cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Discovery of an accreted stellar system within the globular cluster omega Centauri
Creators: name: Ferraro, F. R.
name: Bellazzini, M.
name: Pancino, E.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Recent wide-field photometric surveys (Lee et al.; Pancino et al.) have shown the existence of a previously unknown metal-rich ([Fe/H] -0.6) stellar population in the galactic globular cluster omega Centauri. The discovery of this new component, which comprises only a small percentage (~5%) of the entire cluster population, has added a new piece to the already puzzling picture of the star formation and chemical evolution of this stellar system. In this Letter we show that stars belonging to the newly discovered metal-rich population have a coherent bulk motion with respect to the other cluster stars, thus demonstrating that they formed in an independent self-gravitating stellar system. This is the first clear-cut evidence that extreme metal-rich stars were part of a small stellar system (a satellite of omega Centauri?) that has been accreted by the main body of the cluster. In this case, we are witnessing an in vivo example of hierarchical merging on the sub-galactic scale.
description: 11 pages, 3 figures, accepted for publication in ApJ Letters
MOESM1 of A systematic review of parent based programs to prevent or reduce alcohol consumption in adolescents
Creators: name: Hurley, Erin
name: Dietrich, Timo
name: Rundle-Thiele, Sharyn
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1. Program summary. The table provides a summary of the 13 parent programs included in the review.
Second Order Corrections to Weak Lensing by Large-Scale Structure
Creators: name: Cooray, Asantha
name: Hu, Wayne
Publisher: name: arXiv
Year: 2002
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We calculate corrections to the power spectrum predictions of weak lensing by large scale structure due to higher order effects in the gravitational potential. Using a perturbative approach to third order in transverse displacements, we calculate a second order correction to the angular power spectra of E and B mode shear and convergence resulting from dropping the so-called Born approximation, where one integrates along the unperturbed photon path. We also consider a correction to the power spectra from the coupling between lenses at different redshifts. Both effects generate B-mode shear and the latter also causes a net rotation of the background galaxy images. We show all these corrections are at least two orders of magnitude below the convergence or E-mode power and hence relevant only to future ultra high precision measurements. These analytical calculations are consistent with previous numerical estimates and validate the use of current large scale structure weak lensing predictions for cosmological studies and future use of B-modes as a monitor of systematic effects.
description: 4 pages, 1 figure, submitted to ApJL
Computer-Aided Design of Ligands at Multiple Protein Targets for Multifactorial Diseases
Creators: name: Kalash, Leen
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Structure-based design
Ligand-based design
MD simulations
docking
multi-target ligands
allosteric inhibitors
multifactorial diseases
lung cancer

description: Today, drug discovery predominately focuses on the design of ligands with high selectivity towards a specific biological target. A significant limitation in the case of multi-factorial diseases (e.g. neurodegenerative disorders) is that effective therapy may require multi-target drugs addressing the complexity of multi-factorial pathologies. Here, single- and multi-target ligand design was investigated to discover novel compounds active at multiple proteins/multiple binding sites including allosteric ligands. Calpain-1, a challenging target, was selected to develop and evaluate computational approaches to the discovery of novel ligands. Current selective calpain-1 inhibitors are reported to bind to an allosteric site and their mode of action has remained elusive. To elucidate this, a structure-based virtual screening protocol was implemented to find chemically novel compounds with improved selectivity and a reduced side-effects profile. To develop methods for the discovery of multi-target ligands, a multi-target design approach, which could be beneficial in the treatment of Lung Carcinoma and Neurodegenerative diseases, was investigated. A novel ensemble of proteins was targeted to elevate intracellular cAMP, deemed to be beneficial in these diseases resulting in the discovery of ligands with high binding affinity at three targets, PDE10A, A1 and A2A receptors. In tandem, functional activity at the A2A receptor and PDE10A was investigated, resulting in the discovery of novel compounds, which exhibited anti-proliferative effects in lung carcinoma cell-lines correlating with the co-expression of the two targets and increased cAMP levels. Critically, the dynamics of one amino acid residue, Val84, was identified as a novel conformational descriptor of A2A receptor activation. Overall, novel single- and multi-target ligand design approaches are presented in this work, which could be applicable to a wide range of ligand design problems, across (multi-factorial) disease areas and target families. The findings may facilitate improved design of allosteric calpain-1 inhibitors using the PEF(S) domain, and encourage investigating the therapeutic benefits of dual ligands at the A2A receptor and PDE10A against lung cancer in vivo.
description: IDB Cambridge International Scholarship and ERC Starting Grant (No. 336159)
Additional file 1 of XGBoost-SHAP-based interpretable diagnostic framework for alzheimer’s disease
Creators: name: Yi, Fuliang
name: Yang, Hui
name: Chen, Durong
name: Qin, Yao
name: Han, Hongjuan
name: Cui, Jing
name: Bai, Wenlin
name: Ma, Yifei
name: Zhang, Rong
name: Yu, Hongmei
Publisher: name: figshare
Year: 2023
Subjects: Space Science
Medicine
Cell Biology
Neuroscience
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Cancer

description: Supplementary Material 1
Gravitational waveforms of binary neutron star inspirals using post-Newtonian tidal splicing
Creators: name: Barkett, Kevin
name: Chen, Yanbei
name: Scheel, Mark A.
