cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Grooving Pavement Centerlines for Lane Demarcation
Creators: name: Hughes, Ronald D.
name: Garner, Gordon R.
Publisher: name: Kentucky Transportation Center, University of Kentucky
Year: 1969
Subjects: subject: Transportation Engineering

description: Lane demarcation is conventionally accomplished by use of white traffic paint placed as a skip line. Most traffic paints are beaded by premixing glass beads in the paint, by drop-on applications, or a combination of the two. The retrodirective properties of the beads greatly enhance nighttime visibility during dry weather; however, visibility of the lines is practically nil during wet nighttime driving. Submerged beads cannot redirect the light when the need for guidance is mosL critical. Thermoplastic striping materials have been used to varying degrees of success by numerous agencies. Wet nighttime visibility of thermoplastics, as experienced in Kentucky, is generally far superior to that of conventional beaded paints. Thermoplastics are placed at a thickness of 125 mils and are thereby less likely to become submerged than conventional paints, which are placed at film thicknesses in the order of 14 mils and dry to approzimately 8 mils.  Late in 1965, the California Division of Highways reportedly issued a policy requiring the use of raised pavement markers as a replacement for most painted lines on future freeways and conventional highways. Other agencies have employed raised markers in various forms and have reported excellent to good wet nighttime visibility for markers remaining in place. Major disadvantages of the thermoplastics and raised markers are:      they are quite expensive as compared to paint,     they break or crack under traffic, and     the present loss is high as a result of traffic and snow removal equipment.  In addition, the raised markers are rather difficult to install.  Christensen Diamond Services, Inc. of Salt Lake City, Utah, reportedly introduced the concept of grooving centerlines in an attempt to provide a rumble effect for alerting drivers straying outside their traffic lanes. It was later observed that the painted grooves were more visible at night during wet weather than were normal paint stripes. The concept of grooving and painting centerlines was thus promoted, and, as a result, several test sections were placed on Nebraska highways in the summer of 1968. In order to evaluate the effectiveness of grooving the centerline prior to striping, a section uf newly constructed pavement of I 71 in Carroll County, Kentucky, was chosen for an experimental installation. This interim report covers installation of the grooves and a preliminary evaluation of their value to date.
AJAE Appendix: Estimating Policy Effects on Spatial Market Efficiency: An Extension to the Parity Bounds Model
Creators: name: Muleta, Asfaw Negassa
name: Myers, Robert J.
name: Muleta, Asfaw Negassa
name: Myers, Robert J.
Publisher: name: Unknown
Year: 2007
Subjects: subject: Marketing
subject: FOS: Economics and business

description: The material contained herein is supplementary to the article named in the title and published in the American Journal of Agricultural Economics, May 2007, Volume 89, Issue 2.
MEDICAL DIAGNOSTICS BY MICROSTRUCTURAL ANALYSIS OF BIOLOGICAL LIQUID DRIED PATTERNS AS A PROBLEM OF BIOINFORMATICS
Creators: name: Lebedev-Stepanov, Peter
name: Buzoverya, Marina
name: Shishpor, Irina
name: Vlasov, Konstantin
name: Potekhina, Yulia
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2018

description: Motivation: It is important to develop high-precision computerized methods for quick medical diagnostics based on the unique clinical experience obtained within the past decade. This method provides specialized solutions for diagnostics and the monitoring of specific diseases, identifies reserves of human health, and takes actions to prevent the depletion of these reserves. In this paper we present one of the new directions in bioinformatics, i.e. medical diagnostics by means of an automated expert system on the basis of morphology analysis of digital images of biological liquid dried pattern. Results: The proposed method is a combination of bioinformatics and biochemistry approaches for obtaining diagnostic information from a morphological analysis of standardized dried patterns of biological liquid sessile drop. We conducted our own research in collaboration with medical diagnostic centers and formed an electronic database for the recognition of the following types of diseases: neoplasms; diabetes mellitus; diseases of the circulatory system; cerebrovascular disease; diseases of the digestive system; diseases of the genitourinary system; infectious diseases; factors relevant to the work; factors associated with environmental pollution; factors related to lifestyle. The laboratory instrument for diagnostics of the human body in pathology states has developed and the diagnostic results have been analyzed. Availability: Access to the testing of software can be obtained upon request via the contact email below.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (6) (2018)
AJAE Appendix: The Use of Conditional Cost Functions to Generate Estimable Mixed Demand Systems
Creators: name: Wong, Gary
name: Park, Hoanjae
name: Wong, Gary
name: Park, Hoanjae
Publisher: name: Unknown
Year: 2007
Subjects: Demand and Price Analysis

description: The material contained herein is supplementary to the article named in the title and published in the American Journal of Agricultural Economics, May 2007, Volume 89, Issue 2.
DISTANT JOINING: A SEQUENCE SAMPLING METHOD FOR COMPLEX PHYLOGENIES
Creators: name: Morozov, Alexey
name: Galachyants, Yuri
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2017

