cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Multi-scale energy systems modeling of the renewable energy transition
Creators: name: Pfenninger, Stefan Johannes
Publisher: name: Imperial College London
Year: 2015

description: The majority of greenhouse gas emissions produced by mankind come from the burning of fossil fuels. Therefore, to prevent dangerous climate change, the world needs to completely rebuild the way it uses energy. This transformation is already underway and one of its key features is the rising importance of variable renewable energy, particularly wind and photovoltaics (PV). To better understand this transition, a new energy systems modeling framework is developed, called Calliope. Calliope is designed to deal with data of high spatial and temporal resolution, to run on high-performance computing clusters, to be easily extensible and re-usable and thus allow the rapid development of models targeted at specific problems. A high-resolution modeling system requires high-resolution input data, particularly for the potential power production from renewable power plants. Thus, a method is developed and presented to simulate PV plants by using both meteorological reanalysis and satellite-measured data. To validate these simulations, a database of measured power output data from real PV systems across Europe is built. These methods are applied to two cases. First, scenarios for the British power system with different combinations of three key technology groups -- renewables, nuclear and fossil fuels -- are examined with regards to their cost, emissions, their import dependence and diversity. The results show that costs are similar across a wide range of combinations but that interconnection, storage or clean dispatchable technologies are needed for renewables shares above 80%. Second, the ability of concentrating solar (CSP) and nuclear power plants to provide a stable (baseload) power supply are examined for the case of South Africa, showing that CSP plants have the potential to be cost-competitive, and likely preferable with regards to environmental and investment risks. The methods and results presented here are a contribution towards a better understanding of the energy transition, and by extension, towards improved energy policy and planning.
Synthesis and crystal structure of the first dinuclear zinc complex containing 1,4,7-triazacyclononane and biological properties of the protonated ligand
Creators: name: Qian, Jing
name: Qiao, Wei-Wei
name: Tian, Jin-Lei
Publisher: name: Taylor & Francis
Year: 2018
Subjects: Biophysics
Biochemistry
Medicine
Cell Biology
Environmental Sciences not elsewhere classified
Chemical Sciences not elsewhere classified

description: A new binuclear complex, [Zn2L2Cl4]·2H2O {L = N-aldehyde-N-(4-(benzyloxy)benzyl)-1,4,7triazacyclononane}, was synthesized and characterized by X-ray, elemental analysis, infrared and electronic spectroscopy, and mass spectrometry. The central ion is bridged by the L and lies in a tetrahedral configuration with Zn···Zn distance of 6.283 Å. The complex crystallizes in the triclinic space group Pī. ESI-MS of the complex indicates that the protonated ligand HL+ is the active species. The interaction of HL+ with calf thymus–DNA (CT–DNA) and bovine serum albumin (BSA) was studied by means of various spectroscopic methods, which revealed that HL+ could interact with CT–DNA through groove-binding mode and could quench the intrinsic fluorescence of BSA in a static quenching process. DNA–cleavage experiments indicate that HL+ exhibits efficient DNA–cleavage activity in the presence of H2O2, hydroxyl radical (HO•) may serve as the major cleavage active species, and the pseudo-Michaelis–Menten kinetic parameters (Kcat, KM, Vmax); 2.47 h−1, 2.70 × 10−4 M and 6.68 × 10−4 Mh−1.
On the usage of Flaring Gas Layers to determine the Shape of Dark Matter Halos
Creators: name: Olling, Rob P.
Publisher: name: arXiv
Year: 1995
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: I present a new method of deriving the shape of the dark matter (DM) halos of spiral galaxies. The method relies on the comparison of model predictions with high spectral and spatial resolution HI observations of the gas layer. The potential arising from the {\em total} mass distribution of the galaxy is used in the calculation of the vertical distribution of the gas. I developed a new algorithm to calculate the force field of an arbitrary, azimuthally symmetric, density distribution. This algorithm is used to calculate the forces due to the radially truncated stellar disk as well as of the flaring gas layer. I use a simple two-parameter family of disk-halo models which have essentially the same observed equatorial rotation curve but different vertical forces. This mass model is composed of a stellar disk with constant M/L, and a DM-halo with a given axial ratio. I approximate the radial force due to the gaseous disk, and iteratively determine the vertical force due to the global distribution of the gas. The thickness of the gaseous disk is sensitive to both the flattening of the DM-halo and the self-gravity of the gas, but not to the particular choice of disk-halo decomposition. I show that the determination of the thickness of the gas layer is not restricted to edge-on galaxies, but can be measured for moderately inclined systems as well.
description: 40 pages including 14 Postscript figures (2MByet) also available via anonymous ftp at ftp://parsifal.phys.columbia.edu/pub/olling/ as files Halo-Shape.ps(.Z) (2360 kb, uncompressed), Halo-Shape-txt.ps.Z (the text, 362 kb, uncompressed) Halo-Shape-F##.ps.Z (the figures, 1173 kb, uncompressed)
On the formation history of Galactic double neutron stars
Creators: name: Vigna-Gómez, Alejandro
name: Neijssel, Coenraad J.
