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Search Results: 1 - 10 of 11018 matches for " Joseph Walder "
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Analysing interaction effects in forests using the mark correlation function
Walder O,Walder K
Forest@ , 2007, DOI: -
Abstract: The spatial distribution of trees in forests can be described and modelled by point processes where the points are given by the locations (coordinates) of the trees. Further properties of a tree like height or mean crown radius can be interpreted as so called marks of the considered point process characterising the points or trees in some way. The so called mark correlation function describes the spatial correlation of these marks in the observed point pattern. In this paper we introduce a special mark, the overlapping or crown index. We show that mark correlation functions for the considered marks help to understand interaction effects of forest trees.
Modeling the fine root biomass dispersion using a special influence function
Walder O,Walder K
iForest : Biogeosciences and Forestry , 2008, DOI: 10.3832/ifor0469-0010141
Abstract: This paper presents a successful application of techniques from the adjustment theory for modeling interaction in fine root biomass dispersion. Using special distance and species dependent weightings the influence function for fine root biomass dispersion of two species is estimated. Using the estimated influence functions the fine root biomass is predicted at the locations where the real data was sampled. Goodness of fit of our model is evaluated by comparing sample values and predicted values. However, the results show successful coincidence between sampled and predicted values. Finally, we present an example for the root dispersion in a mixed stand of beeches and spruces in Saxony/Germany.
Analysing interaction effects in forests using the mark correlation function
Walder O,Walder K
iForest : Biogeosciences and Forestry , 2008, DOI: -
Abstract: The spatial distribution of trees in forests can be described and modelled by point processes where the points are given by the locations (coordinates) of the trees. Further properties of a tree like height or mean crown radius can be interpreted as so called marks of the considered point process characterising the points or trees in some way. The so called mark correlation function describes the spatial correlation of these marks in the observed point pattern. In this paper we introduce a special mark, the overlapping or crown index. We show that mark correlation functions for the considered marks help to understand interaction effects of forest trees.
A High-Performing and Cost-Effective SNP Genotyping Method Using rhPCR and Universal Reporters  [PDF]
Kristin Beltz, Daniel Tsang, Junzhou Wang, Scott Rose, Yun Bao, Yu Wang, Katelyn Larkin, Susan Rupp, Daniela Schrepfer, Krishnalekha Datta, Keith Gunderson, Chris Sailor, Scott Hansen, Joseph Dobosy, Lynette Lewis, Aurita Menezes, Joseph Walder, Mark Behlke, Caifu Chen
Advances in Bioscience and Biotechnology (ABB) , 2018, DOI: 10.4236/abb.2018.99034
Abstract: We have developed a novel dual enzyme chemistry called rhAmp® SNP genotyping based on RNase H2-dependent PCR (rhPCR) that provides high signal and specificity for SNP analysis. rhAmp SNP genotyping combines a unique two-enzyme system with 3’ end blocked DNA-RNA hybrid primers to interrogate SNP loci. Activation of the blocked primers occurs upon hybridization to its perfectly matched target, which eliminates or greatly reduces primer dimers. A thermostable hot-start RNase H2 cleaves the primer immediately 5’ of the ribose sugar, releasing the blocking group and allowing primer extension. PCR specificity is further improved with the use of a mutant Taq DNA polymerase, resulting in improved allelic discrimination. Signal generation is obtained using a universal reporter system which requires only two reporter probes for any bi-allelic SNP. 1000 randomly selected SNPs were chosen to validate the 95% design rate of the design pipeline. A subsampling of 130 human SNP targets was tested and achieved a 98% call rate, and 99% call accuracy. rhAmp SNP genotyping assays are compatible with various qPCR instruments including QuantStudioTM 7 Flex, CFX384TM, IntelliQube®, and Biomark HDTM. In comparison to TaqMan®, rhAmp SNP genotyping assays show higher signal (Rn) and greater cluster separation, resulting in more reliable SNP genotyping performance. The rhAmp SNP genotyping solution is suited for high-throughput SNP genotyping applications in humans and plants.
