Residue length and solvation model dependency of elastinlike polypeptides

NASA Astrophysics Data System (ADS)

Bilsel, Mustafa; Arkin, Handan

2010-05-01

We have performed exhaustive multicanonical Monte Carlo simulations of elastinlike polypeptides with a chain including amino acids (valine-proline-glycine-valine-glycine)n or in short (VPGVG)n , where n changes from 1 to 4, in order to investigate the thermodynamic and structural properties. To predict the characteristic secondary structure motifs of the molecules, Ramachandran plots were prepared and analyzed as well. In these studies, we utilized a realistic model where the interactions between all types of atoms were taken into account. Effects of solvation were also simulated by using an implicit-solvent model with two commonly used solvation parameter sets and compared with the vacuum case.

Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions.

PubMed

Najibi, Seyed Morteza; Maadooliat, Mehdi; Zhou, Lan; Huang, Jianhua Z; Gao, Xin

2017-01-01

Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.

Construction of a 3D model of nattokinase, a novel fibrinolytic enzyme from Bacillus natto. A novel nucleophilic catalytic mechanism for nattokinase.

PubMed

Zheng, Zhong-liang; Zuo, Zhen-yu; Liu, Zhi-gang; Tsai, Keng-chang; Liu, Ai-fu; Zou, Guo-lin

2005-01-01

A three-dimensional structural model of nattokinase (NK) from Bacillus natto was constructed by homology modeling. High-resolution X-ray structures of Subtilisin BPN' (SB), Subtilisin Carlsberg (SC), Subtilisin E (SE) and Subtilisin Savinase (SS), four proteins with sequential, structural and functional homology were used as templates. Initial models of NK were built by MODELLER and analyzed by the PROCHECK programs. The best quality model was chosen for further refinement by constrained molecular dynamics simulations. The overall quality of the refined model was evaluated. The refined model NKC1 was analyzed by different protein analysis programs including PROCHECK for the evaluation of Ramachandran plot quality, PROSA for testing interaction energies and WHATIF for the calculation of packing quality. This structure was found to be satisfactory and also stable at room temperature as demonstrated by a 300ps long unconstrained molecular dynamics (MD) simulation. Further docking analysis promoted the coming of a new nucleophilic catalytic mechanism for NK, which is induced by attacking of hydroxyl rich in catalytic environment and locating of S221.

Density functional theory study of the conformational space of an infinitely long polypeptide chain

NASA Astrophysics Data System (ADS)

Ireta, Joel; Scheffler, Matthias

2009-08-01

The backbone conformational space of infinitely long polyalanine is investigated with density-functional theory and mapping the potential energy surface in terms of (L, θ) cylindrical coordinates. A comparison of the obtained (L, θ) Ramachandran-like plot with results from an extended set of protein structures shows excellent conformity, with the exception of the polyproline II region. It is demonstrated the usefulness of infinitely long polypeptide models for investigating the influence of hydrogen bonding and its cooperative effect on the backbone conformations. The results imply that hydrogen bonding together with long-range electrostatics is the main actuator for most of the structures assumed by protein residues.

Virtual Screening of Phytochemicals to Novel Target (HAT) Rtt109 in Pneumocystis Jirovecii using Bioinformatics Tools.

PubMed

Sugumar, Ramya; Adithavarman, Abhinand Ponneri; Dakshinamoorthi, Anusha; David, Darling Chellathai; Ragunath, Padmavathi Kannan

2016-03-01

Pneumocystis jirovecii is a fungus that causes Pneumocystis pneumonia in HIV and other immunosuppressed patients. Treatment of Pneumocystis pneumonia with the currently available antifungals is challenging and associated with considerable adverse effects. There is a need to develop drugs against novel targets with minimal human toxicities. Histone Acetyl Transferase (HAT) Rtt109 is a potential therapeutic target in Pneumocystis jirovecii species. HAT is linked to transcription and is required to acetylate conserved lysine residues on histone proteins by transferring an acetyl group from acetyl CoA to form e-N-acetyl lysine. Therefore, inhibitors of HAT can be useful therapeutic options in Pneumocystis pneumonia. To screen phytochemicals against (HAT) Rtt109 using bioinformatics tool. The tertiary structure of Pneumocystis jirovecii (HAT) Rtt109 was modeled by Homology Modeling. The ideal template for modeling was obtained by performing Psi BLAST of the protein sequence. Rtt109-AcCoA/Vps75 protein from Saccharomyces cerevisiae (PDB structure 3Q35) was chosen as the template. The target protein was modeled using Swiss Modeler and validated using Ramachandran plot and Errat 2. Comprehensive text mining was performed to identify phytochemical compounds with antipneumonia and fungicidal properties and these compounds were filtered based on Lipinski's Rule of 5. The chosen compounds were subjected to virtual screening against the target protein (HAT) Rtt109 using Molegro Virtual Docker 4.5. Osiris Property Explorer and Open Tox Server were used to predict ADME-T properties of the chosen phytochemicals. Tertiary structure model of HAT Rtt 109 had a ProSA score of -6.57 and Errat 2 score of 87.34. Structure validation analysis by Ramachandran plot for the model revealed 97% of amino acids were in the favoured region. Of all the phytochemicals subjected to virtual screening against the target protein (HAT) Rtt109, baicalin exhibited highest binding affinity towards the target protein as indicated by the Molegro score of 130.68 and formed 16 H-bonds. The ADME-T property prediction revealed that baicalin was non-mutagenic, non-tumorigenic and had a drug likeness score of 0.87. Baicalin has good binding with Rtt 109 in Pneumocystis jirovecii and can be considered as a novel and valuable treatment option for Pneumocystis pneumonia patients after subjecting it to invivo and invitro studies.

