bluuebunny/crossref_metadata_2025_split huggingface dataset:
DockTope: a Web-based tool for automated pMHC-I modelling
Authors: Menegatti Rigo Maurício , Amaral Antunes Dinler , Vaz de Freitas Martiela , Fabiano de Almeida Mendes Marcus , Meira Lindolfo , Sinigaglia Marialva , Fioravanti Vieira Gustavo 
Published: December 2015

AbstractThe immune system is constantly challenged, being required to protect the organism against a wide variety of infectious pathogens and, at the same time, to avoid autoimmune disorders. One of the most important molecules involved in these events is the Major Histocompatibility Complex class I (MHC-I), responsible for binding and presenting small peptides from the intracellular environment to CD8+T cells. The study of peptide:MHC-I (pMHC-I) molecules at a structural level is crucial to understand the molecular mechanisms underlying immunologic responses. Unfortunately, there are few pMHC-I structures in the Protein Data Bank (PDB) (especially considering the total number of complexes that could be formed combining different peptides) and pMHC-I modelling tools are scarce. Here, we present DockTope, a free and reliable web-based tool for pMHC-I modelling, based on crystal structures from the PDB. DockTope is fully automated and allows any researcher to construct a pMHC-I complex in an efficient way. We have reproduced a dataset of 135 non-redundant pMHC-I structures from the PDB (Cα RMSD below 1 Å). Modelling of pMHC-I complexes is remarkably important, contributing to the knowledge of important events such as cross-reactivity, autoimmunity, cancer therapy, transplantation and rational vaccine design.
Disintegration of Carbon Dioxide Molecules in a Microwave Plasma Torch
Authors: Kwak Hyoung S. , Uhm Han S. , Hong Yong C. , Choi Eun H. 
Published: December 2015

AbstractA pure carbon dioxide torch is generated by making use of 2.45 GHz microwave. Carbon dioxide gas becomes the working gas and produces a stable carbon dioxide torch. The torch volume is almost linearly proportional to the microwave power. Temperature of the torch flame is measured by making use of optical spectroscopy and thermocouple. Two distinctive regions are exhibited, a bright, whitish region of high-temperature zone and a bluish, dimmer region of relatively low-temperature zone. Study of carbon dioxide disintegration and gas temperature effects on the molecular fraction characteristics in the carbon dioxide plasma of a microwave plasma torch under atmospheric pressure is carried out. An analytical investigation of carbon dioxide disintegration indicates that substantial fraction of carbon dioxide molecules disintegrate and form other compounds in the torch. For example, the normalized particle densities at center of plasma are given by nCO2/nN = 6.12 × 10−3, nCO/nN = 0.13, nC/nN = 0.24, nO/nN = 0.61, nC2/nN = 8.32 × 10−7, nO2/nN = 5.39 × 10−5, where nCO2, nCO, nC, nO, nC2 and nO2 are carbon dioxide, carbon monoxide, carbon and oxygen atom, carbon and oxygen molecule densities, respectively. nN is the neutral particle density. Emission profiles of the oxygen and carbon atom radicals and the carbon monoxide molecules confirm the theoretical predictions of carbon dioxide disintegration in the torch.
Estimating the Attack Ratio of Dengue Epidemics under Time-varying Force of Infection using Aggregated Notification Data
Authors: Coelho Flavio Codeço , Carvalho Luiz Max de 
Published: December 2015

AbstractQuantifying the attack ratio of disease is key to epidemiological inference and public health planning. For multi-serotype pathogens, however, different levels of serotype-specific immunity make it difficult to assess the population at risk. In this paper we propose a Bayesian method for estimation of the attack ratio of an epidemic and the initial fraction of susceptibles using aggregated incidence data. We derive the probability distribution of the effective reproductive number,Rtand use MCMC to obtain posterior distributions of the parameters of a single-strain SIR transmission model with time-varying force of infection. Our method is showcased in a data set consisting of 18 years of dengue incidence in the city of Rio de Janeiro, Brazil. We demonstrate that it is possible to learn about the initial fraction of susceptibles and the attack ratio even in the absence of serotype specific data. On the other hand, the information provided by this approach is limited, stressing the need for detailed serological surveys to characterise the distribution of serotype-specific immunity in the population.
SMC1B is present in mammalian somatic cells and interacts with mitotic cohesin proteins
Authors: Mannini Linda , Cucco Francesco , Quarantotti Valentina , Amato Clelia , Tinti Mara , Tana Luigi , Frattini Annalisa , Delia Domenico , Krantz Ian D. , Jessberger Rolf , Musio Antonio 
Published: December 2015