description: Motivation: Massive parallel phylogenetic analyses allow to reconstruct phylogenetic trees for every gene in genome, typically using a set of potential homologues detected by similarity search against reference databases via BLAST or BLAST-like algorithms. However, given that the amount of similarity hits between query sequence and targets is often too high, it may be necessary to reduce number of sequences for downstream pelogenetic analyses.. Currently available automatic and semi-automatic methods for dataset reduction are error-prone and may depend on additional metadata, whereas reduction “by hand” is labour-intensive and becomes intractable once phylogenetic analysis of multiple genes is to be performed. Results: We propose a distance-based algorithm, termed Distant Joining, for phylogenetic dataset reduction that does not require additional input except sequences analyzed. DJ was shown to robustly subsample a set of sequences with minimal loss of dataset divergence from large and complex sequence data sets. In the context of out study, the underlying assumptions and limitations of different subsampling approaches are discussed, and directions for selection of the subsampling method to build phylogenomic pipelines are provided. Availability: Proof-of-concept Python implementation is available at https://github.com/SynedraAcus/sampler under the terms of CC-BY-4.0 license. Supplementary information: Supplementary data are available at Journal of Bioinformatics and Genomics online.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 3 (5) (2017)
Realization of a deterministic quantum Toffoli gate with a single photon
Creators: name: Ru, Shihao
name: Wang, Yunlong
name: An, Min
name: Wang, Feiran
name: Zhang, Pei
name: Li, Fuli
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum controlled-logic gates, including controlled NOT gate and Toffoli gate, play critical roles in lots of quantum information processing schemes. We design and experimentally demonstrate deterministic Toffoli gate by utilizing orbital-angular-momentum and polarization degrees of freedom of a single photon. In addition, we generate Bell states by using the controlled NOT gate. The effective conversion rate of the Toffoli gate in our experiment is $(95.1\pm3.2)\%$. Furthermore, our experimental setup does not require any auxiliary photons and probabilistic post selections.
description: 6 pages, 5 figures, 2tables
AJAE Appendix: Contract Enforcement, Social Efficiency, and Distribution: Some Experimental Evidence
Creators: name: Wu, Steven Y.
name: Roe, Brian E.
name: Wu, Steven Y.
name: Roe, Brian E.
Publisher: name: Unknown
Year: 2007
Subjects: subject: Marketing
subject: FOS: Economics and business

description: The material contained herein is supplementary to the article named in the title and published in the American Journal of Agricultural Economics, May 2007, Volume 89, Issue 2.
Det lykkelige Barn ved Opdragelsen, eller en Afhandling om Opdragelsen, fra et Barns Fødsel til den modne Alder : indeholdende fornemmelig hvad Foreldre og Lærere have at iagttage ved samme
Creators: name: Scheffer, Frederik Christian
Publisher: name: Trykt paa Kanneworffs Bekostning, som Forlegger
Year: 0

description: Utgitt anonymt. Skrevet av Frederik Christian Scheffer
AJAE Appendix: Brand-Supermarket Demand for Breakfast Cereals and Retail Competition
Creators: name: Chidmi, Benaissa
name: Lopez, Rigoberto A.
name: Chidmi, Benaissa
name: Lopez, Rigoberto A.
Publisher: name: Unknown
Year: 2007
Subjects: Demand and Price Analysis

description: The material contained herein is supplementary to the article named in the title and published in the American Journal of Agricultural Economics, May 2007, Volume 89, Issue 2.
BIOINFORMATICS MODEL OF THE CARAPACE SCUTE PATTERN OF THE RED-EARED SLIDER TRACHEMYS SCRIPTA ELEGANS (WIED-NEUWIED, 1839)
Creators: name: Kiladze, Andrei
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2017

description: The scutes located on the carapace of the red-eared slider Trachemys scripta elegans (Wied-Neuwied, 1839) have been modeled. Bioinformatics modeling of carapace’s scutes were carried out by utilizing the Voronoi decomposition and Delaunay triangulation method. These two geometric techniques allow the patterns of vertebral and costal scutes to be recreated. The proposed model may have a certain value for taxonomy as well as for estimating the symmetry of the morphological structures, which is important for the purposes of biomimetics.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 3 (5) (2017)
Spinless Fermionic ladders in a magnetic field: Phase Diagram
Creators: name: Carr, Sam T.
name: Narozhny, Boris N.
name: Nersesyan, Alexander A.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The system of interacting spinless fermions hopping on a two-leg ladder exhibits a series of quantum phase transitions when subjected to an external magnetic field. At half filling, these are either U(1) Gaussian phase transitions between two phases with distinct types of long-range order or Berezinskii-Kosterlitz-Thouless transitions between ordered and gapless phases.
description: 16 pages, 6 figures
AJAE Appendix: Is There Persistence in the Impact of Emergency Food Aid? Evidence on Consumption, Food Security and Assets in Rural Ethiopia
Creators: name: Gilligan, Daniel O.
name: Hoddinott, John
name: Gilligan, Daniel O.
name: Hoddinott, John
Publisher: name: Unknown
Year: 2007
Subjects: Food Security and Poverty

