bluuebunny/crossref_metadata_2025_split huggingface dataset:
Remodeling of the Rad51 DNA Strand-Exchange Protein by the Srs2 Helicase
Authors: Sasanuma Hiroyuki , Furihata Yuko , Shinohara Miki , Shinohara Akira 
Published: June 2013

Abstract
Homologous recombination is associated with the dynamic assembly and disassembly of DNA–protein complexes. Assembly of a nucleoprotein filament comprising ssDNA and the RecA homolog, Rad51, is a key step required for homology search during recombination. The budding yeast Srs2 DNA translocase is known to dismantle Rad51 filament in vitro. However, there is limited evidence to support the dismantling activity of Srs2in vivo. Here, we show that Srs2 indeed disrupts Rad51-containing complexes from chromosomes during meiosis. Overexpression of Srs2 during the meiotic prophase impairs meiotic recombination and removes Rad51 from meiotic chromosomes. This dismantling activity is specific for Rad51, as Srs2 Overexpression does not remove Dmc1 (a meiosis-specific Rad51 homolog), Rad52 (a Rad51 mediator), or replication protein A (RPA; a single-stranded DNA-binding protein). Rather, RPA replaces Rad51 under these conditions. A mutant Srs2 lacking helicase activity cannot remove Rad51 from meiotic chromosomes. Interestingly, the Rad51-binding domain of Srs2, which is critical for Rad51-dismantling activity in vitro, is not essential for this activity in vivo. Our results suggest that a precise level of Srs2, in the form of the Srs2 translocase, is required to appropriately regulate the Rad51 nucleoprotein filament dynamics during meiosis.
The Kinesin-3, Unc-104 Regulates Dendrite Morphogenesis and Synaptic Development in Drosophila
Authors: Kern Jeannine V , Zhang Yao V , Kramer Stella , Brenman Jay E , Rasse Tobias M 
Published: June 2013

Abstract
Kinesin-based transport is important for synaptogenesis, neuroplasticity, and maintaining synaptic function. In an anatomical screen of neurodevelopmental mutants, we identified the exchange of a conserved residue (R561H) in the forkhead-associated domain of the kinesin-3 family member Unc-104/KIF1A as the genetic cause for defects in synaptic terminal- and dendrite morphogenesis. Previous structure-based analysis suggested that the corresponding residue in KIF1A might be involved in stabilizing the activated state of kinesin-3 dimers. Herein we provide the first in vivo evidence for the functional importance of R561. The R561H allele (unc-104bris) is not embryonic lethal, which allowed us to investigate consequences of disturbed Unc-104 function on postembryonic synapse development and larval behavior. We demonstrate that Unc-104 regulates the reliable apposition of active zones and postsynaptic densities, possibly by controlling site-specific delivery of its cargo. Next, we identified a role for Unc-104 in restraining neuromuscular junction growth and coordinating dendrite branch morphogenesis, suggesting that Unc-104 is also involved in dendritic transport. Mutations in KIF1A/unc-104 have been associated with hereditary spastic paraplegia and hereditary sensory and autonomic neuropathy type 2. However, we did not observe synapse retraction or dystonic posterior paralysis. Overall, our study demonstrates the specificity of defects caused by selective impairments of distinct molecular motors and highlights the critical importance of Unc-104 for the maturation of neuronal structures during embryonic development, larval synaptic terminal outgrowth, and dendrite morphogenesis.
Learning Natural Selection from the Site Frequency Spectrum
Authors: Ronen Roy , Udpa Nitin , Halperin Eran , Bafna Vineet 
Published: June 2013

Abstract
Genetic adaptation to external stimuli occurs through the combined action of mutation and selection. A central problem in genetics is to identify loci responsive to specific selective constraints. Many tests have been proposed to identify the genomic signatures of natural selection by quantifying the skew in the site frequency spectrum (SFS) under selection relative to neutrality. We build upon recent work that connects many of these tests under a common framework, by describing how selective sweeps affect the scaled SFS. We show that the specific skew depends on many attributes of the sweep, including the selection coefficient and the time under selection. Using supervised learning on extensive simulated data, we characterize the features of the scaled SFS that best separate different types of selective sweeps from neutrality. We develop a test, SFselect, that consistently outperforms many existing tests over a wide range of selective sweeps. We apply SFselect to polymorphism data from a laboratory evolution experiment of Drosophila melanogaster adapted to hypoxia and identify loci that strengthen the role of the Notch pathway in hypoxia tolerance, but were missed by previous approaches. We further apply our test to human data and identify regions that are in agreement with earlier studies, as well as many novel regions.
A Bayesian Nonparametric Approach for Mapping Dynamic Quantitative Traits
Authors: Li Zitong , Sillanpää Mikko J 
Published: June 2013

