 1.51-2.80, p < 0.001) and less (OR 0.30, 95% CI 0.22-0.41, p < 0.001) likely to refuse offered vaccines. Those who were willing to be vaccinated cited both personal and public protection as reasons, with some alluding to having a sense of collective responsibility. Conclusion: Dominant narratives of COVID-19 vaccine hesitancy are misconceived as primarily being driven by misinformation. Key indicators of UK vaccine acceptance include prior behaviors, transparency of the scientific process of vaccine development, mistrust in science and leadership and individual political views. Vaccine programmes should leverage the sense of altruism, citizenship and collective responsibility that motivated many participants to get vaccinated.
A Spitzer IRS Spectral Atlas of Luminous 8 micron Sources in the Large Magellanic Cloud
Creators: name: Buchanan, Catherine L.
name: Kastner, Joel H.
name: Forrest, William J.
name: Hrivnak, Bruce J.
name: Sahai, Raghvendra
name: Egan, Michael
name: Frank, Adam
name: Barnbaum, Cecilia
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present an atlas of Spitzer Space Telescope Infrared Spectrograph (IRS) spectra of highly luminous, compact mid-infrared sources in the Large Magellanic Cloud. Sources were selected on the basis of infrared colors and 8 micron (MSX) fluxes indicative of highly evolved, intermediate- to high-mass stars with current or recent mass loss at large rates. We determine the chemistry of the circumstellar envelope from the mid-IR continuum and spectral features and classify the spectral types of the stars. In the sample of 60 sources, we find 21 Red Supergiants (RSGs), 16 C-rich Asymptotic Giant Branch (AGB) stars, 11 HII regions, 4 likely O-rich AGB stars, 4 Galactic O-rich AGB stars, 2 OH/IR stars, and 2 B[e] supergiants with peculiar IR spectra. We find that the overwhelming majority of the sample AGB stars (with typical IR luminosities ~1.0E4 L_sun) have C-rich envelopes, while the O-rich objects are predominantly luminous RSGs with L_IR ~ 1.0E5 L_sun. We determine mean bolometric corrections to the stellar K-band flux densities and find that for carbon stars, the bolometric corrections depend on the infrared color, whereas for RSGs, the bolometric correction is independent of IR color. Our results reveal that objects previously classified as PNe on the basis of IR colors are in fact compact HII regions with very red IRS spectra that include strong atomic recombination lines and PAH emission features. We demonstrate that the IRS spectral classes in our sample separate clearly in infrared color-color diagrams that use combinations of 2MASS data and synthetic IRAC/MIPS fluxes derived from the IRS spectra. On this basis, we suggest diagnostics to identify and classify, with high confidence levels, IR-luminous evolved stars and HII regions in nearby galaxies using Spitzer and near-infrared photometry.
description: 46 pages, 9 figures; accepted for publication in AJ; abstract abridged
CommunityClick: Capturing and Reporting Community Feedback from Town Halls to Improve Inclusivity
Creators: name: Jasim, Mahmood
name: Khaloo, Pooya
name: Wadhwa, Somin
name: Zhang, Amy X.
name: Sarvghad, Ali
name: Mahyar, Narges
Publisher: name: arXiv
Year: 2020
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Local governments still depend on traditional town halls for community consultation, despite problems such as a lack of inclusive participation for attendees and difficulty for civic organizers to capture attendees' feedback in reports. Building on a formative study with 66 town hall attendees and 20 organizers, we designed and developed CommunityClick, a communitysourcing system that captures attendees' feedback in an inclusive manner and enables organizers to author more comprehensive reports. During the meeting, in addition to recording meeting audio to capture vocal attendees' feedback, we modify iClickers to give voice to reticent attendees by allowing them to provide real-time feedback beyond a binary signal. This information then automatically feeds into a meeting transcript augmented with attendees' feedback and organizers' tags. The augmented transcript along with a feedback-weighted summary of the transcript generated from text analysis methods is incorporated into an interactive authoring tool for organizers to write reports. From a field experiment at a town hall meeting, we demonstrate how CommunityClick can improve inclusivity by providing multiple avenues for attendees to share opinions. Additionally, interviews with eight expert organizers demonstrate CommunityClick's utility in creating more comprehensive and accurate reports to inform critical civic decision-making. We discuss the possibility of integrating CommunityClick with town hall meetings in the future as well as expanding to other domains.
