cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Chaotic zone boundary for low free eccentricity particles near an eccentric planet
Creators: name: Quillen, Alice C.
name: Faber, Peter
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We consider particles with low free or proper eccentricity that are orbiting near planets on eccentric orbits. Via collisionless particle integration we numerically find the location of the boundary of the chaotic zone in the planet's corotation region. We find that the distance in semi-major axis between the planet and boundary depends on the planet mass to the 2/7 power and is independent of the planet eccentricity, at least for planet eccentricities below 0.3. Our integrations reveal a similarity between the dynamics of particles at zero eccentricity near a planet in a circular orbit and with zero free eccentricity particles near an eccentric planet. The 2/7 law has been previously explained by estimating the semi-major at which the first order mean motion resonances are large enough to overlap. Orbital dynamics near an eccentric planet could differ due to first order corotation resonances that have strength proportional to the planet's eccentricity. However, we find the corotation resonance width at low free eccentricity is small. Also the first order resonance width at zero free eccentricity is the same as that for a zero eccentricity particle near a planet in a circular orbit. This accounts for insensitivity of the chaotic zone width to planet eccentricity. Particles at zero free eccentricity near an eccentric planet have similar dynamics to those at zero eccentricity near a planet in a circular orbit.
description: accepted for publication in MNRAS
On the Design of Optimization Criteria for Multiple Sequence Alignment
Creators: name: Durand, Dannie
name: Farach-Colton, Martin
Publisher: name: Carnegie Mellon University
Year: 2002
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Multiple sequence alignment (MSA) is important in functional, structural and evolutionary studies of sequence data. While MSA construction has traditionally been an interactive process, the rapid growth of genetic sequence data has engendered a need for automated sequence analysis without human intervention. This requires more accurate methods based on rigorous mathematical models that reflect sequence biology in a realistic way. Focusing on MSA as an optimization problem, we examine the problem of unifying mathematical tractability with biological accuracy in cost function design. In particular, we consider tree alignment, which is often viewed as the most “biological” of the rigorous approaches to MSA. We point out several important pitfalls in current optimization approaches to MSA and identify characteristics for good cost function design. Design issues specific to approximation algorithms are also addressed. We hope these ideas will lead to future research on a biologically realistic and mathematically rigorous approach to MSA.
The Paradox of Industrial Involvement in Engineering Higher Education
Creators: name: Mitra, Srinjoy
name: Raskin, Jean-Pierre
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computers and Society (cs.CY)
subject: FOS: Computer and information sciences

description: This paper discusses the importance of reflective and socially conscious education in engineering schools, particularly within the EE/CS sector. While most engineering disciplines have historically aligned themselves with the demands of the technology industry, the lack of critical examination of industry practices and their impact on justice, equality, and sustainability is self-evident. Today, the for-profit engineering/technology companies, some of which are among the largest in the world, also shape the narrative of engineering education and research in universities. As engineering graduates form the largest cohorts within STEM disciplines in Western countries, they become future professionals who will work, lead, or even establish companies in this industry. Unfortunately, the curriculum within engineering education often lacks a deep understanding of social realities, an essential component of a comprehensive university education. Here we establish this unusual connection with the industry that has driven engineering higher education for several decades and its obvious negative impacts to society. We analyse this nexus and highlight the need for engineering schools to hold a more critical viewpoint. Given the wealth and power of modern technology companies, particularly in the ICT domain, questioning their techno-solutionism narrative is essential within the institutes of higher education.
Complete NNLO QCD Analysis of B -> X_s l^+ l^- and Higher Order Electroweak Effects
Creators: name: Bobeth, Christoph
name: Gambino, Paolo
name: Gorbahn, Martin
name: Haisch, Ulrich
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We complete the next-to-next-to-leading order QCD calculation of the branching ratio for B -> X_s l^+ l^- including recent results for the three-loop anomalous dimension matrix and two-loop matrix elements. These new contributions modify the branching ratio in the low-q^2 region, BR_ll, by about +1% and -4%, respectively. We furthermore discuss the appropriate normalization of the electromagnetic coupling alpha and calculate the dominant higher order electroweak effects, showing that, due to accidental cancellations, they change BR_ll by only -1.5% if alpha(mu) is normalized at mu = O(m_b), while they shift it by about -8.5% if one uses a high scale normalization mu = O(M_W). The position of the zero of the forward-backward asymmetry, q_0^2, is changed by around +2%. After introducing a few additional improvements in order to reduce the theoretical error, we perform a comprehensive study of the uncertainty. We obtain BR_ll(1 GeV^2 <= q^2 <= 6 GeV^2) = (1.57 +- 0.16) x 10^-6 and q_0^2 = (3.76 +- 0.33) GeV^2 and note that the part of the uncertainty due to the b-quark mass can be easily reduced.
