cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
An Improved Measure of Musical Noise Based on Spectral Kurtosis
Creators: name: Torcoli, Matteo
Publisher: name: arXiv
Year: 2021
Subjects: subject: Audio and Speech Processing (eess.AS)
subject: Sound (cs.SD)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: Audio processing methods operating on a time-frequency representation of the signal can introduce unpleasant sounding artifacts known as musical noise. These artifacts are observed in the context of audio coding, speech enhancement, and source separation. The change in kurtosis of the power spectrum introduced during the processing was shown to correlate with the human perception of musical noise in the context of speech enhancement, leading to the proposal of measures based on it. These baseline measures are here shown to correlate with human perception only in a limited manner. As ground truth for the human perception, the results from two listening tests are considered: one involving audio coding and one involving source separation. Simple but effective perceptually motivated improvements are proposed and the resulting new measure is shown to clearly outperform the baselines in terms of correlation with the results of both listening tests. Moreover, with respect to the listening test on musical noise in audio coding, the exhibited correlation is nearly as good as the one exhibited by the Artifact-related Perceptual Score (APS), which was found to be the best objective measure for this task. The APS is however computationally very expensive. The proposed measure is easily computed, requiring only a fraction of the computational cost of the APS.
description: Manuscript accepted for the 2019 IEEE Workshop on Applications of Signal Processing to Audio and Acoustics
First version of the interfaces and interconnections allowing to interact with BIM and multi-simulation information in VR
Creators: name: Ververidis, Dimitrios
name: Gounaridis, Dimitrios
name: Mouzakis, Christos
name: Bava, Vittorio
name: Margariti, Evangelia Vangeli
name: Rousi, Maria
name: Jeg Dudley
name: De Loris, Roberto
name: Nikolopoulos, Spiros
name: Broesamle, Martin
Publisher: name: Zenodo
Year: 2021
Subjects: BIM
CAE
Simulation
Interface

description: Software package and associated report containing the results from T4.1-T4.4, namely interconnection modules, BIM/CAE-Simulation interfaces and high-realistic graphics that will be integrated in WP5, the first prototype.
Asymmetric embedding in brane cosmology
Creators: name: Shtanov, Yuri
name: Viznyuk, Alexander
name: Granda, Luis Norberto
Publisher: name: arXiv
Year: 2008
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We derive a system of cosmological equations for a braneworld with induced curvature which is a junction between several bulk spaces. The permutation symmetry of the bulk spaces is not imposed, and the values of the fundamental constants, and even the signatures of the extra dimension, may be different on different sides of the brane. We then consider the usual partial case of two asymmetric bulk spaces and derive an exact closed system of scalar equations on the brane. We apply this result to the cosmological evolution on such a brane and describe its various partial cases.
description: 10 pages
Quantum circuit synthesis of Bell and GHZ states using projective simulation in the NISQ era
Creators: name: Pires, O. M.
name: Duzzioni, E. I.
name: Marchi, J.
name: Santiago, R.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (cs.LG)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Quantum Computing has been evolving in the last years. Although nowadays quantum algorithms performance has shown superior to their classical counterparts, quantum decoherence and additional auxiliary qubits needed for error tolerance routines have been huge barriers for quantum algorithms efficient use. These restrictions lead us to search for ways to minimize algorithms costs, i.e the number of quantum logical gates and the depth of the circuit. For this, quantum circuit synthesis and quantum circuit optimization techniques are explored. We studied the viability of using Projective Simulation, a reinforcement learning technique, to tackle the problem of quantum circuit synthesis for noise quantum computers with limited number of qubits. The agent had the task of creating quantum circuits up to 5 qubits to generate GHZ states in the IBM Tenerife (IBM QX4) quantum processor. Our simulations demonstrated that the agent had a good performance but its capacity for learning new circuits decreased as the number of qubits increased.
title: Mortality Of Larval Cod Related To Predation By The Hydroid Clytia Gracilis On Georges Bank
Creators: name: Klein-Macphee, G.
name: Sullivan, B. K.
name: Van Keuran, D.
name: Horgan, E.
name: Klos, E.
Publisher: name: ASC 1997 - T
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.Mortality Of Larval Cod Related To Predation By The Hydroid Clytia Gracilis On Georges Bank
Uniform-in-bandwidth consistency for kernel-type estimators of Shannon's entropy
Creators: name: Bouzebda, Salim
name: Elhattab, Issam
Publisher: name: arXiv
Year: 2008
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics

description: We establish uniform-in-bandwidth consistency for kernel-type estimators of the differential entropy. We consider two kernel-type estimators of Shannon's entropy. As a consequence, an asymptotic 100% confidence interval of entropy is provided.
A general approach to the total synthesis of yeuhchukene and its analogues : a novel anti-implantation agent
Creators: name: Lopez Tapia, Francisco Javier
Publisher: name: University of British Columbia
Year: 2010