description: The material contained herein is supplementary to the article named in the title and published in the American Journal of Agricultural Economics, May 2007, Volume 89, Issue 2.
A transport approach to relate asymmetric protein segregation and population growth
Creators: name: Min, Jiseon
name: Amir, Ariel
Publisher: name: arXiv
Year: 2020
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: Many unicellular organisms allocate their key proteins asymmetrically between the mother and daughter cells, especially in a stressed environment. A recent theoretical model is able to predict when the asymmetry in segregation of key proteins enhances the population fitness, extrapolating the solution at two limits where the segregation is perfectly asymmetric (asymmetry $a$ = 1) and when the asymmetry is small ($0 \leq a \ll 1$). We generalize the model by introducing stochasticity and use a transport equation to obtain a self-consistent equation for the population growth rate and the distribution of the amount of key proteins. We provide two ways of solving the self-consistent equation: numerically by updating the solution for the self-consistent equation iteratively and analytically by expanding moments of the distribution. With these more powerful tools, we can extend the previous model by Lin et al. to include stochasticity to the segregation asymmetry. We show the stochastic model is equivalent to the deterministic one with a modified effective asymmetry parameter ($a_{\rm eff}$). We discuss the biological implication of our models and compare with other theoretical models.
description: 21 pages, 11 figures, submitted to JStat
title: Endivia :
title: Directrices para la ejecución del examen de la distinción, la homogeneidad y la estabilidad.
titleType: Subtitle
Creators: name: International Union For The Protection Of New Varieties Of Plants,
Publisher: name: International Union for the Protection of New Varieties of Plants,
Year: 0
Subjects: Witloof Chicory
Group identity.
New Varieties of Plants

description: La finalidad de estas directrices (“directrices de examen”) es elaborar los principios que figuran en la Introducción General (documento TG/1/3) y sus documentos TGP conexos, con objeto de que sirvan de orientación práctica y detallada para el examen armonizado de la distinción, homogeneidad y estabilidad (DHE) y en particular, para identificar los caracteres apropiados para el examen DHE y producir descripciones armonizadas de variedades.
Green's relations on the deformed transformation semigroups
Creators: name: Tsyaputa, G. Y.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Rings and Algebras (math.RA)
subject: Group Theory (math.GR)
subject: FOS: Mathematics
subject: 20M20

description: Green's relations on the deformed finite inverse symmetric semigroup $\mathcal{IS}_n$ and the deformed finite symmetric semigroup $\mathcal{T}_n$ are described.
description: 11 pages
AJAE Appendix: Asset Pricing in Created Markets
Creators: name: Newell, Richard G.
name: Papps, Kerry L.
name: Sanchirico, James N.
name: Newell, Richard G.
name: Papps, Kerry L.
name: Sanchirico, James N.
Publisher: name: Unknown
Year: 2007
Subjects: subject: Marketing
subject: FOS: Economics and business

description: The material contained herein is supplementary to the article named in the title and published in the American Journal of Agricultural Economics, May 2007, Volume 89, Issue 2.
TAXONDC: CALCULATING THE SIMILARITY VALUE OF THE 16S RRNA GENE SEQUENCES OF PROKARYOTES OR ITS REGIONS OF FUNGI
Creators: name: Tarlachkov, Sergey
name: Starodumova, Irina
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2017

description: The TaxonDC program (Taxon Distance Calculator) performs pairwise sequence alignment followed by determining the similarity value between two or more sequences of interest. Unlike widely used programs, TaxonDC makes only pairwise alignment of input sequences that allows avoiding different similarity values depending on the sequences included in the analysis. The similarity values calculated with TaxonDC are the same compared to those calculated using popular identification oriented web-based tool EzBioCloud that makes calculated values comparable with previous ones. In addition, to help prevent discrepancy among different researchers, the problem concerning the influence of an order of the input of analyzed sequences on similarity values is specially considered. To our knowledge, TaxonDC is the only software which includes these capabilities in combination, simplifies and widens calculation of similarity values in systematics of prokaryotes and eukaryotes. The program has easy-to-use interface and can be run on Windows and Linux. Availability and Implementation: The program is available free of charge at https://tarlachkov.ru/en/software/taxondc. Supplementary information: Supplementary data are available at Journal of Bioinformatics and Genomics online.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 3 (5) (2017)
Quantum Computing for Atomic and Molecular Resonances
Creators: name: Bian, Teng
name: Kais, Sabre
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The complex-scaling method can be used to calculate molecular resonances within the Born-Oppenheimer approximation, assuming the electronic coordinates are dilated independently of the nuclear coordinates. With this method, one will calculate the complex energy of a non-Hermitian Hamiltonian, whose real part is associated with the resonance position and the imaginary part is the inverse of the lifetime. In this study, we propose techniques to simulate resonances on a quantum computer. First, we transformed the scaled molecular Hamiltonian to second-quantization and then used the Jordan-Wigner transformation to transform the scaled Hamiltonian to the qubit space. To obtain the complex eigenvalues, we introduce the Direct Measurement method, which is applied to obtain the resonances of a simple one-dimensional model potential that exhibits pre-dissociating resonances analogous to those found in diatomic molecules. Finally, we applied the method to simulate the resonances of the H$_2^-$ molecule. Numerical results from the IBM Qiskit simulators and IBM quantum computers verify our techniques.
description: To be published in J. Chem. Phys. 2021
SIGNIFICANCE OF TARGETED EXOME SEQUENCING AND METHODS OF DATA ANALYSIS IN THE DIAGNOSIS OF GENETIC DISORDERS LEADING TO THE DEVELOPMENT OF EPILEPTIC ENCEPHALOPATHY
Creators: name: Kozhanova, Tatiana
name: Zhilina, Svetlana
name: Mescheryakova, Tatiana
name: Ananieva, Tatiana
name: Luk`Yanova, Evgeniya
name: Prokop`Eva, Natalia
name: Osipova, Karine
name: Aivazyan, Sergrei
name: Kanivets, Ilia
name: Konovalov, Fyodor
name: Tolmacheva, Ekaterina
name: Prityko, Andrei
name: Bruhanova, Natalia
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2017