description: 26 pages, 7 figures; v5: corrected normalisation in Eq. (5), numerical results unchanged
Constraining Warm Inflation with CMB data
Creators: name: Bastero-Gil, Mar
name: Bhattacharya, Sukannya
name: Dutta, Koushik
name: Gangopadhyay, Mayukh Raj
Publisher: name: arXiv
Year: 2017
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We confront the warm inflation observational predictions directly with the latest CMB data. We focus on a linear temperature (T) dissipative coefficient combined with the simplest model of inflation, a quartic chaotic potential. Although excluded in its standard cold inflation version, dissipation reduces the tensor-to-scalar ratio and brings the quartic chaotic model within the observable allowed range. We will use the CosmoMC package to derive constraints on the model parameters: the combination of coupling constants giving rise to dissipation, the effective number of relativistic degrees of freedom contributing to the thermal bath, and the quartic coupling in the inflaton potential. We do not assume a priori a power-law primordial spectrum, neither we fix the no. of e-folds at the horizon exit. The relation between the no. of e-folds and the comoving scale at horizon crossing is derived from the dynamics, depending on the parameters of the model, which allows us to obtain the $k$-dependent primordial power spectrum. We study the two possibilities considered in the literature for the spectrum, with the inflaton fluctuations having a thermal or a non-thermal origin, and discuss the ability of the data to constraint the model parameters.
description: 24 pages, 10 figures, updated with some clarifications and minor changes, JCAP accepted version
Nucleotide-dependent self-assembly of Nucleoside Diphosphate Kinase (NDPK) in vitro.
Creators: name: Morin-Leisk, Jeanne
name: Lee, Christina
Publisher: name: Carnegie Mellon University
Year: 2008
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: In addition to their role in nucleotide homeostasis, members of the Nucleoside Diphosphate Kinase (NDPK) family have been implicated in tumor metastasis, cell migration and vesicle trafficking. Although its role in most cases depends on nucleotide catalysis, a precise understanding of how the catalytic activity of NDPK supports its function in diverse processes is lacking. Here we report that wild type, but not catalytically inactive (H118C) NDPKB, undergoes dynamic self-assembly into ordered 20-25 nm diameter filaments in vitro. Self-assembly is nucleoside triphosphate dependent, GTP being most effective at promoting polymer formation. In addition, polymerization appears to depend on formation of the phosphoryl-Histidine intermediate of the enzyme, suggesting a previously unappreciated conformational change in NDPK during its catalytic cycle. We hypothesize that the observed nucleotide-dependent self-assembly property of NDPKB may reflect a key feature of NDPK enzymes that enables their function in diverse processes.
Linum trigynum 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
Malpighiales
Linaceae
Linum
Linum trigynum

description: Linum trigynum Linnaeus, Species Plantarum 1: 279. 1753.
"Habitat in Monspelii. D. Sauvages." RCN: 2210.
 Replaced synonym of: Linum gallicum L. (1762), nom. illeg.
 Lectotype (Rechinger, Fl. Iranica 106: 9. 1974): Herb. Linn. No. 396.19 (LINN).
 Current name: Linum trigynum L. (Linaceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part L), pp. 610-650 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 635, DOI: 10.5281/zenodo.291971
Infrared Properties of Close Pairs of Galaxies
Creators: name: Geller, Margaret J.
name: Kenyon, Scott J.
name: Barton, Elizabeth J.
name: Jarrett, Thomas H.
name: Kewley, Lisa J.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We discuss spectroscopy and infrared photometry for a complete sample of ~ 800 galaxies in close pairs objectively selected from the CfA2 redshift survey. We use 2MASS to compare near infrared color-color diagrams for our sample with the Nearby Field Galaxy Sample and with a set of IRAS flux-limited pairs from Surace et al. We construct a basic statistical model to explore the physical sources of the substantial differences among these samples. The model explains the spread of near infrared colors and is consistent with a picture where central star formation is triggered by the galaxy-galaxy interaction before a merger occurs. For 160 galaxies we report new, deep JHK photometry within our spectroscopic aperture and we use the combined spectroscopic and photometric data to explore the physical conditions in the central bursts. We find a set of objects with H-K >= 0.45 and with a large F(FIR)/F(H). We interpret the very red H-K colors as evidence for 600-1000 K dust within compact star-forming regions, perhaps similar to super-star clusters identified in individual well-studied interacting galaxies. The galaxies in our sample are candidate ``hidden'' bursts or, possibly, ``hidden'' AGN. Over the entire pair sample, both spectroscopic and photometric data show that the specific star formation rate decreases with the projected separation of the pair. The data suggest that the near infrared color-color diagram is also a function of the projected separation; all of the objects with central near infrared colors indicative of bursts of star formation lie at small projected separation.
description: 32 pages of text, 18 figures, accepted for publication (Astronomical Journal)
Nucleoside diphosphate kinase B (NDKB) scaffolds endoplasmic reticulum membranes in vitro.
