cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Population genomics reveals that an anthropophilic population of $\textit{Aedes aegypti}$ mosquitoes in West Africa recently gave rise to American and Asian populations of this major disease vector
Creators: name: Crawford, JE
name: Alves, JM
name: Palmer, WJ
name: Day, Jonathan
name: Sylla, M
name: Ramasamy, R
name: Surendran, SN
name: Black, WC
name: Pain, A
name: Jiggins, Francis
Publisher: name: Apollo - University of Cambridge Repository
Year: 2017
Subjects: Aedes aegypti
anthropophilic
arboviral diseases
dengue virus
mosquito evolution
vector-borne diseases
Zika virus

description: $\textbf{BACKGROUND}$: The mosquito $\textit{Aedes aegypti}$ is the main vector of dengue, Zika, chikungunya and yellow fever viruses. This major disease vector is thought to have arisen when the African subspecies $\textit{Ae. aegypti}$ formosus evolved from being zoophilic and living in forest habitats into a form that specialises on humans and resides near human population centres. The resulting domestic subspecies, $\textit{Ae. aegypti aegypti}$, is found throughout the tropics and largely blood-feeds on humans. $\textbf{RESULTS}$: To understand this transition, we have sequenced the exomes of mosquitoes collected from five populations from around the world. We found that $\textit{Ae. aegypti}$ specimens from an urban population in Senegal in West Africa were more closely related to populations in Mexico and Sri Lanka than they were to a nearby forest population. We estimate that the populations in Senegal and Mexico split just a few hundred years ago, and we found no evidence of $\textit{Ae. aegypti aegypti}$ mosquitoes migrating back to Africa from elsewhere in the tropics. The out-of-Africa migration was accompanied by a dramatic reduction in effective population size, resulting in a loss of genetic diversity and rare genetic variants. $\textbf{CONCLUSIONS}$: We conclude that a domestic population of $\textit{Ae. aegypti}$ in Senegal and domestic populations on other continents are more closely related to each other than to other African populations. This suggests that an ancestral population of $\textit{Ae. aegypti }$evolved to become a human specialist in Africa, giving rise to the subspecies $\textit{Ae. aegypti aegypti}$. The descendants of this population are still found in West Africa today, and the rest of the world was colonised when mosquitoes from this population migrated out of Africa. This is the first report of an African population of Ae. aegypti aegypti mosquitoes that is closely related to Asian and American populations. As the two subspecies differ in their ability to vector disease, their existence side by side in West Africa may have important implications for disease transmission.
description: This work was funded by European Research Council grant Drosophila Infection 281668 to FMJ, a KAUST AEA award to FMJ and AP, a Medical Research Council Centenary Award to WJP and a National Institutes of Health Ruth L. Kirschstein National Research Service Award to JC.
Additional file 9: of Do sputum or circulating blood samples reflect the pulmonary transcriptomic differences of COPD patients? A multi-tissue transcriptomic network META-analysis
Creators: name: Faner, Rosa
name: Morrow, Jarrett
name: Casas-Recasens, Sandra
name: Cloonan, Suzanne
name: Noell, Guillaume
name: LĂłpez-Giraldo, Alejandra
name: Tal-Singer, Ruth
name: Miller, Bruce
name: Silverman, Edwin
name: AgustĂ­, Alvar
name: Hersh, Craig
Publisher: name: figshare
Year: 2019
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Table S5. Gene Ontology enrichment for the core 60 genes. (PDF 33 kb)
Particle-Antiparticle Asymmetry Due to Non-Renormalizable Effective Interactions
Creators: name: Bouzas, Antonio
name: Cheng, Wai Yan
name: Gelmini, Graciela
Publisher: name: arXiv
Year: 1996
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We consider a model for generating a particle-antiparticle asymmetry through out-of-equilibrium decays of a massive particle due to non-renormalizable, effective interactions.
description: preliminary version, 38 pages; LaTeX source, epsf.sty and EPS files included in tar archive
User-centric Privacy Engineering for the Internet of Things
Creators: name: Barhamgi, Mahmoud
name: Perera, Charith
name: Ghedira, Chirine
name: Benslimane, Djamal
Publisher: name: arXiv
Year: 2018
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: Computers and Society (cs.CY)
subject: FOS: Computer and information sciences

description: User privacy concerns are widely regarded as a key obstacle to the success of modern smart cyber-physical systems. In this paper, we analyse, through an example, some of the requirements that future data collection architectures of these systems should implement to provide effective privacy protection for users. Then, we give an example of how these requirements can be implemented in a smart home scenario. Our example architecture allows the user to balance the privacy risks with the potential benefits and take a practical decision determining the extent of the sharing. Based on this example architecture, we identify a number of challenges that must be addressed by future data processing systems in order to achieve effective privacy management for smart cyber-physical systems.
description: 12 Pages
Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental $\textit{Klebsiella pneumoniae}$
Creators: name: Runcharoen, C
name: Moradigaravand, D
name: Blane, B
name: Paksanont, S
name: Thammachote, J
name: Anun, S
name: Parkhill, Julian
name: Chantratita, N
name: Peacock, Sharon
Publisher: name: Apollo - University of Cambridge Repository
Year: 2017
Subjects: antibiotic resistance
genomic epidemiology
klebsiella pneumoniae
whole genome sequencing