name: Stevenson, Simon
name: Barrett, Jim W.
name: Belczynski, Krzysztof
name: Justham, Stephen
name: de Mink, Selma E.
name: Müller, Bernhard
name: Podsiadlowski, Philipp
name: Renzo, Mathieu
name: Szécsi, Dorottya
name: Mandel, Ilya
Publisher: name: arXiv
Year: 2018
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Double neutron stars (DNSs) have been observed as Galactic radio pulsars, and the recent discovery of gravitational waves from the DNS merger GW170817 adds to the known DNS population. We perform rapid population synthesis of massive binary stars and discuss model predictions, including formation rates, mass distributions, and delay time distributions. We vary assumptions and parameters of physical processes such as mass transfer stability criteria, supernova kick distributions, remnant mass distributions and common-envelope energetics. We compute the likelihood of observing the orbital period-eccentricity distribution of the Galactic DNS population under each of our population synthesis models, allowing us to quantitatively compare the models. We find that mass transfer from a stripped post-helium-burning secondary (case BB) onto a neutron star is most likely dynamically stable. We also find that a natal kick distribution composed of both low (Maxwellian $σ=30\rm~km~s^{-1}$) and high ($σ=265\rm~km~s^{-1}$) components is preferred over a single high-kick component. We find that the observed DNS mass distribution can place strong constraints on model assumptions.
description: 23 pages, 10 main figures, 2 tables, 3 figures in appendices; typos added, references added; Formation rates corrected; Table 1 has an extra column
New Structure In The Shapley Supercluster
Creators: name: Drinkwater, M. J.
name: Parker, Q. A.
name: Proust, D.
name: Quintana, H.
name: Slezak, E.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present new radial velocities for 189 galaxies in a 91 sq. deg region of the Shapley supercluster measured with the FLAIR-II spectrograph on the UK Schmidt Telescope. The data reveal two sheets of galaxies linking the major concentrations of the supercluster. The supercluster is not flattened in Declination as was suggested previously and it may be at least 30 percent larger than previously thought with a correspondingly larger contribution to the motion of the Local Group.
description: LaTex: 2 pages, 1 figure, includes conf_iap.sty style file. To appear in proceedings of The 14th IAP Colloquium: Wide Field Surveys in Cosmology, held in Paris, 1998 May 26--30, eds. S.Colombi, Y.Mellier
An Analytical Method for the NLO QCD Corrections to Double-Higgs Production
Creators: name: Bonciani, Roberto
name: Degrassi, Giuseppe
name: Giardino, Pier Paolo
name: Gröber, Ramona
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We propose a new method to calculate analytically higher-order perturbative corrections and we apply it to the calculation of the two-loop virtual corrections to Higgs pair production through gluon fusion. The method is based on the expansion of the amplitudes in terms of a small Higgs transverse momentum. This approach gives a very good approximation (better than per-mille) of the partonic cross section in the center of mass energy region $\sqrt{\hat{s}} \lesssim 750$ GeV, where $\sim95\%$ of the total hadronic cross section is concentrated. The presented method is general and can be applied in a straightforward way to the computation of virtual higher-order corrections to other $2\to2$ processes, representing an improvement with respect to calculations based on heavy mass expansions.
description: 6 pages, 2 figures; V2: Version accepted for publication
Bipartite field theories and D-brane instantons
Creators: name: Franco, Sebastian
name: García-Valdecasas, Eduardo
name: Uranga, Angel
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study D-brane instantons in systems of D3-branes at toric CY 3-fold singularities. The instanton effect can be described as a backreaction modifying the geometry of the mirror configuration, in which the breaking of $U(1)$ symmetries by the instanton translates into the recombination of gauge D-branes, which also directly generates the instanton-induced charged field theory operator. In this paper we describe the D-brane instanton backreaction in terms of a combinatorial operation in the bipartite dimer diagram of the original theory. Interestingly, the resulting theory is a general Bipartite Field Theory (BFT), defined by a bipartite graph tiling a general (possibly higher-genus) Riemann surface. This provides the first string theory realization of such general BFTs. We study the general properties of the resulting theories, including the construction of the higher-dimensional toric diagrams and the interplay between backreaction and Seiberg duality. In cases where the non-perturbative effects relate to complex deformations, we show that the procedure reproduces and explains earlier existing combinatorial recipes. The combinatorial operation and its properties generalize to an operation on the class of general BFTs, even including boundaries, relating BFTs defined on Riemann surfaces of different genus.
description: 51 pages, 49 figures. Minor corrections
Rumex acutus Linnaeus, 1753, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1753
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Polygonales
Polygonaceae
Rumex
Rumex acutus

description: Rumex acutus, spec. nov.
 10. Rumex floribus hermaphroditis: valvulis dentatis graniferis, foliis cordato-oblongis. Hort. cliff. 138. Mat. med. 176. Fl. suec. 293. Roy. lugdb. 229.