Creators: name: Baughman, Cassandra
name: Morin-Leisk, Jeanne
name: Lee, Christina
Publisher: name: Carnegie Mellon University
Year: 2008
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: The mechanisms that structure the mammalian endoplasmic reticulum (ER) network are not fully understood. Here we show that salt extraction of semi-intact normal rat kidney (NRK) fibroblasts and subsequent incubation of the extracted cells with ATP resulted in dramatic ER network retraction. Under these conditions, addition of a single protein, Nucleoside Diphosphate Kinase B (NDKB), was sufficient to reverse the retraction and to promote ER network extension. The underlying mechanism of membrane extension involved direct lipid binding, as NDKB bound phosphatidylinositol (PtdIns)(4)P, PtdIns(4,5)P(2) and phosphatidic acid (PA); binding to these anionic lipids required clusters of basic residues on the surface of the NDKB hexamer; and amino acid changes in NDKB that blocked lipid binding also blocked ER network extension. Remarkably, purified NDKB transformed a uniform population of synthetic lipid vesicles into extensive membrane networks, and this also required its phospholipid-binding activity. Altogether these results identify a protein sufficient to scaffold extended membrane networks, and suggest a possible role for NDKB-like proteins, as well as phosphoinositides and/or acidic phospholipids, in modulating ER network morphogenesis.
Table of the Moon's Increment in Latitude - Ptolemy's Almagest by Toomer (Gerald J.) (1984) | Type-B (ID n° 338)
Creators: name: Toomer, Gerald J.
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2022
Subjects: Astronomy
History of astronomy
DISHAS
Astronomical table

description: This is a type B edition: A type-B edition corresponds to a critical edition of several table witnesses:
 it is based on several different editions, themselves based on tables from different primary sources.
 A type-B edition can be based on type-A, type-B or type-C editions.
You can find it on the DISHAS project website from this link: https://dishas.obspm.fr/table-edition/338
description: Source: Ptolemy's Almagest, Toomer (Gerald J.), 1984
Linum usitatissimum 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
Malpighiales
Linaceae
Linum
Linum usitatissimum

description: Linum usitatissimum Linnaeus, Species Plantarum 1: 277. 1753.
"Habitat hodie inter segetes Europae australis." RCN: 2204.
 Lectotype (Seegeler in Taxon 38: 278, f. 1. 1989): Herb. Clifford: 114, Linum 1 (BM-000558456).
 Generitype of Linum Linnaeus (vide Hitchcock, Prop. Brit. Bot.: 143. 1929).
 Current name: Linum usitatissimum L. (Linaceae).
 Note: Kulpa & Danert (in Kulturpflanze 3: 342. 1962) indicated a Brander collection (396.1 LINN), not received by Linnaeus until 1756, as type but it cannot be original material for the name. Rechinger (Fl. Iranica 106: 17. 1974) indicated Clifford material as “syntypi”, but the two sheets preserved at BM are not a single collection so Art. 9.15 does not apply. Seegeler is therefore the first to have made an explicit choice of lectotype.
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part L), pp. 610-650 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 635, DOI: 10.5281/zenodo.291971
Sudakov Form Factors
Creators: name: Collins, John C.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The theory of the on-shell Sudakov form factor to all order of logarithms is explained.
description: 42 pages, 21 figures. v2: Update of author's address from that in original publication to current address, and correction of typos
Genome-wide identification and expression analysis of lipoxygenase genes in Tartary buckwheat
Creators: name: Ji, Qiqi
name: Zhang, Tianyuan
name: Zhang, Dong
name: Lv, Shiming
name: Tan, Aijuan
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Plant Biology
subject: Computational Biology

description: Lipoxygenases (LOXs; EC1.13.11.12) are widely involved in plant growth, development, maturation, senescence and stress resistance. LOXs have been studied in many crop species but not in Tartary buckwheat [Fagopyrum tataricum (L.) Gaertn.]. This study aimed to systematically identify and analyze LOX genes in Tartary buckwheat. Eight LOX genes, which were unevenly distributed on five chromosomes, were identified in the Pinu1 Genome database. The data indicated that during long evolution, FtLOX genes were subjected to purifying selection. The conservation of motifs within the 9-LOX and 13-LOX subfamilies supported the results of phylogenetic analyses. All FtLOX proteins contained the LOX family-specific His-(X)4-His-(X)4-His-(X)17-His-(X)8-His motif, suggesting that this motif is essential for protein function. Analyses of physical and chemical properties showed that FtLOX6 might function under both acidic and alkaline conditions. The FtLOX gene promoters contained many light-responsive elements, and transcriptome data further suggested their roles in growth regulation and the response to light. Quantitative real-time polymerase chain reaction analysis of expression differences in plants exposed to different wavelengths of light confirmed that FtLOX1 and FtLOX4–7 could respond to light. Genes co-expressed with FtLOX genes were involved in the photoreaction-related pathway. This study provides a basis for further functional research in order to better understand the biological role of individual LOX gene in Tartary buckwheat.
