cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Madrepora Linnaeus, 1758, gen. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Cnidaria
Anthozoa
Scleractinia
Oculinidae
Madrepora

description: Madrepora [gen. nov.]
Animalia Medusae. Ellis cor. t. 32. f. A. Donat. adriat. t. 6. f. F.
Corallium tubulis stellato-la- mellosis.
* Simplices: Stella unica communi simplici.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 793, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Additional file 1 of A novel amino acid site of N protein could affect the PRRSV-2 replication by regulating the viral RNA transcription
Creators: name: Deng, Hua
name: Xin, Ning
name: Zeng, Fancong
name: Wen, Feng
name: Yi, Heyou
name: Ma, Chunquan
name: Huang, Shujian
name: Zhang, Guihong
name: Chen, Yao
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Virology

description: Additional file 1: Figure S1.The schematic diagram of the PRRSV infectious cDNA clones. Figure S2.The full-length western-blots of N proteinexpression level of A78 and XH-GD. Figure S3. The rest serine sitesdid not affect viral viability, infectivityor replication ability.(A): IFA results. The Marc-145 cells were infectedwith the PRRSV at 0.1MOI. At 48 hpi, the cells were fixed with 4%paraformaldehyde and PBS. Then, the cells were incubated with the N monoclonalantibody, followed by goat anti-mouse IgG (H+L), which was modified by fluoresceinisothiocyanate (FITC). The nuclei were stained with DAPI (Scale bars are 90 um); (B)Growth characterization of the viruses. Themultistep kinetics of the mutated viruses. Marc-145 cells were infected withPRRSV at an MOI of 0.1. Thesupernatants were collected at various time points and titrated. The viraltitres were calculated by the Reed-Muench method. Figure S4. Level of IL-10 mRNA production of A78, the result wascalculated after normalization to XH-GD. The data shown represent the mean ±SD (n=3).
Reminiscences of George Hamilton Combs, Jr., 1951
Publisher: name: Columbia University
Year: 2021
Subjects: Legislators--United States
Lawyers

description: Kansas City: Thomas J. Pendergast machine; Congress, 1927-1929; election of 1932; New York City politics and Tammany Hall, 1932-1950; New York election of 1950; Estes Kefauver investigation
Normal-mode representation of noise cross-correlation in the spherically symmetric case from Asymptotic analysis for dispersion relations and travel times in noise cross-correlations: spherically symmetric case
Creators: name: T. S. Liu
name: H. M. Zhang
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Geophysics
subject: FOS: Earth and related environmental sciences

description: derivations for formulae in sec.1
Precise prediction of the MSSM Higgs boson masses for low MA
Creators: name: Bahl, Henning
name: Hollik, Wolfgang
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Precise predictions for Higgs boson masses in the Minimal Supersymmetric Standard Model can be obtained by combining fixed-order calculations with effective field theory (EFT) methods for the resummation of large logarithms in case of heavy superpartners. This hybrid approach is implemented in the computer code FeynHiggs and has been applied in previous studies for calculating the mass of the lightest CP-even Higgs boson for low, intermediate and high SUSY scales. In these works it was assumed that the non-standard Higgs bosons share a common mass scale with the supersymmetric squark particles, leaving the Standard Model as the low-energy EFT. In this article, we relax this restriction and report on the implemention of a Two-Higgs-Doublet Model (THDM) as effective theory below the SUSY scale into our hybrid approach. We explain in detail the various steps how our EFT calculation is consistently combined with the fixed-order calculation within the code FeynHiggs. In our numerical investigation we find effects on the mass of the lightest CP-even Higgs boson h of up to 9 GeV in scenarios with low $M_A$ , low $\tanβ$ and high SUSY scales, when compared with previous versions of FeynHiggs. Comparisons to other publicly available pure EFT codes with a THDM show good agreement. Effects on the mass of the second lightest CP-even Higgs boson H are found to be negligible in the phenomenologically interesting parameter regions where H can be traded for h as the experimentally observed Higgs particle.
description: 86 pages, 21 figures; small corrections; matches version to be published in JHEP
ZOOTRANS 2010 cruise,Côtes De La Manche R/V
Creators: name: SOUISSI Sami
name: GLIPPA Olivier
name: DEVREKER David
Publisher: name: Sismer
Year: 2010