 Lapathum acutum s. Oxylapathum. Bauh. hist. 2. p. 983. Lob. ic. 284.
 Lapathum acutum. Raj. hist. 175.
 Habitat in Europae succulentis. ♃
description: Published as part of Linnaeus, Carolus, 1753, Species plantarum: exhibentes plantas rite cognitas, ad genera relatas, cum differentiis specificis, nominibus trivialibus, synonymis selectis, locis natalibus, secundum systema sexuale digestas, Stockholm :Laurentius Salvius on page 335, DOI: 10.5281/zenodo.3931989
Chromospheric condensations and magnetic field in a C3.6-class flare studied via He I D3 spectro-polarimetry
Creators: name: Libbrecht, Tine
name: Rodriguez, Jaime de la Cruz
name: Danilovic, Sanja
name: Leenaarts, Jorrit
name: Pazira, Hiva
Publisher: name: arXiv
Year: 2018
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Context. Magnetic reconnection during flares takes place in the corona but a substantial part of flare energy is deposited in the chromosphere. However, high-resolution spectro-polarimetric chromospheric observations of flares are very rare. The most used observables are Ca II 8542 Å and He I 10830 Å. Aims. We aim to study the chromosphere during a C3.6 class flare via spectro-polarimetric observations of the He I D3 line. Methods. We present the first SST/CRISP spectro-polarimetric observations of He I D3. We analyze the data using the inversion code HAZEL, and estimate the LOS velocity and the magnetic field vector. Results. Strong He I D3 emission at the flare footpoints, as well as strong He I D3 absorption profiles tracing the flaring loops are observed during the flare. The He I D3 traveling emission kernels at the flare footpoints exhibit strong chromospheric condensations of up to $\sim$ 60 km/s at their leading edge. Our observations suggest that such condensations result in shocking the deep chromosphere, causing broad and modestly blueshifted He I D3 profiles indicating subsequent upflows. A strong and rather vertical magnetic field of up to $\sim$ 2500 G is measured in the flare footpoints, confirming that the He I D3 line is likely formed in the deep chromosphere at those locations. We provide chromospheric line-of-sight velocity and magnetic field maps obtained via He I D3 inversions. We propose a fan-spine configuration as the flare magnetic field topology. Conclusions. The He I D3 line is an excellent diagnostic to study the chromosphere during flares. The impact of strong condensations on the deep chromosphere has been observed. Detailed maps of the flare dynamics and the magnetic field are obtained.
description: Accepted for publication in A&A
Rumex acutus Linnaeus 1753
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Polygonales
Polygonaceae
Rumex
Rumex acutus

description: Rumex acutus Linnaeus, Species Plantarum 1: 335. 1753.
"Habitat in Europae succulentis." RCN: 2587.
Lectotype (López González in Anales Jard. Bot. Madrid 44: 588. 1987): Herb. Linn. No. 150.5 (S).
Current name: Rumex acutus L. (Polygonaceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part R), pp. 785-805 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 803, DOI: 10.5281/zenodo.291971
Mechanical alignment of suprathermally rotating grains
Creators: name: Lazarian, A.
Publisher: name: arXiv
Year: 1995
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: It is shown that mechanical alignment of grains can be efficient for grains rotating suprathermally, i.e. with kinetic energy substantially exceeding $k$ (the Boltzmann constant) over any temperature in the system. The paper studies suprathermal rotation caused by H$_{2}$ formation and the alignment that takes place due to crossover events. Gaseous bombardment in the course of a crossover as well as both gaseous friction and poisoning of active sites are shown to produce alignment. The first type of alignment happens due to the angular momentum deposited by a corpuscular flux with a grain, the second is caused by the change of the mean time back to crossover due to the interaction with a gaseous flux. We show that the two processes act as to decrease the grain cross section in respect to the flux and we find the Rayleigh reduction factor for the joint action of the two processes as well as the range of applicability of each of the processes. Our study indicates that mechanical alignment can be more widely spread than it is generally accepted.
description: 39 pages, uuencoded Postcript, Accepted to ApJ
Additional file 3: of Association between unhygienic menstrual management practices and prevalence of lower reproductive tract infections: a hospital-based cross-sectional study in Odisha, India
Creators: name: Belen Torondel
name: Sinha, Shalini
name: Mohanty, Jyoti
name: Tapoja Swain
name: Pranati Sahoo
name: Bijaya Panda
name: Arati Nayak
name: Bara, Mary
name: Bilung, Bibiana
name: Cumming, Oliver
name: Pinaki Panigrahi
name: Padmalaya Das
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Biotechnology
subject: Developmental Biology
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Strobe checklist for Cross-sectional studies (Strobe checklist requested from reviewers. It is not referred in the text, but it is added as Additional file 3). (DOC 97 kb)
Measurement of the radial distribution of Cherenkov light generated by TeV gamma-ray air showers
Creators: name: HEGRA Collaboration
name: al, F. Aharonian et
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Using air showers induced by TeV gamma-rays from Mrk 501, the radial distribution of Cherenkov light is investigated. The shower geometry is reconstructed from the stereoscopic shower images obtained with the telescopes of the HEGRA IACT system. We observe a change in the shape of the light pool with shower energy, and with zenith angle. Data are well reproduced by Monte-Carlo air shower simulations.