Observations of SN 2015F suggest a correlation between the intrinsic luminosity of Type Ia supernovae and the shape of their light curves >900 days after explosion
Creators: name: Graur, Or
name: Zurek, David R.
name: Rest, Armin
name: Seitenzahl, Ivo R.
name: Shappee, Benjamin J.
name: Fisher, Robert
name: Guillochon, James
name: Shara, Michael M.
name: Riess, Adam G.
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The late-time light curves of Type Ia supernovae (SNe Ia), observed $>900$ days after explosion, present the possibility of a new diagnostic for SN Ia progenitor and explosion models. First, however, we must discover what physical process (or combination of processes) leads to the slow-down of the late-time light curve relative to a pure $^{56}$Co decay, as observed in SNe 2011fe, 2012cg, and 2014J. We present Hubble Space Telescope observations of SN 2015F, taken $\approx 600-1040$ days past maximum light. Unlike those of the three other SNe Ia, the light curve of SN 2015F remains consistent with being powered solely by the radioactive decay of $^{56}$Co. We fit the light curves of these four SNe Ia in a consistent manner and measure possible correlations between the light curve stretch - a proxy for the intrinsic luminosity of the SN - and the parameters of the physical model used in the fit (e.g., the mass ratio of $^{56}$Co and $^{57}$Co produced in the explosion, or the time at which freeze-out sets in). We propose a new, late-time Phillips-like correlation between the stretch of the SNe and the shape of their late-time light curves, which we parametrize as the difference between their pseudo-bolometric luminosities at 600 and 900 days: $ΔL_{900} = {\rm log}(L_{600}/L_{900})$. This model-independent correlation provides a new way to test which physical process lies behind the slow-down of SN Ia light curves $>900$ days after explosion, and, ultimately, fresh constraints on the various SN Ia progenitor and explosion models.
description: Accepted for publication in ApJ (14 pages, 6 figures, 3 tables)
Embedding right-angled Artin groups into graph braid groups
Creators: name: Sabalka, Lucas
Publisher: name: arXiv
Year: 2005
Subjects: subject: Group Theory (math.GR)
subject: Algebraic Topology (math.AT)
subject: Geometric Topology (math.GT)
subject: FOS: Mathematics

description: We construct an embedding of any right-angled Artin group $G(Δ)$ defined by a graph $Δ$ into a graph braid group. The number of strands required for the braid group is equal to the chromatic number of $Δ$. This construction yields an example of a hyperbolic surface subgroup embedded in a two strand planar graph braid group.
description: 8 pages. Final version, appears in Geometriae Dedicata.
Linum usitatissimum 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
Malpighiales
Linaceae
Linum
Linum usitatissimum

description: Linum usitatum Linnaeus, Flora Anglica: 14. 1754, orth. var.
RCN: 2204.
 Lectotype (Seegeler in Taxon 38: 278, f. 1. 1989): Herb. Clifford: 114, Linum 1 (BM).
 Current name: Linum usitatissimum L. (Linaceae).
 Note: An orthographic variant of L. usitatissimum L. (1753), as noted by Stearn (Introd. Ray’s Syn. Meth. Stirp. Brit.  (Ray Soc. ed.): 68. 1973).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part L), pp. 610-650 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 635, DOI: 10.5281/zenodo.291971
Nuclear magnetic resonance of hemoglobins.
Creators: name: Lukin, Jonathan A.
name: Ho, Chien
Publisher: name: Carnegie Mellon University
Year: 2003
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Nuclear magnetic resonance (NMR) spectroscopy detects the interaction of radiofrequency (rf) radiation with the nuclear spins of molecules placed in an applied magnetic field. Because the spins are sensitive to their environment, and may be coupled to one another both through chemical bonds and through space, NMR can provide a wealth of information on the structure and dynamics of macromolecules. In particular, NMR has proven to be a powerful technique for investigating the structure-function relationship of hemoglobin (Hb). In this chapter, we focus on the procedures involved in applying one-dimensional and two-dimensional NMR spectroscopy to Hb and give examples of the information that may be obtained from this method. We begin with a brief outline of theory; a more complete treatment can be found in several excellent books (1–8). A typical NMR sample may contain approx 3×10−7 mol of Hb, which include ≈1021 hydrogen atoms, each of which has a nucleus (i.e., a proton) with a nuclear spin 1/2. In the presence of an applied magnetic field B 0, each nucleus will occupy one of two possible energy levels, corresponding to the z-component of the spin being either parallel or antiparallel to B 0, which conventionally points along the z-axis. At thermal equilibrium, a slight excess (a few parts in 105) of spins will occupy the lower energy level and be parallel to B 0. This small population difference is crucial to the NMR signal resulting from the absorption of rf energy, which excites spins from the lower to the upper energy state.