description: Epilepsy is the most common serious neurological disorder, and there is a genetic basis in almost 50% of people with epilepsy. The diagnosis of genetic epilepsies makes to estimate reasons of seizures in the patient. Last decade has shown tremendous growth in gene sequencing technologies, which have made genetic tests available. The aim is to show significance of targeted exome sequencing and methods of data analysis in the diagnosis of hereditary syndromes leading to the development of epileptic encephalopathy. We examined 27 patients with с early EE (resistant to antiepileptic drugs), psychomotor and speech development delay in the psycho-neurological department. Targeted exome sequencing was performed for patients without a previously identified molecular diagnosis using 454 Sequencing GS Junior sequencer (Roche) and IlluminaNextSeq 500 platform. As a result of the analysis, specific epilepsy genetic variants were diagnosed in 27 patients. The greatest number of cases was due to mutations in the SCN1A gene (7/27). The structure of mutations for other genes (mutations with a minor allele frequency of less than 0,5% are presented): ALDH7A1 (n=1), CACNA1C (n=1), CDKL5 (n=1), CNTNAP2 (n=2), DLGAP2 (n=2), DOCK7 (n=2), GRIN2B (n=2), HCN1 (n=1), NRXN1 (n=3), PCDH19 (n=1), RNASEH2B (n=2), SLC2A1 (n=1), UBE3A (n=1). The use of the exome sequencing in the genetic practice allows to significantly improve the effectiveness of medical genetic counseling, as it made possible to diagnose certain variants of genetically heterogeneous groups of diseases with similar of clinical manifestations.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 2 (4) (2017)
Determination of the parton distribution functions of the proton from ATLAS measurements of differential $W^\pm$ and $Z$ boson production in association with jets
Creators: name: ATLAS Collaboration
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: This article presents a new set of proton parton distribution functions, ATLASepWZVjet20, produced in an analysis at next-to-next-to-leading order in QCD. The new data sets considered are the measurements of $W^+$ and $W^-$ boson and $Z$ boson production in association with jets in $pp$ collisions at $\sqrt{s} = 8~\mathrm{TeV}$ performed by the ATLAS experiment at the LHC with integrated luminosities of $20.2~\mathrm{fb}^{-1}$ and $19.9~\mathrm{fb}^{-1}$, respectively. The analysis also considers the ATLAS measurements of differential $W^{\pm}$ and $Z$ boson production at $\sqrt{s} = 7~\mathrm{TeV}$ with an integrated luminosity of $4.6~\mathrm{fb}^{-1}$ and deep-inelastic-scattering data from $e^{\pm}p$ collisions at the HERA accelerator. An improved determination of the sea-quark densities at high Bjorken $x$ is shown, while confirming a strange-quark density similar in size to the up- and down-sea-quark densities in the range $x \lesssim 0.02$ found by previous ATLAS analyses.
description: 43 pages in total, author list starts page 28, 11 figures, 4 tables. Published in JHEP. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2019-18
Dilaton Deformations in Closed String Field Theory
Creators: name: Yang, Haitang
name: Zwiebach, Barton
Publisher: name: arXiv
Year: 2005
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The dilaton theorem implies that the contribution to the dilaton potential from cubic interactions of all levels must be cancelled by the elementary quartic self-coupling of dilatons. We use this expectation to test the quartic structure of closed string field theory and to study the rules for level expansion. We explain how to use the results of Moeller to compute quartic interactions of states that, just like the dilaton, are neither primary nor have a simple ghost dependence. Our analysis of cancellations is made richer by discussing simultaneous dilaton and marginal deformations. We find evidence for two facts: as the level is increased quartic interactions become suppressed and closed string field theory may be able to describe arbitrarily large dilaton deformations.
description: 32 pages, 3 figures, LaTeX. v2: Two typos corrected in equation (3.15) and above eqution (2.19). A line added above equation (5.3). v3: a mistake in equation (3.20) corrected
AN IN-SILICO PERSPECTIVE TOWARDS TARGET ABILITY OF AVAILABLE DRUGS IN INFECTIOUS DISEASE TREATMENT: A POSSIBLE STRATEGY
Creators: name: Sarkar, Ram Rup
name: Bhowmick, Rupa
name: Sinha, Noopur
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2017