description: 15 Pages, 8 figures, Latex
Functionalised silica nanoparticles for biomedical imaging
Creators: name: Percival, Sarah Jane
Publisher: name: Imperial College London
Year: 2014

description: Magnetic resonance imaging is one of the most widely used diagnostic techniques in the clinic as it affords many of the attributes sought from a non-invasive imaging modality. The main limitation of MRI is its inherent insensitivity, and as a result only large-scale abnormalities can be detected from a scan. With an increasing demand for earlier cancer diagnosis there has been a move towards imaging the molecular biomarkers that are present from the beginning of the disease process. This thesis describes the development of highly fluorinated, silica nanoparticles to actively target cancer cells for imaging by 19F MRI. Silica nanoparticles were prepared, and their size optimised for the molecular imaging application. A method was developed to modify the nanoparticles with the highest possible number of surface amine groups. These amine groups were conjugated to fluorinated PEG chains, each containing six equivalent 19F nuclei, and the resulting particles had a high 19F content. To provide the particles with the properties required for a molecular imaging probe, a tenth of the surface bound 19F PEG chains were conjugated to targeting peptides and the remainder were coupled to stabilising ligands. Using quantitative characterisation techniques each modification step was optimised and the exact composition of the nanoparticles was determined. To complement 19F MRI, fluorophores were incorporated into the particles for optical detection as this modality offered an accessible, sensitive and inexpensive alternative. Several samples were prepared which incorporated fluorophores at different positions throughout the nanoparticle structure. Adding the fluorophores to the nanoparticle surface was found to produce the most sensitive optical probe. The final particles were used for in vitro targeting studies to assess their potential as molecular imaging probes. Preliminary in vitro assays demonstrated that these particles selectively targeted cancer cells in the M21 cell line when compared to a control.
Rumex aegyptiacus Linnaeus, 1753, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1753
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Polygonales
Polygonaceae
Rumex
Rumex aegyptiacus

description: Rumex aegyptiacus, spec. nov.
 6. Rumex floribus hermaphroditis: valvulis trifido-setaceis: unica granifera. Hort. ups. 89.
 Rumex floribus hermaphroditis, foliis oblongis, valvulis dentato-setaceis longissimis. Wach. ultr. 391.
 Lapathum aegypticum, capsula seminis alba & crenata. Dill. elth. 191. t.158. f.191.
 Lapathum aegyptiacum annuum, parietariae foliis, capsula seminis longius barbata. Till. pis. 43. t.37. f.1.
 Habitat in AEgypto . ☉
description: Published as part of Linnaeus, Carolus, 1753, Species plantarum: exhibentes plantas rite cognitas, ad genera relatas, cum differentiis specificis, nominibus trivialibus, synonymis selectis, locis natalibus, secundum systema sexuale digestas, Stockholm :Laurentius Salvius on page 335, DOI: 10.5281/zenodo.3931989
Rumex aegyptiacus Linnaeus 1753
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Polygonales
Polygonaceae
Rumex
Rumex aegyptiacus

description: Rumex aegyptiacus Linnaeus, Species Plantarum 1: 335. 1753.
"Habitat in Aegypto." RCN: 2583.
Type not designated.
Original material: Herb. Linn. No. 149.17 (S); [icon] in Dillenius, Hort. Eltham. 1: 191, t. 158, f. 191. 1732; [icon] in Tilli, Cat. Pl. Hort. Pisani: 93, t. 37, f. 1. 1723.
Current name: Rumex aegyptiacus L. (Polygonaceae).
Note: El Hadidi & al. (in Taeckholmia 10: 57. 1987) indicated 464.11 (LINN) as type, but this collection lacks the relevant Species Plantarum number (i.e. “6”) and was a post-1753 addition to the herbarium, and is not original material for the name.