description: 32 pages, 5 figures, 4 tables, to be published in ACM Conference on Computer-Supported Cooperative Work and Social Computing (CSCW)
title: The modulatory roles of collagen and endothelial cells on platelet function
Creators: name: Provenzale, Isabella
Publisher: name: University of Reading
Year: 2023

description: Background: 
Platelets are crucial in the regulation of haemostasis and thrombosis. Blood fluid 
dynamics, plasma coagulation factors, vascular endothelial cells (ECs) and the 
underlying collagen-enriched matrix further contribute to thrombus formation. Studies on 
the regulation of this process often lack an integrative approach.
Aims: 
In this thesis we aimed to use novel in vitro methods that integrate the various 
components regulating thrombus formation in human blood to understand: i) the roles of 
collagens, wall shear-rate and platelet glycoprotein VI (GPVI), ii) the endothelial 
regulation of platelet and coagulation activation, and iii) the impact of extracellular matrix 
proteoglycans.
Results: 
Using a microspot-based multiparameter microfluidic approach, we revealed the 
importance of the protein kinase Syk, operating downstream of GPVI, in thrombus 
formation induced by different types of collagens expressed in the vascular extracellular 
matrix. The effects of Syk inhibition on platelet activation under flow were best 
represented by reduced ‘thrombus signature’ parameters. To recapitulate the in vivo 
circumstances, a novel vessel-on-a-chip approach was developed, growing partially 
confluent ECs on collagen- and tissue factor-coated channels. The presence of ECs 
locally suppressed collagen-induced platelet activation and fibrin formation. The latter 
being due to ECs thrombomodulin and a glycocalyx enriched in heparan sulphates. At 
the signalling level, a label-free approach revealed sustained modifications in the platelet 
phospho-proteome after exposure to ECs, linked to alterations in multiple protein kinases 
and even extending after platelet stimulation. In addition, we identified a dual platelet-inhibiting and -activating effect by isolated glycocalyx-derived heparan sulphate 
proteoglycans in thrombus formation.
Conclusions: 
By integrating vascular- and blood-derived components in high-throughput microfluidic 
methods, this thesis disclosed the presence of potent and complex regulatory 
mechanisms of ECs and matrix proteoglycans in the control of flow-dependent human 
thrombus formation. The developed methods promise to be useful for the evaluation of novel antithrombotic agents and for the phenotyping of patients with platelet-related 
disorders.
An Improved Framework for Quantum Gravity
Creators: name: Pereira, J. G.
name: López, D. F.
Publisher: name: arXiv
Year: 2020
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: General relativity has two fundamental problems that render it unsuitable for tackling the gravitational field's quantization. The first problem is the lack of a genuine gravitational variable representing gravitation only, inertial forces apart. The second problem is its incompatibility with quantum mechanics, a problem inherited from the more fundamental conflict of special relativity with quantum mechanics. A procedure to overcome these difficulties is outlined, which amounts to replacing general relativity with its teleparallel equivalent and the Poincaré-invariant special relativity with the de Sitter-invariant special relativity. Those replacements give rise to the de Sitter-modified teleparallel gravity, which does not have the two mentioned problems. It can thus be considered an improved alternative approach to quantum gravity.
description: 15 pages, no figures
Dolichogenidea trachala
Creators: name: Fernandez-Triana, Jose
name: Sakagami, Kota
name: Shimizu, So
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Braconidae
Dolichogenidea
Dolichogenidea trachala

description: D. trachala (Nixon, 1965): Pterostigma brown, without pale spot at base; preapical flagellomeres square; T1 shiny and weakly sculptured; ovipositor sheath as long as metatibia.