name: Varma, Vijay
Publisher: name: arXiv
Year: 2019
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The tidal deformations of neutron stars within an inspiraling compact binary alter the orbital dynamics, imprinting a signature on the gravitational wave signal. Modeling this signal could be done with numerical-relativity simulations, but these are too computationally expensive for many applications. Analytic post-Newtonian treatments are limited by unknown higher-order nontidal terms. This paper further builds upon the "tidal splicing" model in which post-Newtonian tidal terms are "spliced" onto numerical relativity simulations of black-hole binaries. We improve on previous treatments of tidal splicing by including spherical harmonic modes beyond the (2,2) mode, expanding the post-Newtonian expressions for tidal effects to 2.5 order, including dynamical tide corrections, and adding a partial treatment of the spin-tidal dynamics. Furthermore, instead of numerical relativity simulations, we use the spin-aligned binary black hole (BBH) surrogate model "NRHybSur3dq8" to provide the BBH waveforms that are input into the tidal slicing procedure. This allows us to construct spin-aligned, inspiraling TaylorT2 and TaylorT4 splicing waveform models that can be evaluated quickly. These models are tested against existing binary neutron star and black hole-neutron star simulations. We implement the TaylorT2 splicing model as an extension to "NRHybSur3dq8," creating a model that we call "NRHybSur3dq8Tidal."
description: 25 pages, 4 figures, published version
Screening mass responses to the chemical potential at finite temperature
Creators: name: TARO Collaboration
name: Choe, S.
name: de Forcrand, Ph.
name: Pérez, M. García
name: Hioki, S.
name: Liu, Y.
name: Matsufuru, H.
name: Miyamura, O.
name: Nakamura, A.
name: Stamatescu, I. -O.
name: Takaishi, T.
name: Umeda, T.
Publisher: name: arXiv
Year: 2001
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: Responses to chemical potential of the pseudoscalar meson screening mass and the chiral condensate in lattice QCD are investigated. On a $16 \times 8^2 \times \4$ lattice with two flavors of staggered quarks the first and second responses below and above $T_c$ are evaluated. Different behavior in the low and the high temperature phases are observed, which may be explained as a consequence of the chiral symmetry breaking and restoration.
description: Lattice2001(hightemp), 3pages, 3figures
A Systematic Study of Hidden Sector Dark Matter: Application to the Gamma-Ray and Antiproton Excesses
Creators: name: Hooper, Dan
name: Leane, Rebecca K.
name: Tsai, Yu-Dai
name: Wegsman, Shalma
name: Witte, Samuel J.
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: In hidden sector models, dark matter does not directly couple to the particle content of the Standard Model, strongly suppressing rates at direct detection experiments, while still allowing for large signals from annihilation. In this paper, we conduct an extensive study of hidden sector dark matter, covering a wide range of dark matter spins, mediator spins, interaction diagrams, and annihilation final states, in each case determining whether the annihilations are s-wave (thus enabling efficient annihilation in the universe today). We then go on to consider a variety of portal interactions that allow the hidden sector annihilation products to decay into the Standard Model. We broadly classify constraints from relic density requirements and dwarf spheroidal galaxy observations. In the scenario that the hidden sector was in equilibrium with the Standard Model in the early universe, we place a lower bound on the portal coupling, as well as on the dark matter's elastic scattering cross section with nuclei. We apply our hidden sector results to the observed Galactic Center gamma-ray excess and the cosmic-ray antiproton excess. We find that both of these excesses can be simultaneously explained by a variety of hidden sector models, without any tension with constraints from observations of dwarf spheroidal galaxies.
description: 40 pages, 11 figures, matches the JHEP version, references added
Ivanauskiella psamathias
Creators: name: Junnilainen, Jari
name: Karsholt, Ole
name: Nupponen, Kari
name: Kaitila, Jari-Pekka
name: Nupponen, Timo
name: Olschwang, Vladimir
Publisher: name: Zenodo
Year: 2010
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Gelechiidae
Ivanauskiella
Ivanauskiella psamathias

description: Ivanauskiella psamathias (Meyrick, 1895)
Figs. 23–25
Chalk Hills 29.VI.2003 (7 exx.), 30.VI.2003 (3 exx.), 01.VII.2003 (9 exx.), 02.VII.2003 (4 exx.); Moskovo 10.VII.1997 (1♀); Verbljushka 16.VII.1998 (1♂). Genitalia slides: prep. no: 02022503, 02022504 Junnilainen.
 Other material studied: SW Bulgaria, Kresna, 31.V–02.VI.2002 (6♂♂, 2♀), J.-P. Kaitila & J. Junnilainen leg. Genitalia slide: 03011801 Junnilainen.
 Remarks. Ivinskis & Piskunov (1980) introduced a new genus Ivanauskiella and described I. turkmenica Ivinskis & Piskunov, 1980 as its type species. Later I. turkmenica was synonymized with I. psamathias (Piskunov 1990b). The female genitalia of I. psamathias published by Bidzilya et al. (1998) are incorrect and belong to another species, possibly M. nomadella (Zeller, 1868) (see above). Habitually I. psamathias resembles M. nomadella, but the adult is smaller in size and forewings and thorax are more lustrous. A description of the female genitalia is given below. It is new to the European part of Russia.