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part R), pp. 785-805 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 803, DOI: 10.5281/zenodo.291971
Quantitative Estimates of Environmental Effects on the Star Formation Rate of Disk Galaxies in Clusters of Galaxies
Creators: name: Fujita, Yutaka
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: A simple model is constructed to evaluate the change of star formation rate of a disk galaxy due to environmental effects in clusters of galaxies. Three effects, (1) tidal force from the potential well of the cluster, (2) increase of external pressure when the galaxy plows into the intracluster medium, (3) high-speed encounters between galaxies, are investigated. General analysis indicates that the star formation rate increases significantly when the pressure of molecular clouds rises above $\sim 3\times 10^5 cm^{-3} K$ in $\sim 10^8$ yr. The tidal force from the potential well of the cluster increases pressures of molecular clouds in a disk galaxy infalling towards the cluster center. Before the galaxy reaches the cluster center, the star formation rate reaches a maximum. The peak is three to four times larger than the initial value. If this is the main mechanism of the Butcher-Oemler effect, blue galaxies are expected to be located within $\sim 300$ kpc from the center of the cluster. However this prediction is inconsistent with the recent observations. The increase of external pressure when the galaxy plows into the intracluster medium does not change star formation rate of a disk galaxy significantly. The velocity perturbation induced by a single high-speed encounter between galaxies is too small to affect star formation rate of a disk galaxy, while successive high-speed encounters (galaxy harassment) trigger star formation activity because of the accumulation of gas in the galaxy center. Therefore, the galaxy harassment remains as the candidate for a mechanism of the Butcher-Oemler effect.
description: 12 pages, 13 figures. To be published in ApJ
Approximation Methods for Non-linear Gravitational Clustering
Creators: name: Sahni, Varun
name: Coles, Peter
Publisher: name: arXiv
Year: 1995
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We discuss various analytical approximation methods for following the evolution of cosmological density perturbations into the strong (i.e. nonlinear) clustering regime. These methods can be classified into five types: (i) simple extrapolations from linear theory, such as the high--peak model and the lognormal model; (ii) {\em dynamical} approximations, including the Zel'dovich approximation and its extensions; (iii) non--linear models based on purely geometric considerations, of which the main example is the Voronoi model; (iv) statistical solutions involving scaling arguments, such as the hierarchical closure {\em ansatz} for BBGKY, fractal models and the thermodynamic model of Saslaw; (v) numerical techniques based on particles and/or hydrodynamics. We compare the results of full dynamical evolution using particle codes and the various other approximation schemes. To put the models we discuss into perspective, we give a brief review of the observed properties of galaxy clustering and the statistical methods used to quantify it, such as correlation functions, power spectra, topology and spanning trees.
description: 175 pages, 20 figures. To appear in Phys. Rep. 1995. Hard copies of figures/Manuscript available upon request from: varun@iucaa.ernet.in
Additional file 2: of Association between unhygienic menstrual management practices and prevalence of lower reproductive tract infections: a hospital-based cross-sectional study in Odisha, India
Creators: name: Belen Torondel
name: Sinha, Shalini
name: Mohanty, Jyoti
name: Tapoja Swain
name: Pranati Sahoo
name: Bijaya Panda
name: Arati Nayak
name: Bara, Mary
name: Bilung, Bibiana
name: Cumming, Oliver
name: Pinaki Panigrahi
name: Padmalaya Das
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Diagnosis of BV, TV, and Candida infection. Detail explanation about laboratory methods used to diagnosed the studied infections [45, 46]. (DOCX 12 kb)
Rumex alpinus Linnaeus, 1753, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1753
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Polygonales
Polygonaceae
Rumex
Rumex alpinus

description: Rumex alpinus, spec. nov.
 3. Rumex floribus hermaphroditis: valvulis integerrimis graniferis, foliis imis ellipticis. Sauv. monsp. 69. †
 Rumex folio pedali cordato, radice repente. Lemonier. Sauv. monsp. 111.
 Lapathum androgynum obtusifolium, spica confertissima. Hall. helv. 170.
 Lapathum hortense rotundifolium s. montanum. Bauh. pin. 115.
 Lapathum rotundifolium. Clus. hist. 2. p. 69.
 Habitat in Helvetia , Monspelii . ♃
description: Published as part of Linnaeus, Carolus, 1753, Species plantarum: exhibentes plantas rite cognitas, ad genera relatas, cum differentiis specificis, nominibus trivialibus, synonymis selectis, locis natalibus, secundum systema sexuale digestas, Stockholm :Laurentius Salvius on page 334, DOI: 10.5281/zenodo.3931989
Catalyst design for ethylene polymerisation - a study on long-chain branching
Creators: name: Gragert, Maria Magdalena
Publisher: name: Imperial College London
Year: 2014

description: Polyethylene (PE) is the most produced polyolefin worldwide. Since recently discovered long-chain branches (LCB) have been shown to improve the processability, this thesis concentrates on the synthesis of new catalysts capable of producing long-chain branched polyethylene (LCB PE), the investigation of the mechanism which leads to LCB, and the control of the branching degree. The synthesis of new Group IV metal complexes with aromatic carbon-donor ligands which are η1-bound to the metal centre is described. These ligands include biphenyls, diphenylpyridines and terphenyls. Furthermore, an amido complex has been prepared and its synthesis and characterisation is presented herein. All complexes with carbon-based ligands are highly sensitive to air and moisture. Only the use of metal precursors with electron donating ligands enabled the formation of such complexes and it is concluded that electron donating ligands stabilise the electron deficient metal centre and metal-carbon bond. Polymerisation studies showed that the new complexes are active ethylene polymerisation catalysts. Their activity usually increases with temperature. The effect of hydrogen on the polymerisation activity cannot be predicted. Sensitive rheology measurements of the polymer melts revealed the presence of long-chain branches and it has been shown that the Group IV metal complexes with carbon-based ligands described in this thesis are producing LCB PE. Initial experiments towards the investigation of the long-chain branch forming mechanism are described within this thesis. Although not finished, a suitable route to complexes bearing a long alkyl chain has been established, which can be pursued in further studies. A series of tertiary-alkyl amines has been prepared and reacted with a silane to give the targeted aminosilane ligand. The effect of alkyl chain substituents on a cyclopentadienyl ligand in metallocenes has additionally been investigated with respect to the formation of LCB. In order to control the number of LCB in a PE resin, a bicatalytic system involving a bis(imino)pyridineiron catalyst that produces linear PE, an α-diiminenickel catalyst that produces branched PE and a chain transfer agent (CTA) was investigated. The combination of chain shuttling and chain walking as common mechanisms involved in ethylene polymerisation with late transition metal complexes showed to be a promising approach for the control of branching in PE while using ethylene as only monomer feed. Not only can branching be induced by carefully selecting the catalyst ratio and amount of CTA, but it has been shown that chain straightening occurs.