Abstract
In biology, many quantitative traits are dynamic in nature. They can often be described by some smooth functions or curves. A joint analysis of all the repeated measurements of the dynamic traits by functional quantitative trait loci (QTL) mapping methods has the benefits to (1) understand the genetic control of the whole dynamic process of the quantitative traits and (2) improve the statistical power to detect QTL. One crucial issue in functional QTL mapping is how to correctly describe the smoothness of trajectories of functional valued traits. We develop an efficient Bayesian nonparametric multiple-loci procedure for mapping dynamic traits. The method uses the Bayesian P-splines with (nonparametric) B-spline bases to specify the functional form of a QTL trajectory and a random walk prior to automatically determine its degree of smoothness. An efficient deterministic variational Bayes algorithm is used to implement both (1) the search of an optimal subset of QTL among large marker panels and (2) estimation of the genetic effects of the selected QTL changing over time. Our method can be fast even on some large-scale data sets. The advantages of our method are illustrated on both simulated and real data sets.
Fine-Scale Analysis of Parasite Resistance Genes in the Red Flour Beetle, Tribolium castaneum
Authors: Zhong Daibin , Pai Aditi , Wang Mei-Hui , Keech Naomi , Yan Guiyun 
Published: June 2013

Abstract
Parasite infection impacts population dynamics through effects on fitness and fecundity of the individual host. In addition to the known roles of environmental factors, host susceptibility to parasites has a genetic basis that has not been well characterized. We previously mapped quantitative trait loci (QTL) for susceptibility to rat tapeworm (Hymenolepis diminuta) infection in Tribolium castaneum using dominant AFLP markers; however, the resistance genes were not identified. Here, we refined the QTL locations and increased the marker density in the QTL regions using new microsatellite markers, sequence-tagged site markers, and single-strand conformational polymorphism markers. Resistance QTL in three linkage groups (LG3, LG6, and LG8) were each mapped to intervals &lt;1.0 cM between two codominant markers. The effects of 21 genes in the three QTL regions were investigated by using quantitative RT-PCR analysis, and transcription profiles were obtained from the resistant TIW1 and the susceptible cSM strains. Based on transcription data, eight genes were selected for RNA interference analysis to investigate their possible roles in H. diminuta resistance, including cytochrome P450 (LOC657454) and Toll-like receptor 13 (TLR13, LOC662131). The transcription of P450 and TLR13 genes in the resistant TIW1 strains was reduced more than ninefold relative to the control. Moreover, the effects of gene knockdown of P450 and TLR13 caused resistant beetles to become susceptible to tapeworm infection, which strongly suggests an important role for each in T. castaneum resistance to H. diminuta infection.
The RNA-Binding Protein Whi3 Is a Key Regulator of Developmental Signaling and Ploidy inSaccharomyces cerevisiae
Authors: Schladebeck Sarah , Mösch Hans-Ulrich 
Published: June 2013

AbstractIn Saccharomyces cerevisiae, the RNA-binding protein Whi3 controls cell cycle progression, biofilm formation, and stress response by post-transcriptional regulation of the Cdc28-Cln3 cyclin-dependent protein kinase and the dual-specificity protein kinase Yak1. Previous work has indicated that Whi3 might govern these processes by additional, yet unknown mechanisms. In this study, we have identified additional effectors of Whi3 that include the G1 cyclins Cln1/Cln2 and two known regulators of biofilm formation, the catalytic PKA subunit Tpk1 and the transcriptional activator Tec1. We also provide evidence that Whi3 regulates production of these factors by post-transcriptional control and might exert this function by affecting translational elongation. Unexpectedly, we also discovered that Whi3 is a key regulator of cellular ploidy, because haploid whi3Δ mutant strains exhibit a significant increase-in-ploidy phenotype that depends on environmental conditions. Our data further suggest that Whi3 might control stability of ploidy by affecting the expression of many key genes involved in sister chromatid cohesion and of NIP100 that encodes a component of the yeast dynactin complex for chromosome distribution. Finally, we show that absence of Whi3 induces a transcriptional stress response in haploid cells that is relieved by whole-genome duplication. In summary, our study suggests that the RNA-binding protein Whi3 acts as a central regulator of cell division and development by post-transcriptional control of key genes involved in chromosome distribution and cell signaling.
Plastic plasma interaction with plasmas with growing atomic number
Authors: Kasperczuk Andrzej , Pisarczyk Tadeusz , Chodukowski Tomasz , Kalinowska Zofia , Gus’kov Sergey , Demchenko Nikolai , Ullschmied Jiri , Krousky Eduard , Pfeifer Miroslav , Skala Jiri , Klir Daniel , Kravarik Jozef , Kubes Pavel , Cikhardt Jakub , Rezac Karel , Pisarczyk Pawel 
Published: June 2013