description: Published as part of Fernandez-Triana, Jose, Sakagami, Kota & Shimizu, So, 2018, Dolichogenidea maetoi sp. nov. (Hymenoptera: Braconidae) from Japan, the first parasitoid wasp recorded from Hyblaea fortissima (Lepidoptera), pp. 167-175 in Acta Entomologica Musei Nationalis Pragae 58 (1) on page 174, DOI: 10.2478/aemnp-2018-0014, http://zenodo.org/record/3699178
Catálogo 2.0 da Latindex Portugal e os critérios de Ciência Aberta
Creators: name: Seguro de Carvalho, Paula
name: Meireles, Paula
Publisher: name: Zenodo
Year: 2024

description: Apresentação realizada na sessão Pecha Kucha II, da 15ª Conferência Lusófona de Ciência Aberta, na Escola Superior de Enfermagem do Porto (ESEP), de 01 a 04 de outubro de 2024.
Flavor and CP Violation from a QCD-like Hidden Sector
Creators: name: Bensalem, Wafia
name: Stolarski, Daniel
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Confining hidden sectors at the GeV scale are well motivated by asymmetric dark matter and naturalness considerations and can also give interesting collider signatures. Here we study such sectors connected to the Standard Model by a TeV scale mediator charged under both QCD and the dark force. Such a mediator admits a Yukawa coupling between quarks and dark quarks which is generically flavour and $CP$ violating. We show that in contrast to expectation, electric dipole moments do not place a strong constraint on this scenario even with $O(1)$ $CP$-violating phases. We also quantitatively explore constraints from $ΔF=1,2$ processes as a function of the number of dark quark flavours. Finally, we describe the reach of upcoming measurements at Belle-II and KOTO, and we propose new $CP$-odd observables in rare meson decays that may be sensitive to the $CP$-violating nature of the dark sector.
Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis.
Creators: name: Beale, Mathew A
name: Marks, Michael
name: Cole, Michelle J
name: Lee, Min-Kuang
name: Pitt, Rachel
name: Ruis, Christopher
name: Balla, Eszter
name: Crucitti, Tania
name: Ewens, Michael
name: Fernández-Naval, Candela
name: Grankvist, Anna
name: Guiver, Malcolm
name: Kenyon, Chris R
name: Khairullin, Rafil
name: Kularatne, Ranmini
name: Arando, Maider
name: Molini, Barbara J
name: Obukhov, Andrey
name: Page, Emma E
name: Petrovay, Fruzsina
name: Rietmeijer, Cornelis
name: Rowley, Dominic
name: Shokoples, Sandy
name: Smit, Erasmus
name: Sweeney, Emma L
name: Taiaroa, George
name: Vera, Jaime H
name: Wennerås, Christine
name: Whiley, David M
name: Williamson, Deborah A
name: Hughes, Gwenda
name: Naidu, Prenilla
name: Unemo, Magnus
name: Krajden, Mel
name: Lukehart, Sheila A
name: Morshed, Muhammad G
name: Fifer, Helen
name: Thomson, Nicholas R
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Article
/631/326/41/2530
/631/208/457/649
/631/114/739
/692/699/255/1318
/631/326/107
/45
/45/23
/45/22
article

description: Funder: Queensland Government (State of Queensland); doi: https://doi.org/10.13039/501100003550
description: Syphilis, which is caused by the sexually transmitted bacterium Treponema pallidum subsp. pallidum, has an estimated 6.3 million cases worldwide per annum. In the past ten years, the incidence of syphilis has increased by more than 150% in some high-income countries, but the evolution and epidemiology of the epidemic are poorly understood. To characterize the global population structure of T. pallidum, we assembled a geographically and temporally diverse collection of 726 genomes from 626 clinical and 100 laboratory samples collected in 23 countries. We applied phylogenetic analyses and clustering, and found that the global syphilis population comprises just two deeply branching lineages, Nichols and SS14. Both lineages are currently circulating in 12 of the 23 countries sampled. We subdivided T. p. pallidum into 17 distinct sublineages to provide further phylodynamic resolution. Importantly, two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analyses revealed examples of isolates collected within the last 20 years from 14 different countries that had genetically identical core genomes, which might indicate frequent exchange through international transmission. It is striking that most samples collected before 1983 are phylogenetically distinct from more recently isolated sublineages. Using Bayesian temporal analysis, we detected a population bottleneck occurring during the late 1990s, followed by rapid population expansion in the 2000s that was driven by the dominant T. pallidum sublineages circulating today. This expansion may be linked to changing epidemiology, immune evasion or fitness under antimicrobial selection pressure, since many of the contemporary syphilis lineages we have characterized are resistant to macrolides.