AbstractCohesin is an evolutionarily conserved protein complex that plays a role in many biological processes: it ensures faithful chromosome segregation, regulates gene expression and preserves genome stability. In mammalian cells, the mitotic cohesin complex consists of two structural maintenance of chromosome proteins, SMC1A and SMC3, the kleisin protein RAD21 and a fourth subunit either STAG1 or STAG2. Meiotic paralogs in mammals were reported for SMC1A, RAD21 and STAG1/STAG2 and are called SMC1B, REC8 and STAG3 respectively. It is believed that SMC1B is only a meiotic-specific cohesin member, required for sister chromatid pairing and for preventing telomere shortening. Here we show that SMC1B is also expressed in somatic mammalian cells and is a member of a mitotic cohesin complex. In addition, SMC1B safeguards genome stability following irradiation whereas its ablation has no effect on chromosome segregation. Finally, unexpectedly SMC1B depletion impairs gene transcription, particularly at genes mapping to clusters such as HOX and PCDHB. Genome-wide analyses show that cluster genes changing in expression are enriched for cohesin-SMC1B binding.
High-beta, steady-state hybrid scenario on DIII-D
Authors: Petty C.C. , Kinsey J.E. , Holcomb C.T. , DeBoo J.C. , Doyle E.J. , Ferron J.R. , Garofalo A.M. , Hyatt A.W. , Jackson G.L. , Luce T.C. , Murakami M. , Politzer P.A. , Reimerdes H. 
Published: December 2015

Abstract
The potential of the hybrid scenario (first developed as an advanced inductive scenario for high fluence) as a regime for high-beta, steady-state plasmas is demonstrated on the DIII-D tokamak. These experiments show that the beneficial characteristics of hybrids, namely safety factor  ⩾1 with low central magnetic shear, high stability limits and excellent confinement, are maintained when strong central current drive (electron cyclotron and neutral beam) is applied to increase the calculated non-inductive fraction to  ≈100% (≈50% bootstrap current). The best discharges achieve normalized beta of 3.4, IPB98(y,2) confinement factor of 1.4, surface loop voltage of 0.01 V, and nearly equal electron and ion temperatures at low collisionality. A 0D physics model shows that steady-state hybrid operation with Q
fus ~ 5 is feasible in FDF and ITER. The advantage of the hybrid scenario as an advanced tokamak regime is that the external current drive can be deposited near the plasma axis where the efficiency is high; additionally, good alignment between the current drive and plasma current profiles is not necessary as the poloidal magnetic flux pumping self-organizes the current density profile in hybrids with an

tearing mode.
Geodesic acoustic mode investigation in the spherical Globus-M tokamak using multi-diagnostic approach
Authors: Bulanin V.V. , Gusev V.K. , Iblyaminova A.D. , Khromov N.A. , Kurskiev G.S. , Minaev V.B. , Patrov M.I. , Petrov A.V. , Petrov Yu.V. , Sakharov N.V. , Shchegolev P.B. , Tolstyakov S.Yu. , Varfolomeev V.I. , Wagner F. , Yashin Yu. 
Published: December 2015