 Female genitalia (Figs. 24–25). Antrum funnel-shaped, posteriorly broader. Colliculum with broad sclerotized plate. Ductus bursae simple, membranous tube, gradually widening towards corpus bursae. Corpus bursae asymmetrical sack with two separate signa, larger one horned, and smaller one roundish plate with ragged margins. Apophyses anteriores 0.8x length of apophyses posteriores.
 Distribution. Bulgaria, Russia (S Ural, Volga-Don region), Ukraine (Bidzilya 1997). Outside Europe in S Siberia, Mongolia, Turkmenistan and N Africa.
description: Published as part of Junnilainen, Jari, Karsholt, Ole, Nupponen, Kari, Kaitila, Jari-Pekka, Nupponen, Timo & Olschwang, Vladimir, 2010, The gelechiid fauna of the southern Ural Mountains, part II: list of recorded species with taxonomic notes (Lepidoptera: Gelechiidae) 2367, pp. 1-68 in Zootaxa 2367 (1) on page 27, DOI: 10.11646/zootaxa.2367.1.1, http://zenodo.org/record/10093655
Investigating the DNA damage response induced by Typhoid Toxin
Creators: name: Ibler, Angela Erna Maria
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: typhoid toxin
Salmonella Typhi
chronic infection
chronic carriage
DNA damage response
replicative stress
host-pathogen interaction

description: Typhoid toxin is produced by the antimicrobial resistant human pathogen Salmonella Typhi that causes 27 million cases of typhoid fever per year and chronic infections, which retain the pathogen in the population. The toxin is secreted by intracellular Salmonella into the extracellular milieu from where it enters bystander cells and causes DNA damage through its putative nickase activity. Purified typhoid toxin causes typhoid fever symptoms and mortality in animal models, and in animal infection models the toxin facilitates chronic infections by Salmonella. However, it is neither understood how the toxin manipulates the cellular DNA damage response (DDR) nor how this promotes infection. The kinases ATM and ATR are the master regulators of DNA damage response and both lead to the phosphorylation of Histone 2AX at S139 (γH2AX). ATM initiates repair of double strand breaks mainly in G1 phase of the cell cycle, while the ATR repair pathway is activated by single stranded DNA (ssDNA) occurring mainly in S phase due to stalled replication forks. The ssDNA sensor RPA binds to ssDNA to activate the ATR pathway marked by phosphorylation of ATR substrates H2AX, CHK1 and RPA itself. This study found that typhoid toxin induces a canonical DDR with γH2AX accumulating in foci and functioning as a hub for recruiting downstream DNA repair proteins. Strikingly however, a large proportion of cells did not contain γH2AX foci. Instead, novel γH2AX localisation was observed at the nuclear periphery (γH2AX rings) that failed to recruit DNA repair factors. This signified a non-canonical DDR that became the main focus of this project. This toxin-induced γH2AX ring pathway was shown to be replication-dependent: it was exacerbated in S phase, marked by an activated ATR pathway and persistent hyper-phosphorylation of RPA. RPA foci accumulated in cells with γH2AX rings indicating that the cellular pool of RPA might be overwhelmed by toxin-induced damage. Indeed, depletion of RPA by siRNA- mediated knock-down was sufficient to induce ring formation. Conversely, ring formation induced by the toxin was impeded by over-expression of RPA. Thus, the results suggest that toxin-induced damage causes replicative stress by exhausting the cellular pool of RPA. The γH2AX ring pathway was found to drive cells into a senescence-like state, a phenomenon associated with ageing. Induction of senescence via the toxin increased the burden of infection by Salmonella. This study provides evidence of a new virulence mechanism by revealing a novel DDR that leads to cellular senescence, which promotes infection. The work suggests that S. Typhi deploys the toxin to induce local ageing that primes cells for infection, which may be relevant to chronic disease caused by a globally important pathogen.
On compact Riemannian manifolds with convex boundary and Ricci curvature bounded from below
Creators: name: Wang, Xiaodong
Publisher: name: arXiv
Year: 2019
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics

description: We propose a new approach to the study of compact Riemannian manifolds with nonnegative Ricci curvature and strictly convex boundary or positive Ricci curvature and convex boundary. Several conjectures are formulated. Some partial results that support these conjectures are established.
description: to appear in Journal of Geometric Analysis
Conservation Agriculture as a strategy for responding to climate change in dry Mediterranean-type Environments
Creators: name: Mrabet, Rachid
name: Mrabet, Rachid
Publisher: name: Unknown
Year: 2014
Subjects: subject: Agribusiness
subject: Agricultural and Food Policy
subject: Environmental Economics and Policy
subject: Farm Management
subject: Conservation agriculture
subject: Mediterranean climate
subject: ecological intensification
subject: climate-smart agriculture
subject: no-tillage systems.