Abstract
This paper describes the investigation of the influence of target material atomic number (Z) on the laser-produced plasma pressure. For this reason, several target materials representing a wide range of atomic numbers (Z = 3.5 - 73), i.e. plastic (CH), Al, Cu, Ag, and Ta, were used. The results presented show that the plasma pressure decreases with growing atomic number but in a limited range of Z only. For higher Z, starting approximately from Z = 47 (Ag), the plasma pressure becomes constant, as confirmed by interferometric measurements and x-ray plasma imaging.
Consensus of compound-order multi-agent systems with communication delays
Authors: Yang Hong-yong , Guo Lei , Zhu Xun-lin , Cao Ke-cai , Zou Hai-lin 
Published: June 2013

AbstractIn complex environments, many distributed networked systems can only be illustrated with fractional-order dynamics. When multi-agent systems show individual diversity with difference agents, heterogeneous (integer-order and fractional-order) dynamics are used to illustrate the agent systems and compose integerfractional compounded-order systems. Applying Laplace transform and frequency domain theory of the fractional-order operator, the consensus of delayed multi-agent systems with directed weighted topologies is studied. Since an integer-order model is the special case of a fractional-order model, the results in this paper can be extended to systems with integer-order models. Finally, numerical examples are used to verify our results.
A novel method for non-destructive Compton scatter imaging based on the genetic algorithm
Authors: Ashrafi Saleh , Jahanbakhsh Okhtay , Alizadeh Davood , Salehpour Behrooz 
Published: June 2013

Abstract
Compton scattering tomography is widely used in numerous applications such as biomedical imaging, nondestructive industrial testing and environmental survey, etc. This paper proposes the use of the genetic algorithm (GA), which utilizes bio-inspired mathematical models, to construct an image of the insides of a test object via the scattered photons, from a voxel within the object. A NaI(Tl) scintillation detector and a 185 MBq 137Cs gamma ray source were used in the experimental measurements. The obtained results show that the proposed GA based method performs well in constructing images of objects.
Tachyon-polytropic inflation on the brane
Authors: Setare Mohammad , Kamali Vahid 
Published: June 2013

Abstract
We consider the tachyon-brane inflationary universe model in the context of a polytropic gas equation of state. In slow-roll approximation, we discuss general conditions of this model. For exponential potential, in high-energy limit the characteristics of the model are presented. By using the seven-year Wilkinson Microwave Anisotropy Probe (WMAP7) observational data, we constrain the cosmological parameters of the model.
Measurement and modeling of CO2 diffusion coefficient in Saline Aquifer at reservoir conditions
Authors: Azin Reza , Mahmoudy Mohamad , Raad Seyed , Osfouri Shahriar 
Published: June 2013

AbstractStorage of CO2 in deep saline aquifers is a promising techniques to mitigate global warming and reduce greenhouse gases (GHG). Correct measurement of diffusivity is essential for predicting rate of transfer and cumulative amount of trapped gas. Little information is available on diffusion of GHG in saline aquifers. In this study, diffusivity of CO2 into a saline aquifer taken from oil field was measured and modeled. Equilibrium concentration of CO2 at gas-liquid interface was determined using Henry’s law. Experimental measurements were reported at temperature and pressure ranges of 32–50°C and 5900–6900 kPa, respectively. Results show that diffusivity of CO2 varies between 3.52–5.98×10−9 m2/s for 5900 kPa and 5.33–6.16×10−9 m2/s for 6900 kPa initial pressure. Also, it was found that both pressure and temperature have a positive impact on the measures of diffusion coefficient. Liquid swelling due to gas dissolution and variations in gas compressibility factor as a result of pressure decay was found negligible. Measured diffusivities were used model the physical model and develop concentration profile of dissolved gas in the liquid phase. Results of this study provide unique measures of CO2 diffusion coefficient in saline aquifer at high pressure and temperature conditions, which can be applied in full-field studies of carbon capture and sequestration projects.
An exploration of FMCDM approach for evaluating the outcome/success of GSD projects
Authors: Sangaiah Arun , Thangavelu Arun 
Published: June 2013