description: Etude de la dynamique de population des copépodes majoritaires de l'estuaire de la Seine en fonction des cycles de marée et saisonnier - mise en place d'un suivi à long terme.
Pulse sequence designed for robust C-phase gates in SiMOS and Si/SiGe double quantum dots
Creators: name: Güngördü, Utkan
name: Kestner, J. P.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We theoretically analyze the errors in one- and two-qubit gates in SiMOS and Si/SiGe spin qubit experiments, and present a pulse sequence which can suppress the errors in exchange coupling due to charge noise using ideal local rotations. In practice, the overall fidelity of the pulse sequence will be limited only by the quality of the single-qubit gates available: the C-phase infidelity comes out to be $\approx 2.5 \times$ the infidelity of the single-qubit operations. Based on experimental data, we model the errors and show that C-phase gate infidelities can be suppressed by two orders in magnitude. Our pulse sequence is simple and we expect an experimental implementation would be relatively straightforward. We also evaluate the performance of this gate against $1/f$ noise. Assuming a soft ultraviolet cutoff, we show that the pulse sequence designed for quasistatic noise still performs well when the cutoff occurs below $\sim 1$MHz given fast enough one-qubit Rabi frequencies, suppressing the infidelity by an order of magnitude compared to the existing direct adiabatic protocol. We also analyze the effects of nonadiabaticity during finite rise periods, and find that adiabaticity is not a limitation for the current values of exchange coupling.
Reminiscences of George Horace Gallup, 1962
Publisher: name: Columbia University
Year: 2021
Subjects: Statisticians
Readership surveys
Public opinion polls
Journalism
Periodicals--Publishing
Demographic surveys

description: Family background and education; early newspaper readership surveys; journalism teaching 1929-1932; principles of effective advertising; magazine publishing: LITERARY DIGEST, READER'S DIGEST, SATURDAY EVENING POST, LOOK, etc.; postcard polling; Gallup polls from 1933; impressions of Gardner Cowles, Jr., Raymond Rubicam, Douglas Southall Freeman
title: ADCO, Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome V, Cart. 189 (11 H 74), 316 folios, f. 0158r
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2012
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: cartulaire
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome V, Archives départementales de la Côte-d'Or, Cart. 189 (11 H 74), 316 folios, f. 0158r, 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 V, Archives départementales de la Côte-d'Or, Cart. 189 (11 H 74), 316 folios, f. 0158r, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https:// manuscrits.cbma-project.eu/
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
ZOSTERA-ACOUSTIQUE cruise,Haliotis R/V
Creators: name: CORDIER Céline
name: BAJJOUK Touria
Publisher: name: Sismer
Year: 2013

description: Dans le cadre du contrôle de surveillance, la végétation benthique est obligatoirement prise en considération pour 3 raisons majeures : 1) sa position dans le proche littoral, particulièrement exposé aux pollutions continentales; 2) sa réactivité naturelle aux évolutions de la qualité des eaux côtières; 3) sa sensibilité aux perturbations accidentelles du milieu comme les évolutions à long terme du climat. Dans ce contexte, l'objectif principal de la campagne Zostera est la cartographie des herbiers de Zostera marina dans le Golfe du Morbihan et en particulier la détermination de leur limite inférieure par l'utilisation de méthodes acoustiques (sonar interférométrique, sondeur monofaisceau). La campagne a été suivie par deux missions de validation Terrain : observations à l'aide d'un bâti vidéo Haute Définition puis par plongeurs. D'autres mesures ont été effectuées en parallèle : un levé aérien (imagerie hyperspectrale) et des mesures de biomasses sur la zone intertidale à marée basse. L'ensemble de ces données permettra également d'amorcer la réflexion sur l'approche méthodologique de mise à jour de la cartographie de l'habitat "herbiers de zostères" dans le cadre du Rebent en vue de son suivi spatio-temporel et d'avancer les projets de recherche de Dyneco concernant la cartographie prédictive des habitats remarquables.
Determination of the genetic mechanisms responsible for generating diversity in the cattle NK cell receptor repertoire
Creators: name: Sanderson, Nicholas
Publisher: name: Imperial College London
Year: 2014

description: Cattle have expanded the KIR gene repertoire, a polymorphic and polygenic im- munoglobulin family that encode Natural Killer cell receptors specific to MHC class I ligands. In humans, KIR are important mediators of innate immunity to viral pathogens such as HCV and HIV, and there is potential for exploiting cattle KIR diversity as a means of improving animal health. Cattle KIR expansion has occurred independently to humans, the result is a cattle KIR haplotype (CKH) with a completely different gene content. Successful sequencing and assembly of the CKH using whole genome techniques has failed. To interrogate cattle KIR, their function and comparative evolution, the content of a CKH must be estab- lished, then the extent of polymorphism and gene presence/absence variation can be studied. In this project the first CKH has been sequenced and assembled using second generation sequencing of BAC clones. This has provided a reference sequence for whole genome sequence data to be aligned revealing the KIR content of different Bovidae species, including the aurochs, the ancestor to all domesticated cattle. Furthermore genome capture and enrichment was performed to determine polymorphic and polygenic KIR variation within 24 different cattle genomes. The sheep KIR haplotype (SKH) was sequenced using PacBio of BAC clones to enable comparative analysis with cattle. The CKH has expanded through block duplications resulting in 16 discrete KIR loci. The haplotype is dominated by functional inhibitory receptor genes and the attenuated remains of activating KIR. Predicted similarity between au- rochs and modern CKH suggests KIR blocks expanded through natural selection and not artificial selection generated through centuries of domestication. Com- parative analysis of the SKH and CKH reveals that sheep have independently expanded at least five of the shared KIR that cattle have expanded. Cattle KIR are extremely polymorphic, with diversity focused within the Ig domains, regions predicted to interact with ligand.
Figure S1 from Experimental evidence for reduced male allocation under selfing in a simultaneously hermaphroditic animal
Creators: name: Winkler, Lennart
name: Ramm, Steven A.
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 60801 Animal Behaviour

