bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetics of Ascites Resistance and Tolerance in Chicken: A Random Regression Approach
Authors: Kause Antti , van Dalen Sacha , Bovenhuis Henk 
Published: May 2012

Abstract
Resistance and tolerance are two complementary mechanisms to reduce the detrimental effects of parasites, pathogens, and production diseases on host performance. Using body weight and ascites data on domesticated chicken Gallus gallus domesticus, we demonstrate the use of random regression animal model and covariance functions to estimate genetic parameters for ascites resistance and tolerance and illustrate the way individual variation in resistance and tolerance induce both genotype re-ranking and changes in variation of host performance along increasing ascites severity. Tolerance to ascites displayed significant genetic variance, with the estimated breeding values of tolerance slope ranging from strongly negative (very sensitive genotype) to weakly negative (less sensitive). Resistance to ascites had heritability of 0.34. Both traits are hence expected to respond to selection. The two complementary defense strategies, tolerance and resistance, were genetically independent. Ascites induced changes to the correlations between ascites resistance and body weight, with the genetic correlations being weak when birds were ascites-free but moderately negative when both healthy and affected birds were present. This likely results because ascites reduces growth, and thus high ascites incidence is genetically related to low adult body weight. Although ascites induced elevated phenotypic and genetic variances in body weight of affected birds, heritability displayed negligible changes across healthy and affected birds. Ascites induced moderate genotype re-ranking in body weight, with the genetic correlation of healthy birds with mildly affected birds being unity but with severely affected birds 0.45. This study demonstrates a novel approach for exploring genetics of defense traits and their impact on genotype-by-environment interactions.
Two-Phase Analysis in Consensus Genetic Mapping
Authors: Ronin Y , Mester D , Minkov D , Belotserkovski R , Jackson B N , Schnable P S , Aluru S , Korol A 
Published: May 2012

AbstractNumerous mapping projects conducted on different species have generated an abundance of mapping data. Consequently, many multilocus maps have been constructed using diverse mapping populations and marker sets for the same organism. The quality of maps varies broadly among populations, marker sets, and software used, necessitating efforts to integrate the mapping information and generate consensus maps. The problem of consensus genetic mapping (MCGM) is by far more challenging compared with genetic mapping based on a single dataset, which by itself is also cumbersome. The additional complications introduced by consensus analysis include inter-population differences in recombination rate and exchange distribution along chromosomes; variations in dominance of the employed markers; and use of different subsets of markers in different labs. Hence, it is necessary to handle arbitrary patterns of shared sets of markers and different level of mapping data quality. In this article, we introduce a two-phase approach for solving MCGM. In phase 1, for each dataset, multilocus ordering is performed combined with iterative jackknife resampling to evaluate the stability of marker orders. In this phase, the ordering problem is reduced to the well-known traveling salesperson problem (TSP). Namely, for each dataset, we look for order that gives minimum sum of recombination distances between adjacent markers. In phase 2, the optimal consensus order of shared markers is selected from the set of allowed orders and gives the minimal sum of total lengths of nonconflicting maps of the chromosome. This criterion may be used in different modifications to take into account the variation in quality of the original data (population size, marker quality, etc.). In the foregoing formulation, consensus mapping is considered as a specific version of TSP that can be referred to as “synchronized TSP.” The conflicts detected after phase 1 are resolved using either a heuristic algorithm over the entire chromosome or an exact/heuristic algorithm applied subsequently to the revealed small non-overlapping regions with conflicts separated by non-conflicting regions. The proposed approach was tested on a wide range of simulated data and real datasets from maize.
Identification of Mutant Versions of the Spt16 Histone Chaperone That Are Defective for Transcription-Coupled Nucleosome Occupancy in Saccharomyces cerevisiae
Authors: Hainer Sarah J , Charsar Brittany A , Cohen Shayna B , Martens Joseph A 
Published: May 2012

