bluuebunny/crossref_metadata_2025_split huggingface dataset:
Translation of SBGN maps: Process Description to Activity Flow
Authors: Vogt Torsten , Czauderna Tobias , Schreiber Falk 
Published: October 2013

Abstract

Background
The Systems Biology Graphical Notation (SBGN) provides standard graphical languages for representing cellular processes, interactions, and biological networks. SBGN consists of three languages: Process Descriptions (PD), Entity Relationships (ER), and Activity Flows (AF). Maps in SBGN PD are often large, detailed, and complex, therefore there is a need for a simplified illustration.

Results
To solve this problem we define translations of SBGN PD maps into the more abstract SBGN AF maps. We present a template-based translation which allows the user to focus on different aspects of the underlying biological system. We also discuss aspects of laying out the AF map and of interactive navigation between both the PD and the AF map. The methods developed here have been implemented as part of SBGN-ED (http://www.sbgn-ed.org).

Conclusions
SBGN PD maps become much smaller and more manageable when translated into SBGN AF. The flexible translation of PD into AF and related interaction methods are an initial step in translating the different SBGN languages and open the path to future research for translation methods between other SBGN languages.
Health-related quality of life and functional ability in patients with early arthritis during remission steered treatment: results of the IMPROVED study
Authors: Heimans Lotte , Boer Kirsten VC Wevers-de , Koudijs KK Michel , Visser Karen , Goekoop-Ruiterman Yvonne P , Harbers Joop B , Steup-Beekman Gerda M , Lard Leroy R , Grillet Bernard AM , Huizinga Tom WJ , Allaart Cornelia F 
Published: October 2013

Abstract
Introduction
The aim of this study was to investigate patient reported outcomes (PROs) of functional ability and health related quality of life (HRQoL) in patients with early (rheumatoid) arthritis during one year of remission steered treatment.

Methods
In this study, 610 patients with early rheumatoid arthritis (RA) or undifferentiated arthritis (UA) were treated with methotrexate (MTX) and tapered high dose of prednisone. Patients in early remission (Disease Activity Score (DAS) <1.6 after 4 months) tapered prednisone to zero and when in persistent remission, also tapered MTX. Patients not in early remission were randomized to either MTX + hydroxychloroquine + sulphasalazine + prednisone (arm 1) or to MTX + adalimumab (arm 2). Every 4 months, patients filled out the Health Assessment Questionnaire (HAQ) and the McMaster Toronto Arthritis Patient Preference Questionnaire (MACTAR), the Short Form 36 (SF-36) and visual analogue scales (VAS). Change scores were compared between treatment groups. The association with achieving remission was analyzed using linear mixed models.

Results
During year 1, patients who achieved early remission had the most improvement in PROs with scores comparable to the general population. Patients in the randomization arms showed less improvement. Scores were comparable between the arms. There was a significant association between achieving remission and scores of HAQ, MACTAR and physical HRQoL.

Conclusions
In early arthritis, PROs of functional ability and HRQoL after one year of remission steered treatment reach normal values in patients who achieved early remission. In patients not in early remission, who were randomized to two strategy arms, PROs improved less, with similar scores in both treatment arms.

Trial registrations
ISRCTN11916566 and EudraCT2006-006186-16
Transcriptional landscapes of emerging autoimmunity: transient aberrations in the targeted tissue’s extracellular milieu precede immune responses in Sjögren’s syndrome
Authors: Delaleu Nicolas , Nguyen Cuong Q , Tekle Kidane M , Jonsson Roland , Peck Ammon B 
Published: October 2013

Abstract
Introduction
Our understanding of autoimmunity is skewed considerably towards the late stages of overt disease and chronic inflammation. Defining the targeted organ’s role during emergence of autoimmune diseases is, however, critical in order to define their etiology, early and covert disease phases and delineate their molecular basis.

Methods
Using Sjögren’s syndrome (SS) as an exemplary rheumatic autoimmune disease and temporal global gene-expression profiling, we systematically mapped the transcriptional landscapes and chronological interrelationships between biological themes involving the salivary glands’ extracellular milieu. The time period studied spans from pre- to subclinical and ultimately to onset of overt disease in a well-defined model of spontaneous SS, the C57BL/6.NOD-Aec1Aec2 strain. In order to answer this aim of great generality, we developed a novel bioinformatics-based approach, which integrates comprehensive data analysis and visualization within interactive networks. The latter are computed by projecting the datasets as a whole on a priori-defined consensus-based knowledge.