description: Motivation: In early stage of therapeutics, several structure and ligand-based in-silico approaches have aided the modern drug discovery and design. However, such techniques are limited by availability of resolved 3D structures of targets and ligands. At the same time the growing concern of drug resistivity not only demands for new drugs but also the judicious use of presently available drugs. In such a scenario, the utilization of the already available drugs of a target molecule over the different homologous target of wider range of organisms is the better perspective for treatment. This requires confirmation of structural similarity of the targets (enzyme and protein targets) in those organisms. Results: In the present study, based on the structural similarity of the target enzymes shared by different pathogenic micro-organisms, we have reviewed to gain an in-silico perspective of their efficacy in targeting a wider subset of organisms with few available drugs marketed for those. The results suggest efficient binding affinity of such drugs for the enzymes of organisms belonging to the cluster formed on the basis of structurally similarity. Implementation: Such an approach can be adopted to utilize the presently available drugs for a wider range of pathogenic micro-organisms. Supplementary Information: http://journal-biogen.org/article/view/58/25
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 2 (4) (2017)
Machine Knowledge: Creation and Curation of Comprehensive Knowledge Bases
Creators: name: Weikum, Gerhard
name: Dong, Luna
name: Razniewski, Simon
name: Suchanek, Fabian
Publisher: name: arXiv
Year: 2020
Subjects: subject: Artificial Intelligence (cs.AI)
subject: Databases (cs.DB)
subject: FOS: Computer and information sciences

description: Equipping machines with comprehensive knowledge of the world's entities and their relationships has been a long-standing goal of AI. Over the last decade, large-scale knowledge bases, also known as knowledge graphs, have been automatically constructed from web contents and text sources, and have become a key asset for search engines. This machine knowledge can be harnessed to semantically interpret textual phrases in news, social media and web tables, and contributes to question answering, natural language processing and data analytics. This article surveys fundamental concepts and practical methods for creating and curating large knowledge bases. It covers models and methods for discovering and canonicalizing entities and their semantic types and organizing them into clean taxonomies. On top of this, the article discusses the automatic extraction of entity-centric properties. To support the long-term life-cycle and the quality assurance of machine knowledge, the article presents methods for constructing open schemas and for knowledge curation. Case studies on academic projects and industrial knowledge graphs complement the survey of concepts and methods.
description: Submitted to Foundations and Trends in Databases
Noncommutative correction to the entropy of Schwarzschild black hole with GUP
Creators: name: Anacleto, M. A.
name: Brito, F. A.
name: Cruz, S. S.
name: Passos, E.
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: In this paper we study through tunneling formalism, the effect of noncommutativity to Hawking radiation and the entropy of the noncommutative Schwarzschild black hole. In our model we have considered the noncommutativity implemented via the Lorentzian distribution. We obtain non-commutative corrections to the Hawking temperature using the Hamilton-Jacobi method and the Wentzel-Kramers-Brillouin (WKB) approximation. In addition, we found corrections of the logarithmic and other types due to noncommutativity and quantum corrections from the generalized uncertainty principle (GUP) for the entropy of the Schwarzschild black hole.
description: 7 pages, no figure, version published in IJMPA
De Sitter space-times in Entangled Relativity
Creators: name: Minazzoli, Olivier
Publisher: name: arXiv
Year: 2020
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: It is argued that de Sitter space-times might be solutions of entangled relativity once the quantum trace anomaly from matter fields in curved space-times is taken into account. This hypothesis would be an elegant solution to the acceleration of the expansion of the universe within the rigid framework of entangled relativity.
description: 9 pages, no figure
CELNETANALYZER: HIGH-PERFORMANCE JAVA PACKAGE FOR THE TOPOLOGICAL ANALYSIS OF CELLULAR NETWORKS
Creators: name: Grinev, Vasily
name: Kushal, Dmitry
name: Charapovich, Vitaly
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2017

description: Summary: A simple-to-use Java-based software package CelNetAnalyzer was developed. CelNetAnalyzer is managed through a graphical user interface and it returns a comprehensive list of the topological indices including compositional complexity, degree and neighbourhood, clustering, distance, centrality and heterogeneity indices as well as simple cycles and Shannon information entropy of undirected networks. Comparative studies have shown that due to parallelization and use of enhanced and newly developed algorithms, CelNetAnalyzer calculates these parameters significantly faster than competitors. Availability and Implementation: CelNetAnalyzer is an open-source project and free distributed for non-commercial use. Software package, source code, test network and the results of the topological analysis can be downloaded from website of the Department of Genetics at Belarusian State University (http://bio.bsu.by/genetics/grinev_software.html). Supplementary information: Supplementary data are available at Journal of Bioinformatics and Genomics online.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (3) (2017)
Stability, Gain, and Robustness in Quantum Feedback Networks
Creators: name: D'Helon, C.
name: James, M. R.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: This paper concerns the problem of stability for quantum feedback networks. We demonstrate in the context of quantum optics how stability of quantum feedback networks can be guaranteed using only simple gain inequalities for network components and algebraic relationships determined by the network. Quantum feedback networks are shown to be stable if the loop gain is less than one-this is an extension of the famous small gain theorem of classical control theory. We illustrate the simplicity and power of the small gain approach with applications to important problems of robust stability and robust stabilization.
description: 16 pages
A NOVEL ROLLING BASED DNA CRYPTOGRAPHY
Creators: name: Saha, Roni
name: Haque, Rejwana
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2017