Abstract
The highly conserved FACT (Facilitates Chromatin Transactions) complex performs essential functions in eukaryotic cells through the reorganization of nucleosomes. During transcription, FACT reorganizes nucleosomes to allow passage of RNA Polymerase II and then assists in restoring these nucleosomes after RNA Polymerase II has passed. We have previously shown, consistent with this function, that Spt16 facilitates repression of the Saccharomyces cerevisiae SER3 gene by maintaining nucleosome occupancy over the promoter of this gene as a consequence of intergenic transcription of SRG1 noncoding DNA. In this study, we report the results of a genetic screen to identify mutations in SPT16 that derepress SER3. Twenty-five spt16 mutant alleles were found to derepress SER3 without causing significant reductions in either SRG1 RNA levels or Spt16 protein levels. Additional phenotypic assays indicate that these mutants have general transcription defects related to altered chromatin structure. Our analyses of a subset of these spt16 mutants reveal defects in SRG1 transcription-coupled nucleosome occupancy over the SER3 promoter. We provide evidence that these mutants broadly impair transcription-coupled nucleosome occupancy at highly transcribed genes but not at lowly transcribed genes. Finally, we show that one consequence shared by these mutations is the reduced binding of mutant Spt16 proteins across SRG1 and other highly transcribed genes. Taken together, our results highlight an important role for Spt16 in orchestrating transcription-coupled nucleosome assembly at highly transcribed regions of the genome, possibly by facilitating the association of Spt16 during this process.
Regulation of Histone Gene Expression in Budding Yeast
Authors: Eriksson Peter R , Ganguli Dwaipayan , Nagarajavel V , Clark David J 
Published: May 2012

AbstractWe discuss the regulation of the histone genes of the budding yeast Saccharomyces cerevisiae. These include genes encoding the major core histones (H3, H4, H2A, and H2B), histone H1 (HHO1), H2AZ (HTZ1), and centromeric H3 (CSE4). Histone production is regulated during the cell cycle because the cell must replicate both its DNA during S phase and its chromatin. Consequently, the histone genes are activated in late G1 to provide sufficient core histones to assemble the replicated genome into chromatin. The major core histone genes are subject to both positive and negative regulation. The primary control system is positive, mediated by the histone gene-specific transcription activator, Spt10, through the histone upstream activating sequences (UAS) elements, with help from the major G1/S-phase activators, SBF (Swi4 cell cycle box binding factor) and perhaps MBF (MluI cell cycle box binding factor). Spt10 binds specifically to the histone UAS elements and contains a putative histone acetyltransferase domain. The negative system involves negative regulatory elements in the histone promoters, the RSC chromatin-remodeling complex, various histone chaperones [the histone regulatory (HIR) complex, Asf1, and Rtt106], and putative sequence-specific factors. The SWI/SNF chromatin-remodeling complex links the positive and negative systems. We propose that the negative system is a damping system that modulates the amount of transcription activated by Spt10 and SBF. We hypothesize that the negative system mediates negative feedback on the histone genes by histone proteins through the level of saturation of histone chaperones with histone. Thus, the negative system could communicate the degree of nucleosome assembly during DNA replication and the need to shut down the activating system under replication-stress conditions. We also discuss post-transcriptional regulation and dosage compensation of the histone genes.
Progression of Periodontal Destruction and the Roles of Advanced Glycation End Products in Experimental Diabetes
Authors: Chang Po‐Chun , Chien Li‐Ying , Yeo Jin Fei , Wang Yi‐Ping , Chung Min‐Chun , Chong Li Yen , Kuo Mark Yen‐Ping , Chen Chun‐Hao , Chiang Huan‐Ching , Ng Benjamin N. , Lee Qi Qi , Phay Yong Kang , Ng Jeffery R. , Erk Kok Yong 
Published: May 2012