Virtual Screening of Phytochemicals to Novel Target (HAT) Rtt109 in Pneumocystis Jirovecii using Bioinformatics Tools

PubMed Central

Adithavarman, Abhinand Ponneri; Dakshinamoorthi, Anusha; David, Darling Chellathai; Ragunath, Padmavathi Kannan

2016-01-01

Introduction Pneumocystis jirovecii is a fungus that causes Pneumocystis pneumonia in HIV and other immunosuppressed patients. Treatment of Pneumocystis pneumonia with the currently available antifungals is challenging and associated with considerable adverse effects. There is a need to develop drugs against novel targets with minimal human toxicities. Histone Acetyl Transferase (HAT) Rtt109 is a potential therapeutic target in Pneumocystis jirovecii species. HAT is linked to transcription and is required to acetylate conserved lysine residues on histone proteins by transferring an acetyl group from acetyl CoA to form e-N-acetyl lysine. Therefore, inhibitors of HAT can be useful therapeutic options in Pneumocystis pneumonia. Aim To screen phytochemicals against (HAT) Rtt109 using bioinformatics tool. Materials and Methods The tertiary structure of Pneumocystis jirovecii (HAT) Rtt109 was modeled by Homology Modeling. The ideal template for modeling was obtained by performing Psi BLAST of the protein sequence. Rtt109-AcCoA/Vps75 protein from Saccharomyces cerevisiae (PDB structure 3Q35) was chosen as the template. The target protein was modeled using Swiss Modeler and validated using Ramachandran plot and Errat 2. Comprehensive text mining was performed to identify phytochemical compounds with antipneumonia and fungicidal properties and these compounds were filtered based on Lipinski’s Rule of 5. The chosen compounds were subjected to virtual screening against the target protein (HAT) Rtt109 using Molegro Virtual Docker 4.5. Osiris Property Explorer and Open Tox Server were used to predict ADME-T properties of the chosen phytochemicals. Results Tertiary structure model of HAT Rtt 109 had a ProSA score of -6.57 and Errat 2 score of 87.34. Structure validation analysis by Ramachandran plot for the model revealed 97% of amino acids were in the favoured region. Of all the phytochemicals subjected to virtual screening against the target protein (HAT) Rtt109, baicalin exhibited highest binding affinity towards the target protein as indicated by the Molegro score of 130.68 and formed 16 H-bonds. The ADME-T property prediction revealed that baicalin was non-mutagenic, non-tumorigenic and had a drug likeness score of 0.87. Conclusion Baicalin has good binding with Rtt 109 in Pneumocystis jirovecii and can be considered as a novel and valuable treatment option for Pneumocystis pneumonia patients after subjecting it to invivo and invitro studies. PMID:27134887

Isolation and in silico analysis of a novel H+-pyrophosphatase gene orthologue from the halophytic grass Leptochloa fusca

NASA Astrophysics Data System (ADS)

Rauf, Muhammad; Saeed, Nasir A.; Habib, Imran; Ahmed, Moddassir; Shahzad, Khurram; Mansoor, Shahid; Ali, Rashid

2017-02-01

Structure prediction can provide information about function and active sites of protein which helps to design new functional proteins. H+-pyrophosphatase is transmembrane protein involved in establishing proton motive force for active transport of Na+ across membrane by Na+/H+ antiporters. A full length novel H+-pyrophosphatase gene was isolated from halophytic grass Leptochloa fusca using RT-PCR and RACE method. Full length LfVP1 gene sequence of 2292 nucleotides encodes protein of 764 amino acids. DNA and protein sequences were used for characterization using bioinformatics tools. Various important potential sites were predicted by PROSITE webserver. Primary structural analysis showed LfVP1 as stable protein and Grand average hydropathy (GRAVY) indicated that LfVP1 protein has good hydrosolubility. Secondary structure analysis showed that LfVP1 protein sequence contains significant proportion of alpha helix and random coil. Protein membrane topology suggested the presence of 14 transmembrane domains and presence of catalytic domain in TM3. Three dimensional structure from LfVP1 protein sequence also indicated the presence of 14 transmembrane domains and hydrophobicity surface model showed amino acid hydrophobicity. Ramachandran plot showed that 98% amino acid residues were predicted in the favored region.