X-ray Properties of Intermediate-mass Black Holes in Active Galaxies
Creators: name: Greene, Jenny E.
name: Ho, Luis C.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present a pilot study of the X-ray properties of intermediate-mass (~10^5-10^6 M_sun) black holes in active galaxies using the Chandra X-ray telescope. Eight of the 10 active galaxies are detected with a significance of at least 3 sigma, with X-ray luminosities in the range L_(0.5-2 keV) ~ 10^41-10^43 ergs/s. The optical-to-X-ray flux ratios are consistent with expectations, given the known correlations between alpha_ox and ultraviolet luminosity, while a couple of objects appear to be anomalously X-ray weak. The range of 0.5--2 keV photon indices we measure, 1 < Gamma_s < 2.7, is entirely consistent with values found in samples of more luminous sources with more massive black holes. Black hole mass evidently is not a primary driver of soft X-ray spectral index. On the other hand, we do find evidence for a correlation between X-ray power-law slope and both X-ray luminosity and Eddington ratio, which may suggest that X-ray emission mechanisms weaken at high Eddington ratio. Such a weakening may explain the X-ray weakness of one of our most optically luminous objects.
description: Submitted to ApJ on 7 April 2006, but still awaiting referee's report; 8 pages, 4 figures, uses emulateapj5.sty
Word-Entity Duet Representations for Document Ranking
Creators: name: Xiong, Chenyan
name: Callan, Jamie
name: Liu, Tie-Yan
Publisher: name: arXiv
Year: 2017
Subjects: subject: Information Retrieval (cs.IR)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: This paper presents a word-entity duet framework for utilizing knowledge bases in ad-hoc retrieval. In this work, the query and documents are modeled by word-based representations and entity-based representations. Ranking features are generated by the interactions between the two representations, incorporating information from the word space, the entity space, and the cross-space connections through the knowledge graph. To handle the uncertainties from the automatically constructed entity representations, an attention-based ranking model AttR-Duet is developed. With back-propagation from ranking labels, the model learns simultaneously how to demote noisy entities and how to rank documents with the word-entity duet. Evaluation results on TREC Web Track ad-hoc task demonstrate that all of the four-way interactions in the duet are useful, the attention mechanism successfully steers the model away from noisy entities, and together they significantly outperform both word-based and entity-based learning to rank systems.
Constraints on Large Extra Dimensions with Bulk Neutrinos
Creators: name: Cao, Qing-Hong
name: Gopalakrishna, Shrihari
name: Yuan, C. -P.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We consider right-handed neutrinos propagating in $δ$ (large) extra dimensions, whose only coupling to Standard Model fields is the Yukawa coupling to the left-handed neutrino and the Higgs boson. These theories are attractive as they can explain the smallness of the neutrino mass, as has already been shown. We show that if $δ$ is bigger than two, there are strong constraints on the radius of the extra dimensions, resulting from the experimental limit on the probability of an active state to mix into the large number of sterile Kaluza-Klein states of the bulk neutrino. We also calculate the bounds on the radius resulting from requiring that perturbative unitarity be valid in the theory, in an imagined Higgs-Higgs scattering channel.
description: 24 pages, 4 figures, revtex4. v2: Minor typos corrected, references added
General relativistic radiation magnetohydrodynamics simulations of supercritical accretion onto magnetized neutron star; -modeling of ultra luminous x-ray pulsars
Creators: name: Takahashi, Hiroyuki R.
name: Ohsuga, Ken
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: By performing 2.5-dimensional general relativistic radiation magnetohydrodynamic simulations, we demonstrate supercritical accretion onto a non-rotating, magnetized neutron star, where the magnetic field strength of dipole fields is $10^{10}$ G on the star surface. We found the supercritical accretion flow consists of two parts; the accretion columns and the truncated accretion disk. The supercritical accretion disk, which appears far from the neutron star, is truncated at around $\sim 3R_*$ ($R_*=10^6$ cm is the neutron star radius), where the magnetic pressure via the dipole magnetic fields balances with the radiation pressure of the disks. The angular momentum of the disk around the truncation radius is effectively transported inward through magnetic torque by dipole fields, inducing the spin up of a neutron star. The evaluated spin up rate, $\sim -10^{-11}$ s s$^{-1}$, is consistent with the recent observations of the ultra luminous X-ray pulsars. Within the truncation radius, the gas falls onto neutron star along dipole fields, which results in a formation of accretion columns onto north and south hemispheres. The net accretion rate and the luminosity of the column are $\sim 66L_{\rm Edd}/c^2$ and $\lesssim 10L_{\rm Edd}$, where $L_{\rm Edd}$ is the Eddington luminosity and c is the light speed. Our simulations support a hypothesis whereby the ultra luminous X-ray pulsars are powered by the supercritical accretion onto the magnetized neutron stars.
description: 9 pages, 3 figures, 1 table, Accepted for publication in ApJL
Linum virginianum 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
Malpighiales
Linaceae
Linum
Linum virginianum

description: Linum virginianum Linnaeus, Species Plantarum 1: 279. 1753.