description: $\textbf{BACKGROUND}$: $\textit{Klebsiella pneumoniae}$ is a gram-negative bacterial species capable of occupying a broad range of environmental and clinical habitats. Known as an opportunistic pathogen, it has recently become a major causative agent of clinical infections worldwide. Despite growing knowledge about the highly diverse population of $\textit{K. pneumoniae}$, the evolution and clinical significance of environmental $\textit{K. pneumoniae}$, as well as the relationship between clinical and environmental $\textit{K. pneumoniae}$, are poorly defined. $\textbf{METHODS}$: We isolated and sequenced $\textit{K. pneumoniae}$ from in-patients in a single hospital in Thailand, as well as hospital sewage, and surrounding canals and farms within a 20-km radius. $\textbf{RESULTS}$: Phylogenetic analysis of 77 K. pneumoniae (48 clinical and 29 non-clinical isolates) demonstrated that the two groups were intermixed throughout the tree and in some cases resided in the same clade, suggesting recent divergence from a common ancestor. Phylogenetic comparison of the 77 Thai genomes with 286 $\textit{K. pneumoniae}$ from a global collection showed that Thai isolates were closely related to the clinical sub-population of the global collection, indicating that Thai clinical isolates belonged to globally circulating lineages. Dating of four Thai $\textit{K. pneumoniae}$ clades indicated that they emerged between 50 and 150 years ago. Despite their phylogenetic relatedness, virulence factors and β-lactamase resistance genes were more numerous in clinical than in environmental isolates. Our results indicate that clinical and environmental $\textit{K. pneumoniae}$ are closely related, but that hospitals may select for isolates with a more resistant and virulent genotype. $\textbf{CONCLUSIONS}$: These findings highlight the clinical relevance of environmental K. pneumoniae isolates.
description: CR and NC were supported by grants from the Royal Thai Golden Jubilee studentship scheme (PHD/0116/2556), Thailand, and the Newton Fund, UK and Thailand One Health University Network. This publication also presents independent research supported by the Health Innovation Challenge Fund (HICF-T5-342 and WT098600), a parallel funding partnership between the UK Department of Health and Wellcome Trust.
Brown Measure Support and the Free Multiplicative Brownian Motion
Creators: name: Hall, Brian
name: Kemp, Todd
Publisher: name: arXiv
Year: 2018
Subjects: subject: Functional Analysis (math.FA)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: Probability (math.PR)
subject: Quantum Physics (quant-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: The free multiplicative Brownian motion $b_{t}$ is the large-$N$ limit of Brownian motion $B_t^N$ on the general linear group $\mathrm{GL}(N;\mathbb{C})$. We prove that the Brown measure for $b_{t}$---which is an analog of the empirical eigenvalue distribution for matrices---is supported on the closure of a certain domain $Σ_{t}$ in the plane. The domain $Σ_t$ was introduced by Biane in the context of the large-$N$ limit of the Segal--Bargmann transform associated to $\mathrm{GL}(N;\mathbb{C})$. We also consider a two-parameter version, $b_{s,t}$: the large-$N$ limit of a related family of diffusion processes on $\mathrm{GL}(N;\mathbb{C})$ introduced by the second author. We show that the Brown measure of $b_{s,t}$ is supported on the closure of a certain planar domain $Σ_{s,t}$, generalizing $Σ_t$, introduced by Ho. In the process, we introduce a new family of spectral domains related to any operator in a tracial von Neumann algebra: the {\em $L^p_n$-spectrum} for $n\in\mathbb{N}$ and $p\ge 1$, a subset of the ordinary spectrum defined relative to potentially-unbounded inverses. We show that, in general, the support of the Brown measure of an operator is contained in its $L_2^2$-spectrum.
description: 30 pages, 6 figures
Additional file 3: of Exploring the unmapped DNA and RNA reads in a songbird genome
Creators: name: Laine, Veronika
name: Gossmann, Toni
name: Oers, Kees Van
name: Visser, Marcel
name: Groenen, Martien
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Plant Biology

description: Figure S2. Neighbour-Joining phylogenetic tree between the newly constructed mitochondria (blue), the already existing reference mitochondria (green) and 123 sequences of NADH dehydrogenase subunit 2 (ND2) gene from both Parus major and Parus minor. (PDF 228 kb)
Scalable String and Suffix Sorting: Algorithms, Techniques, and Tools
Creators: name: Bingmann, Timo
Publisher: name: arXiv
Year: 2018
Subjects: subject: Data Structures and Algorithms (cs.DS)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: This dissertation focuses on two fundamental sorting problems: string sorting and suffix sorting. The first part considers parallel string sorting on shared-memory multi-core machines, the second part external memory suffix sorting using the induced sorting principle, and the third part distributed external memory suffix sorting with a new distributed algorithmic big data framework named Thrill.
description: 396 pages, dissertation, Karlsruher Instituts f\"ur Technologie (2018). arXiv admin note: text overlap with arXiv:1101.3448 by other authors
La edad de la prosa
Creators: name: Carlos, Liscano
name: Liscano, Carlos
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2022
Subjects: Prison
Dictature
Cárcel
Dictadura