‘It’s All Done With Mirrors’: V.S. Ramachandran and the Material Culture of Phantom Limb Research

PubMed Central

Guenther, Katja

2016-01-01

This article examines the material culture of neuroscientist Vilayanur S. Ramachandran’s research into phantom limbs. In the 1990s Ramachandran used a ‘mirror box’ to ‘resurrect’ phantom limbs and thus to treat the pain that often accompanied them. The experimental success of his mirror therapy led Ramachandran to see mirrors as a useful model of brain function, a tendency that explains his attraction to work on ‘mirror neurons’. I argue that Ramachandran’s fascination with and repeated appeal to the mirror can be explained by the way it allowed him to confront a perennial problem in the mind and brain sciences, that of the relationship between a supposedly immaterial mind and a material brain. By producing what Ramachandran called a ‘virtual reality’, relating in varied and complex ways to the material world, the mirror reproduced a form of psycho-physical parallelism and dualistic ontology, while conforming to the materialist norms of neuroscience today. PMID:27292324

Beyond basins: φ,ψ preferences of a residue depend heavily on the φ,ψ values of its neighbors.

PubMed

Hollingsworth, Scott A; Lewis, Matthew C; Karplus, P Andrew

2016-09-01

The Ramachandran plot distributions of nonglycine residues from experimentally determined structures are routinely described as grouping into one of six major basins: β, PII , α, αL , ξ and γ'. Recent work describing the most common conformations adopted by pairs of residues in folded proteins [i.e., (φ,ψ)2 -motifs] showed that commonly described major basins are not true single thermodynamic basins, but are composed of distinct subregions that are associated with various conformations of either the preceding or following neighbor residue. Here, as documentation of the extent to which the conformational preferences of a central residue are influenced by the conformations of its two neighbors, we present a set of φ,ψ-plots that are delimited simultaneously by the φ,ψ-angles of its neighboring residues on both sides. The level of influence seen here is typically greater than the influence associated with considering the identities of neighboring residues, implying that the use of this heretofore untapped information can improve the accuracy of structure prediction algorithms and low resolution protein structure refinement. © 2016 The Protein Society.

Atomic structure of unligated laccase from Cerrena maxima at 1.76 A with molecular oxygen and hydrogen peroxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhukova, Yu. N., E-mail: amm@ns.crys.ras.ru; Lyashenko, A. V.; Lashkov, A. A.

2010-05-15

The three-dimensional structure of unligated laccase from Cerrena maxima was established by X-ray diffraction at 1.76-A resolution; R{sub work} = 18.07%, R{sub free} = 21.71%, rmsd of bond lengths, bond angles, and chiral angles are 0.008 A, 1.19{sup o}, and 0.077{sup o}, respectively. The coordinate error for the refined structure estimated from the Luzzati plot is 0.195 A. The maximum average error in the atomic coordinates is 0.047 A. A total of 99.4% of amino-acid residues of the polypeptide chain are in the most favorable, allowable, and accessible regions of the Ramachandran plot. The three-dimensional structures of the complexes ofmore » laccase from C. maxima with molecular oxygen and hydrogen peroxide were determined by the molecular simulation. These data provide insight into the structural aspect of the mechanism of the enzymatic cycle. The structure factors and the refined atomic coordinates were deposited in the Protein Data Bank (PDB-ID code is 3DIV).« less

Atomistic model of the spider silk nanostructure

NASA Astrophysics Data System (ADS)

Keten, Sinan; Buehler, Markus J.

2010-04-01

Spider silk is an ultrastrong and extensible self-assembling biopolymer that outperforms the mechanical characteristics of many synthetic materials including steel. Here we report atomic-level structures that represent aggregates of MaSp1 proteins from the N. Clavipes silk sequence based on a bottom-up computational approach using replica exchange molecular dynamics. We discover that poly-alanine regions predominantly form distinct and orderly beta-sheet crystal domains while disorderly structures are formed by poly-glycine repeats, resembling 31-helices. These could be the molecular source of the large semicrystalline fraction observed in silks, and also form the basis of the so-called "prestretched" molecular configuration. Our structures are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content.

The rate of cis-trans conformation errors is increasing in low-resolution crystal structures.