Results
Applying these methodologies revealed extensive susceptibility loci-dependent aberrations in salivary gland homeostasis and integrity preceding onset of overt disease by a considerable amount of time. These alterations coincided with innate immune responses depending predominantly on genes located outside of the SS-predisposing loci Aec1 and Aec2. Following a period of transcriptional stability, networks mapping the onset of overt SS displayed, in addition to natural killer, T- and B-cell-specific gene patterns, significant reversals of focal adhesion, cell-cell junctions and neurotransmitter receptor-associated alterations that had prior characterized progression from pre- to subclinical disease.

Conclusions
This data-driven methodology advances unbiased assessment of global datasets an allowed comprehensive interpretation of complex alterations in biological states. Its application delineated a major involvement of the targeted organ during the emergence of experimental SS.
Molecular characterization and in vitro differentiation of feline progenitor-like amniotic epithelial cells
Authors: Rutigliano Lucia , Corradetti Bruna , Valentini Luisa , Bizzaro Davide , Meucci Aurora , Cremonesi Fausto , Lange-Consiglio Anna 
Published: October 2013

Abstract
Introduction
While amniotic mesenchymal cells have been isolated and characterized in different species, amniotic epithelial cells (AECs) have been found only in humans and horses and are recently considered valid candidates in regenerative medicine. The aim of this work is to obtain and characterize, for the first time in the feline species, presumptive stem cells from the epithelial portion of the amnion (AECs) to be used for clinical applications.

Methods
In our study, we molecularly characterized and induced in vitro differentiation of feline AECs, obtained after enzymatic digestion of amnion.

Results
AECs displayed a polygonal morphology and the mean doubling time value was 1.94 ± 0.04 days demonstrating the high proliferating capacity of these cells. By RT-PCR, AECs expressed pluripotent (Oct4, Nanog) and some mesenchymal markers (CD166, CD44) suggesting that an epithelial-mesenchymal transition may occur in these cells that lack the hematopoietic marker CD34. Cells also showed the expression of embryonic marker SSEA-4, but not SSEA-3, as demonstrated by immunocytochemistry and flow cytometry. Moreover, the possibility to use feline AECs in cell therapies resides in their low immunogenicity, due to the absence of MHC-II antigen expression. After induction, AECs differentiated into the mesodermic and ectodermic lineages, demonstrating high plasticity.

Conclusions
In conclusion, feline AECs appear to be a readily obtainable, highly proliferative, multipotent and non-immunogenic cell line from a source that may represent a good model system for stem cell biology and be useful in allogenic cell-based therapies in order to treat tissue lesions, especially with loss of substance.
L-functions ofp-adic characters
Authors: Davis Christopher , Wan Daqing 
Published: October 2013

AbstractWe define ap-adic character to be a continuous homomorphism fromForp> 2, we use the ring of big Witt vectors overto exhibit a bijection betweenp-adic characters and sequences (ci)(i,p)=1of elements inindexed by natural numbers relatively prime top, and for which. To such ap-adic character we associate anL-function, and we prove that thisL-function isp-adic meromorphic if the corresponding sequence (ci) is overconvergent. If more generally the sequence isClog-convergent, we show that the associatedL-function is meromorphic in the open disk of radiusqC. Finally, we exhibit examples ofClog-convergent sequences with associatedL-functions which are not meromorphic in the disk of radiusqC+∊for any∊> 0.
Projective metric number theory
Authors: Ghosh Anish , Haynes Alan 
Published: October 2013

Abstract

In this paper we consider the probabilistic theory of Diophantine approximation in projective space over a completion of ℚ. Using the projective metric studied in [Ann. Sc. Norm. Super. Pisa Cl. Sci. (4) 23 (1996), no. 2, 211–248] we prove the analogue of Khintchine's theorem in projective space. For finite places and in higher dimension, we are able to completely remove the condition of monotonicity and establish the analogue of the Duffin–Schaeffer conjecture.
Microbial xylitol production from culm of Sasa kurilensis using the yeast Candida magnoliae
Authors: Miura Masahiro , Seo Tomoaki , Shimotori Yasutaka , Aoyama Masakazu , Nakatani Hisayuki , Nishikoori Masatomo 
Published: October 2013