description: Manuscrit original du récit "El informante".
description: Manuscrito original del relato "El informante".
description: Notes/Notas : Stylo noir et bleu. 4 pages non numérotées. Passages du "Diario de la cárcel" aux pages 48 [1984-05-06], 52 [1984-05-07], 56 [1984-05-09], 59 [1984-05-11], 67 [1984-05-21], 75 [1984-05-22], 113 et 114 [1984-06-07].
description: Bolígrafo negro y azul. Pasajes del "Diario de la cárcel" en la páginas 48 [1984-05-06], 52 [1984-05-07], 56 [1984-05-09], 59 [1984-05-11], 67 [1984-05-21], 75 [1984-05-22], 113 et 114 [1984-06-07]
description: Source: Cote / Código : CL-AA3-01-C0
description: Source: Localisation / Ubicación del archivo : Archivo Carlos Liscano – Montevideo, Uruguay
description: Relation: CL-AA4-01
description: Bibliographic citation: Liscano Carlos, « El Informante y otros relatos », Montevideo, Trilce, 1997.
description: created: 1972/1984
Chrysosplenium oppositifolium 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
Saxifragales
Saxifragaceae
Chrysosplenium
Chrysosplenium oppositifolium

description: Chrysosplenium oppositifolium Linnaeus, Species Plantarum 1: 398. 1753.
"Habitat in Belgio, Anglia, Canada locis umbrosis humentibus." RCN: 3138.
 Lectotype (Gornall in Jarvis & al., Regnum Veg. 127: 33. 1993): [icon] " Saxifraga aurea " in Dodoëns, Stirp. Hist. Pempt., ed. 2: 316. 1616.
 Generitype of Chrysosplenium Linnaeus (vide Hitchcock, Prop. Brit. Bot.: 154. 1929).
 Current name:  Chrysosplenium oppositifolium  L. (Saxifragaceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part C), pp. 370-473 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 416, DOI: 10.5281/zenodo.291971
A Heavy Top Quark From Flavor-Universal Colorons
Creators: name: Popovic, Marko B.
name: Simmons, Elizabeth H.
Publisher: name: arXiv
Year: 1998
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Ordinary technicolor and extended technicolor cannot produce the heavy top quark unaided. We demonstrate that a flavor-universal extension of the color interactions combined with an extended hypercharge sector that singles out the third generation can provide the necessary assistance. We discuss current experimental constraints and suggest how collider experiments can search for the predicted new heavy gauge bosons.
description: 14 pages, 3 figures, LaTeX, updated reference, fixed typo
Analysis of feed as an ecological factor of influence on the organism of a productive animal under conditions of increased anthropogenic load on agroecosystems
Creators: name: Portiannyk, Serhii Vasylovych
name: Mamenko, Oleksii Mykhailovych
Publisher: name: Zenodo
Year: 2022
Subjects: toxic metals, cadmium, lead, copper, zinc, mineral elements