description: DNA Cryptography can be defined as a hiding data in terms of DNA Sequence. In this paper we propose a new DNA Encryption Technique where three different types of ordering is use to make binary data into cipher text. The main stages of this encryption technique are: Key Analysis, Data and Key Arrangement, Roll in encoding, Secondary Arrangement and Shifting. Decryption process has six main steps to obtain the original binary data from the encrypted data and key. Decryption steps are: Key Analysis, Shifting, Secondary Arrangement, Key Arrangement, Roll-out decoding, Data Arrangement. Here key size is half of binary data and the key varies from data to data so key is used as one time pad. In this paper we also discuss the implementation from sample data and security analysis for this given method. Motivation: Most of the existing methods use static representation of DNA base to convert binary to DNA sequence but here we avoid this step but finally we are able to convert them into DNA sequence. In our proposed method DNA base do not contain static value. It makes it harder to decipher the encrypted data. For most of the existing method security totally depends on key. Sometimes almost same key can reveal a part of real data. Here we worked with the frequency of DNA base of the key so here 1% bit mismatch can produce totally different result so data does not reveal. So security depends on its frequency as well. Results: In the algorithm change of a single base of key can affect on whole data so even 99.99% matched key can’t reveal any part of the original data. Besides that, this algorithm produce comparatively smaller encrypted data and every bit of encrypted data contains dynamic value so it is harder to break. Availability: We used Matlab-V2015(a) for simulation of the algorithm.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (3) (2017)
APPLICATIONS OF SOME NEW TRANSMUTED CUMULATIVE DISTRIBUTION FUNCTIONS IN POPULATION DYNAMICS
Creators: name: Iliev, Anton
name: Kyurkchiev, Vesselin
name: Kyurkchiev, Nikolay
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2017

description: Motivation: In literature, several transformations exists to obtain a new cumulative distribution function (cdf) using other(s) well-known cdf(s). Results: In this note we find applications of some new cumulative distribution function transformations to construct a family of sigmoidal functions based on the Verhulst logistic function. We prove estimates for the Hausdorff approximation of the shifted Heaviside step function by means of this family. Numerical examples, illustrating our results are given.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (3) (2017)
Comparative Planetary Atmospheres: Models of TrES-1 and HD209458b
Creators: name: Fortney, J. J.
name: Marley, M. S.
name: Lodders, K.
name: Saumon, D.
name: Freedman, R.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present new self-consistent atmosphere models for transiting planets TrES-1 and HD209458b. The planets were recently observed with the Spitzer Space Telescope in bands centered on 4.5 and 8.0 $μ$m, for TrES-1, and 24 $μ$m, for HD209458b. We find that standard solar metallicity models fit the observations for HD209458b. For TrES-1, which has an T_eff ~300 K cooler, we find that models with a metallicity 3-5 times enhanced over solar abundances can match the 1$σ$ error bar at 4.5 $μ$m and 2$σ$ at 8.0$μ$m. Models with solar abundances that included energy deposition into the stratosphere give fluxes that fall within the 2$σ$ error bars in both bands. The best-fit models for both planets assume that reradiation of absorbed stellar flux occurs over the entire planet. For all models of both planets we predict planet/star flux ratios in other Spitzer bandpasses.
description: Accepted to the Astrophysical Journal Letters, May 17, 2005
ZERO-INFLATED NEGATIVE BINOMIAL REGRESSION FOR DIFFERENTIAL ABUNDANCE TESTING IN MICROBIOME STUDIES
Creators: name: Zhang, Xinyan
name: Mallick, Himel
name: Yi, Nengjun
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2016

description: Motivation: The human microbiome plays an important role in human health and disease. The composition of the human microbiome is influenced by multiple factors and understanding these factors is critical to elucidate the role of the microbiome in health and disease and for development of new diagnostics or therapeutic targets based on the microbiome. 16S ribosomal RNA (rRNA) gene targeted amplicon sequencing is a commonly used approach to determine the taxonomic composition of the bacterial community. Operational taxonomic units (OTUs) are clustered based on generated sequence reads and used to determine whether and how the abundance of microbiome is correlated with some characteristics of the samples, such as health/disease status, smoking status, or dietary habit. However, OTU count data is not only overdispersed but also contains an excess number of zero counts due to undersampling. Efficient analytical tools are therefore needed for downstream statistical analysis which can simultaneously account for overdispersion and sparsity in microbiome data.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 2 (2) (2016)
Institutionalization of economic neoliberalism in the international system with emphasis on international agreements on trade and finance
Creators: name: Salgado Garza, Enrique
Publisher: name: University of British Columbia
Year: 2009