description: Sex allocation plasticity under selfing vs. outcrossing conditions in Macrostomum hystrix
Heterophyton F. G. Wang 2014, nom. nov.
Creators: name: Wang, Fa-Guo
name: Xing, Fu-Wu
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Pteridopsida
Heterophyton

description: Heterophyton F.G. Wang, nom. nov.
Replaced name: Allophyton X.W. Wu (1982: 53), nom. illeg., non Allophyton Brandegee (1914: 62).
Type:— Heterophyton dengqenensis (X.W. Wu) F.G. Wang.
Etymology: Named from Greek heteros, “different,” and phyton, “plant”. The words heteros and allos essentially have the same meaning in botanical Latin.
One species in Xizang, China:
description: Published as part of Wang, Fa-Guo & Xing, Fu-Wu, 2014, Heterophyton, a new substitute name for Allophyton X. W. Wu (Pteridopsida), pp. 299-300 in Phytotaxa 163 (5) on page 299, DOI: 10.11646/phytotaxa.163.5.6, http://zenodo.org/record/5132505
Role of correlated two-pion exchange in $K^+ N$ scattering
Creators: name: Hoffmann, M.
name: Durso, J. W.
name: Holinde, K.
name: Pearce, B. C.
name: Speth, J.
Publisher: name: arXiv
Year: 1995
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: A dynamical model for S-- and P--wave correlated $2 π$ (and $K \bar K$) exchange between a kaon and a nucleon is presented, starting from corresponding $N \bar N \rightarrow K \bar K$ amplitudes in the pseudophysical region, which have been constructed from nucleon, $Δ$--isobar and hyperon ($Λ$, $Σ$) exchange Born terms and a realistic meson exchange model of the $ππ\rightarrow K \bar K$ and $K \bar K \rightarrow K \bar K$ amplitude. The contribution in the s--channel is then obtained by performing a dispersion relation over the unitarity cut. In the $ρ$--channel, considerable ambiguities exist, depending on how the dispersion integral is performed. Our model, supplemented by short range interaction terms, is able to describe empirical $K^+ N$ data below pion production threshold in a satisfactory way.
description: 24 pages, REVTEX, figures available from the authors
Development of a three-dimensional fracture model for the combined finite-discrete element method
Creators: name: Guo, Liwei
Publisher: name: Imperial College London
Year: 2014