"Habitat in Virginia, Pensylvania." RCN: 2214.
 Lectotype (Fernald in Rhodora 37: 428. 1935): Kalm, Herb. Linn. No. 396.24 (LINN).
 Current name: Linum virginianum L. (Linaceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part L), pp. 610-650 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 635, DOI: 10.5281/zenodo.291971
Інтеграція компатибілізму Денета зі стохастичною моделлю свідомості: нові перспективи для свободи волі
Creators: name: Котенко Валерій
Publisher: name: Zenodo
Year: 2025

description: Проблема свободи волі залишається центральною у філософії та нейронауці. Чи є наші рішення продуктом детермінованих процесів, чи ми маємо справжню свободу вибору? Компатибілізм, зокрема в інтерпретації Деніела Денета, стверджує, що свобода волі сумісна з детермінізмом завдяки складній обробці інформації в мозку. У цій статті ми пропонуємо інтеграцію компатибілізму Денета зі стохастичною моделлю свідомості, яка враховує нейронну варіативність як джерело множинності можливостей. Замість спекулятивних квантових ефектів ми фокусуємося на стохастичних процесах у нейронах, таких як випадкові флуктуації в синаптичній передачі, які можуть імітувати варіативність, необхідну для свободи волі. Ця модель поєднує філософський підхід із нейронауковими даними, пропонуючи перевіряєму парадигму.
Linum viscosum Linnaeus 1762
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
Malpighiales
Linaceae
Linum
Linum viscosum

description: Linum viscosum Linnaeus, Species Plantarum, ed. 2, 1: 398. 1762.
"Habitat in montibus Bononiensibus, Sumano, Augustae vindelicorum, Ingolstadii." RCN: 2206.
Type not designated.
Original material: none traced.
 Current name: Linum viscosum L. (Linaceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part L), pp. 610-650 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 635, DOI: 10.5281/zenodo.291971
Novel multisample scheme for inferring phylogenetic markers from whole genome tumor profiles.
Creators: name: Ayshwarya  Subramanian
name: Shackney, Stanley E.
name: Schwartz, Russell
Publisher: name: Carnegie Mellon University
Year: 2013
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Computational cancer phylogenetics seeks to enumerate the temporal sequences of aberrations in tumor evolution, thereby delineating the evolution of possible tumor progression pathways, molecular subtypes, and mechanisms of action. We previously developed a pipeline for constructing phylogenies describing evolution between major recurring cell types computationally inferred from whole-genome tumor profiles. The accuracy and detail of the phylogenies, however, depend on the identification of accurate, high-resolution molecular markers of progression, i.e., reproducible regions of aberration that robustly differentiate different subtypes and stages of progression. Here, we present a novel hidden Markov model (HMM) scheme for the problem of inferring such phylogenetically significant markers through joint segmentation and calling of multisample tumor data. Our method classifies sets of genome-wide DNA copy number measurements into a partitioning of samples into normal (diploid) or amplified at each probe. It differs from other similar HMM methods in its design specifically for the needs of tumor phylogenetics, by seeking to identify robust markers of progression conserved across a set of copy number profiles. We show an analysis of our method in comparison to other methods on both synthetic and real tumor data, which confirms its effectiveness for tumor phylogeny inference and suggests avenues for future advances.
Modelling the Pan-Spectral Energy Distribution of Starburst Galaxies: III. Emission Line Diagnostics of Ensembles of Evolving HII Regions
Creators: name: Dopita, Michael A.
name: Fischera, Joerg
name: Sutherland, Ralph S.
name: Kewley, Lisa J.
name: Leitherer, Claus
name: Tuffs, Richard J.
name: Popescu, Cristina C.
name: van Breugel, Wil
name: Groves, Brent A.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We build, as far as theory will permit, self consistent model HII regions around central clusters of aging stars. These produce strong emission line diagnostics applicable to either individual HII regions in galaxies, or to the integrated emission line spectra of disk or starburst galaxies. The models assume that the expansion and internal pressure of individual HII regions is driven by the net input of mechanical energy from the central cluster, be it through winds or supernova events. This eliminates the ionization parameter as a free variable, replacing it with a parameter which depends on the ratio of the cluster mass to the pressure in the surrounding interstellar medium. These models explain why HII regions with low abundances have high excitation, and demonstrate that at least part of the warm ionized medium is the result of overlapping faint, old, large, and low pressure HII regions. We present line ratios (at both optical and IR wavelengths) which provide reliable abundance diagnostics for both single HII regions or for integrated galaxy spectra, and we find a number that can be used to estimate the mean age of the cluster stars exciting individual HII regions.