description: Mediterranean agriculture is highly vulnerable to climate change. A crop production strategy that responds to climate change must address both adaptability and mitigation aspects, and should also contribute to decreasing the overall agricultural carbon footprint in the economy. Over the past decades, there have been concerted efforts to promote such strategy through application of conservation agriculture (CA). CA is a set of soil management practices that minimize the disruption of the soil's structure, composition and natural biodiversity. Despite high diversity in the types of crops grown, all forms of CA share 4 core principles. These include (i) maintenance of permanent or semi-permanent soil cover, (ii) direct seeding with minimum soil disturbance, (iii) regular crop rotations or sequences and (iv) integrated weed control. It also uses or promotes where possible or needed various management practices such as utilization of green manures/cover crops, integrated pest and disease management, use of well adapted, high yielding varieties and good quality seeds, efficient water management and controlled traffic over agricultural soils. The origins, inventions and evolution of CA principles and practices are embedded in North and South American farming societies who, out of necessity, had to respond to the severe erosion and land degradation problems and productivity declines on their agricultural soils due to “intensive” tillage-based production agriculture. CA is currently practiced on 117 million hectares in all continents and all ecologies, including the dry Mediterranean environments. Presently, CA is advertised as a climate-smart agriculture permitting to (i) cope with drought and climate variability, (ii) invert erosion processes, (iii) mitigate greenhouse gas emissions, and (iv) sustain food production and tackle food security. For Mediterranean environments, many researchers believe that agriculture has the potential of becoming a much larger sink for CO2, if CA principles are followed. In fact, the accumulated scientific and farmer’s evidences have shown that CA can successfully provide a range of unequivocal productivity, socio-economic and environmental co-benefits to the producers and the society at large. To achieve these benefits, CA needs heightened attention in agricultural policy processes and strategies from national to regional levels. This paper is addressing these issues in order to smooth policy shifts to CA in dry Mediterranean areas.
Electric and Magnetic Fluxes in SU(2) Yang-Mills Theory
Creators: name: von Smekal, Lorenz
name: de Forcrand, with Philippe
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We measure the free energies in SU(2) of static fundamental charges and center monopoles. Dual to temporal center fluxes, the former provide a well-defined (dis)order parameter for deconfinement. In contrast, the monopole free energies vanish in the thermodynamic limit at all temperatures and are thus irrelevant for the transition.
description: 3 pages, LaTeX2e (espcrc2.sty), 4 figures (epsfig), for Lattice2002(topology)
Development of a novel SupraChoroidal-to-Optic-NervE (SCONE) drug delivery system
Creators: name: Chiang, Bryce
name: Heng, Kathleen
name: Jang, Kyeongwoo
name: Dalal, Roopa
name: Liao, Yaping Joyce
name: Myung, David
name: Goldberg, Jeffrey L
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Space Science
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences

description: Targeted drug delivery to the optic nerve head may be useful in the preclinical study and later clinical management of optic neuropathies, however, there are no FDA-approved drug delivery systems to achieve this. The purpose of this work was to develop an optic nerve head drug delivery technique. Different strategies to approach the optic nerve head were investigated, including standard intravitreal and retroorbital injections. A novel SupraChoroidal-to-Optic-NervE (SCONE) delivery was optimized by creating a sclerotomy and introducing a catheter into the suprachoroidal space. Under direct visualization, the catheter was guided to the optic nerve head. India ink was injected. The suprachoroidal approach was performed in New Zealand White rabbit eyes in vivo (25 animals total). Parameters, including microneedle size and design, catheter design, and catheter tip angle, were optimized ex vivo and in vivo. Out of the candidate optic nerve head approaches, intravitreal, retroorbital, and suprachoroidal approaches were able to localize India ink to within 2 mm of the optic nerve. The suprachoroidal approach was further investigated, and after optimization, was able to deposit India ink directly within the optic nerve head in up to 80% of attempts. In eyes with successful SCONE delivery, latency and amplitude of visual evoked potentials was not different than the naïve untreated eye. SCONE delivery can be used for targeted drug delivery to the optic nerve head of rabbits without measurable toxicity measured anatomically or functionally. Successful development of this system may yield novel opportunities to study optic nerve head-specific drug delivery in animal models, and paradigm-shifting management strategies for treating optic neuropathies. Here we demonstrate data on a new method for targeted delivery to the optic nerve head, addressing a significant unmet need in therapeutics for optic neuropathies.
Dirhinosia cervinella
Creators: name: Junnilainen, Jari
name: Karsholt, Ole
name: Nupponen, Kari
name: Kaitila, Jari-Pekka
name: Nupponen, Timo
name: Olschwang, Vladimir
Publisher: name: Zenodo
Year: 2010
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Gelechiidae
Dirhinosia
Dirhinosia cervinella

description: Dirhinosia cervinella (Eversmann, 1844)
Chalk Hills 03–07.VI.1998, 10.VI.2001, 29.VI–02.VII.2003; Kuvandyk 13–16.VI.1998, 04.VII.2003; Sakmara river 20–21. VI.1996; Suleimanovo 14. VI:2001; Verbljushka 10–12.VI.1998, 28.VI.2003; Zesnokovka 09. VI.2001; Zirgan 24. VI.1999. A total of 108 exx. Genitalia slide: K. Nupponen prep. no. 2/ 19.X.2008 (♂).