description: Three-dimensional fracture simulation is a big challenge to computational mechanics because of the complicated fracture surface geometry and the difficulty of characterising different failure and interaction mechanisms in complex three-dimensional stress fields. As an attempt to improve the ability of numerical methods to simulate discrete fractures in quasi-brittle materials, a three-dimensional fracture model is developed in the context of the combined finite-discrete element method. The proposed fracture model is capable of simulating the whole fracturing process for both tensile and shear fracture initiation and propagation, including pre-peak hardening deformation, post-peak strain softening, transition from continuum to discontinuum, and explicit interaction between discrete fracture surfaces. An adaptive remeshing algorithm is developed to simulate discrete fractures with less mesh dependency. This algorithm can accurately refine tetrahedral elements based on the local stress field, and update the local mesh as fractures propagate. As a further development of the fixed-mesh-based fracture model, it is incorporated into a two-way fluid-solid coupling model and it is successfully applied to simulate a hydraulic fracturing problem. A comprehensive numerical simulation is carried out by applying the proposed three-dimensional fracture model to investigate explicit fracture development and to evaluate the damage mechanisms of concrete armour units on breakwaters. Dolosse units are simulated in drop tests and pendulum tests. The dropping of an assembly of CORE-LOCTM units of prototype scale is simulated under an imaginary extreme loading condition. The whole structural response of the CORE-LOCTM units is accurately captured and the transient dynamic response including that by fracturing is explicitly characterised. To investigate fracture network formation and growth in multi-layered rock, two-dimensional and polyaxial deformation simulations are conducted. Three-dimensional stress heterogeneity caused by fracturing is accurately captured. The results show the three-dimensional fracture model is capable of generating realistic fracture patterns according to geomechanical principles of rock failure.
Proton inelastic scattering to continuum studied with antisymmetrized molecular dynamics
Creators: name: Tanaka, Eiji I.
name: Ono, Akira
name: Horiuchi, Hisashi
name: Maruyama, Tomoyuki
name: Engel, Andreas
Publisher: name: arXiv
Year: 1995
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Intermediate energy (p,p$'$x) reaction is studied with antisymmetrized molecular dynamics (AMD) in the cases of $^{58}$Ni target with $E_p = 120$ MeV and $^{12}$C target with $E_p = $ 200 and 90 MeV. Angular distributions for various $E_{p'}$ energies are shown to be reproduced well without any adjustable parameter, which shows the reliability and usefulness of AMD in describing light-ion reactions. Detailed analyses of the calculations are made in the case of $^{58}$Ni target and following results are obtained: Two-step contributions are found to be dominant in some large angle region and to be indispensable for the reproduction of data. Furthermore the reproduction of data in the large angle region $θ\agt 120^\circ$ for $E_{p'}$ = 100 MeV is shown to be due to three-step contributions. Angular distributions for $E_{p'} \agt$ 40 MeV are found to be insensitive to the choice of different in-medium nucleon-nucleon cross sections $σ_{NN}$ and the reason of this insensitivity is discussed in detail. On the other hand, the total reaction cross section and the cross section of evaporated protons are found to be sensitive to $σ_{NN}$. In the course of the analyses of the calculations, comparison is made with the distorted wave approach.
description: 16 pages, 7 Postscript figures
Deploying Jupyter Notebooks at scale on XSEDE resources for Science Gateways and workshops
Creators: name: Zonca, Andrea
name: Sinkovits, Robert S.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: Jupyter Notebooks have become a mainstream tool for interactive computing in every field of science. Jupyter Notebooks are suitable as companion applications for Science Gateways, providing more flexibility and post-processing capability to the users. Moreover they are often used in training events and workshops to provide immediate access to a pre-configured interactive computing environment. The Jupyter team released the JupyterHub web application to provide a platform where multiple users can login and access a Jupyter Notebook environment. When the number of users and memory requirements are low, it is easy to setup JupyterHub on a single server. However, setup becomes more complicated when we need to serve Jupyter Notebooks at scale to tens or hundreds of users. In this paper we will present three strategies for deploying JupyterHub at scale on XSEDE resources. All options share the deployment of JupyterHub on a Virtual Machine on XSEDE Jetstream. In the first scenario, JupyterHub connects to a supercomputer and launches a single node job on behalf of each user and proxies back the Notebook from the computing node back to the user's browser. In the second scenario, implemented in the context of a XSEDE consultation for the IRIS consortium for Seismology, we deploy Docker in Swarm mode to coordinate many XSEDE Jetstream virtual machines to provide Notebooks with persistent storage and quota. In the last scenario we install the Kubernetes containers orchestration framework on Jetstream to provide a fault-tolerant JupyterHub deployment with a distributed filesystem and capability to scale to thousands of users. In the conclusion section we provide a link to step-by-step tutorials complete with all the necessary commands and configuration files to replicate these deployments.
description: 7 pages, 3 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, USA
MOESM5 of Expanding the clinical and genetic spectrum of Heimler syndrome
Creators: name: Gao, Feng-Juan
name: Hu, Fang-Yuan
name: Xu, Ping
name: Qi, Yu-He
name: Li, Jian-Kang
name: Zhang, Yong-Jin
name: Chen, Fang
name: Chang, Qing
name: Song, Fang
name: Shen, Si-Mai
name: Xu, Ge-Zhi
name: Wu, Ji-Hong
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Virology
subject: Computational Biology

description: Additional file 5: Table S3. Reported pathogenic variants in PEX1, PEX6, and PEX26 in the Human Gene Mutation Database associated with Zellweger syndrome.
Comment on ``Large-space shell-model calculations for light nuclei''
Creators: name: Csoto, Attila
name: Lovas, Rezso G.
Publisher: name: arXiv
Year: 1995
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: In a recent publication Zheng, Vary, and Barrett reproduced the negative quadrupole moment of Li-6 and the low-lying positive-parity states of He-5 by using a no-core shell model. In this Comment we question the meaning of these results by pointing out that the model used is inadequate for the reproduction of these properties.
description: Latex with Revtex, 1 postscript figure in separate file
Central Activity in the Barred Galaxy NGC 3367
Creators: name: Garcia-Barreto, J. A.
name: Rudnick, L.
name: Franco, J.
name: Martos, M.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We report the radio continuum structure of the barred galaxy NGC 3367 with an angular resolution of 4''.5. The radio structure indicates emission from the disk and from a triple source consisting of the nucleus straddled by extended sources (the lobes). The triple source shows an excess of radio continuum emission compared to the emission expected from the total radio - Halpha correlation, suggesting a non-thermal origin probably related to AGN activity and no to star formation processes. The triple source is about 12 kpc in diameter at a P.A. 40, close (but not aligned) to that of the stellar bar P.A. 65. Only the southwest lobe is polarized. The polarizatrion asymmetry between the two lobes suggests that the triple source axis is slightly out of the plane.
description: 13 latex pages, 8 figures. To appear in Astronomical Journal, July 1998
title: ADCO, Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome III, Cart. 187 (11 H 72), f. 0021v
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2012
name: Petot, Frédéric
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: LaMOP
subject: Chartes de la Bourgogne du Moyen Âge
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. 0021v, 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. 0021v, 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
Global bio-systems modulation and the translational metabolic physiology of bariatric surgery
Creators: name: Ashrafian, Hutan
Publisher: name: Imperial College London
Year: 2013