description: This thesis concerns a general approach to the total synthesis of yuehchukene 2 and its analogues. Yuehchukene has a potent anti-implantation activity. It also lacks the estrogenic side effect of most compounds with similar biological activity. However, it is somewhat unstable and this could bring some problems when administered to humans. Development of a versatile synthesis of yuehchukene capable of producing a variety of analogous structures in order to fully exploit the pharmacological properties of this novel molecular system and/or to make a more stable product without losing its biological properties was the central objective of this project. Specifically, the total synthesis of yuehchukene 2 and its analogue 6a-ep/-yuehchukene 25 are described. After some preliminary studies, it was found that a kinetic carboxylation (lithium 2,6-di-tert-butyl-4-methylphenoxide, CO₂) of isophorone 26 followed by a reduction (NaBH₄) produced stereoselectively cis-hydroxyacid 46 in good yield. The latter was transformed into indoleacid 48 by dibenzoylation (PhCOCI, DMAP) and treatment with indolylmagnesium iodide. The key intermediate trans-ketone 60 was obtained by treatment of 48 with oxalyl chloride followed by indolylmagnesium iodide. Epimerization of 60 to the more stable cis-ketone 24 was accomplished quantitatively under basic conditions (MeONa/MeOH, reflux). Reduction (LiAlH₄) and dibenzoylation (PhCOCI, DMAP, Et₃N) of 24 furnished the benzoate 68 which was subjected to a nucleophilic substitution with indolylmagnesium iodide to give N-benzoylyuehchukene 69. The latter transformation also gave the interesting compound 75 which was submitted to an X-Ray diffraction analysis. The total synthesis of yuehchukene 2 was then achieved by methanolysis (NaOMe/MeOH) of 69. As far as the synthesis of 6a-epi-yuehchukene 25 is concerned, it was found that, after a thorough study, it was best to transform trans-ketone 60 into its SEM-derivative 85 (SEM-CI,NaH). The latter was reduced (DIBAL) and acetylated (Ac₂O, DMAP, Et₃N) to produce stereoselectively the acetate 87 which, by treatment with indolylmagnesium iodide, furnished SEM-trans-yuehchukene 88. The newly incorporated indole group bears a 1,3-diaxial-like interaction with the β-methyl group at C-7. Unlike 88, tosylacetate 82 gave the compound 84. Finally, the total synthesis of 6a-epi-yuehchukene was accomplished by deprotection of the indole system. Various compounds from this study are now under investigation at WHO and in Hong Kong but, unfortunately, biological results are unavailable at present. [Formula Omitted]
Spin matrix elements in 2D Ising model on the finite lattice
Creators: name: Bugrij, A. I.
name: Lisovyy, O.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We present explicit formulas for all spin matrix elements in the 2D Ising model with the nearest neighbor interaction on the finite periodic square lattice. These expressions generalize the known results [Phys. Rev. D19, (1979), 2477--2479; hep-th/0107117; hep-th/0112167] (coincide with them in the appropriate limits) and fulfill the test of straightforward transfer matrix calculations for finite $N$.
description: old paper (2003) posted for archival purposes
title: Broad-Scale Patterns Of High Frequency Volume Backscattering On Georges Bank During Late Spring/Early Summer Of 1994, 1995, 1996, And 1997
Creators: name: Wiebe, Peter H.
name: Stanton, T.M.
name: Benfield, M.
name: Greene, C.H.
name: Mutlu, E.
Publisher: name: ASC 1997 - T
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.High frequency (120 and 420 kHz) sound was used to survey sound scatterers in the waterover Georges Bank on broad-scale cruises during late springlearly summer 1994, 1995, 1996, and1997. Data were collected from a towed body with down looking transducers along the tracklines between stations on 45 transect legs [1441 km] in June 1994 arid 39 transect legs in July1995, June 1996, and June 97 each with -1350 km.
Knots are Generic Stable Phases in Semiflexible Polymers
Creators: name: Majumder, Suman
name: Marenz, Martin
name: Paul, Subhajit
name: Janke, Wolfhard
Publisher: name: arXiv
Year: 2021
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible polymers has not been explored much. Here, via extensive replica exchange Monte Carlo simulation we investigate the same for a bead-stick and a bead-spring homopolymer model that covers the whole range from flexible to stiff. We establish the fact that the presence of stable knotted phases in the phase diagram is dependent on the ratio $r_b/r_{\rm{min}}$ where $r_b$ is the equilibrium bond length and $r_{\rm{min}}$ is the distance for the strongest nonbonded contacts. Our results provide evidence for both models that if the ratio $r_b/r_{\rm{min}}$ is outside a small window around unity then depending on the bending stiffness one always encounters stable knotted phases along with the usual frozen and bent-like structures at low temperatures. These findings prompt us to conclude that knots are generic stable phases in semiflexible polymers.
Phylogenetic patterns and conservation among North American members of the genus Agalinis (Orobanchaceae)
Creators: name: Pettengill, James B
name: Neel, Maile C
Publisher: name: Springer Nature
Year: 2008
Subjects: rbcL
Bootstrap Support
Calyx Lobe
Incomplete Lineage Sorting
Corolla Lobe