 Distribution. Russia (S Ural, the Caucasus, Altai, Lower Volga), Ukraine, Bulgaria, Hungary, Croatia, Turkey (Tokár & Gozmány 2004).
 Remarks. This species was described from S Ural. Recently it was found also in the Altai Mountains (K. Nupponen, unpublished).
description: Published as part of Junnilainen, Jari, Karsholt, Ole, Nupponen, Kari, Kaitila, Jari-Pekka, Nupponen, Timo & Olschwang, Vladimir, 2010, The gelechiid fauna of the southern Ural Mountains, part II: list of recorded species with taxonomic notes (Lepidoptera: Gelechiidae) 2367, pp. 1-68 in Zootaxa 2367 (1) on page 27, DOI: 10.11646/zootaxa.2367.1.1, http://zenodo.org/record/10093655
Microfluidics for Cell Culture and Single Cell Assays
Creators: name: Roode, Lianne Wei Yu
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Microfluidics
Microgels
Cell Culture

description: Elucidating molecular processes that govern cell function is paramount in forming a basis for understanding human health and treating disease. Research is presently limited by investigating in bulk, where information on critical subsets of cells is lost through averaging across an entire population. Therefore, biological and biomedical fields have become increasingly interested in methods that enable the handling of cells individually and facilitate studies into cellular heterogeneity. Existing techniques, however, are often associated with high costs and limited throughput. To address these shortcomings, my PhD has focussed on the methodological advancement of cell culture and assay techniques by taking advantage of the reduced size and volume scales of microfluidics. This dissertation describes the development of two micro-scale cell culturing platforms. The first approach involves the generation of hydrogel-based microgels for cell encapsulation. The system aims to provide a versatile and high throughput platform that imposes minimal cellular stress and uses readily available materials to reduce costs compared to existing methods. The potential of cell-laden microgels as an assay system is demonstrated by performing a digital toxicity assay, which demonstrates the ability to record individual cell responses. Furthermore, the formation of composite and core-shell microgels is explored to provide control over the internal structure and composition of the microgels. Using this approach, the platform is shown to be easily adaptable to incorporate various materials, such as extracellular matrix-like components, to provide a biomimetic microenvironment that more closely matches physiological tissue conditions in comparison to conventional two-dimensional methods. This system facilitates three- dimensional cell culture and spheroid formation of various cell types, including adherent cells that require a scaffolding structure. The second approach focusses on neuronal cell culture directly on-chip, where cells are compartmentalised by the microstructures of the microfluidic device. Modulation of the device explores the isolation of axon growth between donor and acceptor cells to facilitate the study of infectious tau protein propagation involved in neurodegenerative diseases. Collectively, this dissertation represents my work in combining microfluidic techniques with cell studies to develop platforms that will readily enable research into cellular heterogeneity and individual cellular processes.
description: ERC, funding for 3 years of PhD study; CRUK, partial funding for collaborative project
Additional file 6 of Sand supplementation favors tropical seagrass Thalassia hemprichii in eutrophic bay: implications for seagrass restoration and management
Creators: name: Jiang, Zhijian
name: Liu, Songlin
name: Cui, Lijun
name: He, Jialu
name: Fang, Yang
name: Premarathne, Chanaka
name: Li, Linglan
name: Wu, Yunchao
name: Huang, Xiaoping
name: Kumar, Manoj
Publisher: name: figshare
Year: 2022
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: Additional file 6: Table S3. Results of Levene’s test of homogeneity of flavonoid.
Characterising the gene regulatory landscape of CD4+ T cells
Creators: name: Glinos, Dafni Anna
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: regulatory T cell
immune system
transcriptomics
quantitative trait loci
GWAS
autoimmunity
CD4 T cell
CD28 costimulation
ChiP-seq
ATAC-seq
differential gene expression
humans

description: Despite the high prevalence of immune-mediated diseases, the molecular mechanisms by which they arise and the influence of genetic variation in the predisposition to disease are not well understood. Immune susceptibility loci identified by genome wide association studies (GWAS) overlap with active regulatory elements in CD4+ T cells, and particularly in regulatory T cells (Tregs). CD4+ T cells are the orchestrators of the adaptive immune response and their dysfunction has been associated with immune-mediated disorders through uncontrolled activation and resistance to downregulation, which is usually mediated by Tregs. T cell activation requires the combination of T cell receptor (TCR) recognition of an antigen and CD28 co-stimulation. The role of CD28 co-stimulation requirement in the activation of different T cell subsets has been understudied. Here, I assessed the role of immune disease variants in modulating pathways underlying T cell activation and Treg function. For that, I activated CD4+ T cells using different intensities of CD28 and TCR signals, followed by genome-wide transcriptome and chromatin profiling of naive and memory cells. I observed that CD28 plays a critical role in the expression of genes involved in effector functions, cell cycle regulation in memory T cells and in disease susceptibility. I profiled the gene expression regulatory landscape in Tregs using a combination of genomic assays. Due to the scarce Treg numbers in peripheral blood I first optimised the ChIPmentation (ChM) sequencing protocol to profile H3K4me3 and H3K27ac histone modifications in Tregs. I combined it with chromatin accessibility and gene expression profiling in resting and stimulated Tregs from ten donors. I observed cases of alternative transcription, such as alternative splicing and promoter, induced by stimulation, which could be predicted by changes in the chromatin landscape. Finally, I assessed how genetic variability impacts the function of Tregs and how this can lead to autoimmunity. I carried a quantitative trait locus (QTL) mapping using RNA-seq, ATAC-seq, H3K4me3 and H3K27ac ChM-seq data from Tregs isolated from 100 individuals. Additionally, I processed publicly available data from naive T cells to distinguish the Treg specific effects from generic CD4+ T cell signals. I recapitulated known colocalisations between QTLs and immune GWAS loci, and identified previously unknown Treg specific colocalisations. My findings highlight the value of carrying QTL studies in rare immune cell types relevant to the disease.