description: 22 pages. 18 figures. Accepted for publication in Astrophysical journal Supplements. Electronic tabular material is available on request to Michael.Dopita@anu.edu.au
7.2 Making Research Data Repositories Visible – The re3data.org Registry
Creators: name: Frank Scholze, Heinz Pampel
Publisher: name: Zenodo
Year: 2015
Subjects: data, repositiories, visibility, registry

description: Researchers require infrastructures that ensure a maximum of accessibility, stability and reliability to facilitate working with and sharing of research data. Such infrastructures are being increasingly summarised under the term Research Data Repositories (RDR). The project re3data.org – Registry of Research Data Repositories – began to index research data repositories in 2012 and offers researchers, funding organisations, libraries and publishers an overview of the heterogeneous research data repository landscape. In December 2014 re3data.org listed more than 1,030 research data repositories, which are described in detail using the re3data.org schema (http://dx.doi.org/10.2312/re3.003). Information icons help researchers to identify easily an adequate repository for the storage and reuse of their data. This talk describes the heterogeneous RDR landscape and presents a typology of institutional, disciplinary, multidisciplinary and project-specific RDR. Further, it outlines the features of re3data. org and it shows current developments for integration into data management planning tools and other services. By the end of 2015 re3data.org and Databib (Purdue University, USA) will merge their services, which will then be managed under the auspices of DataCite. The aim of this merger is to reduce duplication of effort and to serve the research community better with a single, sustainable registry of research data repositories. The talk will present this organisational development as a best practice example for the development of international research information services. Frank Scholze has been Director of Library Services at the Karlsruhe Institute of Technology (KIT) since January 2010. KIT is the merger of the University of Karlsruhe and one of the National Research Centers within the Helmholtz Association. He chairs the DINI (German Initiative for Networked Information) working group on electronic publishing and has been involved in a series of digital library projects. He is a member of a number of scientific boards and councils (among them DFG (German Research Foundation), FIZ Karlsruhe, DARIAH-DE and German Classification Society). Before he joined the KIT, he was a Programme Manager at the Ministry of Science Research and the Arts Baden-Württemberg and Head of the Public Services Department at Stuttgart University Library. He holds an MA in Art History and English Literature and a BSc in Library and Information Science.
Photon and its hadronic interaction
Creators: name: Krawczyk, Maria
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: A short overview of basics aspects of hadronic interaction of the photon is presented.
description: Introduction to PHOTON2003, 2 pages, 2 ps figures, espcrc2.sty, to appear in Proceedings
Novel entries in a fungal biofilm matrix encyclopedia.
Creators: name: Zarnowski, Robert
name: Westler, William M
name: Lacmbouh, Ghislain Ade
name: Marita, Jane M.
name: Bothe, Jameson R.
name: Bernhardt, Jörg
name: Sahraoui, Anissa Lounes-Hadj
name: Fontaine, Joël
name: Hiram  Sanchez
name: Hatfield, Ronald D.
name: Ntambi, James M.
name: Jeniel E. Nett
name: Mitchell, Aaron
name: Andes, David R.
Publisher: name: Carnegie Mellon University
Year: 2014
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Virulence of Candida is linked with its ability to form biofilms. Once established, biofilm infections are nearly impossible to eradicate. Biofilm cells live immersed in a self-produced matrix, a blend of extracellular biopolymers, many of which are uncharacterized. In this study, we provide a comprehensive analysis of the matrix manufactured by Candida albicans both in vitro and in a clinical niche animal model. We further explore the function of matrix components, including the impact on drug resistance. We uncovered components from each of the macromolecular classes (55% protein, 25% carbohydrate, 15% lipid, and 5% nucleic acid) in the C. albicans biofilm matrix. Three individual polysaccharides were identified and were suggested to interact physically. Surprisingly, a previously identified polysaccharide of functional importance, β-1,3-glucan, comprised only a small portion of the total matrix carbohydrate. Newly described, more abundant polysaccharides included α-1,2 branched α-1,6-mannans (87%) associated with unbranched β-1,6-glucans (13%) in an apparent mannan-glucan complex (MGCx). Functional matrix proteomic analysis revealed 458 distinct activities. The matrix lipids consisted of neutral glycerolipids (89.1%), polar glycerolipids (10.4%), and sphingolipids (0.5%). Examination of matrix nucleic acid identified DNA, primarily noncoding sequences. Several of the in vitro matrix components, including proteins and each of the polysaccharides, were also present in the matrix of a clinically relevant in vivo biofilm. Nuclear magnetic resonance (NMR) analysis demonstrated interaction of aggregate matrix with the antifungal fluconazole, consistent with a role in drug impedance and contribution of multiple matrix components. Importance: This report is the first to decipher the complex and unique macromolecular composition of the Candida biofilm matrix, demonstrate the clinical relevance of matrix components, and show that multiple matrix components are needed for protection from antifungal drugs. The availability of these biochemical analyses provides a unique resource for further functional investigation of the biofilm matrix, a defining trait of this lifestyle.