Virialization of cosmological structures in models with time varying equation of state
Creators: name: Basilakos, Spyros
name: Voglis, Nikos
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We study the virialization of the cosmic structures in the framework of flat cosmological models where the dark energy component plays an important role in the global dynamics of the universe. In particular, our analysis focuses on the study of the spherical matter perturbations, as the latter decouple from the background expansion and start to ``turn around'' and finally collapse. We generalize this procedure taking into account models with an equation of state which vary with time, and provide a complete formulation of the cluster virialization attempting to address the nonlinear regime of structure formation. In particular, assuming that clusters have collapsed prior to the epoch of $z_{\rm f}\simeq 1.4$, in which the most distant cluster has been found, we show that the behavior of the spherical collapse model depends on the functional form of the equation of state.
description: 8 pages, 4 figures, MNRAS in press
ОПТИМИЗАЦИЯ ХИРУРГИЧЕСКОГО ДОСТУПА ПРИ РЕЗЕКЦИИ ГЛУБИННЫХ ОПУХОЛЕЙ ГОЛОВНОГО МОЗГА У ДЕТЕЙ.
Creators: name: Акрамов, О.З.
name: Аблязов, О.В.
name: Назарова, Л.А.
name: Ташматов, С.А.
name: Хусниддинов, Ш.Р.
Publisher: name: Zenodo
Year: 2024

description: В этом тезисе будут рассмотрены вопросы оптимизации доступа при удалении глубинно расположенных опухолей у детей. Не смотря на развитие современных нейрохирургических возможностей и техник, глубинно расположенные опухоли представляют собой сложный вызов даже опытному нейрохирургу из-за вовлечения функционально значимых структур. В нашем исследовании мы попытались оптимизировать доступы к глубинно расположенным опухолям окружёнными функционально значимыми зонами, с минимальным повреждением, максимальным сохранением естественной анатомии и неврологической функции, а также качества жизни у детей с нейроонкологической проблемой.
Dolichogenidea victor
Creators: name: Fernandez-Triana, Jose
name: Sakagami, Kota
name: Shimizu, So
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Braconidae
Dolichogenidea
Dolichogenidea victor

description: D. victor (Wilkinson, 1941): Pterostigma entirely brown; T1 mostly smooth; ovipositor sheath longer than metatibia (more than 1.5 times).
description: Published as part of Fernandez-Triana, Jose, Sakagami, Kota & Shimizu, So, 2018, Dolichogenidea maetoi sp. nov. (Hymenoptera: Braconidae) from Japan, the first parasitoid wasp recorded from Hyblaea fortissima (Lepidoptera), pp. 167-175 in Acta Entomologica Musei Nationalis Pragae 58 (1) on page 175, DOI: 10.2478/aemnp-2018-0014, http://zenodo.org/record/3699178
Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture.