Background: Progression of diabetes‐associated periodontal destruction and the roles of advanced glycation end products (AGEs) are investigated.Methods: Diabetes was induced by streptozocotin injection, and periodontitis was induced via silk ligature placement with Porphyromonas gingivalis lipopolysaccharide injection in 64 Sprague‐Dawley rats for 7 to 21 days. The quality of alveolar bone and attachment loss (AL) were measured by microcomputed tomography and histology. Destruction profiles were evaluated by histology, histochemistry, immunohistochemistry, and quantitative assessments of inflammatory cells, expression of receptors for AGEs (RAGE), tartrate‐resistant acid phosphatase, and proliferating cell nuclear antigen.Results: Without periodontitis induction, there was no obvious morphologic change in the periodontium, although slight elevations of AGEs and RAGE levels were noted in animals with diabetes. In the group with experimental periodontitis, significant periodontal bone loss was noted in animals both with and without diabetes from day 7, with more progressive bone loss in animals with diabetes during days 14 to 21. Histologically, the disruption of attachment and inflammation were observed from day 7, but subsequently subsided in animals without diabetes. A stronger and more prolonged response with significant AL was observed in animals with diabetes. Stronger inflammation, attenuated and persistent resorptive activity, and weaker proliferating potential were demonstrated by animals with diabetes. AGE deposition and RAGE expression were noted in animals without diabetes but with periodontitis, although levels were considerably elevated in the later stages in animals with diabetes.Conclusions: Diabetes augments periodontal destruction by reducing the proliferating capability and activating resorptive activities. Presence of the AGE‐RAGE axis without diabetes implies that it is involved in the regulation of inflammation.
Estimating Horizontal Well PI to Develop Giant Carbonate Reservoir with Artificial Lift
Authors: Al-Otaibi Majid , Pardo Cesar H. , Gunarto Ronny , Kanfar Mohammed 
Published: May 2012

Abstract
Productivity index (PI) is one of the most important well parameters required to have an optimum reservoir development plan in terms of well spacing, number of wells required and ensuring the deliverability of the production target. Having correct PI estimation is also crucial to optimize artificial lift system design when required.
The paper discusses the methodology to estimate horizontal well PI using limited actual data from existing vertical well performances in a giant field that is still in the development phase. Vertical wells’ Pi's were calculated based on the pressure transient analysis, taking into account the correction for stabilized bottom hole flowing pressure (Pwf) and reservoir pressure (Pr). As a means of quality control, the calculated vertical well PI was compared against the radial flow equation using the transmissibility value obtained from the well test data. Vertical wells PI maps were constructed then verified against the reservoir properties distribution, which are well developed in the crest of the field. Converting PIs from vertical to horizontal well configuration involved an analytical calculation that was further tested against actual PI results. The ratio between horizontal and vertical well's PI is obtained by comparing Joshi's and Darcy's equation. Conversion factors per reservoir and area were determined and applied to generate horizontal PI contour maps. These maps were used to assign a PI value to each of the future producers in the field. The estimated values exhibited a reasonable match with actual existing data. Notwithstanding this match, minor discrepancies between estimated and actual PI are analyzed in this paper to further improve the proposed methodology. Reservoir heterogeneities and effective lateral length which contributes to the total well flow are the main reasons for the differences. The impact of the effective lateral length on the actual PI was evaluated and sensitized for better prediction of the well performance, whereas the reservoir heterogeneity influence was assessed using a correlation that includes the known petrophysical properties to estimate the PI of new drilled and undrilled wells.
A Singularly Perturbed Convection Diffusion Turning Point Problem with an Interior Layer
Authors: O'Riordan Eugene , Quinn Jason 
Published: May 2012

Abstract A finite difference scheme on special piecewise-uniform grids
condensing in tA linear singularly perturbed interior turning point problem with a continuous convection coefficient is examined in this paper. Parameter uniform numerical methods composed of monotone finite difference operators and piecewise-uniform Shishkin meshes, are constructed and analysed for this class of problems. A refined Shishkin mesh is placed around the location of the interior layer and we consider disrupting the centre point of this fine mesh away from the point where the convection coefficient is zero. Numerical results are presented to illustrate the theoretical parameter-uniform error bounds established.
Maximum Norm a Posteriori Error Estimation For a Time-dependent Reaction-diffusion Problem
Authors: Kopteva Natalia , Linß Torsten 
Published: May 2012

Abstract A semilinear second-order singularly perturbed parabolic equation in one
space dimension is considered.
For this equation, we give computable a posteriori error estimates
in the maximum norm for a difference scheme that uses Backward-Euler in
time and central differencing in space.
Sharp L¹-norm bounds for the Green's function of the parabolic operator
and its derivatives are derived that form the basis of the a posteriori
error analysis.
Numerical results are presented.
Divergence Preserving Interpolation on Anisotropic Quadrilateral Meshes
Authors: Braack Malte , Lube Gert , Röhe Lars 
Published: May 2012