description: This thesis is a description and analysis of the inclusion of neoliberal norms in international rules and practices. Neoliberalism is a normative framework composed of norms for economic liberalization, privatization, and monetarism. Particular emphasis is made on the institutionalization of neoliberal norms in international agreements on trade and finance. The method of investigation is documentary research and analysis. The general conclusions are that (a) since 1971 neoliberalism has been institutionalized in the international system; (b) the norms of economic neoliberalism are prescribed in several international agreements on trade and finance; and (c) the institutionalization of economic neoliberalism in the international system has considerable implications for international politics.
Vortex and translational currents due to broken time-space symmetries
Creators: name: Denisov, S.
name: Zolotaryuk, Y.
name: Flach, S.
name: Yevtushenko, O.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We consider the classical dynamics of a particle in a $d=2,3$-dimensional space-periodic potential under the influence of time-periodic external fields with zero mean. We perform a general time-space symmetry analysis and identify conditions, when the particle will generate a nonzero averaged translational and vortex currents. We perform computational studies of the equations of motion and of corresponding Fokker-Planck equations, which confirm the symmetry predictions. We address the experimentally important issue of current control. Cold atoms in optical potentials and magnetic traps are among possible candidates to observe these findings experimentally.
description: 4 pages, 2 figures
title: Erinnerungen an Ferdinand Freiligrath und Gottfried Kinkel
title: beim Besuche des Dichterheimes im Freiligrath-Meloshause
titleType: Subtitle
Creators: name: Kellermann
Publisher: name: [Verlag nicht ermittelbar]
Year: 1906
Subjects: subject: 920 Biografien, Genealogie, Insignien
subject: Nachruf
subject: Weimar
subject: Freiligrath, Ferdinand
subject: Kinkel, Gottfried
subject: Zürich

description: In: Weimarische Neueste Nachrichten, 1906, 4, 1
DNA STRUCTURE, REPLICATION AND GENOME VARIABILITY CORRELATION
Creators: name: Shabalkin, Igor
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2016

description: The study of special features of a new molecular DNA structure synthesis based on the fact that monomers transpositions can occur in the backbone of polymer chains according to the mathematical law known as a Fibonacci numerical series and «the Golden ratio» was performed. The example of the formation of a new DNA model demonstrates that there are dimers of three types in DNA structure: • Dimers with phosphodiester bond P-O-C, [(s-p) + (s-p)]; [(p-s)+(p-s)]; • Dimers with phosphatic bond P-O-P, [(s-p) + (p-s)]; • Dimers with glycosidic bond C-O-C, [(p-s)+(s-p)]. Dimers of the [(s-p) + (p-s)] type are of special importance for the process of replication. For example, if an enzyme catalyst (DNA polymerase) interacts in the backbone of matrix thread with a dimer of [(s-p) + (p-s)] type during the replication process it leads to a thread break. The growth of the daughter thread does not occur until the enzyme catalyst finds the transition point to another matrix thread of DNA, which contains in its backbone monomers similar to those, necessary for the activity of the given DNA polymerase. Thus, during the process of replication the genetic material is redistributed in the cell, and each daughter thread gets the information about genes belonging to both matrix threads of DNA molecule. This pattern of cell genome changing may manifest itself in phenotype or genotype of the body in different ways.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (1) (2016)
Combinatorics of renormalization as matrix calculus
Creators: name: Ebrahimi-Fard, K.
name: Gracia-Bondia, J. M.
name: Guo, L.
name: Varilly, J. C.
Publisher: name: arXiv
Year: 2005
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We give a simple presentation of the combinatorics of renormalization in perturbative quantum field theory in terms of triangular matrices. The prescription, that may be of calculational value, is derived from first principles, to wit, the ``Birkhoff decomposition'' in the Hopf-algebraic description of renormalization by Connes and Kreimer.
description: 10 pages, revised version, typos corrected, to appear in Phys. Lett. B
MOLECULAR TAXONOMY AND THE EVOLUTION THEORY IN LIGHT OF EMERGING BIOINFORMATIC AND COSMOLOGICAL DATA
Creators: name: Shchyogolev, Sergei
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2016

description: A brief review is given of recent advances in the taxonomic study of organisms and current views on biological evolution and the origin of life. A discussion is presented on how the treelike and net components contribute to the topology of phylogenetic constructs, with account taken of the prevailing role of horizontal gene transfer in prokaryote evolution and life. Approaches are described to the rational selection and practical use of phylogenetic markers (including 16S rRNA gene DNA sequences) in biomedical (including metagenomic) applications with traditional and nontraditional (large) amounts of molecular genetic data. Emerging results from taxonomic studies of the Earth’s biota and the methods of their generation are demonstrated. It is noted that the current developments in particle physics and in cosmology have important implications for solving paradoxes associated with the vanishingly small probability of some fundamental processes of prebiological and biological evolution.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (1) (2016)
Phase transition and Quasinormal modes for Charged black holes in 4D Einstein-Gauss-Bonnet gravity
Creators: name: Zhang, Ming
name: Zhang, Chao-Ming
name: Zou, De-Cheng
name: Yue, Rui-Hong
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this paper, we study the quasinormal modes(QNMs) of massless scalar perturbations to probe the Van der Waals like small and large black holes(SBH/LBH) phase transition of (charged) AdS black holes in the 4-dimensional Einstein Gauss-Bonnet gravity. We find that the signature of this SBH/LBH phase transition in the isobaric process can be detected since the slopes of the QNMs frequencies change drastically different in small and large black holes near the critical point. The obtained results further support that the QNMs can be a dynamic probe of the thermodynamic properties in black holes.
Yang--Mills Monopoles in Extremal Reissner--Nordström Black Hole Metric
Creators: name: Zhang, Xiangqin
name: Yang, Yisong
Publisher: name: arXiv
Year: 2020
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 34B40, 35J50, 81T13, 83C57