Large-deviations/thermodynamic approach to percolation on the complete graph
Creators: name: Biskup, Marek
name: Chayes, Lincoln
name: Smith, S. Alex
Publisher: name: arXiv
Year: 2005
Subjects: subject: Probability (math.PR)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 60C05; 60F10; 05C80

description: We present a large-deviations/thermodynamic approach to the classic problem of percolation on the complete graph. Specifically, we determine the large-deviation rate function for the probability that the giant component occupies a fixed fraction of the graph while all other components are ``small.'' One consequence is an immediate derivation of the ``cavity'' formula for the fraction of vertices in the giant component. As a by-product of our analysis we compute the large-deviation rate functions for the probability of the event that the random graph is connected, the event that it contains no cycles and the event that it contains only ``small'' components.
description: 16 pages, 1 figure; revised version accomodating literature remarks of the referees
Liparia graminifolia Linnaeus 1771
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
Liparia
Liparia graminifolia

description: Liparia graminifolia Linnaeus, Mantissa Plantarum Altera: 268. 1771.
"Habitat ad Cap. b. spei arenosis." RCN: 5432.
 Lectotype (Schutte & Van Wyk in Taxon 43: 579. 1994): Tulbagh 5, Herb. Linn. No. 910.3 (LINN).
 Current name: Liparia graminifolia L. (Fabaceae: Faboideae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part L), pp. 610-650 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 635, DOI: 10.5281/zenodo.291971
Shock-cloud interaction in the Vela SNR II. Hydrodynamic model
Creators: name: Miceli, M.
name: Reale, F.
name: Orlando, S.
name: Bocchino, F.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: In the framework of the study of the X-ray and optical emission in supernova remnants we focus on an isolated X-ray knot in the northern rim of the Vela SNR (Vela FilD), whose X-ray emission has been studied and discussed in Paper I. We aim at understanding the physical origin of the X-ray and optical emission in FilD, at understanding the role of the different physical processes at work, and at obtaining a key for the interpretation of future X-ray observations of SNRs. To this end we have pursued an accurate ``forward'' modeling of the interaction of the Vela SNR shock with an ISM cloud. We perform hydrodynamic simulations and we directly compare the observables synthesized from the simulations with the data. We explore four different model setups, choosing the values of the physical parameters on the basis of our preliminary analysis of the X-ray data. We synthesize X-ray emission maps and spectra filtered through the XMM-Newton EPIC-MOS instrumental response. The impact of a shock front at 6 million Kelvin on an elliptical cloud 30 times denser than the ambient medium describes well the shock-cloud interaction processes in the Vela FilD region in terms of spectral properties and morphology of the X-ray and optical emission. The bulk of the X-ray emission in the FilD knot originates in the cloud material heated by the transmitted shock front, but significant X-ray emission is also associated to the cloud material, which evaporates, as an effect of thermal conduction, in the intercloud medium. The physical origin of the FilD optical emission is associated to thermal instabilities. In the FilD knot the X-ray emission associated to the reflected shock front is negligible.
description: 13 pages, 11 figures, accepted for publication in Astronomy & Astrophysics. For the version of the paper with high resolution images, please see http://www.astropa.unipa.it/Library/preprint.html
ECFA-Summary: Higgs, gamma-gamma and e-gamma physics
Creators: name: Krawczyk, Maria
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Recent results obtained within ECFA/DESY and ECFA Study by the Higgs and gamma gamma /e gamma physics working groups are presented.
description: Talk at EPS2003, 3 pages, 15 eps figures, svepj.clo and svjour.cls
Supplementary document for Anisotropic scattering characteristics of nanoparticles in different morphologies: from the point of view of photothermal therapy - 5015457.pdf
Creators: name: Chen, Qin
name: Ren, Yatao
name: Yin, Yanmei
name: Qi, Hong
Publisher: name: Optica Publishing Group
Year: 2021
Subjects: Uncategorized

description: Supproting Information
NOTUNG: a program for dating gene duplications and optimizing gene family trees.
Creators: name: Chen, Kevin
name: Durand, Dannie
name: Farach-Colton, Martin
Publisher: name: Carnegie Mellon University
Year: 2000
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Large scale gene duplication is a major force driving the evolution of genetic functional innovation. Whole genome duplications are widely believed to have played an important role in the evolution of the maize, yeast, and vertebrate genomes. The use of evolutionary trees to analyze the history of gene duplication and estimate duplication times provides a powerful tool for studying this process. Many studies in the molecular evolution literature have used this approach on small data sets, using analyses performed by hand. The rapid growth of genetic sequence data will soon allow similar studies on a genomic scale, but such studies will be limited unless the analysis can be automated. Even existing data sets admit alternative hypotheses that would be too tedious to consider without automation. In this paper, we describe a program called NOTUNG that facilitates large scale analysis, using both rooted and unrooted trees. When tested on trees analyzed in the literature, NOTUNG consistently yielded results that agree with the assessments in the original publications. Thus, NOTUNG provides a basic building block for inferring duplication dates from gene trees automatically and can also be used as an exploratory analysis tool for evaluating alternative hypotheses.