description: Feed for farm animals is an environmental factor that has a significant impact on various physiological functions, productivity, health, and homeostasis of the body. It is the subject of research in many sciences, including ecology. Scientists in different countries of the world have begun to pay special attention to the study of the ecological safety of animal feed, which is associated with the urbanization of settlements, the development of industry, oil and gas production, accidents on main gas pipelines, mining of coal and gas, the placement of agricultural land by large cars, and livestock farms not far from the developed industrial center of metallurgical complex enterprises, etc., which leads to soil pollution with toxic heavy metals, and then migration and accumulation of elements in plants from the produced feed included in the rations. The aim of the research was to establish the quality and biological completeness of feed rations of dairy cows in enterprises located near environmentally unfavorable anthropogenic objects. The object of research included norms of rations, corn silage, alfalfa haylage, corn turf, fodder beets, grain hay, cereals and legumes hay, alfalfa hay. To conduct a scientific experiment on the production of cow’s milk, plant-based feed from four farms located around an industrial city and not far from sources of anthropogenic pollution was selected. Laboratory analysis of selected average feed samples for the content of mineral elements, including toxic metals Cd and Pb, was carried out by the atomic absorption method. Statistical data processing was carried out using the STATISTICA software package version 10.0. The analysis of feed shows not only an increased concentration of heavy metals, but also a low content of vital essential macro- and microelements in plants (feed) against this background, which was typical for all farms. In such conditions, the problem of producing high-quality biologically valuable ecologically safe milk arises. Therefore, in case of local contamination of agroecosystems and ration feeds with heavy metals, especially Cd and Pb, it is necessary to take into account the actual nutritional value of feed, ensure the rationing of essential and non-essential elements in the diet and develop new feed additives, mineral and vitamin premixes of antidote action, homeostasis of an intoxicated organism, increasing the productivity of cows, improving their health status and obtaining environmentally friendly milk. Further research is aimed at constant environmental monitoring of various mineral elements, primarily toxic heavy metals in the feed of farms specializing in milk production in different regions of Ukraine, forest-steppe and Polissya.
Strong Eigenstate Thermalization within a Generalized Shell in Noninteracting Integrable Systems
Creators: name: Ishii, Takashi
name: Mori, Takashi
Publisher: name: arXiv
Year: 2018
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Integrable systems do not obey the strong eigenstate thermalization hypothesis (ETH), which has been proposed as a mechanism of thermalization in isolated quantum systems. It has been suggested that an integrable system reaches a steady state described by a generalized Gibbs ensemble (GGE) instead of thermal equilibrium. We prove that a generalized version of the strong ETH holds for noninteracting integrable systems with translation invariance. Our generalized ETH states that any pair of energy eigenstates with similar values of local conserved quantities looks similar with respect to local observables, such as local correlations. This result tells us that an integrable system relaxes to a GGE for any initial state that has subextensive fluctuations of macroscopic local conserved quantities. Contrary to the previous derivations of the GGE, it is not necessary to assume the cluster decomposition property for an initial state.
description: 6 pages
Normal Modes of the B=4 Skyrme Soliton
Creators: name: Barnes, Chris
name: Baskerville, Kim
name: Turok, Neil
Publisher: name: arXiv
Year: 1997
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The Skyrme model of nuclear physics requires quantisation if it is to match observed nuclear properties. A simple technique is used to find the normal mode spectrum of the baryon number B=4 Skyrme soliton, representing the $α$ particle. We find sixteen vibrational modes and classify them under the cubic symmetry group $O_h$ of the static solution. The spectrum possesses a remarkable structure, with the lowest energy modes lying in those representations expected from an approximate correspondence between Skyrmions and BPS monopoles. The next mode up is the `breather', and above that are higher multipole breathing modes.
description: 4 pages, RevTex file and two figures, the former requiring spectrum.eps, the latter requiring 17 eps files sh.sol*.eps which are included. Replaced version corrects one typo in the Table, replacing the representation F_1^- with F_2^- for the omega=.513 mode
Radiative corrections to sfermion mass splittings
Creators: name: Yamada, Youichi
Publisher: name: arXiv
Year: 1996
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We study the one-loop radiative corrections to the SU(2) breaking mass splittings between sfermions in SU(2) doublets in the Minimal Supersymmetric Standard Model. At tree-level, the differences of mass squared $m_{\tilde{f}_{1L}}^2-m_{\tilde{f}_{2L}}^2$ of SU(2) doublet sfermions $(\tilde{f}_1, \tilde{f}_2)_L$ in the first two generations are determined by $\tanβ$, and are universal to sleptons and squarks. The radiative correction, however, breaks this relation. The typical deviation from the universality between sleptons and squarks is within $\pm0.05$ in terms of the ``effective $\cos2β$''. We also study the SUSY parameter dependence of the deviation. For very heavy sfermions, the relative corrections become large.
description: 11 pages (LaTeX) and 8 figures (postscript), to be published
Improving effect size estimation and statistical power with multi-echo fMRI and its impact on understanding the neural systems supporting mentalizing
Creators: name: Lombardo, Michael V
name: Auyeung, Bonnie
name: Holt, Rosemary
name: Waldman, Jack
name: Ruigrok, Amber
name: Mooney, Natasha
name: Bullmore, Edward
name: Baron-Cohen, Simon
name: Kundu, Prantik
Publisher: name: Apollo - University of Cambridge Repository
Year: 2016
Subjects: multi-echo EPI
statistical power
denoising
task-fMRI
mentalizing
cerebellum