PubMed

Croll, Tristan Ian

2015-03-01

Cis-peptide bonds (with the exception of X-Pro) are exceedingly rare in native protein structures, yet a check for these is not currently included in the standard workflow for some common crystallography packages nor in the automated quality checks that are applied during submission to the Protein Data Bank. This appears to be leading to a growing rate of inclusion of spurious cis-peptide bonds in low-resolution structures both in absolute terms and as a fraction of solved residues. Most concerningly, it is possible for structures to contain very large numbers (>1%) of spurious cis-peptide bonds while still achieving excellent quality reports from MolProbity, leading to concerns that ignoring such errors is allowing software to overfit maps without producing telltale errors in, for example, the Ramachandran plot.

Structure prediction and binding sites analysis of curcin protein of Jatropha curcas using computational approaches.

PubMed

Srivastava, Mugdha; Gupta, Shishir K; Abhilash, P C; Singh, Nandita

2012-07-01

Ribosome inactivating proteins (RIPs) are defense proteins in a number of higher-plant species that are directly targeted toward herbivores. Jatropha curcas is one of the biodiesel plants having RIPs. The Jatropha seed meal, after extraction of oil, is rich in curcin, a highly toxic RIP similar to ricin, which makes it unsuitable for animal feed. Although the toxicity of curcin is well documented in the literature, the detailed toxic properties and the 3D structure of curcin has not been determined by X-ray crystallography, NMR spectroscopy or any in silico techniques to date. In this pursuit, the structure of curcin was modeled by a composite approach of 3D structure prediction using threading and ab initio modeling. Assessment of model quality was assessed by methods which include Ramachandran plot analysis and Qmean score estimation. Further, we applied the protein-ligand docking approach to identify the r-RNA binding residue of curcin. The present work provides the first structural insight into the binding mode of r-RNA adenine to the curcin protein and forms the basis for designing future inhibitors of curcin. Cloning of a future peptide inhibitor within J. curcas can produce non-toxic varieties of J. curcas, which would make the seed-cake suitable as animal feed without curcin detoxification.

Comments on `Area and power efficient DCT architecture for image compression' by Dhandapani and Ramachandran

NASA Astrophysics Data System (ADS)

Cintra, Renato J.; Bayer, Fábio M.

2017-12-01

In [Dhandapani and Ramachandran, "Area and power efficient DCT architecture for image compression", EURASIP Journal on Advances in Signal Processing 2014, 2014:180] the authors claim to have introduced an approximation for the discrete cosine transform capable of outperforming several well-known approximations in literature in terms of additive complexity. We could not verify the above results and we offer corrections for their work.

Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking.

PubMed

Sokkar, Pandian; Mohandass, Shylajanaciyar; Ramachandran, Murugesan

2011-07-01

We present a comparative account on 3D-structures of human type-1 receptor (AT1) for angiotensin II (AngII), modeled using three different methodologies. AngII activates a wide spectrum of signaling responses via the AT1 receptor that mediates physiological control of blood pressure and diverse pathological actions in cardiovascular, renal, and other cell types. Availability of 3D-model of AT1 receptor would significantly enhance the development of new drugs for cardiovascular diseases. However, templates of AT1 receptor with low sequence similarity increase the complexity in straightforward homology modeling, and hence there is a need to evaluate different modeling methodologies in order to use the models for sensitive applications such as rational drug design. Three models were generated for AT1 receptor by, (1) homology modeling with bovine rhodopsin as template, (2) homology modeling with multiple templates and (3) threading using I-TASSER web server. Molecular dynamics (MD) simulation (15 ns) of models in explicit membrane-water system, Ramachandran plot analysis and molecular docking with antagonists led to the conclusion that multiple template-based homology modeling outweighs other methodologies for AT1 modeling.

Conformational features of cepacian: the exopolysaccharide produced by clinical strains of Burkholderia cepacia.

PubMed

Nogueira, Carlos E Sampaio; Ruggiero, Jose R; Sist, Paola; Cescutti, Paola; Urbani, Ranieri; Rizzo, Roberto

2005-04-11

Conformational energy calculations and molecular dynamics investigations, both in water and in dimethyl sulfoxide, were carried out on the exopolysaccharide cepacian produced by the majority of the clinical strains of Burkholderia cepacia, an opportunistic pathogen causing serious lung infection in patients affected by cystic fibrosis, The investigation was aimed at defining the structural and conformational features, which might be relevant for clarification of the structure-function relationships of the polymer. The molecular dynamics calculations were carried out by Ramachandran-type energy plots of the disaccharides that constitute the polymer repeating unit. The dynamics of an oligomer composed of three repeating units were investigated in water and in Me2SO, a non-aggregating solvent. Analysis of the time persistence of hydrogen bonds showed the presence of a large number of favourable interactions in water, which were less evident in Me2SO. The calculations on the cepacian chain indicated that polymer conformational features in water were affected by the lateral chains, but were also largely dictated by the presence of solvent. Moreover, the large number of intra-chain hydrogen bonds in water disappeared in Me2SO solution, increasing the average dimension of the polymer chains.

Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Phi, Psi) energy maps and conformers in the gas phase, ether, and water.

PubMed

Wang, Zhi-Xiang; Duan, Yong

2004-11-15

The effects of solvation on the conformations and energies of alanine dipeptide (AD) have been studied by ab initio calculations up to MP2/cc-pVTZ//MP2/6-31G**, utilizing the polarizable continuum model (PCM) to mimic solvation effects. The energy surfaces in the gas phase, ether, and water bear similar topological features carved by the steric hindrance, but the details differ significantly due to the solvent effects. The gas-phase energy map is qualitatively consistent with the Ramachandran plot showing seven energy minima. With respect to the gas-phase map, the significant changes of the aqueous map include (1) the expanded low-energy regions, (2) the emergence of an energy barrier between C5-beta and alpha(R)-beta(2) regions, (3) a clearly pronounced alpha(R) minimum, a new beta-conformer, and the disappearance of the gas-phase global minimum, and (4) the shift of the dominant region in LEII from the gas-phase C7(ax) region to the alpha(L) region. These changes bring the map in water to be much closer to the Ramachandran plot than the gas-phase map. The solvent effects on the geometries include the elongation of the exposed N-H and C=O bonds, the shortening of the buried HN--CO peptide bonds, and the enhanced planarity of the peptide bonds. The energy surface in ether has features similar to those both in the gas phase and in water. The free energy order computed in the gas phase and in ether is in good agreement with experimental studies that concluded that C5 and C7(eq) are the dominant species in both the gas phase and nonpolar solvents. The free energy order in water is consistent with the experimental observation that the dominant C7(eq) in the nonpolar solvent was largely replaced by P(II)-like (i.e., beta) and alpha(R) in the strong polar solvents. Based on calculations on AD + 4H(2)O and other AD-water clusters, we suggest that explicit water-AD interactions may distort C5 and beta (or alpha(R) and beta) to an intermediate conformation. Our analysis also shows that the PCM calculations at the MP2/cc-pVTZ//MP2/6-31G** level give good descriptions to the bulk solvent polarization effect. The results presented in this article should be of sufficient quality to characterize the peptide bonds in the gas phase and solvents. The energy surfaces may serve as the basis for developing of strategies enabling the inclusion of solvent polarization in the force field.

SLC5A8-mediated Switching of STAT3 from a Pro-oncogenic Signal into a Proapoptotic Signal in Breast Cancer. Revision

DTIC Science & Technology

2009-06-01

Breast Cancer Selvakumar Elangovan,1,∗ Rajneesh Pathania,1,* Sabarish Ramachandran,1 Sudha Ananth, 1 Ravi Padia,1 Elangovan Gopal,1 Nikki Harvel2...Leslyn Hawthrown2, Thomas R . Boetter,3 Sylvia B. Smith,4 Puttur D. Prasad, 1 Vadivel Ganapathy1 and Muthusamy Thangaraju1, 5 Departments of...of mammary tumorigenesis and accelerated lung metastasis Sabarish Ramachandran, 1,∗ Selvakumar Elangovan, 1,∗ Rajneesh Pathania, 1 Sathananth

Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.

PubMed

Aliev, Abil E; Courtier-Murias, Denis

2010-09-30

Experimental NMR verification of MD simulations using 12 different force fields (AMBER, CHARMM, GROMOS, and OPLS-AA) and 5 different water models has been undertaken to identify reliable MD protocols for structure and dynamics elucidations of small open chain peptides containing Gly and Pro. A conformationally flexible tetrapeptide Gly-Pro-Gly-Gly was selected for NMR (3)J-coupling, chemical shift, and internuclear distance measurements, followed by their calculations using 2 μs long MD simulations in water. In addition, Ramachandran population maps for Pro-2 and Gly-3 residues of GPGG obtained from MD simulations were used for detailed comparisons with similar maps from the protein data bank (PDB) for large number of Gly and Pro residues in proteins. The MD simulations revealed strong dependence of the populations and geometries of preferred backbone and side chain conformations, as well as the time scales of the peptide torsional transitions on the force field used. On the basis of the analysis of the measured and calculated data, AMBER99SB is identified as the most reliable force field for reproducing NMR measured parameters, which are dependent on the peptide backbone and the Pro side chain geometries and dynamics. Ramachandran maps showing the dependence of conformational populations as a function of backbone ϕ/ψ angles for Pro-2 and Gly-3 residues of GPGG from MD simulations using AMBER99SB, AMBER03, and CHARMM were found to resemble similar maps for Gly and Pro residues from the PDB survey. Three force fields (AMBER99, AMBER99ϕ, and AMBER94) showed the least satisfactory agreement with both the solution NMR and the PDB survey data. The poor performance of these force fields is attributed to their propensity to overstabilize helical peptide backbone conformations at the Pro-2 and Gly-3 residues. On the basis of the similarity of the MD and PDB Ramachandran plots, the following sequence of transitions is suggested for the Gly backbone conformation: α(L) ⇆ β(PR) ⇆ β(S) ⇆ β(P) ⇆ α, where backbone secondary structures α(L) and α are associated with helices and turns, β(P) and β(PR) correspond to the left- and right-handed polyproline II structures and β(S) denotes the fully stretched backbone conformation. Compared to the force field dependence, less significant, but noteworthy, variations in the populations of the peptide backbone conformations were observed. For different solvent models considered, a correlation was noted between the number of torsional transitions in GPGG and the water self-diffusion coefficient on using TIP3P, TIP4P, and TIP5P models. In addition to MD results, we also report DFT derived Karplus relationships for Gly and Pro residues using B972 and B3LYP functionals.