description: North American Agalinis Raf. species represent a taxonomically challenging group and there have been extensive historical revisions at the species, section, and subsection levels of classification. The genus contains many rare species, including the federally listed endangered species Agalinis acuta. In addition to evaluating the degree to which historical classifications at the section and subsection levels are supported by molecular data sampled from 79 individuals representing 29 Agalinis species, we assessed the monophyly of 27 species by sampling multiple individuals representing different populations of those species. Twenty-one of these species are of conservation concern in at least some part of their range. Phylogenetic relationships estimated using maximum likelihood analyses of seven chloroplast DNA loci (aligned length = 11 076 base pairs (bp) and the nuclear ribosomal DNA ITS (internal transcribed spacer) locus (733 bp); indicated no support for the historically recognized sections except for Section Erectae. Our results suggest that North American members of the genus comprise six major lineages, however we were not able to resolve branching order among many of these lineages. Monophyly of 24 of the 29 sampled species was supported based on significant branch lengths of and high bootstrap support for subtending branches. However, there was no statistical support for the monophyly of A. acuta with respect to Agalinis tenella and Agalinis decemloba. Although most species were supported, deeper relationships among many species remain ambiguous. The North American Agalinis species sampled form a well supported, monophyletic group within the family Orobanchaceae relative to the outgroups sampled. Most hypotheses regarding section- and subsection-level relationships based on morphology were not supported and taxonomic revisions are warranted. Lack of support for monophyly of Agalinis acuta leaves the important question regarding its taxonomic status unanswered. Lack of resolution is potentially due to incomplete lineage sorting of ancestral polymorphisms among recently diverged species; however the gene regions examined did distinguish among almost all other species in the genus. Due to the important policy implications of this finding we are further evaluating the evolutionary distinctiveness of A. acuta using morphological data and loci with higher mutation rates.
title: Horizontal Convergence And Dispersion Over The Southern Flank Of Georges Bank
Creators: name: Churchill, James H.
name: Manning, James P.
Publisher: name: ASC 1997 - T
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.A goal of the GLOBEC Georges Bank program is to better understand the impact of currents on the recruitment of cod and haddock to Georges Bank. A premiseof the program is that most of the cod and haddock which recruit to the juvenile population over the Bank' s crest have been passively carried from the principal spawning region over the Bank's northeast peak (e.g. Smith et al., 1981; Lough, 1984; Lough and Boltz, 1989).
Substochastic semigroups and densities of piecewise deterministic Markov processes
Creators: name: Tyran-Kaminska, Marta
Publisher: name: arXiv
Year: 2008
Subjects: subject: Functional Analysis (math.FA)
subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 47D06 (Primary) 60J25, 60J35, 60J75 (Secondary)

description: Necessary and sufficient conditions are given for a substochastic semigroup on $L^1$ obtained through the Kato--Voigt perturbation theorem to be either stochastic or strongly stable. We show how such semigroups are related to piecewise deterministic Markov process, provide a probabilistic interpretation of our results, and apply them to fragmentation equations.
description: 26 pages; corrected typos
Total cross-section and rapidity gap survival probability at the LHC through an eikonal with soft gluon resummation
Creators: name: Achilli, Andrea
name: Hegde, Rohit
name: Godbole, Rohini M.
name: Grau, Agnes
name: Pancheri, Giulia
name: Srivastava, Yogi
Publisher: name: arXiv
Year: 2007
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: New results are presented for total ${\rm pp}/ {\rm \bar p p}$ cross-sections, in the framework of our QCD based model (GGPS). This is an improved eikonal mini-jet model, where soft gluon radiation tames the fast energy rise normally present in mini-jet models. We discuss the variability in our predictions and provide a handy parametrization of our results for the LHC. We find that our model predictions span the range $σ_{tot}^{LHC}=100 ^{+10}_{-13} mb$. While this matches nicely with the range of most other models, it does not agree with recent ones which include a "hard" Pomeron, even though our model does include hard scattering. We compute the survival probability for Large Rapidity Gap (LRG) events at the LHC and at the Tevatron. These events are relevant, for example, for Higgs signal in the $WW$ fusion process. We also explore whether measurements of the total cross-sections at the LHC can help us sharpen the model parameters and hence estimates for these survival probabilities, further.
description: 15 pages, 3 figures, LaTeX
Localization of the Helical Edge States in the Absense of External Magnetic Field
Creators: name: Bubis, A. V.
name: Mikhailov, N. N.
name: Dvoretsky, S. A.
name: Nasibulin, A. G.
name: Tikhonov, E. S.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Theoretically, the helical edge states of two-dimensional topological insulators are protected from coherent backscattering due to nonmagnetic disorder provided electron interactions are not too strong. Experimentally, the edges typically do not demonstrate the systematic and robust quantization, at the same time little is known about the sub-Kelvin temperature behavior. Here, we report the surprising localization of the edge states in an 8 nm HgTe quantum well in zero magnetic field at millikelvin temperatures. Additionally, the magnetoresistance data at 0.5 K for the edges few micrometers long suggests the field-dependent localization length $l_B\propto B^{-α}$, with $α$ ranging approximately from $1.6$ to $2.8$ at fields $B\lesssim0.1\,\text{T}$ and $α\approx1.1$ at higher fields up to $0.5\,\text{T}$. In the frame of disordered interacting edge, these values of $α$ correspond to the Luttinger liquid parameters $K\approx 0.9-1.1$ and $K\approx 0.6$, respectively. We discuss possible scenarios which could result in the zero magnetic field localization.
An exploratory factor analysis of post-concussion syndromes in Thai people after head injury: A psychometric properties study
Creators: name: Chanokporn Jitpanya
name: Kanjana Kinklaykan
name: Tanita Puengching
Publisher: name: Faculty of Medicine Chulalongkorn University
Year: 2019
Subjects: Head injury, psychometrics, post-concussion syndromes, Rivermead Post-Concussion Symptoms Questionnaire