CONTEMPORARY SCULPTURE IN UZBEKISTAN: ITS STATUS, TRADITIONS, INNOVATIONS, AND CULTURAL DEVELOPMENT
Creators: name: Khatamov, Azamat
Publisher: name: Zenodo
Year: 2025

description: This article analyzes the development of contemporary sculpture art in Uzbekistan, examining its historical, cultural, and aesthetic significance. Uzbekistan’s rich cultural heritage has played an important role in the formation and development of sculpture art. In recent years, under the influence of new technologies and global trends, sculpture has acquired new forms, incorporating new materials and styles. The article deeply explores the contemporary trends in Uzbek sculpture, the creative styles of artists, and the strategies of state support being implemented. It also discusses how sculpture is being integrated into the changing global culture and the tourism industry.
Numerical-relativity simulations of long-lived remnants of binary neutron star mergers
Creators: name: De Pietri, Roberto
name: Feo, Alessandra
name: Font, José A.
name: Löffler, Frank
name: Pasquali, Michele
name: Stergioulas, Nikolaos
Publisher: name: arXiv
Year: 2019
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We analyze the properties of the gravitational wave signal emitted after the merger of a binary neutron star system when the remnant survives for more than a 80 ms (and up to 140ms). We employ four different piecewise polytropic equations of state supplemented by an ideal fluid thermal component. We find that the post-merger phase can be subdivided into three phases: an early post-merger phase (where the quadrupole mode and a few subdominant features are active), the intermediate post-merger phase (where only the quadrupole mode is active) and the late post-merger phase (where convective instabilities trigger inertial modes). The inertial modes have frequencies somewhat smaller than the quadrupole modes. In one model, we find an interesting association of a corotation of the quadrupole mode in parts of the star with a revival of its amplitude. The gravitational wave emission of inertial modes in the late post-merger phase is concentrated in a narrow frequency region and is potentially detectable by the planned third-generation detectors. This allows for the possibility of probing not only the cold part of the equation of state, but also its dependence on finite temperature. In view of these results, it will be important to investigate the impact of various type of viscosities on the potential excitation of inertial modes in binary neutron star merger remnants.
description: 20 pages, 16 figures. Improved text and one appendix added
Incompatibility of antimalarial drugs: challenges in formulating combination products for malaria
Creators: name: Mhango, Ellen K. G.
name: Sveinbjornsson, Benjamin R.
name: Snorradottir, Bergthora S.
name: Gizurarson, Sveinbjorn
Publisher: name: Taylor & Francis
Year: 2024
Subjects: Biochemistry
Physical Sciences not elsewhere classified
Pharmacology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Mathematical Sciences not elsewhere classified
Cancer
Computational Biology

description: Lipophilic drugs require more advance formulation, especially if the intention is to make solutions or semisolid formulations. This also accounts for most antimalarial drugs. Although some of these antimalarial drugs are soluble in lipid vehicles, few of them, such as lumefantrine (LF), are also poorly soluble in oily vehicles. Trying to dissolve and formulate LF as a liquid formulation together with other antimalarial drugs is, therefore, a major task. When mixed in solution together with artemether (AR), precipitation occurs, sometimes with LF precipitating out on its own, and sometimes with AR precipitating out alongside LF. In this study, it was hypothesized that the use of fatty acids could lead to enhanced solubility in lipid formulation. Addition of the fatty acid solved the dissolution challenges, making LF soluble for over a year at room temperature (21–23 °C); but further research is needed to test the mechanism of action of the fatty acid. In addition, design of experiments (MODDE® 13) revealed that the amount of fatty acid in the formulation was the only significant factor for LF precipitation.
Autonomous Dynamical System of Einstein-Gauss-Bonnet Cosmologies
Creators: name: Chatzarakis, N.
name: Oikonomou, V. K.