description: Functional magnetic resonance imaging (fMRI) research is routinely criticized for being statistically underpowered due to characteristically small sample sizes and much larger sample sizes are being increasingly recommended. Additionally, various sources of artifact inherent in fMRI data can have detrimental impact on effect size estimates and statistical power. Here we show how specific removal of non-BOLD artifacts can improve effect size estimation and statistical power in task-fMRI contexts, with particular application to the social-cognitive domain of mentalizing/theory of mind. Non-BOLD variability identification and removal is achieved in a biophysical and statistically principled manner by combining multi-echo fMRI acquisition and independent components analysis (ME-ICA). Without smoothing, group-level effect size estimates on two different mentalizing tasks were enhanced by ME-ICA at a median rate of 24% in regions canonically associated with mentalizing, while much more substantial boosts (40- 149%) were observed in non-canonical cerebellar areas. Effect size boosting occurs via reduction of non-BOLD noise at the subject-level and consequent reductions in betweensubject variance at the group-level. Smoothing can attenuate ME-ICA-related effect size improvements in certain circumstances. Power simulations demonstrate that ME-ICArelated effect size enhancements enable much higher-powered studies at traditional sample sizes. Cerebellar effects observed after applying ME-ICA may be unobservable with conventional imaging at traditional sample sizes. Thus, ME-ICA allows for principled design-agnostic non-BOLD artifact removal that can substantially improve effect size estimates and statistical power in task-fMRI contexts. ME-ICA could mitigate some issues regarding statistical power in fMRI studies and enable novel discovery of aspects of brain organization that are currently under-appreciated and not well understood.
description: This work was supported by a Wellcome Trust project grant to SB-C and ETB. MVL was supported by the Wellcome Trust and fellowships from Jesus College, Cambridge and the British Academy. PK was supported by the National Institutes of Health–Cambridge Scholars Program. ETB is employed half-time by the University of Cambridge and halftime by GlaxoSmithKline (GSK).
description: This is the author accepted manuscript. It first appeared from Elseiver at http://dx.doi.org/10.1016/j.neuroimage.2016.07.022.
Low-luminosity AGN and X-ray binary populations in COSMOS star-forming galaxies
Creators: name: Fornasini, Francesca M.
name: Civano, Francesca
name: Fabbiano, Giuseppina
name: Elvis, Martin
name: Marchesi, Stefano
name: Miyaji, Takamitsu
name: Zezas, Andreas
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present an X-ray stacking analysis of $\sim$75,000 star-forming galaxies between $0.11.3$ exhibit a significant X-ray excess indicating nuclear emission. The AGN emission is strongly correlated with stellar mass but does not exhibit an additional correlation with SFR. The hardness ratios of the high-redshift stacks indicate that the AGN are substantially obscured ($N_{\mathrm{H}}\sim10^{23}$ cm$^{-2}$). These obscured AGN are not identified by IRAC color selection and have $L_X\sim10^{41}-10^{43}$ erg s$^{-1}$, consistent with accretion at an Eddington rate of $\sim10^{-3}$ onto $10^7-10^8 M_{\odot}$ black holes. Combining our results with other X-ray studies suggests that AGN obscuration depends on stellar mass and an additional variable, possibly the Eddington rate.
description: 24 pages, 12 figures, 3 tables (2 tables available in full online or by request)
Additional file 7: of Do sputum or circulating blood samples reflect the pulmonary transcriptomic differences of COPD patients? A multi-tissue transcriptomic network META-analysis
Creators: name: Faner, Rosa
name: Morrow, Jarrett
name: Casas-Recasens, Sandra
name: Cloonan, Suzanne
name: Noell, Guillaume
name: LĂłpez-Giraldo, Alejandra
name: Tal-Singer, Ruth
name: Miller, Bruce
name: Silverman, Edwin
name: AgustĂ­, Alvar
name: Hersh, Craig
Publisher: name: figshare
Year: 2019
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Figure S3. Association between consensus gene modules and lung function in each cohort. (DOCX 96 kb)
Solving large nonlinear generalized eigenvalue problems from Density Functional Theory calculations in parallel
Creators: name: Bendtsen, Claus
name: Nielsen, Ole H.
name: Hansen, Lars B.
Publisher: name: arXiv
Year: 2000
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The quantum mechanical ground state of electrons is described by Density Functional Theory, which leads to large minimization problems. An efficient minimization method uses a selfconsistent field (SCF) solution of large eigenvalue problems. The iterative Davidson algorithm is often used, and we propose a new algorithm of this kind which is well suited for the SCF method, since the accuracy of the eigensolution is gradually improved along with the outer SCF-iterations. Best efficiency is obtained for small-block-size iterations, and the algorithm is highly memory efficient. The implementation works well on both serial and parallel computers, and good scalability of the algorithm is obtained.
description: 20 pages, 4 figures. Accepted for Applied Numerical Mathematics (Elsevier)
Additional file 2: of Exploring the unmapped DNA and RNA reads in a songbird genome
Creators: name: Laine, Veronika
name: Gossmann, Toni
name: Oers, Kees Van
name: Visser, Marcel
name: Groenen, Martien
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified

description: Figure S1. Newly constructed and annotated mitochondria of the reference bird. (PDF 125 kb)
Phase separation in disordered exclusion models
Creators: name: Krug, Joachim
Publisher: name: arXiv
Year: 1999
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: The effect of quenched disorder in the one-dimensional asymmetric exclusion process is reviewed. Both particlewise and sitewise disorder generically induces phase separation in a range of densities. In the particlewise case the existence of stationary product measures in the homogeneous phase implies that the critical density can be computed exactly, while for sitewise disorder only bounds are available. The coarsening of phase-separated domains starting from a homogeneous initial condition is addressed using scaling arguments and extremal statistics considerations. Some of these results have been obtained previously in the context of directed polymers subject to columnar disorder.
description: 15 pages, 4 figures
Additional file 8: of Do sputum or circulating blood samples reflect the pulmonary transcriptomic differences of COPD patients? A multi-tissue transcriptomic network META-analysis
Creators: name: Faner, Rosa
name: Morrow, Jarrett
name: Casas-Recasens, Sandra
name: Cloonan, Suzanne
name: Noell, Guillaume
name: LĂłpez-Giraldo, Alejandra
name: Tal-Singer, Ruth
name: Miller, Bruce
name: Silverman, Edwin
name: AgustĂ­, Alvar
name: Hersh, Craig
Publisher: name: figshare
Year: 2019
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Plant Biology