description: Chulalongkorn Medical Journal, 63, 4, 239-244
Valley-dependent Corner States in Honeycomb Photonic Crystal without Inversion Symmetry
Creators: name: Phan, Huyen Thanh
name: Liu, Feng
name: Wakabayashi, Katsunori
Publisher: name: arXiv
Year: 2021
Subjects: subject: Optics (physics.optics)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We study topological states of honeycomb photonic crystals in absence of inversion symmetry using plane wave expansion and finite element methods. The breaking of inversion symmetry in honeycomb lattice leads to contrasting topological valley indices, i.e., the valley-dependent Chern numbers in momentum space. We find that the topological corner states appear for 60$^\circ$ degree corners, but absent for other corners, which can be understood as the sign flip of valley Chern number at the corner. Our results provide an experimentally feasible platform for exploring valley-dependent higher-order topology in photonic systems.
description: 13 pages, 6 figures
Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids
Creators: name: Loh, Yong-Hwee E
name: Katz, Lee S
name: Mims, Meryl C
name: Kocher, Thomas D
name: Yi, Soojin V
name: Streelman, J Todd
Publisher: name: Springer Nature
Year: 2008
Subjects: Additional Data File
Genetic Cluster
Joint Genome Institute
Cichlid Species
Species Flock

description: Cichlid fish from East Africa are remarkable for phenotypic and behavioral diversity on a backdrop of genomic similarity. In 2006, the Joint Genome Institute completed low coverage survey sequencing of the genomes of five phenotypically and ecologically diverse Lake Malawi species. We report a computational and comparative analysis of these data that provides insight into the mechanisms that make closely related species different from one another. We produced assemblies for the five species ranging in aggregate length from 68 to 79 megabase pairs, identified putative orthologs for more than 12,000 human genes, and predicted more than 32,000 cross-species single nucleotide polymorphisms (SNPs). Nucleotide diversity was lower than that found among laboratory strains of the zebrafish. We collected around 36,000 genotypes to validate a subset of SNPs within and among populations and across multiple individuals of about 75 Lake Malawi species. Notably, there were no fixed differences observed between focal species nor between major lineages. Roughly 3% to 5% of loci surveyed are statistical outliers for genetic differentiation (FST) within species, between species, and between major lineages. Outliers for FST are candidate genes that may have experienced a history of natural selection in the Malawi lineage. We present a novel genome sequencing strategy, which is useful when evolutionary diversity is the question of interest. Lake Malawi cichlids are phenotypically and behaviorally diverse, but they appear genetically like a subdivided population. The unique structure of Lake Malawl cichlid genomes should facilitate conceptually new experiments, employing SNPs to identity genotype-phenotype association, using the entire species flock as a mapping panel.
A simple spontaneously active Hebbian learning model: homeostasis of activity and connectivity, and consequences for learning and epileptogenesis
Creators: name: Hsu, David
name: Tang, Aonan
name: Hsu, Murielle
name: Beggs, John M.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: FOS: Biological sciences

description: A spontaneously active neural system that is capable of continual learning should also be capable of homeostasis of both firing rate and connectivity. Experimental evidence suggests that both types of homeostasis exist, and that connectivity is maintained at a state that is optimal for information transmission and storage. This state is referred to as the critical state. We present a simple stochastic computational Hebbian learning model that incorporates both firing rate and critical homeostasis, and we explore its stability and connectivity properties. We also examine the behavior of our model with a simulated seizure and with simulated acute deafferentation. We argue that a neural system that is more highly connected than the critical state (i.e., one that is "supercritical") is epileptogenic. Based on our simulations, we predict that the post-seizural and post-deafferentation states should be supercritical and epileptogenic. Furthermore, interventions that boost spontaneous activity should be protective against epileptogenesis.
description: 37 pages, 1 table, 7 figures
Indoor air microbial counts in dormitory of nursing students, Bangkok
Creators: name: Pipat Luksamijarulkul
name: Maneenut Wutthikarn
name: Poolsuk Janepanish Visudtibhan
name: Pisit Vatanasomboon
Publisher: name: Faculty of Medicine Chulalongkorn University
Year: 2019
Subjects: Indoor air, bacterial counts, fungal counts, nursing student dormitory