Publisher: name: arXiv
Year: 2019
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this paper, we study the phase space of cosmological models in the context of Einstein-Gauss-Bonnet theory. More specifically, we consider a generalized dynamical system that encapsulates the main features of the theory and for the cases that this is rendered autonomous, we analyze its equilibrium points and stable and unstable manifolds corresponding to several distinct cosmological evolutions. As we demonstrate, the phase space is quite rich and contains invariant structures, which dictate the conditions under which the theory may be valid and viable in describing the evolution Universe during different phases. It is proved that a stable equilibrium point and two invariant manifolds leading to the fixed point, have both physical meaning and restrict the physical aspects of such a rich in structure modified theory of gravity. More important we prove the existence of a heteroclinic orbit which drives the evolution of the system to a stable fixed point. However, while on the fixed point the Friedman constraint corresponding to a flat Universe is satisfied, the points belonging to the heteroclinic orbit do not satisfy the Friedman constraint. We discuss the origin of this intriguing issue in some detail.
description: Revised Version, AoP Accepted
The Circum-Galactic Environment of Bright IRAS Galaxies
Creators: name: Krongold, Y.
name: Dultzin-Hacyan
name: Marziani, P.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: This paper studies systematically, for the first time, the circumgalactic environment of bright IRAS galaxies as defined by Soifer et al. (1989). While the role of gravitational interaction for luminous and ultraluminous IRAS galaxies has been well established by various studies, the situation is by far more obscure in the IR luminosity range of the bright IRAS sample, 10^{10}Lsol < Lfir < 10^{11} Lsol. To easily identify nearby companion galaxies, the bright IRAS sample was restricted to 87 objects with redshift range 0.008 < z < 0.018 and galactic latitude > 30^{o}. A control sample, selected from the Center for Astrophysics redshift survey catalogue, includes 90 objects matching the Bright IRAS sample for distribution of isophotal diameter, redshift, and morphological type. From a search of nearby companion galaxies within 250 Kpc on the second-generation Digitized Sky Survey (DSS-II), we found that the circumgalactic environment of the Bright IRAS galaxies contains more large companions than the galaxies in the optically selected control sample, and is similar to that of Seyfert 2 galaxies. We found a weak correlation over a wide range of far IR luminosity (10^9 Lsol < Lfir < 10^{12.5}Lsol) between projected separation and Lfir, which confirms a very close relationship between star formation rate of a galaxy and the strength of gravitational perturbations. We also find that the far IR colors depend on whether a source is isolated or interacting. Finally, we discuss the intrinsic difference and evolution expectations for the bright IRAS galaxies and the control sample, as well as the relationship between starbursting and active galaxies.
description: 10 pages, 5 figs, 2 tables. Accepted for publication in ApJ
Ultra-subwavelength focusing and giant magnetic-field enhancement in a low-loss one-way waveguide based on remanence
Creators: name: Xu, Jie
name: Deng, Xiaohua
name: Zhang, Hang
name: Wu, Chiaho
name: Wubs, Martijn
name: Xiao, Sanshui
name: Shen, Linfang
Publisher: name: arXiv
Year: 2019
Subjects: subject: Optics (physics.optics)
subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: The subwavelength focusing based on surface plasmon polaritons (SPP) has been widely explored in tapered metallic structures. However, the efficiency of energy localization is relatively weak, largely due to high propagation loss and strong back reflection. Here, we propose a straight-tapered 3-dimensional (3D) one-way surface magnetoplasmon (SMP) waveguide with the ending surface of $\sim 10^{-4}λ_0 \times 10^{-4}λ_0$ to achieve energy focusing in the microwave regime. Due to low propagation loss of SMP, we achieve huge magnetic field enhancement in such an ultra-subwavelength area, by five orders of magnitude. Instead of using an external static magnetic field, our proposed SMP waveguide relies on remanence, which is very convenient for operating practical 3D applications. These results show promising applications in magnetic-field enhancing or quenching fluorescence, luminescence or nonlinearity of 2D materials, novel scanning near-field microwave microscopy and energy storage.
Schrödinger functional at N_f=-2
Creators: name: Gehrmann, Bernd
name: Kurth, Stefan
name: Rolf, Juri
name: Wolff, Ulli
Publisher: name: arXiv
Year: 2001
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: We study the Schrödinger functional coupling for lattice Yang-Mills theory coupled to an improved bosonic spinor field, which corresponds to QCD with minus two light flavors. This theory serves as a less costly testcase than QCD for the scaling of the coupling.
description: Lattice2001(improvement) 3 pages, 4 figures
Quantum fluctuations and electronic transport through strongly interacting quantum dots
Creators: name: Costi, T. A.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We study electronic transport through a strongly interacting quantum dot by using the finite temperature extension of Wilson's numerical renormalization group (NRG) method. This allows the linear conductance to be calculated at all temperatures and in particular at very low temperature where quantum fluctuations and the Kondo effect strongly modify the transport. The quantum dot investigated has one active level for transport and is modeled by an Anderson impurity model attached to left and right electron reservoirs. The predictions for the linear conductance are compared to available experimental data for quantum dots in heterostructures. The spin-resolved conductance is calculated as a function of gate voltage, temperature and magnetic field strength and the spin-filtering properties of quantum dots in a magnetic field are described.
description: 9 pages, 8 eps figures, proceedings paper for 2nd Hvar workshop on Concepts in Correlated Electrons
Photometric observations of 9 Near-Earth Objects
Creators: name: Szabo, Gy.
name: Csak, B.
name: Sarneczky, K.
name: Kiss, L. L.