description: We show that the closed-form monotone solution linking two different vacuum states, for the exterior Yang--Mills wave equation over the extremal Reissner--Nordström spacetime found in a recent work of Bizoń and Kahl, is the unique solution to an associated domain-wall type energy minimization problem. We also derive the accompanying interior Yang--Mills wave equation within the same formalism. We obtain a few more closed-form solutions, regular and singular, among other solutions of oscillatory behavior, and discuss several interesting features of the solutions based on some energy consideration.
description: 16 pages, 2 figure
W-boson production in TMD factorization
Creators: name: Gutierrez-Reyes, Daniel
name: Leal-Gomez, Sergio
name: Scimemi, Ignazio
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: Nuclear Experiment (nucl-ex)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: At hadron colliders, the differential cross section for $W$ production can be factorized and it is sensitive transverse momentum dependent distributions (TMD) for low boson transverse momentum. While, often, the corresponding non-perturbative QCD contributions are extrapolated from $Z$ boson production, here we use an existing extraction (based on the code Artemide) of TMD which includes data coming from Drell-Yan and semi-inclusive deep inelastic scattering, to provide checks and predictions for the $W$ case. Including fiducial cuts with different configurations and kinematical power corrections, we consider transverse momentum dependent cross sections within several intervals of the vector boson transverse mass. We perform the same study for the $p_T^{W^-}/p_T^{W^+}$ and $p_T^Z/p_T^W$ distributions. We compare our predictions with recent extractions of these quantities at ATLAS and CMS and results from TeVatron. The results encourage a broader experimental and phenomenological work, and a deeper study of TMD for the $W$ case.
description: v3: version accepted for publication; table added, some plots revised
The Choice of Marketing Cooperative in a Transition Agriculture
Creators: name: Ferto, Imre
name: Bakucs, Lajos Zoltan
name: Szabo, Gabor G.
name: Ferto, Imre
name: Bakucs, Lajos Zoltan
name: Szabo, Gabor G.
Publisher: name: Unknown
Year: 2007
Subjects: Agribusiness

description: The agriculture in transition countries can be described by considerable uncertainties. In these countries public institutions are ineffective in ensuring contract enforcement. The absence of enforceable contract to set up any kind of vertical co-ordination has become difficult. In addition, this creates severe barriers for price discovery involving high transaction costs to co-ordinate market exchanges. Although there is a wealth of literature on marketing cooperative, but research on their role in transition agriculture is scarce. This paper tries to contribute to this gap. In this paper we have analysed the potential benefits and costs of the marketing cooperatives in Hungary employing transaction cost economics framework. The results presented add to a small literature on the marketing cooperatives in transition agriculture. We found that the quantity, the existence of contract, flexibility and trust are the most important factor for farmers to selling their product via cooperative. The cluster analysis provides some additional insights regarding farmers' choices. Namely, direct benefits including price, input finance extension services and speed of payments from cooperative membership have also important role. The most striking result is that the diversification and reputation has positive influences on the share of cooperative. Furthermore, large farmers have less willingness to sell their product to the cooperative. Surprisingly, asset specificity has rather negative effects on the share of cooperative.
Dynamical contribution into enzyme catalytic efficiency
Creators: name: Sitnitsky, A. E.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Biological Physics (physics.bio-ph)
subject: Biomolecules (q-bio.BM)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: A realistic physical model for the so called rate promoting vibration (RPV) at enzyme action is constructed. The origin of the RPV is assumed to be an oscillating electric field produced by long-lived localized vibrational modes in protein dynamics, namely, by the so called discrete breather (DB) in secondary structure. The strength of interaction of the RPV with the reaction coordinate is evaluated and its effect on the reaction acceleration is assessed within the framework of modern theory for thermally activated escape rate at periodic driving. We reveal the phenomenon of resonant activation in our model elucidating why the frequency of the RPV in the range $100\div200 cm^{-1}$ was chosen by the evolution of enzymes as an optimal one. The effect of the RPV on the reaction acceleration is shown to vary from moderate one (up to $10^3\div10^4$) in the case of three-site DB to enormous (up to $10^6\div10^8$) in the case of five-site DB and thus can significantly contribute into enzyme catalytic efficiency. Also the model is shown to be compatible with the known functional dependence of enzymatic reaction rates on solvent viscosity.
description: 19 LaTex pages, 3 eps figures, final version, accepted for publication to Physica A