description: Chulalongkorn Medical Journal, 63, 4, 245-252
title: The Relation Between The Spatial Distribution Of Early Juvenile Cod (Gadus Morhua L.) And Zooplankton Biomass In The Barents Sea
Creators: name: Helle, Kristin
name: Pennington, Michael
Publisher: name: ASC 1997 - T
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.The year dass strength of Arcto-Norwegian eod (Gadus morhua L.) in the Barents Seais extrernely variable. One of the key indicators for a possible strong year dass is watertemperature since good year dasses rnay be produeed in warm years while they seIdomif ever occur in cold years. Water temperature alone is not sufficient to produce a goodyear dass.
v-RIO1 – an atypical protein kinase from the parasitic nematode Trichostrongylus vitrinus
Creators: name: Hu, Min
name: LaRonde-LeBlanc, Nicole
name: Sternberg, Paul W
name: Gasser, Robin B
Publisher: name: Springer Nature
Year: 2008
Subjects: Parasitic Nematode
Amino Acid Sequence Data
Atypical Protein Kinase
Gene M01B12
Eukaryotic Protein Kinase

description: Protein kinases are key enzymes that regulate a wide range of cellular processes, including cell-cycle progression, transcription, DNA replication and metabolic functions. These enzymes catalyse the transfer of phosphates to serine, threonine and tyrosine residues, thus playing functional roles in reversible protein phosphorylation. There are two main groups, namely eukaryotic protein kinases (ePKs) and atypical protein kinases (aPKs); RIO kinases belong to the latter group. While there is some information about RIO kinases and their roles in animals, nothing is known about them in parasites. This is the first study to characterise a RIO1 kinase from any parasite. A full-length cDNA (Tv-rio-1) encoding a RIO1 protein kinase (Tv-RIO1) was isolated from the economically important parasitic nematode Trichostrongylus vitrinus (Order Strongylida). The uninterrupted open reading frame (ORF) of 1476 nucleotides encoded a protein of 491 amino acids, containing the characteristic RIO1 motif LVHADLSEYNTL. Tv-rio-1 was transcribed at the highest level in the third-stage larva (L3), and a higher level in adult females than in males. Comparison with homologues from other organisms showed that protein Tv-RIO1 had significant homology to related proteins from a range of metazoans and plants. Amino acid sequence identity was most pronounced in the ATP-binding motif, active site and metal binding loop. Phylogenetic analyses of selected amino acid sequence data revealed Tv-RIO1 to be most closely related to the proteins in the species of Caenorhabditis. A structural model of Tv-RIO1 was constructed and compared with the published crystal structure of RIO1 of Archaeoglobus fulgidus (Af-Rio1). This study provides the first insights into the RIO1 protein kinases of nematodes, and a foundation for further investigations into the biochemical and functional roles of this molecule in biological processes in parasitic nematodes.
Association of vitamin D-related genetic variations and the susceptibility among Thai children with biliary atresia
Creators: name: Kanjaporn Sirisomboonlarp
name: Natthaya Chuaypen
name: Sittisak Honsawek
name: Palittiya Sintusek
name: Voranush Chongsrisawat
name: Pisit Tangkijvanich
Publisher: name: Faculty of Medicine Chulalongkorn University
Year: 2019
Subjects: Biliary atresia, single nucleotide polymorphism, genetic variants, vitamin D, chronic liver diseases

description: Chulalongkorn Medical Journal, 63, 4, 253-260
Probing superconductivity in MgB2 confined to magnetic field tuned cylinders by means of critical fluctuations
Creators: name: Weyeneth, S.
name: Schneider, T.
name: Zhigadlo, N. D.
name: Karpinski, J.
name: Keller, H.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report and analyze reversible magnetization measurements on a high quality MgB2 single crystal in the vicinity of the zero field transition temperature, T_c=38.83 K, at several magnetic fields up to 300 Oe, applied along the c-axis. Though MgB2 is a two gap superconductor our scaling analysis uncovers remarkable consistency with 3D-xy critical behavior, revealing that close to criticality the order parameter is a single complex scalar as in 4He. This opens up the window onto the exploration of the magnetic field induced finite size effect, whereupon the correlation length transverse to the applied magnetic field H_i applied along the i-axis cannot grow beyond the limiting magnetic length L_Hi, related to the average distance between vortex lines. We find unambiguous evidence for this finite size effect. It implies that in type II superconductors, such as MgB2, there is the 3D to 1D crossover line H_pi and xi denotes the critical amplitudes of the correlation lengths above and below T_c along the respective axis. Consequently, above H_pi(T) and T
Coordination complexes of trivalent non-transition metal ions
Creators: name: Smith, Alexis
Publisher: name: University of British Columbia
Year: 2010