Few Ramachandran Angle Changes Provide Interaction Strength Increase in Aβ42 versus Aβ40 Amyloid Fibrils

NASA Astrophysics Data System (ADS)

Bastidas, Oscar H.; Green, Benjamin; Sprague, Mary; Peters, Michael H.

2016-11-01

The pathology of Alzheimer’s disease can ultimately be traced to the increased aggregation stability of Aβ42 peptides which possess two extra residues (Ile 41 & Ala 42) that the non-pathological strain (Aβ40) lacks. We have found Aβ42 fibrils to exhibit stronger energies in inter-chain interactions and we have also identified the cause for this increase to be the result of different Ramachandran angle values in certain residues of the Aβ42 strain compared to Aβ40. These unique angle configurations result in the peptide planes in the fibril structures to be more vertical along the fibril axis for Aβ42 which thus reduces the inter-atomic distance between interacting atoms on vicinal peptide chains thereby increasing the electrostatic interaction energies. We lastly postulate that these different Ramachandran angle values could possibly be traced to the unique conformational folding avenues sampled by the Aβ42 peptide owing to the presence of its two extra residues.

On Ramachandran angles, closed strings and knots in protein structure

NASA Astrophysics Data System (ADS)

Chen, Si; Niemi, Antti J.

2016-08-01

The Ramachandran angles (φ,\\psi ) of a protein backbone form the vertices of a piecewise geodesic curve on the surface of a torus. When the ends of the curve are connected to each other similarly, by a geodesic, the result is a closed string that in general wraps around the torus a number of times both in the meridional and the longitudinal directions. The two wrapping numbers are global characteristics of the protein structure. A statistical analysis of the wrapping numbers in terms of crystallographic x-ray structures in the protein data bank (PDB) reveals that proteins have no net chirality in the ϕ direction but in the ψ direction, proteins prefer to display chirality. A comparison between the wrapping numbers and the concept of folding index discloses a non-linearity in their relationship. Thus these three integer valued invariants can be used in tandem, to scrutinize and classify the global loop structure of individual PDB proteins, in terms of the overall fold topology.

Ramachandran analysis of conserved glycyl residues in homologous proteins of known structure.

PubMed

Lakshmi, Balasubramanian; Sinduja, Chandrasekaran; Archunan, Govind; Srinivasan, Narayanaswamy

2014-06-01

High conservation of glycyl residues in homologous proteins is fairly frequent. It is commonly understood that glycine tends to be highly conserved either because of its unique Ramachandran angles or to avoid steric clash that would arise with a larger side chain. Using a database of aligned 3D structures of homologous proteins we identified conserved Gly in 288 alignment positions from 85 families. Ninety-six of these alignment positions correspond to conserved Gly residue with (φ, ψ) values allowed for non-glycyl residues. Reasons for this observation were investigated by in-silico mutation of these glycyl residues to Ala. We found in 94% of the cases a short contact exists between the C(β) atom of the introduced Ala with the atoms which are often distant in the primary structure. This suggests the lack of space even for a short side chain thereby explaining high conservation of glycyl residues even when they adopt (φ, ψ) values allowed for Ala. In 189 alignment positions, the conserved glycyl residues adopt (φ, ψ) values which are disallowed for Ala. In-silico mutation of these Gly residues to Ala almost always results in steric hindrance involving C(β) atom of Ala as one would expect by comparing Ramachandran maps for Ala and Gly. Rare occurrence of the disallowed glycyl conformations even in ultrahigh resolution protein structures are accompanied by short contacts in the crystal structures and such disallowed conformations are not conserved in the homologues. These observations raise the doubt on the accuracy of such glycyl conformations in proteins. © 2014 The Protein Society.