Abstract For the solution of incompressible fluid models with inf-sup stable
finite element pairs for velocity and pressure, interpolation
operators are desirable which preserve the property of discrete zero
divergence and enjoy the same local approximation properties as
standard interpolation operators. In this work, we show how an
anisotropic interpolation operator can be modified preserving the
discrete divergence and maintaining certain anisotropic
interpolation properties. Beside the construction of such an
operator for special anisotropic meshes, we discuss the
applicability of anisotropic grid resolution of boundary layers for
incompressible low-turbulent flow problems.
A Note on the Convergence Analysis of a Diffuse-domain Approach
Authors: Franz Sebastian , Roos Hans-Görg , Gärtner Roland , Voigt Axel 
Published: May 2012

Abstract We analyse the error behaviour of a diffuse-domain approximation of
an elliptic differential equation. In one dimension and for a
half-plane problem in two dimensions an approximation quality of
order one in the interface parameter is shown.
Some supporting numerical experiments are also presented.
A Local Projection Stabilization Method with Shock Capturing and Diagonal Mass Matrix for Solving Non-stationary Transport Dominated Problems
Authors: Schieweck Friedhelm , Skrzypacz Piotr 
Published: May 2012

AbstractWe consider a time-dependent convection diffusion equation in the
transport dominated case.
As a stabilization method in space we propose a new variant of Local
Projection Stabilization (LPS) which uses special enriched bubble functions
such that L²-orthogonal local basis functions can be constructed.
L²-orthogonal basis functions lead to a diagonal mass matrix which is
advantageous for time discretization.
We use the discontinuous Galerkin method of polynomial order one for the
discretization in time which is superconvergent of order three at the
endpoints of the time intervals.
In order to avoid the remaining oscillations in the LPS-solution we
add for each time step
in the space discretization an extra shock capturing term which acts only
locally on those mesh cells where an error-indicator is relatively large.
The novelty in the shock capturing term is that the scaling factor in
front of the additive diffusion term is computed from a
low order post-processing error.
As a result we obtain both, an oscillation-free discrete solution and
the information about the local regions where this solution is still
inaccurate due to some smearing. The latter information can be used to
create in each time step an adaptively refined space mesh.
Whereas
the numerical experiments are restricted to one space dimension
the proposed ideas work also in the multi-dimensional spatial case.
The numerical tests show that the discrete solution with shock capturing
is oscillation-free and of optimal accuracy in the regions outside of
the shock.
The effect of rapid and depot testosterone and estradiol on spatial performance in water maze
Authors: Hodosy Julius , Ostatnikova Daniela , Riljak Vladimír , Myslivecek Jaromir , Celec Peter 
Published: May 2012

AbstractMen and women differ in some cognitive functions including spatial abilities. These differences seem to be affected by sex steroids, but the results are controversial. The aim of this work is to describe the effects of rapid or depot testosterone and estradiol on spatial memory in rats. Thirty-two adult male Wistar rats were divided into 6 groups. Five groups were gonadectomized, and one group was left as control. Castrated groups received sterile oil, testosterone isobutyras, testosterone propionate, estradiol dipropionate or estradiol benzoate. We evaluated spatial performance (escape latency, overall improvement, and time in the quadrant after platform removal) of the rats in a spatial water maze. Animals receiving exogenous sex steroids showed higher plasma concentrations of the particular hormones. Experimental groups improved during the acquisition spatial trials in the water maze. No significant differences between the groups during probe trial were found. In overall improvement, the testosterone depot and estradiol depot groups showed less improvement in comparison to the control groups (P<0.05). No differences in respect to administered hormones were found in corresponding receptor gene expression in hippocampus. In conclusion, exogenous testosterone affects spatial memory of adult castrated males.
Antimicrobial activity, total phenolic content and flavonoid concentrations of Teucrium species
Authors: Stanković Milan , Stefanović Olgica , Čomić Ljiljana , Topuzović Marina , Radojević Ivana , Solujić Slavica 
Published: May 2012