description: Lathaxride(III) complexes of three potentially heptadentate Schiff base ligands were prepared by addition of lanthanide(III) salts to a solution containing a slight excess of ligand in the presence of poorly coordinating chloride ions or strongly coordinating nitrate ions. The complexes La(hatren), La(datren)(CH₃0H) and La(trac) were isolated in the presence of chloride ions, and were found to have the ligand bound in a hexadentate or heptadentate fashion. We were unable to isolate analogous complexes with the heavier lanthanides (Ln = Pr, Nd, Gd, Dy, Yb, Lu). The complexes Ln(H₃L)(NO₃)₃ (Ln = La, Pr, Nd, Gd, Dy, Yb; H₃L = H₃hatren, H₃datren) and Ln(H₃trac)(NO₃)₃ (Ln = Pr, Nd, Gd, Dy, Yb) were isolated in the presence of nitrate ions, and were found to have the Schiff base ligand bound in a tridentate fashion ( where H₃datren = tris(2'-hydroxy-4',5'-dimethylacetopheniminoethyl)amine; H₃trac = tris(3-aza-4-methylhept-4-ene-6-one)amine; and H₃hatren = tris(2'-hydroxyacetophenirninoethyl)amine) All products were characterized by infrared and mass spectroscopy, and by elemental analysis. ¹H-NMR spectroscopy indicated that the complexes were solution labile and dissociated in DMSO to yield free ligand and solvated lanthanide(III) ions. The crystal structure of Gd(H₃trac)(NO₃)₃ was determined. The gadolinium(III) ion is nine coordinate. H₃trac is bound only through its three oxygen donor atoms, and the nitrate ions are bound in a bidentate fashion to the gadolinium center. Aluminum (III) and gallium(III) complexes of 2-chloromethyl-5-hydroxy-4H-pyran-4-one (Hck) were isolated from a basic aqueous solution. The complexes Al(ck)₃ and Ga(ck)₃ were characterized by ¹H-NMR (CDCI₃), infrared and mass spectroscopy, as well as by elemental analysis. Al(ck)₃ was also characterized by ²⁷Al-NMR in CDCI₃.
Transcriptional responses to biologically relevant doses of UV-B radiation in the model archaeon, Halobacteriumsp. NRC-1
Creators: name: Boubriak, Ivan
name: Ng, Wooi Loon
name: DasSarma, Priya
name: DasSarma, Shiladitya
name: Crowley, David J
name: McCready, Shirley J
Publisher: name: Springer Nature
Year: 2008
Subjects: Transcriptional Response
Nucleotide Excision Repair
Halophilic Archaea
Cyclobutane Pyrimidine Dimer
Stall Fork

description: Most studies of the transcriptional response to UV radiation in living cells have used UV doses that are much higher than those encountered in the natural environment, and most focus on short-wave UV (UV-C) at 254 nm, a wavelength that never reaches the Earth's surface. We have studied the transcriptional response of the sunlight-tolerant model archaeon, Halobacterium sp. NRC-1, to low doses of mid-wave UV (UV-B) to assess its response to UV radiation that is likely to be more biologically relevant. Halobacterium NRC-1 cells were irradiated with UV-B at doses equivalent to 30 J/m2 and 5 J/m2 of UV-C. Transcriptional profiling showed that only 11 genes were up-regulated 1.5-fold or more by both UV-B doses. The most strongly up-regulated gene was radA1 (vng2473), the archaeal homologue of RAD51/recA recombinase. The others included arj1 (vng779) (recJ-like exonuclease), top6A (vng884) and top6B (vng885) (coding for Topoisomerase VI subunits), and nrdJ (vng1644) (which encodes a subunit of ribonucleotide reductase). We have found that four of the consistently UV-B up-regulated genes, radA1 (vng2473), vng17, top6B (vng885) and vng280, share a common 11-base pair motif in their promoter region, TTTCACTTTCA. Similar sequences were found in radA promoters in other halophilic archaea, as well as in the radA promoter of Methanospirillum hungatei. We analysed the transcriptional response of a repair-deficient ΔuvrA (vng2636) ΔuvrC (vng2381) double-deletion mutant and found common themes between it and the response in repair proficient cells. Our results show a core set of genes is consistently up-regulated after exposure to UV-B light at low, biologically relevant doses. Eleven genes were up-regulated, in wild-type cells, after two UV-B doses (comparable to UV-C doses of 30 J/m2 and 5 J/m2), and only four genes were up-regulated by all doses of UV-B and UV-C that we have used in this work and previously. These results suggest that high doses of UV-C radiation do not necessarily provide a good model for the natural response to environmental UV. We have found an 11-base pair motif upstream of the TATA box in four of the UV-B up-regulated genes and suggest that this motif is the binding site for a transcriptional regulator involved in their response to UV damage in this model archaeon.
title: A Preliminary Description Of The Heat Budget, Southern Flank Of Georges Bank, Spring-Summer, 1995
Creators: name: Beardsley, R.C.
name: Lentz, S. J.
name: Weller, R. A.
name: Irish, J. D.
name: Brink, K. H.
name: Limeburner, R.
name: Manning, J. D.
Publisher: name: ASC 1997 - T
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.This report is a Preliminary Description Of The Heat Budget, Southern Flank Of Georges Bank, Spring-Summer, 1995
PRFdb: A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals
Creators: name: Belew, Ashton T
name: Hepler, Nicholas L
name: Jacobs, Jonathan L
name: Dinman, Jonathan D
Publisher: name: Springer Nature
Year: 2008
Subjects: Minimum Free Energy
Sequence Window
Ribosomal Frameshift
Mammalian Gene Collection