Extension of the Genetic Algorithm Based Malware Strategy Evolution Forecasting Model for Botnet Strategy Evolution Modeling

DTIC Science & Technology

2010-11-01

CHEN, Yan; PAXSON, Vern (2009). Automating Analysis of Large- Scale Botnet Probing Events. ASIACCS 󈧍: Proceedings of the 4th International...2004). Email Virus Propagation Modeling and Analysis. Technical report TRCSE- 03-04. – University of Massachussets, 2004. [37] RAMACHANDRAN, Krishna ...20, 8 pp. [38] STANIFORD, Stuart; PAXSON, Vern ; WEAVER, Nicholas (2002). How to 0wn the Internet in Your Spare Time. Proceedings of the 11 th

Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics

NASA Astrophysics Data System (ADS)

Sicard, François; Senet, Patrick

2013-06-01

Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers, however, from the same limitation, i.e., the non-trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachandran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates, and does not depend on the alignment to an arbitrarily chosen reference structure as usual in Cartesian PCA. We illustrate the robustness of this method in the case of a reference model protein, the small and very diffusive Met-enkephalin pentapeptide. We propose a justification a posteriori of the considered number of CVs necessary to bias the metadynamics simulation in terms of the one-dimensional free-energy profiles associated with Ramachandran dihedral angles along the amino-acid sequence.

Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics.

PubMed

Sicard, François; Senet, Patrick

2013-06-21

Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers, however, from the same limitation, i.e., the non-trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachandran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates, and does not depend on the alignment to an arbitrarily chosen reference structure as usual in Cartesian PCA. We illustrate the robustness of this method in the case of a reference model protein, the small and very diffusive Met-enkephalin pentapeptide. We propose a justification a posteriori of the considered number of CVs necessary to bias the metadynamics simulation in terms of the one-dimensional free-energy profiles associated with Ramachandran dihedral angles along the amino-acid sequence.

Molecular characterization of alkaline protease of Bacillus amyloliquefaciens SP1 involved in biocontrol of Fusarium oxysporum.

PubMed

Guleria, Shiwani; Walia, Abhishek; Chauhan, Anjali; Shirkot, C K

2016-09-02

An alkaline protease gene was amplified from genomic DNA of Bacillus amyloliquefaciens SP1 which was involved in effective biocontrol of Fusarium oxysporum. We investigated the antagonistic capacity of protease of B. amyloliquifaciens SP1, under in vitro conditions. The 5.62 fold purified enzyme with specific activity of 607.69U/mg reported 24.14% growth inhibition of F. oxysporum. However, no antagonistic activity was found after addition of protease inhibitor i.e. PMSF (15mM) to purified enzyme. An 1149bp nucleotide sequence of protease gene encoded 382 amino acids of 43kDa and calculated isoelectric point of 9.29. Analysis of deduced amino acid sequence revealed high homology (86%) with subtilisin E of Bacillus subtilis. The B. amyloliquefaciens SP1 protease gene was expressed in Escherichiax coli BL21. The expressed protease was secreted into culture medium by E. coli and exhibited optimum activity at pH8.0 and 60°C. The most reliable three dimensional structure of alkaline protease was determined using Phyre 2 server which was validated on the basis of Ramachandran plot and ERRAT value. The expression and structure prediction of the enzyme offers potential value for commercial application in agriculture and industry. Copyright © 2016 Elsevier B.V. All rights reserved.

Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model

PubMed Central

Mitra, Rajib; Jordan, Michael I.; Dunbrack, Roland L.

2010-01-01

Distributions of the backbone dihedral angles of proteins have been studied for over 40 years. While many statistical analyses have been presented, only a handful of probability densities are publicly available for use in structure validation and structure prediction methods. The available distributions differ in a number of important ways, which determine their usefulness for various purposes. These include: 1) input data size and criteria for structure inclusion (resolution, R-factor, etc.); 2) filtering of suspect conformations and outliers using B-factors or other features; 3) secondary structure of input data (e.g., whether helix and sheet are included; whether beta turns are included); 4) the method used for determining probability densities ranging from simple histograms to modern nonparametric density estimation; and 5) whether they include nearest neighbor effects on the distribution of conformations in different regions of the Ramachandran map. In this work, Ramachandran probability distributions are presented for residues in protein loops from a high-resolution data set with filtering based on calculated electron densities. Distributions for all 20 amino acids (with cis and trans proline treated separately) have been determined, as well as 420 left-neighbor and 420 right-neighbor dependent distributions. The neighbor-independent and neighbor-dependent probability densities have been accurately estimated using Bayesian nonparametric statistical analysis based on the Dirichlet process. In particular, we used hierarchical Dirichlet process priors, which allow sharing of information between densities for a particular residue type and different neighbor residue types. The resulting distributions are tested in a loop modeling benchmark with the program Rosetta, and are shown to improve protein loop conformation prediction significantly. The distributions are available at http://dunbrack.fccc.edu/hdp. PMID:20442867

Motion of the drawing hand induces a progressive increase in muscle activity of the non-dominant hand in Ramachandran's mirror-box therapy.