Abstract
A sugar solution containing 31 g l-1 xylose was prepared from the culm of Sasa kurilensis by hydrolysis with 2% sulfuric acid with a liquor-to-solid ratio of 6 (g g-1) at 121°C for 1 h. During acid hydrolysis, also some byproducts were generated, such as acetic acid, furfural, 5-hydroxymethylfurfral, and low molecular weight phenolics, which inhibit bioconversion of xylose to xylitol. Except for acetic acid, these inhibitors were successfully removed from the hydrolysate by contacting with a steam-activated charcoal (15 g l-1 dose) for 24 h. Bioconversion of the detoxified hydrolysate to xylitol by the yeast, Candida magnoliae, was investigated under various microaerobic conditions. The oxygen transfer rate (OTR) varied from 8.4 to 27.6 mmol-O2 l-1 h-1. The maximum xylitol yield (0.62 g-xylitol g-xylose-1) was attained at the OTR of 1.2 mmol-O2 l-1 h-1. An additional increase in the OTR brought about cell growth, which consumed xylose. A proper control of the oxygen supply is necessary to produce efficiently xylitol from the culm hydrolysate.
Analysis of the Flicker Level Produced by a Fixed-Speed Wind Turbine
Authors: Suppioni Vinicius , P. Grilo Ahda 
Published: October 2013

Abstract
In this article, the analysis of the flicker emission during continuous operation of a mid-scale fixed-speed wind turbine connected to a distribution system is presented. Flicker emission is investigated based on simulation results, and the dependence of flicker emission on short-circuit capacity, grid impedance angle, mean wind speed, and wind turbulence is analyzed. The simulations were conducted in different programs in order to provide a more realistic wind emulation and detailed model of mechanical and electrical components of the wind turbine. Such aim is accomplished by using FAST (Fatigue, Aerodynamics, Structures, and Turbulence) to simulate the mechanical parts of the wind turbine, Simulink/MatLab to simulate the electrical system, and TurbSim to obtain the wind model. The results show that, even for a small wind generator, the flicker level can limit the wind power capacity installed in a distribution system.
Inverse problems for the ground penetrating radar
Authors: Kabanikhin S. I. , Nurseitov D. B. , Shishlenin M. A. , Sholpanbaev B. B. 
Published: October 2013

Abstract.
We consider the continuation problem from the time-like surface for the 2D Maxwell equation. The problem is formulated in an operator form . We describe and justify gradient methods for minimizing the cost functional for the continuation and coefficient inverse problems. The results of a computational experiment are presented.
Comparative Genome Mapping Between Chinook Salmon (Oncorhynchus tshawytscha) and Rainbow Trout (O. mykiss) Based on Homologous Microsatellite Loci
Authors: Naish Kerry A , Phillips Ruth B , Brieuc Marine S O , Newton Lyndsay R , Elz Anna E , Park Linda K 
Published: October 2013

Abstract
Comparative genome mapping can rapidly facilitate the transfer of DNA sequence information from a well-characterized species to one that is less described. Chromosome arm numbers are conserved between members of the teleost family Salmonidae, order Salmoniformes, permitting rapid alignment of large syntenic blocks of DNA between members of the group. However, extensive Robertsonian rearrangements after an ancestral whole-genome duplication event has resulted in different chromosome numbers across Salmonid taxa. In anticipation of the rapid application of genomic data across members of the Pacific salmon genus Oncorhynchus, we mapped the genome of Chinook salmon (O. tshawytscha) by using 361 microsatellite loci and compared linkage groups to those already derived for a well-characterized species rainbow trout (O. mykiss). The Chinook salmon female map length was 1526 cM, the male map 733 cM, and the consensus map between the two sexes was 2206 cM. The average female to male recombination ratio was 5.43 (range 1−42.8 across all pairwise marker comparisons). We detected 34 linkage groups that corresponded with all chromosome arms mapped with homologous loci in rainbow trout and inferred that 16 represented metacentric chromosomes and 18 represented acrocentric chromosomes. Up to 13 chromosomes were conserved between the two species, suggesting that their structure precedes the divergence between Chinook salmon and rainbow trout. However, marker order differed in one of these linkage groups. The remaining linkage group structures reflected independent Robertsonian chromosomal arrangements, possibly after divergence. The putative linkage group homologies presented here are expected to facilitate future DNA sequencing efforts in Chinook salmon.
Bounded pseudo-hoops with internal states
Authors: Ciungu Lavinia 
Published: October 2013