description: Table S4. Core 60 genes in common between the yellow meta-analysis module and brown consensus module with the p-value <0.1 for association with FEV1 % predicted. (PDF 38 kb)
Poor neutralization and rapid decay of antibodies to SARS-CoV-2 variants in vaccinated dialysis patients.
Creators: name: Bassi, Jessica
name: Giannini, Olivier
name: Silacci-Fregni, Chiara
name: Pertusini, Laura
name: Hitz, Paolo
name: Terrot, Tatiana
name: Franzosi, Yves
name: Muoio, Francesco
name: Saliba, Christian
name: Meury, Marcel
name: Dellota, Exequiel A
name: Dillen, Josh R
name: Hernandez, Patrick
name: Czudnochowski, Nadine
name: Cameroni, Elisabetta
name: Beria, Nicola
name: Ventresca, Mariangela
name: Badellino, Alberto
name: Lavorato-Hadjeres, Soraya
name: Lecchi, Elisabetta
name: Bonora, Tecla
name: Mattiolo, Matteo
name: Trinci, Guido
name: Garzoni, Daniela
name: Bonforte, Giuseppe
name: Forni-Ogna, Valentina
name: Giunzioni, Davide
name: Berwert, Lorenzo
name: Gupta, Ravindra
name: Ferrari, Paolo
name: Ceschi, Alessandro
name: Cippà, Pietro
name: Corti, Davide
name: Lanzavecchia, Antonio
name: Piccoli, Luca
Publisher: name: Apollo - University of Cambridge Repository
Year: 2022
Subjects: Research Article
Biology and life sciences
Medicine and health sciences

description: Funder: Swiss Kidney Foundation
description: Patients on dialysis are at risk of severe course of SARS-CoV-2 infection. Understanding the neutralizing activity and coverage of SARS-CoV-2 variants of vaccine-elicited antibodies is required to guide prophylactic and therapeutic COVID-19 interventions in this frail population. By analyzing plasma samples from 130 hemodialysis and 13 peritoneal dialysis patients after two doses of BNT162b2 or mRNA-1273 vaccines, we found that 35% of the patients had low-level or undetectable IgG antibodies to SARS-CoV-2 Spike (S). Neutralizing antibodies against the vaccine-matched SARS-CoV-2 and Delta variant were low or undetectable in 49% and 77% of patients, respectively, and were further reduced against other emerging variants. The fraction of non-responding patients was higher in SARS-CoV-2-naïve hemodialysis patients immunized with BNT162b2 (66%) than those immunized with mRNA-1273 (23%). The reduced neutralizing activity correlated with low antibody avidity. Patients followed up to 7 months after vaccination showed a rapid decay of the antibody response with an average 21- and 10-fold reduction of neutralizing antibodies to vaccine-matched SARS-CoV-2 and Delta variant, which increased the fraction of non-responders to 84% and 90%, respectively. These data indicate that dialysis patients should be prioritized for additional vaccination boosts. Nevertheless, their antibody response to SARS-CoV-2 must be continuously monitored to adopt the best prophylactic and therapeutic strategy.
Cicer arietinum 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
Fabales
Fabaceae
Cicer
Cicer arietinum

description: Cicer arietinum Linnaeus, Species Plantarum 2: 738. 1753.
"Habitat inter Hispaniae, Italiae segetes." RCN: 5430.
 Lectotype (Verdcourt in Milne-Redhead & Polhill, Fl. Trop. E. Africa, Leguminosae 4: 1065. 1971): Herb. Clifford: 370, Cicer 1 α (BM-000646701).
 Generitype of Cicer Linnaeus.
 Current name:  Cicer arietinum  L. (Fabaceae: Faboideae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part C), pp. 370-473 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 416, DOI: 10.5281/zenodo.291971
Scalar Field Cosmologies with Viscous Fluid
Creators: name: Chimento, Luis P.
name: Jakubi, Alejandro S.
Publisher: name: arXiv
Year: 1995
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We investigate cosmological models with a free scalar field and a viscous fluid. We find exact solutions for a linear and nonlinear viscosity pressure. Both yield singular and bouncing solutions. In the first regime, a de Sitter stage is asymptotically stable, while in the second case we find power-law evolutions for vanishing cosmological constant.
description: 8 pages, LaTeX. To be published in International Journal of Modern Physics D
title: Rapport de voyage, De Grasse (1924) : Ligne de croisière en Orient, 1934
Creators: name: De Batz, Pierre
name: De Valon, Pierre
name: Mallet, Louis
name: Thoreux, Pierre
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2024
Subjects: subject: Compagnie Générale Transatlantique
subject: Transports maritimes - Histoire
subject: Marine marchande
subject: Journaux de bord