Abstract
The results of a multi-diagnostic approach for geodesic acoustic mode (GAM) studies in the spherical torus Globus-M are presented. The GAM oscillations of radial electric field, plasma density and magnetic field were simultaneously observed. The spatial structures of crucial plasma parameters are exhibited and discussed. The intermittent character of the GAM manifests itself as a modulation at two time-scales: equilibrium time scale and the characteristic time for limit-cycle oscillations. The mutual influence of GAM oscillations and turbulence is demonstrated by bicoherence analysis.
Integrating, summarizing and visualizing GWAS-hits and human diversity with DANCE (Disease-ANCEstry networks)
Authors: Araújo Gilderlanio S. , Lima Lucas Henrique C. , Schneider Silvana , Leal Thiago P. , da Silva Ana Paula C. , Vaz de Melo Pedro O. S. , Tarazona-Santos Eduardo , Scliar Marília O. , Rodrigues Maíra R. 
Published: December 2015

Abstract
Motivation: The 1000 Genomes Project (1KGP) and thousands of Genome-Wide Association Studies (GWAS) performed during the last years have generated an enormous amount of information that needs to be integrated to better understand the genetic architecture of complex diseases in different populations. This integration is important in areas such as genetics, epidemiology, anthropology, as well as admixture mapping design and GWAS-replications. Network-based approaches that explore the genetic bases of human diseases and traits have not yet incorporated information on genetic diversity among human populations.
Results: We propose Disease-ANCEstry networks (DANCE), a graph-based web tool that allows to integrate and visualize information on human complex phenotypes and their GWAS-hits, as well as their risk allele frequencies in different populations. DANCE provides an interactive way to explore the human SNP–Disease Network and its projection, a Disease–Disease Network. With these functionalities, DANCE fills a gap in our ability to handle and understand the knowledge generated by GWAS and 1KGP. We provide a number of case studies that show how DANCE can be used to explore the relationships between human complex diseases, their genetic bases and variability in different human populations.
Availability and implementation: DANCE is freely available at http://ldgh.com.br/dance/. We recommend using DANCE with Mozilla Firefox, Safari, Chrome or Internet Explorer (v9 or v10).
Contact: gilderlanio@gmail.com or maira.r.rodrigues@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Identifying environmental factors associated with the genetic structure of the New Zealand scallop: linking seascape genetics and ecophysiological tolerance
Authors: Silva Catarina N. S. , Gardner Jonathan P. A. 
Published: December 2015

AbstractUnderstanding the processes responsible for shaping the spatial genetic patterns of species is critical for predicting evolutionary dynamics and defining significant evolutionary and/or management units. Here, we investigated the potential role of environmental factors in shaping the genetic structure of the endemic New Zealand scallop Pecten novaezelandiae using a seascape genetics approach. For this, we assayed genetic variation at 12 microsatellite markers in 952 individuals collected from 14 sites throughout New Zealand, and used data for 9 site-specific environmental variables (3 geospatial and 6 environmental variables). Our results indicate that a combination of environmental factors may be contributing to the observed patterns of genetic differentiation, but in particular, freshwater discharge and suspended particulate matter concentration were identified as being important. Environmental variation in these parameters may be acting as a barrier to gene flow. In terms of their ecophysiology, scallops are not particularly tolerant of high concentrations of either freshwater input or suspended sediment, making the identification of an association between these environmental variables and genetic variation particularly relevant across the full distributional range of this species. Although geographic distance between populations was also an important variable explaining the genetic variation among populations, it appears that levels of genetic differentiation are not a simple function of interpopulation distance. This study has identified previously unknown environmental factors that may be acting on the genetic structure of the New Zealand scallop and highlights the utility of seascape genetic studies to better understand the processes shaping the genetic structure of organisms.
On the relation between face and object recognition in developmental prosopagnosia: Systematic association but no dissociation
Authors: Gerlach Christian , Klargaard Solja K. , Starrfelt Randi 
Published: December 2015