Publisher: name: arXiv
Year: 2001
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present new CCD observations of nine Near-Earth Asteroids carried out between February, 1999 and July, 2000. The bulk of the data was acquired through an R_C filter, while the minor planet 11405 was observed without filter. We could determine synodic periods and amplitudes for 5 asteroids, 699: 3.3 h, 0.18 mag; 1866: 2.7 h, 0.12 mag; 1999 JD6: 7.68 h, 1.2 mag; 2000 GK137: 4.84 h, 0.27 mag; 2000 NM: 9.24 h, 0.30 mag. Based on observations taken at different phases, we could infer a phase parameter m of 0.018+/-0.005 for 1865 Cerberus. An epoch-method yielded a sidereal period of 0.27024003(5) d for this object with retrograde rotation. The remaining 3 objects have only partial coverage, thus no firm conclusion on their synodic period is possible.
description: 8 pages, 12 figures, accepted for publication in A&A
A new approach to search for free neutron-antineutron oscillations using coherent neutron propagation in gas
Creators: name: Gudkov, V.
name: Nesvizhevsky, V. V.
name: Protasov, K. V.
name: Snow, W. M.
name: Voronin, A. Yu.
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Coherent forward neutron propagation in gas is discussed as a new approach to search for neutron-antineutron oscillations ($ n-\bar{n}$), which violate both $B$ and $B-L$ conservation. We show that one can increase the probability of neutron - antineutron transitions to essentially the free neutron oscillation rate in the presence of a nonzero external magnetic field by tuning the density of an appropriate mixture of gases so that the neutron optical potential of the gas cancels that from an external magnetic field.
EFFECTS OF CLIMATE CHANGE ON COCOA PRODUCTION IN ONDO STATE, NIGERIA
Creators: name: Oseni, Joseph Olumide
name: Oseni, Joseph Olumide
Publisher: name: Unknown
Year: 2011
Subjects: Agribusiness
Crop Production/Industries
Environmental Economics and Policy

description: The paper examined the effects of climate change on cocoa production in Ondo State, Nigeria. When talking about climate change and its effects, it is important to make adjustments and interventions in order to manage the losses or take advantages of opportunities presented by it. These adjustments or interventions are known as adaptation (IPCC, 2001). Cocoa has been the second largest foreign exchange earner after crude oil and has also contributed significantly to infrastructural development in the country. Given this importance, one would expect it to be produced on a large scale and its production should be on the increase to boost the nation’s foreign exchange earnings. But despite the nation’s commitment to increase its production, it is still being faced with the problems of climate change which cannot be controlled by man. It is because of this that a study to determine the effects of climatic change on cocoa production and how farmers are able to adapt to the changing climatic conditions is being carried out.
Bryotropha rossica Anikin & Piskunov 1996
Creators: name: Junnilainen, Jari
name: Karsholt, Ole
name: Nupponen, Kari
name: Kaitila, Jari-Pekka
name: Nupponen, Timo
name: Olschwang, Vladimir
Publisher: name: Zenodo
Year: 2010
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Gelechiidae
Bryotropha
Bryotropha rossica

description: Bryotropha rossica Anikin & Piskunov, 1996
Burannoe 12.VI.2001, 3.VII.2003; Chalk Hills 3–7.VI.1998, 22.VI.1999, 11.VI.2001, 29.VI–2.VII.2003; Guberlja 25.VI.2003; Novoiletzk 9.VI.1998, Verbljushka 27.VI.2003. A total of 81 exx. Genitalia slides: Hendriksen 4986, 5022, 5023; Rutten 591, 593, 595, 604, 619, 620, 633.
 Distribution. SE part of European Russia. Recently found in Estonia (Jürivete 2004) and Ukraine (Bidzilya & Budashkin 2009).
 Remarks. This species was described from lower Volga region.
 The sequence of species in the genus Bryotropha follows that of Karsholt & Rutten (2005).
description: Published as part of Junnilainen, Jari, Karsholt, Ole, Nupponen, Kari, Kaitila, Jari-Pekka, Nupponen, Timo & Olschwang, Vladimir, 2010, The gelechiid fauna of the southern Ural Mountains, part II: list of recorded species with taxonomic notes (Lepidoptera: Gelechiidae) 2367, pp. 1-68 in Zootaxa 2367 (1) on page 27, DOI: 10.11646/zootaxa.2367.1.1, http://zenodo.org/record/10093655
Steady one-dimensional domain wall motion in biaxial ferromagnets: mapping of the Landau-Lifshitz equation to the sine-Gordon equation
Creators: name: Rama-Eiroa, Ricardo
name: Otxoa, Rubén M.
name: Roy, Pierre E.
name: Guslienko, Konstantin Y.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Motivated by the difference between the dynamics of magnetization textures in ferromagnets and antiferromagnets, the Landau-Lifshitz equation of motion is explored. A typical one-dimensional domain wall in a bulk ferromagnet with biaxial magnetic anisotropy is considered. In the framework of Walker-type of solutions of steady-state ferromagnetic domain wall motion, the reduction of the non-linear Landau-Lifshitz equation to a Lorentz-invariant sine-Gordon equation typical for antiferromagnets is formally possible for velocities lower than a critical velocity of the topological soliton. The velocity dependence of the domain wall energy and the domain wall width are expressed in the relativistic-like form in the limit of large ratio of the easy-plane/easy-axis anisotropy constants. It is shown that the mapping of the Landau-Lifshitz equation of motion to the sine-Gordon equation can be performed only by going beyond the steady-motion Walker-type of solutions.