description: Chapitrage : Rapports d'inspecteurs - Rapport général / du capitaine - Rapport du commissaire - Rapport du second - Rapport de l'officier de sécurité - Rapport de l'officier de navigation - Rapport du médecin - Rapport contentieux
description: Source: French Lines & Compagnies, 1997 004 4979-07
description: Coverage: 1934-03-25/1934-04-10
Holographic derivation of $ q $ SYK spectrum with Yang-Baxter shift
Creators: name: Roychowdhury, Dibakar
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: In this Letter, based on the notion of gauge/gravity duality, we compute $ q $ SYK spectra in the presence of Yang-Baxter (YB) deformations. The gravitational counterpart of this duality turns out to be the YB deformed Almheiri-Polchinski (AP) model embodied with hyperbolic potential for the dilaton. Following Kaluza-Klein reduction on $ (AdS_2)_η\times (S^1/ Z_2) $, we compute the deformed Green's function that reproduces the original $ q $ SYK spectrum in the limit of vanishing deformations.
description: Latex, 12 pages, To appear in PLB
A faster horse on a safer trail: generalized inference for the efficient reconstruction of weighted networks
Creators: name: Parisi, Federica
name: Squartini, Tiziano
name: Garlaschelli, Diego
Publisher: name: arXiv
Year: 2018
Subjects: subject: Physics and Society (physics.soc-ph)
subject: FOS: Physical sciences

description: Due to the interconnectedness of financial entities, estimating certain key properties of a complex financial system (e.g. the implied level of systemic risk) requires detailed information about the structure of the underlying network. However, since data about financial linkages are typically subject to confidentiality, network reconstruction techniques become necessary to infer both the presence of connections and their intensity. Recently, several "horse races" have been conducted to compare the performance of the available financial network reconstruction methods. These comparisons, however, were based on arbitrarily-chosen similarity metrics between the real and the reconstructed network. Here we establish a generalised maximum-likelihood approach to rigorously define and compare weighted reconstruction methods. Our generalization maximizes the conditional entropy to solve the problem represented by the fact that the density-dependent constraints required to reliably reconstruct the network are typically unobserved. The resulting approach admits as input any reconstruction method for the purely binary topology and, conditionally on the latter, exploits the available partial information to infer link weights. We find that the most reliable method is obtained by "dressing" the best-performing binary method with an exponential distribution of link weights having a properly density-corrected and link-specific mean value and propose two unbiased (in the sense of maximum conditional entropy) variants of it. While the one named CReMA is perfectly general (as a particular case, it can place optimal weights on a network whose topology is known), the one named CReMB is recommended both in case of full uncertainty about the network topology and if the existence of some links is certain. In these cases, the CReMB is faster and reproduces empirical networks with highest generalised likelihood.
description: 19 pages, 4 figures, 1 table
Stellar Feedback and the Energy Budget of Late-Type Galaxies: Missing Baryons and Core Creation
Creators: name: Katz, Harley
name: Desmond, Harry
name: Lelli, Federico
name: McGaugh, Stacy
name: Di Cintio, Arianna
name: Brook, Chris
name: Schombert, James
Publisher: name: arXiv
Year: 2018
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: In a $Λ$CDM cosmology, galaxy formation is a globally inefficient process: it is often the case that far fewer baryons are observed in galaxy disks than expected from the cosmic baryon fraction. The location of these "missing baryons" is unclear. By fitting halo profiles to the rotation curves of galaxies in the SPARC data set, we measure the "missing baryon" mass for individual late-type systems. Assuming that haloes initially accrete the cosmological baryon fraction, we show that the maximum energy available from supernovae is typically not enough to completely eject these "missing baryons" from a halo, but it is often sufficient to heat them to the virial temperature. The energy available from supernovae has the same scaling with galaxy mass as the energy needed to heat or eject the "missing baryons", indicating that the coupling efficiency of the feedback to the ISM may be constant with galaxy virial mass. We further find that the energy available from supernova feedback is always enough to convert a primordial cusp into a core and has magnitude consistent with what is required to heat the "missing baryons" to the virial temperature. Taking a census of the baryon content of galaxies with ${\rm 10^9
description: 16 pages, 8 figures, MNRAS accepted
title: Jahreshefte der Gesellschaft für Naturkunde in Württemberg, Bd. 170 Nr. 2 (2014): Jahreshefte der Gesellschaft für Naturkunde in Württemberg, 170. Jahrgang, Heft 2
title: Jahreshefte der Gesellschaft für Naturkunde in Württemberg, 170. Jahrgang, Heft 2
titleType: AlternativeTitle
Creators: name: Jahreshefte Der Gesellschaft Für Naturkunde In Württemberg
Publisher: name: Jahreshefte der Gesellschaft für Naturkunde in Württemberg
Year: 2021