Abstract
This study presents a fuzzy multi-criteria decision making (FMCDM) approach for analyzing the influential factors affecting the outcome/success of global software development (GSD) projects. The main aim of this study is to demonstrate the potential of proposed methodology based on FMCDM which is used to measure the offshore/onsite teams’ partnership quality dimensions and underlying the influential factors towards the outcome of GSD projects. The uncertainty and subjective vagueness within the decision making process are dealing with fuzzy linguistic terms quantified in an interval scale [0,1]. The proposed FMDCM framework is used to determine the priority weights of partnership quality factors and rating the GSD project outcome/success from the service provider perspective into three dimensions: service quality, schedule and cost improvement. The predicted GSD project outcome values are obtained to facilitate organization and to determine the impact of offshore/on-site teams’ partnership quality towards success of GSD project outcome otherwise initiate actions to improve the GSD project outcome. This study established survey research method that involves thirty-eight critical influential factors evaluated by twenty software professionals for their assessment of GSD projects outcome in India.
Integration of thermophysiological body model in CFD
Authors: Pichurov George , Stankov Peter 
Published: June 2013

Abstract
A two-node mathematical model of the human thermophysiological system has been integrated into a Computational Fluid Dynamic (CFD) simulation of the airflow in a room. Temperature inputs from the CFD are used by the model to evaluate the dry and latent heat flux from the body surface and output them as boundary conditions. This is an iterative process and convergence is ensured by under-relaxation of the latent heat flux. The model also considers the dry and latent heat resistance of clothing. Numerical predictions of the body heat loss and airflow are compared against physical measurements in a climate chamber. Good agreement was observed when using the low Reynolds number turbulence model. The integrated simulation performs well under wide set of conditions, predicting body core and skin temperature, blood flow, skin wittedness, as well as the transfer of heat and moisture released by the body into the room.
A fractal circular polarized RFID tag antenna
Authors: Chaouki Guesmi , Ferchichi Abdelhak , Gharsallah Ali 
Published: June 2013

Abstract
In this paper, we present a novel fractal antenna for radiofrequency identification (RFID) tags. The proposed antenna has a resonant frequency equal to 2.45GHz and circular polarization. The fractal technique was very useful to obtain a miniaturization of antenna size by more than 30%. The gain and directivity of the antenna are acceptable for the desired RFID application. All the results are obtained using CST Microwave simulation tool.
Correlation between permanent deformation-related performance parameters of asphalt concrete mixes and binders
Authors: Adorjányi Kálmán , Füleki Péter 
Published: June 2013

Abstract
This paper examines methods to predict the performance of hot asphalt concrete mixes based on performance parameters of binders. Specifically, relationships between binder parameters determined from multiple stress creep and recovery tests were correlated to the creep parameters of hot asphalt concrete mixes obtained from cyclic load compression testing. For the determination of creep parameters, a modified expression of the creep curve is proposed to cover the entire spectrum of permanent deformation; including the tertiary creep phase. Non-recoverable compliance, unrecovered strain, and recoverable strain of binders show good correlation to creep parameters of hot asphalt concrete mixes such as creep rate and high temperature performance ratio. Additionally, unrecovered strain and non-recoverable compliance of binders correlates well with mean rut depth of asphalt concrete mixes. However, no correlation has been detected between the difference in non-recoverable compliance of binders and permanent deformation parameters of asphalt concrete mixes.
Coordinated signal control for arterial intersections using fuzzy logic
Authors: Kermanian Davood , Zare Assef , Balochian Saeed 
Published: June 2013