description: The global pandemic of obesity continues to escalate worldwide and results in severe multisystem metabolic dysfunction in the expanding population of its sufferers. It is associated with the concurrent pathologies of type 2 diabetes, cardiovascular disease, cancer and sleep apnea, which have also increased in prevalence over the past decade. Obesity can be mapped in social networks and is recognised as a fundamental element of the metabolic syndrome contributing to the global burden of diabesity and oncobesity. Its impact on global health has resulted in a massive burden on healthcare services and is among the most prominent contributors to mounting healthcare costs. Despite its pathological impact, the non-surgical management of obesity through behavioural, lifestyle and pharmacotherapies has not offered dependable benefits in severely obese patients. Bariatric surgery has demonstrated consistent weight loss in morbidly obese subjects and is increasingly performed worldwide to treat morbid obesity. Furthermore, these operations may produce beneficial metabolic effects especially with respect to improvement in type 2 diabetes and the metabolic syndrome. Understanding surgical weight loss mechanisms and metabolic modulation is required to enhance patient benefits and operative outcomes. A surgical model of Roux-en-Y gastric bypass (RYGB) was developed as an experimental platform to investigate the metabolic effects of bariatric surgery. The model was studied through a systems biology approach to characterize systemic and gastro-intestinal surgical metabolic modulation. Analysis of postoperative faecal samples from this rodent model revealed a powerful shift in gut microbial ecology and also highlighted the role of RYGB surgery in regulating the cross-talk between the gut microbiome and its mammalian host. Similar metabolic changes were also identified in human subjects undergoing bariatric surgery. Analysis of plasma and cardiac tissue revealed shifts in metabolic activity, reflected by enhanced cardiac energy metabolism. Overall, the results of this work identify some of the potential mechanisms behind bariatric surgical weight loss and systemic metabolic enhancement. This study not only supports the term metabolic surgery but also identifies the global multi-systemic benefits of bariatric surgical procedures. As such, the findings presented in this thesis may in future contribute to the enhancement of current bariatric procedures and the development of the next-generation of innovative metabolic therapies.
Molecular Simulation of Diffusive Mass Transport in Porous Materials
Creators: name: Frentrup, Hendrik
Publisher: name: Imperial College London
Year: 2014