AbstractIn vitro antimicrobial activity of 21 crude extracts obtained from seven taxa of the genus Teucrium (T. chamaedrys, T. montanum, T. arduini, T. polium, T. scordium subsp. scordium, T. scordium subsp. scordioides and T. botrys) was tested against bacterial and fungal species. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined using a microdilution analysis method. Total phenolic content and flavonoid concentrations were measured spectrophotometrically. Total phenols were determined using Folin-Ciocalteu reagent and their amounts ranged from 28.49 up to 159.84 mg CA/g of extract (chlorogenic acid equivalent). The amounts of flavonoids ranged from 38.17 up to 190.45 mg RU/g of extract (rutin equivalent).The plant extracts showed greater potential of antibacterial than antifungal activity. A relationship was found between total phenolics and biological activity. The highest level of total phenols was measured in the methanol extracts, which demonstrated higher antimicrobial activity than acetone and ethyl acetate extracts. Staphylococcus aureus ATCC 25923 appeared to be the most sensitive organism. Our results indicate that Teucrium spp extracts are rich sources of phenolic compounds and are promising candidates for further development as natural antimicrobial agents.
Integrin CD11b Negatively Regulates TLR9-Triggered Dendritic Cell Cross-Priming by Upregulating microRNA-146a
Authors: Bai Yi , Qian Cheng , Qian Li , Ma Feng , Hou Jin , Chen Yongjian , Wang Qingqing , Cao Xuetao 
Published: May 2012

Abstract
Dendritic cells (DCs) play critical roles in cross-priming to induce the CTL response against infection; however, the molecular mechanisms for the regulation of DC cross-priming need to be investigated further, which may help to improve the potency of DC vaccines through engineering modifications. Our previous studies showed that β2 integrin CD11b could control TLR-triggered NK cell cytotoxicity and macrophage inflammatory responses. CD11b is also abundantly expressed in DCs, but it is unknown whether CD11b participates in the regulation of DC cross-priming for the CTL response. Also, because microRNAs (miRNAs) are important regulators of the immune response, it remains unclear whether miRNAs are regulated by CD11b in DCs. In this study, we showed that CD11b deficiency upregulated TLR9-triggered, but not TLR4-triggered, IL-12p70 production in DCs, subsequently promoting DC cross-priming of the CTL response. Further experiments showed that CD11b selectively promoted TLR9-triggered miR-146a upregulation in DCs by sustaining late-phase NF-κB activation. Additionally, Notch1, a known positive regulator of IL-12p70 production in DCs, was confirmed to be directly targeted by miR-146a. miR-146a upregulation and Notch1 repression were determined to be responsible for the reduced IL-12p70 production in TLR9-triggered wild-type DCs compared with that in CD11b-deficient DCs. Therefore, CD11b and downstream miR-146a may be new negative regulators for DC cross-priming by suppressing Notch1 expression and IL-12p70 production. Our data indicate a new mechanism for the regulation of DC cross-priming through integrins and miRNAs.
Mammalian Target of Rapamycin Integrates Diverse Inputs To Guide the Outcome of Antigen Recognition in T Cells
Authors: Waickman Adam T. , Powell Jonathan D. 
Published: May 2012

Abstract
T cells must integrate a diverse array of intrinsic and extrinsic signals upon Ag recognition. Although these signals have canonically been categorized into three distinct events—Signal 1 (TCR engagement), Signal 2 (costimulation or inhibition), and Signal 3 (cytokine exposure)—it is now appreciated that many other environmental cues also dictate the outcome of T cell activation. These include nutrient availability, the presence of growth factors and stress signals, as well as chemokine exposure. Although all of these distinct inputs initiate unique signaling cascades, they also modulate the activity of the evolutionarily conserved serine/threonine kinase mammalian target of rapamycin (mTOR). Indeed, mTOR serves to integrate these diverse environmental inputs, ultimately transmitting a signaling program that determines the fate of newly activated T cells. In this review, we highlight how diverse signals from the immune microenvironment can guide the outcome of TCR activation through the activation of the mTOR pathway.