Rumex alpinus Linnaeus 1753
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Polygonales
Polygonaceae
Rumex
Rumex alpinus

description: Rumex alpinus Linnaeus, Species Plantarum 1: 334. 1753, nom. cons.
"Habitat in Helvetia, Monspelii." RCN: 2598.
Conserved type (Cafferty & Snogerup in Taxon 49: 571. 2000): Herb. Linn. No. 464.35 (LINN).
Current name: Rumex alpinus L. (Polygonaceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part R), pp. 785-805 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 803, DOI: 10.5281/zenodo.291971
Cosmological Adaptive Mesh Refinement
Creators: name: Norman, Michael L.
name: Bryan, Greg L.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We describe a grid-based numerical method for 3D hydrodynamic cosmological simulations which is adaptive in space and time and combines the best features of higher order--accurate Godunov schemes for Eulerian hydrodynamics with adaptive particle--mesh methods for collisionless particles. The basis for our method is the structured adaptive mesh refinement (AMR) algorithm of Berger & Collela (1989), which we have extended to cosmological hydro + N-body simulations. The resulting multiscale hybrid method is a powerful alternative to particle-based methods in current use. The choices we have made in constructing this algorithm are discussed, and its performance on the Zeldovich pancake test problem is given. We present a sample application of our method to the problem of first structure formation. We have achieved a spatial dynamic range $L_{box}/Δx > 250,000$ in a 3D multispecies gas + dark matter calculation, which is sufficient to resolve the formation of primordial protostellar cloud cores starting from linear matter fluctuations in an expanding FRW universe.
description: 14 pages, 3 figures (incl. one large color PS) to appear in "Numerical Astrophysics 1998", eds. S. Miyama & K. Tomisaka, Tokyo, March 10-13, 1998
Simulating tidal turbines with multi-scale mesh optimisation techniques
Creators: name: Abolghasemi, Mohammad Amin
Publisher: name: Imperial College London
Year: 2016

description: Embedding tidal turbines within simulations of realistic large-scale tidal flows is a highly multi-scale problem that poses significant computational challenges. Herein this problem is tackled using actuator disc momentum (ADM) theory and Reynolds-averaged Navier-Stokes (RANS) with, for the first time, dynamically adaptive mesh optimisation techniques. This enables the mesh to be refined dynamically in time and only in the locations required, thus making optimal use of limited computational resources. Ambient turbulence intensity has a significant effect on the structure of the turbine wake and its recovery. Therefore, both $k-\omega$ and $k-\omega$ SST RANS models have been implemented within the Fluidity framework in order to account for the effects of turbulence. The model is validated against three sets of experiments and a comparison against a similar OpenFOAM model is also presented to portray the benefits of the finite element discretisation scheme employed in the Fluidity ADM-RANS model. With the aid of the ADM-RANS model, the eddy viscosity value used in depth-averaged models is tuned to improve the wake structures predicted. Thereafter, OpenTidalFarm (OTF) is used to optimise turbine positions in order to maximise the total extracted power from an array. The depth-averaged results are then compared against 3D simulations of the arrays of tidal turbines using the ADM-RANS model, thus allowing for an investigation into the accuracy of the adjoint-based optimisation used in OTF for the first time. Finally, a methodology for embedding the ADM-RANS model within large scale simulations with real tidal forcing and bathymetry is presented. This allows for an accurate prediction of the power output from an array at a realistic tidal site and it can also provide valuable information on how the local and global flows are affected.