description: Ever increasing control over the shape and form of a material's nanoscale features provokes the pursuit of a detailed understanding for the main factors influencing fluid transport. It is sought to facilitate the intelligent design of novel materials used in membrane separation processes. In addition to a strong dependence on molecular mobility, mass transport is heavily influenced by thermodynamic effects. Isolating thermodynamic and mobility effects is useful to understand the significant driving forces for mass transport through porous materials and their selective characteristics. However, experimental techniques are limited in probing this behaviour at the nanometre scale. In response to experimental challenges, the present study makes extensive use of the ability of molecular simulations to reflect the molecular character of nanoscale diffusion and identify equilibrium and transport properties individually. First, this work investigates diffusive mass transport inside a planar slit pore focusing on the influence of solid-fluid interactions, pore width, and fluid density. The influence of solid-fluid interactions, in particular, have often been neglected in studies of mass transport in porous solids. The vast variety of functionalised nano-materials is virtually endless and has spurred interest in this area. Equilibrium simulations were employed to determine self- and collective diffusivities and Grand Canonical insertions were used for the determination of thermodynamic factors. In addition, this work showcases the implementation of a highly efficient Non-Equilibrium Molecular Dynamics (NEMD) method through which effective transport was studied. The method was used to determine effective diffusivities which incorporate thermodynamic effects, the dominating contribution to transport for dense fluids. It is well suited to observe effective fluid transport in confined spaces as opposed to measuring self-diffusion, a measure for single-particle mobility only. The method is effective in studying mass transport in model systems as well as more realistic, complex geometries. As a second exemplary case, gas permeation through an atomistically detailed model of a high free-volume polymer was simulated explicitly with the NEMD approach. In addition to determining permeability and solubility directly from NEMD simulations, the results also shed light on the permeation mechanism of the penetrant gases, suggesting a departure from the expected pore-hopping mechanism due to the considerable accessibility of permeation paths.
Constraints on $Σ$ Nucleus Dynamics from Dirac Phenomenology of $Σ^-$ Atoms
Creators: name: Mares, J.
name: Friedman, E.
name: Gal, A.
name: Jennings, B. K.
Publisher: name: arXiv
Year: 1995
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Strong interaction level shifts and widths in $Σ^-$ atoms are analyzed by using a $Σ$ nucleus optical potential constructed within the relativistic mean field approach. The analysis leads to potentials with a repulsive real part in the nuclear interior. The data are sufficient to establish the size of the isovector meson--hyperon coupling. Implications to $Σ$ hypernuclei are discussed.
description: 18 pages, RevTex, 4 uuencoded figures, subm. Nucl.Phys.A
unyt: Handle, manipulate, and convert data with units in Python
Creators: name: Goldbaum, Nathan J.
name: ZuHone, John A.
name: Turk, Matthew J.
name: Kowalik, Kacper
name: Rosen, Anna L.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: Software that processes real-world data or that models a physical system must have some way of managing units. While simple approaches like the understood convention that all data are in a unit system (such as the MKS SI unit system) do work in practice, they are fraught with possible sources of error both by developers and users of the software. In this paper we present unyt, a Python library based on NumPy and SymPy for handling data that has units. It is designed both to aid quick interactive calculations and to be tightly integrated into a larger Python application or library. We compare unyt with two other Python libraries for handling units, Pint and astropy.units, and find that unyt is faster, has higher test coverage, and has fewer lines of code.
description: 11 pages, 6 figures. Submitted to the Journal of Open Source Software. The source code is available at https://github.com/yt-project/unyt and the documentation is available at http://unyt.readthedocs.io/en/latest/. Accepted for publication in the Journal of Open Source Software
Body sensor networks: smart monitoring solutions after reconstructive surgery
Creators: name: Kwasnicki, Richard Mark
Publisher: name: Imperial College London
Year: 2014

description: Advances in reconstructive surgery are providing treatment options in the face of major trauma and cancer. Body Sensor Networks (BSN) have the potential to offer smart solutions to a range of clinical challenges. The aim of this thesis was to review the current state of the art devices, then develop and apply bespoke technologies developed by the Hamlyn Centre BSN engineering team supported by the EPSRC ESPRIT programme to deliver post-operative monitoring options for patients undergoing reconstructive surgery. A wireless optical sensor was developed to provide a continuous monitoring solution for free tissue transplants (free flaps). By recording backscattered light from 2 different source wavelengths, we were able to estimate the oxygenation of the superficial microvasculature. In a custom-made upper limb pressure cuff model, forearm deoxygenation measured by our sensor and gold standard equipment showed strong correlations, with incremental reductions in response to increased cuff inflation durations. Such a device might allow early detection of flap failure, optimising the likelihood of flap salvage. An ear-worn activity recognition sensor was utilised to provide a platform capable of facilitating objective assessment of functional mobility. This work evolved from an initial feasibility study in a knee replacement cohort, to a larger clinical trial designed to establish a novel mobility score in patients recovering from open tibial fractures (OTF). The Hamlyn Mobility Score (HMS) assesses mobility over 3 activities of daily living: walking, stair climbing, and standing from a chair. Sensor-derived parameters including variation in both temporal and force aspects of gait were validated to measure differences in performance in line with fracture severity, which also matched questionnaire-based assessments. Monitoring the OTF cohort over 12 months with the HMS allowed functional recovery to be profiled in great detail. Further, a novel finding of continued improvements in walking quality after a plateau in walking quantity was demonstrated objectively. The methods described in this thesis provide an opportunity to revamp the recovery paradigm through continuous, objective patient monitoring along with self-directed, personalised rehabilitation strategies, which has the potential to improve both the quality and cost-effectiveness of reconstructive surgery services.
Track structure simulation of low energy electron damage to DNA using Geant4-DNA
Creators: name: Mokari, Mojtaba
name: Alamatsaz, Mohammad Hassan
name: Moeini, Hossein
name: Babaei-Brojeny, Ali Akbar
name: Taleei, Reza
Publisher: name: arXiv
Year: 2018
Subjects: subject: Biological Physics (physics.bio-ph)
subject: Medical Physics (physics.med-ph)
subject: FOS: Physical sciences