description: The Programmed Ribosomal Frameshift Database (PRFdb) provides an interface to help researchers identify potential programmed -1 ribosomal frameshift (-1 PRF) signals in eukaryotic genes or sequences of interest. To identify putative -1 PRF signals, sequences are first imported from whole genomes or datasets, e.g. the yeast genome project and mammalian gene collection. They are then filtered through multiple algorithms to identify potential -1 PRF signals as defined by a heptameric slippery site followed by an mRNA pseudoknot. The significance of each candidate -1 PRF signal is evaluated by comparing the predicted thermodynamic stability (ΔG°) of the native mRNA sequence against a distribution of ΔG° values of a pool of randomized sequences derived from the original. The data have been compiled in a user-friendly, easily searchable relational database. The PRFdB enables members of the research community to determine whether genes that they are investigating contain potential -1 PRF signals, and can be used as a metasource of information for cross referencing with other databases. It is available on the web at http://dinmanlab.umd.edu/prfdb .
PageRank without hyperlinks: Reranking with PubMed related article networks for biomedical text retrieval
Creators: name: Lin, Jimmy
Publisher: name: Springer Nature
Year: 2008
Subjects: Related Article
Test Collection
Relevance Judgment
Text Retrieval
Retrieval Effectiveness

description: Graph analysis algorithms such as PageRank and HITS have been successful in Web environments because they are able to extract important inter-document relationships from manually-created hyperlinks. We consider the application of these techniques to biomedical text retrieval. In the current PubMed® search interface, a MEDLINE® citation is connected to a number of related citations, which are in turn connected to other citations. Thus, a MEDLINE record represents a node in a vast content-similarity network. This article explores the hypothesis that these networks can be exploited for text retrieval, in the same manner as hyperlink graphs on the Web. We conducted a number of reranking experiments using the TREC 2005 genomics track test collection in which scores extracted from PageRank and HITS analysis were combined with scores returned by an off-the-shelf retrieval engine. Experiments demonstrate that incorporating PageRank scores yields significant improvements in terms of standard ranked-retrieval metrics. The link structure of content-similarity networks can be exploited to improve the effectiveness of information retrieval systems. These results generalize the applicability of graph analysis algorithms to text retrieval in the biomedical domain.
Quantum control landscape for ultrafast generation of single-qubit phase shift quantum gates
Creators: name: Volkov, Boris O.
name: Morzhin, Oleg V.
name: Pechen, Alexander N.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: In this work, we consider the problem of ultrafast controlled generation of single-qubit phase shift quantum gates. Globally optimal control is a control which realizes the gate with maximal possible fidelity. Trap is a control which is optimal only locally but not globally. It was shown before that traps do not exist for controlled generation of arbitrary single-qubit quantum gates for sufficiently long times, as well as for fast control of quantum gates other than phase shift gates. Ultrafast generation of phase-shift gates was missed in the previous analysis. In this work we show, combining analytical and numerical optimization methods such as Gradient Ascent Pulse Engineering (GRAPE), differential evolution, and dual annealing, that control landscape for ultrafast generation of phase shift gates is also free of traps. Mathematical analysis of quantum control landscapes, which aims to prove either absence or existence of traps for quantum control objective functionals, is an important topic in quantum control. In this work, we provide a rigorous analysis of quantum control landscapes for ultrafast generation of single-qubit quantum gates and show, combining analytical methods based on a sophisticated analysis of spectrum of the Hessian, and numerical optimization methods such as Gradient Ascent Pulse Engineering (GRAPE), differential evolution, and dual annealing, that control landscape for ultrafast generation of phase shift gates is free of traps.
description: 23 pages, 3 figures
Optimizing Replica Exchange Moves For Molecular Dynamics
Creators: name: Nadler, Walter
name: Hansmann, Ulrich H. E.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Quantitative Methods (q-bio.QM)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Computational Physics (physics.comp-ph)
subject: Biomolecules (q-bio.BM)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: In this short note we sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations as well as new applications of the method.
description: 4 pages, 3 figures; revised version (1 figure added), PRE in press
title: Spatial Evolution Of Cod (Gadus Morhua) And Haddock (Melanogrammus Aeglefinus) Year Classes On The Scotian Shelf As Inferred From Growth Variation Of Juveniles
Creators: name: Shackell, N. L.
name: Frank, K.T.
name: Shore, J.
name: C.Hannah
name: J.Loder
Publisher: name: ASC 1997 - T
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.The structure of groundfish populations on the Scotian Shelf is known only in a general sense. While adjacentpopulations are more likely to mix, the extent of mixing is unknown. Documentation of large-scale migration ofgroundfish year classes are rare yet are inferred to be a result of egg/larval advection or post-larval dispersion.
Azimuthal correlations of forward dijets in d+Au collisions at RHIC
Creators: name: Marquet, Cyrille
Publisher: name: arXiv
Year: 2008
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Measuring correlations between forward dijets in deuteron-gold collisions at RHIC will further test the Color Glass Condensate (CGC) picture of the nuclear wavefunction at small-x, which successfully predicted the suppressed production of high-p_T particles at forward rapidities in d+Au collisions: R_dA<1. I present predictions for the correlation in azimuthal angle between forward dijets in the CGC framework, with both multiple scatterings and non-linear QCD evolution at small-x taken into account.
description: 4 pages, 1 figure, Proceedings of the 20th International Conference on Ultra-Relativistic Nucleus Nucleus Collisions (QM08), Jaipur, India, February 4-10 2008
Detection of co-eluted peptides using database search methods
Creators: name: Alves, Gelio
name: Ogurtsov, Aleksey Y
name: Kwok, Siwei
name: Wu, Wells W
name: Wang, Guanghui
name: Shen, Rong-Fong
name: Yu, Yi-Kuo
Publisher: name: Springer Nature
Year: 2008
Subjects: Receiver Operating Characteristic
Receiver Operating Characteristic Curve
Complex Protein Mixture
Compound Spectrum
Theoretical Fragment