Abstract
State MV-algebras were introduced by Flaminio and Montagna as MV-algebras with internal states. Di Nola and Dvurečenskij presented the notion of state-morphism MV-algebra which is a stronger variation of a state MV-algebra. Rachůnek and Šalounová introduced state GMV-algebras (pseudo-MV algebras) and state-morphism GMV-algebras, while the state BL-algebras and state-morphism BL-algebras were defined by Ciungu, Dvurečenskij and Hyčko. Recently, Dvurečenskij, Rachůnek and Šalounová presented state Rℓ-monoids and state-morphism Rℓ-monoids. In this paper we study these concepts for more general fuzzy structures, namely pseudo-hoops and we present state pseudo-hoops and state-morphism pseudo-hoops.
On algebras with a generalized implication
Authors: Yon Yong , Kim Kyung 
Published: October 2013

Abstract
We introduce the notion of gi-algebra as a generalization of dual BCK-algebra, and define the notions of strong, commutative and transitive gi-algebra, and then we show that an interval ↑l = {a ∈ P | l ≤ a} in a strong and commutative gi-algebra P is a lattice. Also, we define a congruence relation ∼D on a transitive gi-algebra P and show that the quotient set P/∼D is a gi-algebra and a dual BCK-algebra.
Homomorphism-homogeneous monounary algebras
Authors: Jungábel Éva , Mašulović Dragan 
Published: October 2013

Abstract
In 2006, P. J. Cameron and J. Nešetřil introduced the following variant of homogeneity: we say that a structure is homomorphism-homogeneous if every homomorphism between finitely generated substructures of the structure extends to an endomorphism of the structure. In several recent papers homomorphism-homogeneous objects in some well-known classes of algebras have been investigated (e.g. lattices and semilattices), while finite homomorphism-homogeneous groups were described in 1979 under the name of finite quasiinjective groups. In this paper we characterize homomorphism-homogenous monounary algebras of arbitrary cardinalities.
Mixed-mean inequality for submatrix
Authors: Si Lin , Zhao Suyun 
Published: October 2013

Abstract
For an m × n matrix B = (b
ij)m×n
with nonnegative entries b
ij, let B(k, l) denote the set of all k × l submatrices of B. For each A ∈ B(k, l), let a
A and g
A denote the arithmetic mean and geometric mean of elements of A respectively. It is proved that if k is an integer in ($$\tfrac{m}
{2}$$,m] and l is an integer in ($$\tfrac{n}
{2}$$, n] respectively, then $$\left( {\prod\limits_{A \in B\left( {k,l} \right)} {a_A } } \right)^{\tfrac{1}
{{\left( {_k^m } \right)\left( {_l^n } \right)}}} \geqslant \frac{1}
{{\left( {_k^m } \right)\left( {_l^n } \right)}}\left( {\sum\limits_{A \in B\left( {k,l} \right)} {g_A } } \right),$$ with equality if and only if b
ij is a constant for every i, j.
Characterization of summability methods with high indices
Authors: Sarigol Mehmet 
Published: October 2013

Abstract
In this paper we establish a set of necessary and sufficient conditions in order that |C, 0|k ⇒ |R, p
n|s and |R, p
n|k ⇒ |C, 0|s for the case 1 < k ≤ s < ∞. As a corollary, we obtain that a crucial assumption of [BOR, H.: A new result on the high indices theorem, Analysis 29 (2009), 403–405] is omitted and that the other one is not only sufficient but also necessary for his consequence to hold.
Some convergence theorems for total asymptotically nonexpansive mappings in Banach spaces
Authors: Chang Shih-sen , Joseph Lee H. , Chan Chi 
Published: October 2013

Abstract
The purpose of this paper is to establish some new approximation theorems of common fixed points for a countable family of total asymptotically quasi-nonexpansive mappings in Banach spaces which generalize and improve the corresponding theorems of Chidume et al. [J. Math. Anal. Appl. 333 (2007), 128–141], [J. Math. Anal. Appl. 326 (2007), 960–973], [Internat. J. Math. Math. Sci. 2009, Article ID 615107, 17 pp.] and others.
Coefficient inequalities for univalent starlike functions
Authors: Obradović Milutin , Ponnusamy Saminathan 
Published: October 2013