description: Due to the physical and chemical processes that are involved, interactions of ionizing radiations with cells lead to single- and double-strand breaks (SSB and DSB) and base damage to DNA cells. The damage may kill the cells or may be mis-repaired and lead to genetic diseases and cancers. Track structure Monte Carlo simulation of the DNA damage provides types of the damage and their frequencies. In the present work, to derive initial DNA damage, we used the Geant4-DNA code to simulate the physical, physico-chemical and chemical stages of interactions of incident beams of 100 eV to 4.5 keV electrons. By considering the direct damage of electrons and also the indirect hydroxyl radical damage to the DNA, in a simulation, simple and complex damages to SSB and DSB were investigated. Moreover, the yield of damage and the probability of types of DNA damage were evaluated. The results of these calculations were compared with the existing experimental data and the other simulations. For electrons with energies lower than 500 eV, there were differences between our results and published data which are basically due to the existing differences in the physical (electron ionization, excitation cross sections) and chemical models of Geant4-DNA, the chemical processes considered in the simulations, DNA geometry, and the selected parameters for damage threshold as compared to the other codes. In the present work, the effect of the threshold energy of the strand breaks was also evaluated.
description: 6 figures, 4 tables, 21 pages
Subjective wellbeing: a perspective on health care and health policy
Creators: name: Lee, Henry Adam
Publisher: name: Imperial College London
Year: 2014

description: The nature and resource constraints of modern health care has led to increased reliance on rigorous treatment targets and detailed policy guidelines. Whilst well intentioned, this can shift the focus away from patients themselves and places emphasis on arbitrary measures of output or performance that can relate poorly to how people experience and benefit from health care. Considerable effort and resources are spent on health care interventions, but policy makers and clinicians may be left without a clear understanding of how these treatments actually affect people in the experience of their lives. Subjective wellbeing (SWB) is a broad category of phenomena that includes people’s emotional responses, domain satisfactions (e.g., health or work), and global judgements of life satisfaction. Measures of SWB offer a means to gauge the impact of changes and events in the lives of individuals. In recent years, there has been increasing interest in the use of SWB in shaping public policy (e.g. in relation to environmental and economic policies). In my thesis, I examine for the first time the ways in which measures of SWB can be used directly within a health care setting and to inform health policy decisions. In doing so, I have drawn on my understanding of clinical environments and health care systems as a practising clinician to bring a new perspective to the way that SWB is considered and used in health care and to how it can be applied in determining health policy. I explore the use of SWB at both the macro and micro levels of policy making and address the challenges faced when using measures of SWB in these ways. At the macro level, I examine the limitations and challenges of existing methods and examine where using SWB would have the most impact. I also focus on the use of SWB measures at a micro level, setting out a new model of patient experience with reference to SWB. My thesis sets out original methods for SWB data collection developed through innovative empirical work. This work into hernia surgery and on the SWB of the staff and inpatients of an acute NHS hospital has generated new data sets in clinical populations. I discuss the implications of this research and explain how, when and where SWB measures, when used in health care, can be used in health policy. All too often we lose sight of what really matters in life, and the world of heath care is no exception. Through the application of measures of SWB in health care, I offer a novel perspective that ensures a greater focus is placed on the way that patients experience health interventions when developing health policy.
Madrepora astroites Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Cnidaria
Anthozoa
Scleractinia
Oculinidae
Madrepora
Madrepora astroites

description: Madrepora astroites [spec. nov.]
M. composita, stellis subrotundis concavis coadunatis. Hort. cliff. 481.
Olear. mus. 74. t. 34. f. 5.
Bocc. mus. 1. t. 5. f. 4. Astroites V.
Gesn. fig. 35.
Worm. mus. 68.
Plot. oxon. 87. t. 2. f. 6, 7. Astroites.
Boet. lap. 298.
Sloan. jam. 1. p. 54. t. 21. Lapis Astroites s. stellaris.
Aldr. mus. 872. t. 877, 878, 879. Stellatus lapis.
Habitat .. fossilis.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 796, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Tables S3-S5 from Experimental evidence for reduced male allocation under selfing in a simultaneously hermaphroditic animal
Creators: name: Winkler, Lennart
name: Ramm, Steven A.
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 60801 Animal Behaviour

description: Supplementary analyses exploring potential effects of body size
MOESM1 of The in vivo impact of MsLAC1, a Miscanthus laccase isoform, on lignification and lignin composition contrasts with its in vitro substrate preference
Creators: name: He, Feng
name: Machemer-Noonan, Katja
name: Golfier, Philippe
name: Unda, Faride
name: Dechert, Johanna
name: Zhang, Wan
name: Hoffmann, Natalie
name: Samuels, Lacey
name: Mansfield, Shawn
name: Rausch, Thomas
name: Wolf, Sebastian
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Additional file 1: Table. S1. Primers used for cloning and colony PCR in this study. Table. S2. Primers used for quantitative real-time PCR analysis. Figure S1. Phylogenetic tree including putative laccases of Miscanthus and laccase proteins from Brachypodium distachyon. Figure S2. Multiple sequence alignment of MsLAC1 with other laccase proteins known to be involved in lignification. Figure S3. Time course of spectral change in reaction mixtures containing cinnamyl, p-coumaryl or coniferyl alcohol, respectively, co-incubated with purified rMsLAC1 protein. Figure S4. Under long-day condition, ectopic expression of MsLAC1 (p35S::MsLAC1) in Arabidopsis ecotype Col-0 reduces stem growth. Figure S5. Structural sugar contents in different Arabidopsis lines after ectopic expression of MsLAC1 (p35S:MsLAC1, see Figure S4).
Reminiscences of George Rublee, 1951
Publisher: name: Columbia University
Year: 2021
Subjects: Lawyers
Government executives
Negotiation
Presidents--Election--1912.--United States
Presidents--Election--1928.--United States
World War, 1914-1918
Arbitration (International law)