Fabrication of doxorubicin-gated mesoporous polydopamine nanoplatforms for multimode imaging-guided synergistic chemophotothermal therapy of tumors
Creators: name: Yang, Min
name: Zhang, Ningnan
name: Zhang, Tao
name: Yin, Xian
name: Shen, Jie
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer

description: A versatile theranostic agent that integrated with therapeutic and diagnostic functions is extremely essential for cancer theranostic. Herein, a multifunctional theranostic nanoplatform (PFP@MPDA-DOX) based on perfluoropentane (PFP) encapsulated mesoporous polydopamine (MPDA) is elaborately designed, followed by gating of drug doxorubicin (DOX) for preventing cargo leaking. The MPDA with pH-responsive biodegradation behavior was served as nanocarrier, which also endows the nanoplatform with a large cavity for PFP filling. The nanoparticles were then gated with DOX molecule by Michael addition and/or Schiff base reaction to shield the leaking of PFP during the blood circulation before the tumor tissue is reached. Also, such nanotheranostic exhibits high photothermal conversion efficiency of 45.6%, which can act as an intelligent nanosystem for photothermal therapy (PTT) and photoacoustic (PA) imaging. Moreover, the liquid-gas phase transition of PFP arising upon exposure to an 808 nm laser and thus produced the bubbles for ultrasound (US) imaging. The subsequent PFP@MPDA-DOX-mediated synergetic chemotherapy (contributed by the DOX gatekeeper) and PTT (contributed by the MPDA) shows excellent anticancer activity, which has been systematically evaluated both in vitro and in vivo. All these positive results certify that the facile incorporation of the antitumor drug gatekeeper and MPDA into one theranostic nanoplatform shows general potential for multimode PA/US imaging and combination chemotherapy/PTT of tumors.
Computational analysis of blood flow and stress patterns in the aorta of patients with Marfan syndrome
Creators: name: Singh, Shelly Deokie
Publisher: name: Imperial College London
Year: 2016

description: Personalised external aortic root support (PEARS) was designed to prevent progressive aortic dilatation, and the associated risk of aortic dissection, in patients with Marfan syndrome by providing an additional support to the aorta. The objective of this thesis was to understand the biomechanical implications of PEARS surgery as well as to investigate the altered haemodynamics associated with the disease and its treatment. Finite element (FE) models were developed using patient-specific aortic geometries reconstructed from pre and post-PEARS magnetic resonance (MR) images of three Marfan patients. The wall and PEARS materials were assumed to be isotropic, incompressible and linearly elastic. A static load on the inner wall corresponding to the patients’ pulse pressure was applied with a zero-displacement constraint at all boundaries. Results showed that peak aortic stresses and displacements before PEARS were located at the sinuses of Valsalva but following PEARS surgery, they were shifted to the aortic arch, at the intersection between the supported and unsupported aorta. The zero-displacement constraint at the aortic root was subsequently removed and replaced with downward motion measured from in vivo images. This revealed significant increases in the longitudinal wall stress, especially in the pre-PEARS models. Computational fluid dynamics (CFD) models were developed to evaluate flow characteristics. The correlation-based transitional Shear Stress Transport (SST-Tran) model was adopted to simulate potential transitional and turbulence flow during part of the cardiac cycle and flow waveforms derived from phase-contrast MR images were imposed at the inlets. Qualitative patterns of the haemodynamics were similar pre- and post-PEARS with variations in mean helicity flow index (HFI) of -10%, 35% and 20% in the post-PEARS aortas of the three patients. A fluid-structure interaction (FSI) model was developed for one patient, pre- and post-PEARS in order to examine the effect of wall compliance on aortic flow as well as the effect of pulsatile flow on wall stress. This model excluded the sinuses and was based on the laminar flow assumption. The results were similar to those obtained using the rigid wall and static structural models, with minor quantitative differences. Considering the higher computational cost of FSI simulations and the relatively small differences observed in peak wall stress, it is reasonable to suggest that static structural models would be sufficient for wall stress prediction. Additionally, aortic root motion had a more profound effect on wall stress than wall compliance. Further studies are required to assess the statistical significance of the findings outlined in this thesis. Recommendations for future work were also highlighted, with emphasis on model assumptions including material properties, residual stress and boundary conditions.