AbstractThere is an ongoing debate about whether face recognition and object recognition constitute separate domains. Clarification of this issue can have important theoretical implications as face recognition is often used as a prime example of domain-specificity in mind and brain. An important source of input to this debate comes from studies of individuals with developmental prosopagnosia, suggesting that face recognition can be selectively impaired. We put the selectivity-hypothesis to test by assessing the performance of 10 subjects with developmental prosopagnosia on demanding tests of visual object processing involving both regular and degraded drawings. None of the individuals exhibited a dissociation between face and object recognition, and as a group they were significantly more affected by degradation of objects than control participants. Importantly, we also find positive correlations between the severity of the face recognition impairment and the degree of impaired performance with degraded objects. This suggests that the face and object deficits are systematically related rather than coincidental. We conclude that at present, there is no strong evidence in the literature on developmental prosopagnosia supporting domain-specific accounts of face recognition.
An evolutionary hourglass of herbivore-induced transcriptomic responses inNicotiana attenuata
Authors: Durrant Matthew , Boyer Justin , Baldwin Ian T. , Xu Shuqing 
Published: December 2015

AbstractHerbivore induced defences are robust, evolve rapidly and activated in plants when specific elicitors, frequently found in the herbivores’ oral secretions (OS) are introduced into wounds during attack. How these complex induced defences evolve remains unclear. Here, we show that herbivore-induced transcriptomic responses in a wild tobacco, Nicotiana attenuata, display an evolutionary hourglass: the pattern that characterises the transcriptomic evolution of embryogenesis in animals, plants, and fungi. While relatively young and rapidly evolving genes involved in signal perception and processing to regulate defence metabolite biosynthesis are recruited both early (1 h) and late (9-21 h) in the defence elicitation process, a group of highly conserved and older genes involved in transcriptomic regulation are activated in the middle stage (5 h). The appearance of the evolutionary hourglass architecture in both developmental and defence elicitation processes may reflect the importance of robustness and evolvability in the signalling of these important biological processes.
Recent progresses in bus-ducts design
Authors: Faiz J. , Ehya H. , Takbash A.M. , Shojaee S. , Hamidian M. , Ghorbani A. 
Published: December 2015

Purpose
– Electrical energy distribution systems must be low losses systems in order to enhance the system efficiency. Therefore, it is preferred to distribute electrical energy by bus-ducts in the place of cables over all energy levels and decrease the losses. The purpose of this paper is to focus on a comprehensive survey of various aspects of bus-ducts design including electromagnetic, mechanical and thermal. Advantages and disadvantages of different available design techniques are reviewed.

Design/methodology/approach
– Different works on various bus-based power transmission and distribution systems are reviewed. Generally these are done in three categories including systems modeling methods, heat transfer in the systems, short circuit and electromagnetic force. The attempt is made to provide geometrical and materials specifications in order to present the analyzed system well.

Findings
– Different types of bus-ducts from used materials, voltage level and insulation types are reviewed. Bus-duct modeling techniques are introduced which can be easily applied for bus-ducts design. Electromagnetic field distribution, thermal pattern inside and outside of the bus-duct in normal and short circuit modes and finally mechanical considerations are dominant factors which must be taken into account in the bus-ducts design. This leads to an optimal design of bus-ducts which prolong the life span of the bus-ducts fixed in the installations.

Originality/value
– This paper for the first time systematically reviews the latest state of arts in the design of bus-ducts for efficient electrical energy distribution. It summarizes a variety of design techniques applicable to bus-ducts design.
Shaping inductor geometry for casting functionally graded composites
Authors: Golak Slawomir , Kordos Mirosław 
Published: December 2015

Purpose
– The attractiveness of functionally graded composites lies in the possibility of a gradual spatial change of their properties such as hardness, strength and wear resistance. The purpose of this paper is to discuss the use of electromagnetic buoyancy to separate the reinforcement particles during the casting process of such a composite.

Design/methodology/approach
– The basic problem encountered in the process of casting composites is to obtain electromagnetic buoyancy and simultaneously to avoid a flow of the liquid metal which destroys the desired composite structure. In this paper the authors present the methodology of numerical optimization of inductor geometry in order to homogenize the electromagnetic force field distribution.

Findings
– The optimization method based on searching the solution subspace created by applying knowledge of the modelled process physics proved better than the universal local optimization methods. These results were probably caused by the complex shape of the criterion function hypersurface characterized by the presence of local minima.

Practical implications
– Due to their characteristics, functionally graded composites are of great interest to the automotive, aerospace and defense industries. In the case of metal matrix composites casting techniques (as the presented one) are the most effective methods of producing functionally graded materials.