Abstract
Every day growth of the vehicles has become one of the biggest problems of urbanism especially in major cities. This can waste people’s time, increase the fuel consumption, air pollution, and increase the density of cars and vehicles. Fuzzy controllers have been widely used in many consumer products and industrial applications with success over the past two decades. This article proposes a comprehensive model of urban traffic network using state space equations and then using Fuzzy Logic Tool Box and SIMULINK Program MATLAB a fuzzy controller in order to optimize and coordinate signal control at two intersections at an arterial road. The fuzzy controller decides to extend, early cut or terminate a signal phase and phase sequence to ensure smooth flow of traffic with minimal waiting time and length of queue. Results show that the performance of the proposed traffic controller at novel fuzzy model is better that of conventional controllers under normal and abnormal traffic conditions.
Biodiesel production from low cost and renewable feedstock
Authors: Gude Veera , Grant Georgene , Patil Prafulla , Deng Shuguang 
Published: June 2013

AbstractSustainable biodiesel production should: a) utilize low cost renewable feedstock; b) utilize energy-efficient, nonconventional heating and mixing techniques; c) increase net energy benefit of the process; and d) utilize renewable feedstock/energy sources where possible. In this paper, we discuss the merits of biodiesel production following these criteria supported by the experimental results obtained from the process optimization studies. Waste cooking oil, non-edible (low-cost) oils (Jatropha curcas and Camelina Sativa) and algae were used as feedstock for biodiesel process optimization. A comparison between conventional and non-conventional methods such as microwaves and ultrasound was reported. Finally, net energy scenarios for different biodiesel feedstock options and algae are presented.
Genotype by environment interaction and yield stability analysis of quality protein maize genotypes in Terai Region of Nepal
Authors: Shrestha Jiban 
Published: June 2013

Grain yield stability for the new maize genotypes is an important target in maize breeding programs. The main objective of this study was to identify stable high yielding quality protein maize (QPM) genotypes under various locations and years in terai region of Nepal. Six quality protein maize genotypes along with Poshilo Makai-1 (Standard Check) and Farmer’s Variety (Local Check) were tested at three different locations namely Ayodhyapuri-2, Devendrapur, Madi, Chitwan; Rajahar-8, Bartandi, Rajahar, Nawalparasi; Mangalpur-2, Rampur, Chitwan during 2011 and 2012 spring and winter seasons under rainfed condition. The experiment was conducted using Randomized Complete Block Design with two replications in farmer’s fields. There was considerable variation among genotypes and environments for grain yield. The analysis of variance showed that mean squares of environments (E) was highly significant and genotypes (G) and genotype x environment interaction (GEI) were non significant. The genotypes S03TLYQ-AB02 and RampurS03FQ02 respectively produced the higher mean grain yield 5422±564 kg/ha and 5274±603 kg/ha across the locations. Joint regression analysis showed that RampurS03FQ02 and S03TLYQ-AB02 with regression coefficient 1.10 and 1.22 respectively are the most stable genotypes over the tested environments. The coefficient of determination (R2) for genotypes Rampur S03FQ02 and S03TLYQ-AB02 were as high as 0.954, confirming their high predictability to stability. Further confirmation from GGE biplot analysis showed that maize genotype S03TLYQ-AB02 followed by Rampur S03FQ02 were more stable and adaptive genotypes across the tested environments. Thus these genotypes could be recommended to farmers for general cultivation.DOI: http://dx.doi.org/10.3126/ijasbt.v1i2.8202 Int J Appl Sci Biotechnol, Vol. 1(2): 75-79
A study of air borne fungal distribution and species diversity in Hill Fort Region of Channagiri, Karnataka, India
Authors: Thirumala S. , M. Pradeep Nathu , Aravinda H. B. 
Published: June 2013

Air borne fungi of Hill fort region of Channagiri is studied with help of Petriplate exposure method using Pottato dextrose agar media, petriplate exposure time is 15min. Sampling is taken in the month of January 2013 total 74 fungal colonies represented 07 fungal types were observed during the present investigation period. Environmental condition plays an importance role in the distribution of the fungal spores. Out of 07 fungal species most numbers of fungi are anamorphic groups. The fungal species were Aspergillus, Pencillium, Curvilaria, Cladosporium, Fusarium Rhizopus, Alternaria species were identified. Aspergillus species (47.2%) showing maximum contribution is observed where as Rhizopus shows minimum contribution.DOI: http://dx.doi.org/10.3126/ijasbt.v1i2.8203 Int J Appl Sci Biotechnol, Vol. 1(2): 60-62