Abstract
Let A be the class of analytic functions in the unit disk $$\mathbb{D}$$ with the normalization f(0) = f′(0) − 1 = 0. In this paper the authors discuss necessary and sufficient coefficient conditions for f ∈ A of the form $$\left( {\frac{z}
{{f(z)}}} \right)^\mu = 1 + b_1 z + b_2 z^2 + \ldots$$ to be starlike in $$\mathbb{D}$$ and more generally, starlike of some order β, 0 ≤ β < 1. Here µ is a suitable complex number so that the right hand side expression is analytic in $$\mathbb{D}$$ and the power is chosen to be the principal power. A similar problem for the class of convex functions of order β is open.
Microsatellite primers in the weedy annual herb Anacyclus clavatus (Asteraceae) and four closely related species
Authors: Agudo Alicia , Picó F. Xavier , Álvarez Inés 
Published: October 2013

• Premise of the study: Nuclear microsatellite primers were developed for the weedy herb Anacyclus clavatus to study the genetic structure of hybrid zones with closely related taxa in the western Mediterranean Basin, where different floral phenotypes are present.• Methods and Results: We obtained two microsatellite libraries using next‐generation sequencing and Sanger sequencing of cloned restriction fragments. A total of 13 polymorphic and 11 monomorphic loci were identified in three Iberian populations of A. clavatus. The primers amplified di‐ and trinucleotide repeats with 1–8 alleles per locus. Most primers also amplified in A. homogamos, A. monanthos, A. radiatus, and A. valentinus.• Conclusions: These results indicate the utility of these markers in A. clavatus for population genetic and hybridization studies as well as their applicability across the genus.
Artificial neural network and statistical models for predicting the basic geotechnical properties of soils from electrical measurements
Authors: Boadu Fred Kofi , Owusu‐Nimo Frederick , Achampong Francis , Ampadu Samuel I.K. 
Published: October 2013

ABSTRACTThe ability to predict the geotechnical properties of subsurface soils using non‐invasive geophysical measurements can be undeniably useful to the geotechnical engineer. Using laboratory data, we assess the potential of artificial neural networks to investigate the relations between geotechnical and electrical parameters characterizing a variety of soils. The geotechnical parameters are: fines content, mean grain size, mean pore size and the specific surface area. The electrical parameters obtained from low‐frequency electrical measurements (4 Hz) include the resistivity amplitude, phase shift and the loss tangent. Relations that can be used to predict the geotechnical parameters of a soil given its electrical parameters are developed. The predictive capabilities of the neural networks are compared with traditional multivariate regression models. The performances of the neural network and regression models in predicting (a) the geotechnical parameter given the same electrical parameters as inputs and (b) the electrical parameters given the same geotechnical parameters as inputs are compared. In both cases, the neural network outperforms the multivariate regression as the neural network is able to capture and model the non‐linear and complex relationships among the variables. The relative importance of the geotechnical parameters on the overall electrical conduction was examined using the neural networks. The results indicate that mean grain size and fines content are the two geotechnical parameters that influence phase‐shift values the most; fines content and mean pore size influence the resistivity amplitude the most, whilst fines content and mean grain size influence the loss tangent the most. It was observed that of the four geotechnical parameters, the mean grain size influences the measured resistivity values the least.
Pressure dependence of seismic Q – a microcrack‐based petrophysical model
Authors: Dobróka Mihály , Molnár Judit Somogyi , Szűcs Péter , Turai Endre 
Published: October 2013

ABSTRACTThe pressure dependence of the quality factor of acoustic waves is an extensively explored rock physical problem. To reasonably interpret laboratory measurements, a petrophysical model is required which provides the physical explanation of the nonlinear pressure dependence of the seismic quality factor. In this paper we highlight important features of seismic wave attenuation and propagation under varying pressure which contribute to creating a petrophysical model. The model is starting from the idea that microcracks are opened and closed under varying pressure. Within the confines of the model, differential equations are set up describing the relationship between microcrack density and confining pressure as well as between quality factor and microcrack density. Combining these equations, a three‐parameter expression is derived which has clear physical meaning. We found that the pressure dependence of the quality factor can be well described by a three‐parameter exponential equation in the form which gives also the physical meaning of pressure versus quality factor connection. The physical explanation of each parameter is clarified in the paper, i.e. is the quality factor at zero pressure, is the possible range of quality factor and is a new petrophysical parameter (the logarithmic stress sensitivity). The model was applied on measurement data sets adopted from the literature. The material parameters of the model were determined by using linearized inversion method and the laboratory measurements were compared to the theoretical data. The theoretical data matched accurately with measured data proving that the petrophysical model applies well in practice.