description: Oberschwäbische Botaniker aus fünf Jahrhunderten...001-643
Dirac Operator and Spectral Geometry
Creators: name: Esposito, Giampiero
Publisher: name: arXiv
Year: 1997
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: This paper is devoted to mathematical and physical properties of the Dirac operator and spectral geometry. Spin-structures in Lorentzian and Riemannian manifolds, and the global theory of the Dirac operator, are first analyzed. Elliptic boundary-value problems, index problems for closed manifolds and for manifolds with boundary, Bott periodicity and K-theory are then presented. This makes it clear why the Dirac operator is the most fundamental, in the theory of elliptic operators on manifolds. The topic of spectral geometry is developed by studying non-local boundary conditions of the Atiyah-Patodi-Singer type, and heat-kernel asymptotics for operators of Laplace type on manifolds with boundary. The emphasis is put on the functorial method, which studies the behaviour of differential operators, boundary operators and heat-kernel coefficients under conformal rescalings of the background metric. In the second part, a number of relevant physical applications are studied: non-local boundary conditions for massless spin-1/2 fields, massless spin-3/2 potentials on manifolds with boundary, geometric theory of massive spin-3/2 potentials, local boundary conditions in quantum supergravity, quark boundary conditions, one-loop quantum cosmology, conformally covariant operators and Euclidean quantum gravity.
description: 205 pages, plain Tex. In the revised version, section 6.3 has been amended
Learning with privileged information via adversarial discriminative modality distillation
Creators: name: Garcia, Nuno C.
name: Morerio, Pietro
name: Murino, Vittorio
Publisher: name: arXiv
Year: 2018
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Heterogeneous data modalities can provide complementary cues for several tasks, usually leading to more robust algorithms and better performance. However, while training data can be accurately collected to include a variety of sensory modalities, it is often the case that not all of them are available in real life (testing) scenarios, where a model has to be deployed. This raises the challenge of how to extract information from multimodal data in the training stage, in a form that can be exploited at test time, considering limitations such as noisy or missing modalities. This paper presents a new approach in this direction for RGB-D vision tasks, developed within the adversarial learning and privileged information frameworks. We consider the practical case of learning representations from depth and RGB videos, while relying only on RGB data at test time. We propose a new approach to train a hallucination network that learns to distill depth information via adversarial learning, resulting in a clean approach without several losses to balance or hyperparameters. We report state-of-the-art results on object classification on the NYUD dataset and video action recognition on the largest multimodal dataset available for this task, the NTU RGB+D, as well as on the Northwestern-UCLA.
description: Accepted to IEEE Transactions on Pattern Analysis and Machine Intelligence
Progress in One-Loop QCD Computations
Creators: name: Bern, Z.
name: Dixon, L.
name: Kosower, D. A.
Publisher: name: arXiv
Year: 1996
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We review progress in calculating one-loop scattering amplitudes required for next-to-leading-order corrections to QCD processes. The underlying technical developments include the spinor helicity formalism, color decompositions, supersymmetry, string theory, factorization and unitarity. We provide explicit examples illustrating these techniques.
description: To appear in Annual Reviews of Nuclear and Particle Science (1996)
Additional file 6: of Do sputum or circulating blood samples reflect the pulmonary transcriptomic differences of COPD patients? A multi-tissue transcriptomic network META-analysis
Creators: name: Faner, Rosa
name: Morrow, Jarrett
name: Casas-Recasens, Sandra
name: Cloonan, Suzanne
name: Noell, Guillaume
name: LĂłpez-Giraldo, Alejandra
name: Tal-Singer, Ruth
name: Miller, Bruce
name: Silverman, Edwin
name: AgustĂ­, Alvar
name: Hersh, Craig
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified

description: Figure S2. Dendrogram of consensus co-expression network including Lung Tissue-1, Lung Tissue-2 and Sputum datasets. (DOCX 48 kb)
Cichorium endivia 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
Asterales
Asteraceae
Cichorium
Cichorium endivia

description: Cichorium endivia Linnaeus, Species Plantarum 2: 813. 1753.
“Habitat– - - –” RCN: 5922.
 Lectotype (Alavi in Jafri & El-Gadi, Fl. Libya 107: 320. 1983): Herb. Linn. No. 962.3 (LINN).
 Current name:  Cichorium endivia  L. (Asteraceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part C), pp. 370-473 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 416, DOI: 10.5281/zenodo.291971
Bericht der Gesellschaft für Naturkunde in Württemberg 2014
Creators: name: Schriftleitung Der Gesellschaft Für Naturkunde In Württemberg
Publisher: name: Jahreshefte der Gesellschaft für Naturkunde in Württemberg
Year: 2014

description: Jahreshefte der Gesellschaft für Naturkunde in Württemberg, Bd. 170 Nr. 1 (2014): Jahreshefte der Gesellschaft für Naturkunde in Württemberg, 170. Jahrgang, Heft 1