description: Current experimental techniques, especially those applying liquid chromatography mass spectrometry, have made high-throughput proteomic studies possible. The increase in throughput however also raises concerns on the accuracy of identification or quantification. Most experimental procedures select in a given MS scan only a few relatively most intense parent ions, each to be fragmented (MS2) separately, and most other minor co-eluted peptides that have similar chromatographic retention times are ignored and their information lost. We have computationally investigated the possibility of enhancing the information retrieval during a given LC/MS experiment by selecting the two or three most intense parent ions for simultaneous fragmentation. A set of spectra is created via superimposing a number of MS2 spectra, each can be identified by all search methods tested with high confidence, to mimick the spectra of co-eluted peptides. The generated convoluted spectra were used to evaluate the capability of several database search methods – SEQUEST, Mascot, X!Tandem, OMSSA, and RAId_DbS – in identifying true peptides from superimposed spectra of co-eluted peptides. We show that using these simulated spectra, all the database search methods will gain eventually in the number of true peptides identified by using the compound spectra of co-eluted peptides. Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section.
title: U.S. Globec Long-Term Moored Program
Creators: name: D.Irish, James
name: C.Beardsley, Robert
name: H.Brink, Kenneth
name: Williams, William J.
Publisher: name: ASC 1997 - T
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.As part of the U.S. GLOBEC NW Atlantic/Georges Bank program, a long-term moored array has been deployed and maintained on Georges Bank as part of the broad scale survey component to help measure the long-term variability ofboth physical and biological characteristics on the Bank.
The photospheric environment of a solar pore with light bridge
Creators: name: Giordano, S.
name: Berrilli, F.
name: Del Moro, D.
name: Penza, V.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Pores are one of the various features forming in the photosphere by the emergence of magnetic field onto the solar surface. They lie at the border between tiny magnetic elements and larger sunspots. Light bridges, in such structures, are bright features separating umbral areas in two or more irregular regions. Commonly, light bridges indicate that a the merging of magnetic regions or, conversely, the breakup of the area is underway. We investigate the velocity structure of a solar pore (AR10812) with light bridge, and of the quiet solar photosphere nearby, analyzing high spatial and spectral resolution images. The pore area has been observed with the Interferometric BI-dimensional Spectrometer (IBIS) at the Dunn Solar Telescope, acquiring monochromatic images in the Ca II 854.2 nm line and in the Fe I 709.0 nm line as well as G-band and broad-band images. We also computed the Line of Sight (LoS) velocity field associated to the Fe I and Fe II photospheric lines. The amplitude of the LoS velocity fluctuations, inside the pore, is smaller than that observed in the quiet granulation near the active region. We computed the azimuthal average LoS velocity and derived its radial profile. The whole pore is characterized by a downward velocity -200 m/s and by an annular downflow structure with an average velocity of -350 m/s with respect to the nearby quiet sun. The light bridge inside the pore, when observed in the broad-band channel of IBIS and in the red wing of Ca II 854.2 nm line, shows an elongated dark structure running along its axis, that we explain with a semi-analytical model. In the highest resolution LoS velocity images the light bridge shows a profile consistent with a convective roll: a weak upflow, 50-100m/s, in correspondence of the dark lane, flanked by a downflow, -(200-300) m/s.
description: 7 pages, 10 figures
Assessing Dialogue Systems with Distribution Distances
Creators: name: Xiang, Jiannan
name: Liu, Yahui
name: Cai, Deng
name: Li, Huayang
name: Lian, Defu
name: Liu, Lemao
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: An important aspect of developing dialogue systems is how to evaluate and compare the performance of different systems. Existing automatic evaluation metrics are based on turn-level quality evaluation and use average scores for system-level comparison. In this paper, we propose to measure the performance of a dialogue system by computing the distribution-wise distance between its generated conversations and real-world conversations. Specifically, two distribution-wise metrics, FBD and PRD, are developed and evaluated. Experiments on several dialogue corpora show that our proposed metrics correlate better with human judgments than existing metrics.
description: 7 pages, 2 figures