Creators: name: Álvarez, Eva G
name: Demeulemeester, Jonas
name: Otero, Paula
name: Jolly, Clemency
name: García-Souto, Daniel
name: Pequeño-Valtierra, Ana
name: Zamora, Jorge
name: Tojo, Marta
name: Temes, Javier
name: Baez-Ortega, Adrian
name: Rodriguez-Martin, Bernardo
name: Oitaben, Ana
name: Bruzos, Alicia L
name: Martínez-Fernández, Mónica
name: Haase, Kerstin
name: Zumalave, Sonia
name: Abal, Rosanna
name: Rodríguez-Castro, Jorge
name: Rodriguez-Casanova, Aitor
name: Diaz-Lagares, Angel
name: Li, Yilong
name: Raine, Keiran M
name: Butler, Adam P
name: Otero, Iago
name: Ono, Atsushi
name: Aikata, Hiroshi
name: Chayama, Kazuaki
name: Ueno, Masaki
name: Hayami, Shinya
name: Yamaue, Hiroki
name: Maejima, Kazuhiro
name: Blanco, Miguel G
name: Forns, Xavier
name: Rivas, Carmen
name: Ruiz-Bañobre, Juan
name: Pérez-Del-Pulgar, Sofía
name: Torres-Ruiz, Raúl
name: Rodriguez-Perales, Sandra
name: Garaigorta, Urtzi
name: Campbell, Peter J
name: Nakagawa, Hidewaki
name: Van Loo, Peter
name: Tubio, Jose MC
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Article
/631/67/1858
/631/208/69
/631/67/1504/1610/4029
/45/23
/14/32
article

description: Most cancers are characterized by the somatic acquisition of genomic rearrangements during tumour evolution that eventually drive the oncogenesis. Here, using multiplatform sequencing technologies, we identify and characterize a remarkable mutational mechanism in human hepatocellular carcinoma caused by Hepatitis B virus, by which DNA molecules from the virus are inserted into the tumour genome causing dramatic changes in its configuration, including non-homologous chromosomal fusions, dicentric chromosomes and megabase-size telomeric deletions. This aberrant mutational mechanism, present in at least 8% of all HCC tumours, can provide the driver rearrangements that a cancer clone requires to survive and grow, including loss of relevant tumour suppressor genes. Most of these events are clonal and occur early during liver cancer evolution. Real-time timing estimation reveals some HBV-mediated rearrangements occur as early as two decades before cancer diagnosis. Overall, these data underscore the importance of characterising liver cancer genomes for patterns of HBV integration.
Existence of travelling-wave solutions and local well-posedness of the Fowler equation
Creators: name: Alvarez-Samaniego, Borys
name: Azerad, Pascal
Publisher: name: arXiv
Year: 2008
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: We study the existence of travelling-waves and local well-posedness in a subspace of $C_b^1(\mathbb{R})$ for a nonlinear evolution equation recently proposed by Andrew C. Fowler to study the dynamics of dunes.
description: 21 pages
Dolichogenidea varifemur
Creators: name: Fernandez-Triana, Jose
name: Sakagami, Kota
name: Shimizu, So
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Braconidae
Dolichogenidea
Dolichogenidea varifemur

description: D. varifemur (Abdinbekova, 1969): Flagellomeres 14 and 15 square to slightly elongate; metafemur brown, legs brown to yellow-brown. No further details available to properly assess this species.
description: Published as part of Fernandez-Triana, Jose, Sakagami, Kota & Shimizu, So, 2018, Dolichogenidea maetoi sp. nov. (Hymenoptera: Braconidae) from Japan, the first parasitoid wasp recorded from Hyblaea fortissima (Lepidoptera), pp. 167-175 in Acta Entomologica Musei Nationalis Pragae 58 (1) on page 175, DOI: 10.2478/aemnp-2018-0014, http://zenodo.org/record/3699178
Inferring solar differential rotation through normal-mode coupling using Bayesian statistics
Creators: name: Kashyap, Samarth G.
name: Das, Srijan Bharati
name: Hanasoge, Shravan M.
name: Woodard, Martin F.