El cuerpo fragmentado
Paul Walder
Polis : Revista de la Universidad Bolivariana , 2004,
Abstract:
La palabra circulante. Territorialización económica del lenguaje
Paul Walder
Polis : Revista de la Universidad Bolivariana , 2004,
Abstract:
Studies of CP-conserving and CP-violating Bs mixing parameters with the D0 experiment
James Walder
Physics , 2007,
Abstract: This paper summarises the recent results of the Run IIa D0 experiment at the Tevatron Collider at Fermilab on the observable parameters of the $B_{s}$ meson. A measurement of the branching fraction $B_s->D_s^{(*)}D_s^{(*)}$ is reported, which provides an estimate of the width difference $\Delta\Gamma_{s}^{CP}/\Delta\Gamma_{s}$. Through the decay $B_{s} \to J/\psi \phi$ the width difference $\Delta\Gamma_{s}$ is extracted, and for the first time a constraint is set on the CP-violating phase $\phi_{s}$, although a four-fold ambiguity remains. This result is combined with other D0 measurements to yield $\Delta\Gamma_{s}=0.13\pm0.09 {\rm ps^{-1}}$, $\phi_{s} = -0.70^{+0.47}_{-0.39}$.
Rank k Cholesky Up/Down-dating on the GPU: gpucholmodV0.2
Christian Walder
Computer Science , 2010,
Abstract: In this note we briefly describe our Cholesky modification algorithm for streaming multiprocessor architectures. Our implementation is available in C++ with Matlab binding, using CUDA to utilise the graphics processing unit (GPU). Limited speed ups are possible due to the bandwidth bound nature of the problem. Furthermore, a complex dependency pattern must be obeyed, requiring multiple kernels to be launched. Nonetheless, this makes for an interesting problem, and our approach can reduce the computation time by a factor of around 7 for matrices of size 5000 by 5000 and k=16, in comparison with the LINPACK suite running on a CPU of comparable vintage. Much larger problems can be handled however due to the O(n) scaling in required GPU memory of our method.
RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers
Joseph R Dobosy, Scott D Rose, Kristin R Beltz, Susan M Rupp, Kristy M Powers, Mark A Behlke, Joseph A Walder
BMC Biotechnology , 2011, DOI: 10.1186/1472-6750-11-80
Abstract: Pyrococcus abyssi (P.a.) RNase H2 was used to enable PCR to be performed using blocked primers containing a single ribonucleotide residue which are activated via cleavage by the enzyme (rhPCR). Cleavage occurs 5'-to the RNA base following primer hybridization to the target DNA. The requirement of the primer to first hybridize with the target sequence to gain activity eliminates the formation of primer-dimers and greatly reduces misamplification of closely related sequences. Mismatches near the scissile linkage decrease the efficiency of cleavage by RNase H2, further increasing the specificity of the assay. When applied to the detection of single nucleotide polymorphisms (SNPs), rhPCR was found to be far more sensitive than standard allele-specific PCR. In general, the best discrimination occurs when the mismatch is placed at the RNA:DNA base pair.rhPCR eliminates the formation of primer dimers and markedly improves the specificity of PCR with respect to off-target amplification. These advantages of the assay should find utility in challenging qPCR applications such as genotyping, high level multiplex assays and rare allele detection.Quantitative PCR (qPCR) is usually performed in real-time mode using fluorescence detection methods. In one commonly used format (the 5'-nuclease assay), qPCR involves three oligonucleotides wherein the forward and reverse primers direct DNA amplification spanning the hybridization site for a third fluorescently labeled oligonucleotide probe. The probe typically contains a fluorescence reporter dye and a quencher. Separation of the reporter and quencher due to cleavage of the probe by the 5'-nuclease activity of the DNA polymerase leads to an increase of fluorescence and a detectable signal [1-3]. Quantitative PCR can also use nucleic acid binding dyes such as SYBR? Green or Eva Green? that increase fluorescence in the presence of double-stranded DNA (dsDNA). Nucleic acid binding dye systems use only two oligonucleotides, the forward and
Radiative cooling instability in 1D colliding flows
Rolf Walder,Doris Folini
Physics , 1996,
Abstract: Radiative shock waves show a strong cooling instability at temperatures above approximately 2 times 10^5 K. We numerically investigate this instability by simulating different astronomical objects in which colliding flows play an outstanding role: Wind bubbles, supernova remnants, and colliding winds. Computing the flow of each object over a large part of its evolutionary time and resolving all physically relevant scales, we find several phenomenologically different types of this instability. If two smooth flows collide, the instability follows a periodic limit cycle with two modes being important. The connection between the radiative loss function and the mode and type of the overstability is discussed. The collision of non-smooth flows can temporarily result in an aperiodic evolution of the system. After a characteristic relaxation time the instability then becomes periodic again. Such disturbances as well as violent types of the instability can excite oscillations of the thin layer of cold compressed gas downstream of the shock, which in turn can influence the stability of the radiative shock.
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