Originality/value
– The paper presents the optimization of a new process of casting functionally graded composites in a low-frequency alternating electromagnetic field. The process involves problems that did not occur previously in the area of electromagnetic processing of materials. The paper proposes the use of special design of inductors to homogenize the electromagnetic force field.
Joint power control and beamforming in MIMO relays
Authors: Shirvani Moghaddam Shahriar , Alibeigi Maryam 
Published: December 2015

Purpose
– In this paper, a wireless network consisting of multiple source-destination pairs, which communicate peer-to-peer with the help of multiple Amplify-and-Forward relays is considered. The purpose of this paper is to minimize the total relay transmit power subject to a sum rate threshold.

Design/methodology/approach
– It is shown that finding a beamforming matrix which satisfies the investigation’s goal is a non-convex optimization problem. Therefore, a semidefinite relaxation technique is used to turn it into a semidefinite programming problem. Thus, it can be effectively solved by interior point methods.

Findings
– Simulation results show that the total relay transmit power decreases with the number of relays. In addition, it is shown that relays’ power consumption decreases when the quality of uplink and/or downlink channels improves. In order to compare the proposed optimization algorithm to two conventional approaches, energy efficiency criterion used for performance comparison and complexity order for evaluating computational complexity. Although the proposed algorithm does not change the order of complexity, it needs a few more iterations to find the best result which leads to a double the processing time compared to existing approaches.

Originality/value
– In the present optimization problem, coefficient ß is used instead of a constant factor 2 in the original optimization problem. It is shown that by changing parameter ß between 1 and 2, a lower power consumption for a target sum rate can be achieved.
Semi-analytical determination of inductances in windings with axial and azimuthal wires
Authors: Dumont de Chassart Corentin , Van Beneden Maxence , Kluyskens Virginie , Dehez Bruno 
Published: December 2015

Purpose
– Optimizing an electromechanical device often requires a significant number of evaluations of the winding inductance. In order to reduce drastically the computing costs associated with the calculation of inductances, the purpose of this paper is to propose a semi-analytical toolbox to calculate inductances in any winding made of axial and azimuthal wires and lying in the air.

Design/methodology/approach
– First, this paper presents a typical rectangular, spiral winding and the way its geometry is approximated for inductance calculations. Second, the basic formulas to calculate inductances of various windings arrangements are provided. The analytical model of the inductances is exposed, and the formulas for the inductances are derived. Finally, a validation is proposed by comparing analytical predictions to 3D FE simulations results and experimental measurements.

Findings
– The semi-analytical predictions agree with the finite element methods (FEM) and experimental data. Furthermore, the calculation of the inductances was done using much fewer resources with the semi-analytical model than with FEM.

Research limitations/implications
– The analytical formula for the mutual inductance between coaxial circular arcs is a series with an infinite number of terms which should be truncated appropriately. This is necessary because the term are found using a recurrence formula which may be unstable for a high number of terms.

Practical implications
– The paper includes implications for the optimization of electromechanical devices comprising windings made of axial and azimuthal pieces of wires.

Originality/value
– The main original result resides in the analytical expression of Neumann’s integral for the inductance between two coaxial circular arcs.
Double-diffusive natural convective boundary-layer flow of a nanofluid over a stretching sheet with magnetic field
Authors: Akbar Noreen , Khan z , Nadeem S , khan W 
Published: December 2015

Purpose
– The purpose of this paper, is to study the MHD double-diffusive natural convection of a nanofluid over a linearly stretching sheet using the Buongiorno model.

Design/methodology/approach
– The transport equations are transformed into coupled similarity equations. The numerical self-similar solutions are compared with the literature for the special case of pure fluid flow and found to be in good agreement. Graphical results are presented to illustrate the effects of various fluid flow, heat transfer and nano concentration parameters for both assisting and opposing flows.

Findings
– It is found that the heat transfer rate increases as nanoparticles and salt are suspended in water. It is also found that dual solutions exist for the stretching parameter.

Originality/value
– First paper on this model for stretching sheet.