name: Tromp, Jeroen
Publisher: name: arXiv
Year: 2021
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Normal-mode helioseismic data analysis uses observed solar oscillation spectra to infer perturbations in the solar interior due to global and local-scale flows and structural asphericity. Differential rotation, the dominant global-scale axisymmetric perturbation, has been tightly constrained primarily using measurements of frequency splittings via "$a$-coefficients". However, the frequency-splitting formalism invokes the approximation that multiplets are isolated. This assumption is inaccurate for modes at high angular degrees. Analysing eigenfunction corrections, which respect cross coupling of modes across multiplets, is a more accurate approach. However, applying standard inversion techniques using these cross-spectral measurements yields $a$-coefficients with a significantly wider spread than the well-constrained results from frequency splittings. In this study, we apply Bayesian statistics to infer $a$-coefficients due to differential rotation from cross spectra for both $f$-modes and $p$-modes. We demonstrate that this technique works reasonably well for modes with angular degrees $\ell=50-291$. The inferred $a_3-$coefficients are found to be within $1$ nHz of the frequency splitting values for $\ell > 200$. We also show that the technique fails at $\ell < 50$ owing to the insensitivity of the measurement to the perturbation. These results serve to further establish mode coupling as an important helioseismic technique with which to infer internal structure and dynamics, both axisymmetric (e.g., meridional circulation) and non-axisymmetric perturbations.
description: 20 pages, 11 figures
A Journey Through Garden Algebras
Creators: name: Bellucci, Stefano
name: Gates,, Sylvester James
name: Orazi, Emanuele
Publisher: name: arXiv
Year: 2006
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The main purpose of these lectures is to give a pedagogical overview on the possibility to classify and relate off-shell linear supermultiplets in the context of supersymmetric mechanics. A special emphasis is given to a recent graphical technique that turns out to be particularly effective for describing many aspects of supersymmetric mechanics in a direct and simplifying way.
description: 50 pages, based on lectures delivered at the Winter School on Modern Trends in Supersymmetric Mechanics 7 - 12 March 2005, Frascati, Italy
Elicitation on pre-verbal subjects and topichood
Creators: name: Rudolph, Johnny (Soni)
name: Drummond, Emily
Publisher: name: California Language Archive, University of California, Berkeley
Year: 2022
Subjects: subject: nkr

description: Elicitation on the overlap between pre-verbal subjects and topichood, using two original storyboards. The first video file only covers a single data point, cut off by internet connectivity issues; the second video file contains both storyboard elicitations.
Significant enhancement of room temperature ferromagnetism in surfactant coated polycrystalline Mn doped ZnO particles
Creators: name: Jayakumar, O. D.
name: Gopalakrishnan, I. K.
name: Sudakar, C.
name: Kadam, R. M.
name: Kulshreshtha, S. K.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report a surfactant assisted synthesis of Mn doped ZnO polycrystalline samples showing robust room temperature ferromagnetism as characterized by X-ray diffraction analysis, Transmission Electron Microscopy, Electron Paramagnetic Resonance and DC magnetization mearurements. This surfactant assisted synthesis method, developed by us, is found to be highly reproducible. Further, it can also be extended to the synthesis of other transition metal doped ZnO.
description: 10 pages, 6 figures
A Reverse Augmented Constraint preconditioner for Lagrange multiplier methods in contact mechanics
Creators: name: Franceschini, Andrea
name: Frigo, Matteo
name: Janna, Carlo
name: Ferronato, Massimiliano
Publisher: name: arXiv
Year: 2021
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics
subject: 65F08, 65N55

description: Frictional contact is one of the most challenging problems in computational mechanics. Typically, it is a tough nonlinear problem often requiring several Newton iterations to converge and causing troubles also in the solution to the related linear systems. When contact is modeled with the aid of Lagrange multipliers, the impenetrability condition is enforced exactly, but the associated Jacobian matrix is indefinite and needs a special treatment for a fast numerical solution. In this work, a constraint preconditioner is proposed where the primal Schur complement is computed after augmenting the zero block. The name Reverse is used in contrast to the traditional approach where only the structural block undergoes an augmentation. Besides being able to address problems characterized by singular structural blocks, often arising in contact mechanics, it is shown that the proposed approach is significantly cheaper than traditional constraint preconditioning for this class of problems and it is suitable for an efficient HPC implementation through the Chronos parallel package. Our conclusions are supported by several numerical experiments on mid- and large-size problems from various applications. The source files implementing the proposed algorithm are freely available on GitHub.
description: 20 pages, 12 figures, 4 tables