MOESM1 of Role of phosphate limitation and pyruvate decarboxylase in rewiring of the metabolic network for increasing flux towards isoprenoid pathway in a TATA binding protein mutant of Saccharomyces cerevisiae
Creators: name: Wadhwa, Manisha
name: Sumana Srinivasan
name: Bachhawat, Anand
name: K. Venkatesh
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Physiology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Table S1. Different spt15 variants for phenotypic improvement. Table S2. List of strains used in the study. Table S3. A. Parameters for simulations of flux balance distribution B. Transcriptomic constraints for flux balance distribution of 102a. C. Transport/Diffusion constraints. Table S4. ATP production and consumption normalized to 100 units of glucose. Table S5. List of upregulated and downregulated reactions in 102a (mutant) (without transcriptomic changes) in comparison to 101a (control). Table S6. Phosphate production and consumption normalized to 100 units of glucose. Table S7. Growth rate of 101a and 102a at different concentration of phosphate. Table S8. NADH production and consumption normalized to 100 units of glucose. Table S9. NADPH production and consumption normalized to 100 units of glucose. Table S10. List of oligonucleotides and their sequence used in the study. Fig. S1. Growth curve kinetics of S. cerevisiae BY4741 strain carrying either control 101a (SPT15WT) or mutant 102a plasmid (spt15_Ala101Thr). Fig. S2. Detailed flux distribution in central metabolism of control 101a (SPT15WT) and mutant 102a (spt15_Ala101Thr) strain without transcriptomic changes. Fig. S3. Schematic representation of plasmid maps (A) pRS416TEF-RtPSY1 (B) pRS315TEF-RtCRTI_Ala393Thr (C) pRS313TEF-SPT15WT (D) pRS313TEF-spt15_Ala101Thr (E) pRS314TEF-PDC6. RtPSY1, RtCRTI_Ala393Thr corresponds to phytoene synthase and hyperactiveÂ mutant of phytoene dehydrogenase from Rhodosporidium toruloides, SPT15WT, spt15_Ala101Thr corresponds to TATA binding protein, SPT15 wild type and mutant of SPT15 from Saccharomyces cerevisiae, PDC6 corresponds to pyruvate decarboxylase 6 gene from S. cerevisiae. TEF promoter- promoter from Translation elongation factor gene, GPD promoter- promoter from Glyceraldehyde-3-phosphate dehydrogenase gene, CYC1 terminator- terminator from cytochrome C gene. URA3, LEU2, TRP1 and HIS3 are auxotrophic markers for yeast, S. cerevisiae.
The Cosmological Bias Factor of Damped Lyman Alpha systems: Dependence on Metal Line Strength
Creators: name: Pérez-Ràfols, Ignasi
name: Miralda-Escudé, Jordi
name: Arinyo-i-Prats, Andreu
name: Font-Ribera, Andreu
name: Mas-Ribas, Lluís
Publisher: name: arXiv
Year: 2018
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We measure the cosmological bias factor of DLAs from their cross-correlation with the Ly$α$ forest absorption, as a function of the DLA metal strength, defined from an average of equivalent widths of the strongest detectable low-ionization metal lines. A clear increase of the bias factor with metal strength is detected, as expected from a relation of metallicity and velocity dispersion with host halo mass. The relation is stronger after the metal strength is corrected for the HI column density, to make it more related to metallicity instead of metal column density. After correcting for the effects of measurement errors of the metal strength parameter, we find that the bias factor of DLAs with the weakest metal lines is close to unity, consistent with an origin in dwarf galaxies with host halo masses $\sim10^{10} M_{\odot}$, whereas the most metal rich DLAs have a bias factor as large as $b_{\rm DLA} \sim 3$, indicative of massive galaxies or galaxy groups in host halos with masses $\sim 10^{12} M_{\odot}$. Our result confirms the physical origin of the relation of bias factors measured from cross-correlation studies to the host halos of the absorbers.
description: 18 pages, 5 figures, 2 tables, accepted to MNRAS
Determination of Malmquist Bias and Selection Effects from Monte-Carlo Simulations
Creators: name: Freudling, Wolfram
name: Da Costa, Luiz N.
name: Wegner, Gary
name: Giovanelli, Riccardo
name: Haynes, Martha P.
name: Salzer, John J.
Publisher: name: arXiv
Year: 1995
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Maps of the peculiar velocity field derived from distance relations are affected by Malmquist type bias and selection effects. Because of the large number of interdependent effects, they are in most cases difficult to treat analytically. Monte Carlo simulations are used to understand and evaluate these effects. In these simulations the ``true'' spatial distribution and relevant properties of galaxies as well as selection effects and observational uncertainties are realistically modeled. The results of the simulation can directly be applied to correct observed peculiar velocity maps. The simulation is used to investigate biases in samples of measured peculiar velocities by Lynden-Bell et al. (1988), Willick (1990) and the new sample of spiral galaxies by Haynes et al. (1993). Based on the results obtained from the application of our method to toy models we find that the method is a useful tool to estimate the bias induced both by inhomogeneities and selection effects. This is a crucial step for the analysis of the Haynes \etal sample which was selected with a redshift dependent criterion.
description: accepted for publication in The Astronomical Journal, LaTex file using aaspptwo.sty macros, 18 pages + 15 figures, figures not included. A postscript version including all figures can be obtained from ftp://ecf.hq.eso.org/pub/preprints/malmquist.ps (2.8 MByte or 0.9 Mbyte for the compressed version)
title: ADCO, Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome III, Cart. 187 (11 H 72), f. 0022r
Creators: name: de la Côte d'Or, Archives départementales
name: CG21/F.PETOT/2012
name: Petot, Frédéric
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: cartulaire
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome III, Archives départementales de la Côte-d'Or, Cart. 187 (11 H 72), f. 0022r, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome III, Archives départementales de la Côte-d'Or, Cart. 187 (11 H 72), f. 0022r, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https:// manuscrits.cbma-project.eu/
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v