description: Early life and law career; Ballinger-Pinchot controversy; election of 1912; Federal Trade Commission; World War I government work; Dwight Morrow and United States relations with Mexico, 1928-1930; election of 1928; London Naval Conference, 1930; adviser to the Colombian government, 1930-1932; Leticia dispute between Peru and Colombia, 1932; coal arbitrator, 1933; war debts; German refugee relief, 1938
High Energy Phenomena in Clusters of Galaxies
Creators: name: Blasi, P.
name: Colafrancesco, S.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Several phenomena in high energy astrophysics have been recently related to clusters of galaxies and to cosmic ray interactions occurring inside these structures. In many of these phenomena the observable effects depend on the energy density of cosmic rays confined in the Intra Cluster (IC) medium, which is a poorly known quantity. We propose here that useful indications about this quantity can be obtained from present and future observations of galaxy clusters in the radio and hard X-ray frequency ranges.
description: 5 pages, 3 Figures, Latex (using espcrc2,epsfig), to appear in the Proceedings of the TAUP97, Eds. A. DiCredico et al., in press. Send comments to S.Colafrancesco: cola@coma.mporzio.astro.it
The roles of cofactors protein S and factor V in the TFPI anticoagulant pathway
Creators: name: Reglinska-Matveyev, Natalia
Publisher: name: Imperial College London
Year: 2014

description: Tissue factor pathway inhibitor (TFPI) is a principal inhibitor of the initiation of coagulation through inhibition of factor (F) Xa and tissue factor (TF)/FVIIa. While TFPI on its own is a poor inhibitor of FXa, protein S acts as cofactor for TFPI through interaction with TFPI Kunitz 3 domain, greatly enhancing FXa inhibition (~10-fold). The aim of my thesis was to further characterise the molecular basis underlying the TFPI cofactor function of protein S by identifying the complementary functional interaction site on protein S required for TFPI enhancement. I have screened over 40 protein S variants comprising substitutions spanning the whole protein S molecule and have identified the C-terminal sex hormone-binding globulin (SHBG)-like domain to be important for the enhancement of TFPI-mediated inhibition of thrombin generation in plasma. This was demonstrated using a protein S/growth arrest-specific 6 (Gas6) chimera, in which the SHBG-like domain was replaced with the corresponding domain in Gas6. Further examination of this chimera using FXa inhibition assays together with direct binding studies confirmed that the protein S SHBG-like domain is essential for the interaction with TFPI and the enhancement of TFPI-mediated inhibition of FXa. TFPI has also been reported to bind to FV in circulation. In my thesis I have aimed to evaluate the effects of FV interaction with TFPI upon its inhibition of FXa. While FV did not enhance TFPI on its own, it further enhanced the inhibition of FXa by TFPI in the presence of protein S (~32-fold by comparison to TFPI alone), suggesting that FV acts together with protein S as a synergistic cofactor for TFPI. Co-immunoprecipitation experiments revealed a direct interaction between TFPI and FV which was augmented by the presence of protein S. I propose that FV, in cooperation with protein S localise TFPI to the activated membrane surface in a position favourable for the efficient inhibition of FXa. Collectively, my findings shed light on the molecular mechanisms of TFPI enhancement by its cofactors protein S and FV.
The Role of Strangeness in Ultrarelativistic Nuclear Collisions
Creators: name: Sollfrank, Josef
name: Heinz, Ulrich
Publisher: name: arXiv
Year: 1995
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We review the progress in understanding the strange particle yields in nuclear collisions and their role in signalling quark-gluon plasma formation. We report on new insights into the formation mechanisms of strange particles during ultrarelativistic heavy-ion collisions and discuss interesting new details of the strangeness phase diagram. In the main part of the review we show how the measured (multi-)strange particle abundances can be used as a testing ground for chemical equilibration in nuclear collisions, and how the results of such an analysis lead to important constraints on the collision dynamics and space-time evolution of high energy heavy-ion reactions.
description: 82 pages, uuencoded compressed postscript file. The full postscript file can also be obtained via www at http://www.physics.helsinki.fi/tft/tft_preprints.html or via anonymous ftp at ftp://rock.helsinki.fi/pub/preprints/tft/Year1995/HU-TFT-95-27/paper.ps.Z or directly from authors. To appear in Quark-Gluon Plasma 2, R.C Hwa (Eds)