PubMed

Furukawa, Kiminobu; Suzuki, Harue; Fukuda, Jun

2012-11-01

To observe the real-time muscle activity of bilateral hands while subjects draw circles under 2 conditions: with and without using Ramachandran's mirror-box. A total of 24 healthy volunteers. Subjects drew 4 circles sequentially using their dominant hand with the other hand at rest, both with and without looking at a mirror image. Circles were marked by 8 dots on the paper, which subjects connected up to draw the shape. The activity of the bilateral first dorsal interosseus muscles was recorded using surface electromyography. Muscle activity of the dominant hand remained constant during each task. In contrast, muscle activity of the non-dominant hand increased under the condition of watching the image in the mirror, but was low under the non-watching condition. Furthermore, muscle activity of the non-dominant hand increased over the duration of the task. However, wide variation between subjects was observed under the mirror-image condition. Increased muscle action potential of the non-dominant hand may be induced by the circle drawing task of the dominant hand during Ramachandran's mirror-box therapy, which supports previous observations of increased brain activity caused by watching a mirror image.

Nanostructure and molecular mechanics of spider dragline silk protein assemblies

PubMed Central

Keten, Sinan; Buehler, Markus J.

2010-01-01

Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 31-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre. PMID:20519206

Nanostructure and molecular mechanics of spider dragline silk protein assemblies.

PubMed

Keten, Sinan; Buehler, Markus J

2010-12-06

Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 3₁-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre.

Transcriptome mining and in silico structural and functional analysis of ascorbic acid and tartaric acid biosynthesis pathway enzymes in rose-scanted geranium.

PubMed

Narnoliya, Lokesh K; Sangwan, Rajender S; Singh, Sudhir P

2018-06-01

Rose-scented geranium (Pelargonium sp.) is widely known as aromatic and medicinal herb, accumulating specialized metabolites of high economic importance, such as essential oils, ascorbic acid, and tartaric acid. Ascorbic acid and tartaric acid are multifunctional metabolites of human value to be used as vital antioxidants and flavor enhancing agents in food products. No information is available related to the structural and functional properties of the enzymes involved in ascorbic acid and tartaric acid biosynthesis in rose-scented geranium. In the present study, transcriptome mining was done to identify full-length genes, followed by their bioinformatic and molecular modeling investigations and understanding of in silico structural and functional properties of these enzymes. Evolutionary conserved domains were identified in the pathway enzymes. In silico physicochemical characterization of the catalytic enzymes revealed isoelectric point (pI), instability index, aliphatic index, and grand average hydropathy (GRAVY) values of the enzymes. Secondary structural prediction revealed abundant proportion of alpha helix and random coil confirmations in the pathway enzymes. Three-dimensional homology models were developed for these enzymes. The predicted structures showed significant structural similarity with their respective templates in root mean square deviation analysis. Ramachandran plot analysis of the modeled enzymes revealed that more than 84% of the amino acid residues were within the favored regions. Further, functionally important residues were identified corresponding to catalytic sites located in the enzymes. To, our best knowledge, this is the first report which provides a foundation on functional annotation and structural determination of ascorbic acid and tartaric acid pathway enzymes in rose-scanted geranium.

Self-Complementarity within Proteins: Bridging the Gap between Binding and Folding

PubMed Central

Basu, Sankar; Bhattacharyya, Dhananjay; Banerjee, Rahul

2012-01-01

Complementarity, in terms of both shape and electrostatic potential, has been quantitatively estimated at protein-protein interfaces and used extensively to predict the specific geometry of association between interacting proteins. In this work, we attempted to place both binding and folding on a common conceptual platform based on complementarity. To that end, we estimated (for the first time to our knowledge) electrostatic complementarity (Em) for residues buried within proteins. Em measures the correlation of surface electrostatic potential at protein interiors. The results show fairly uniform and significant values for all amino acids. Interestingly, hydrophobic side chains also attain appreciable complementarity primarily due to the trajectory of the main chain. Previous work from our laboratory characterized the surface (or shape) complementarity (Sm) of interior residues, and both of these measures have now been combined to derive two scoring functions to identify the native fold amid a set of decoys. These scoring functions are somewhat similar to functions that discriminate among multiple solutions in a protein-protein docking exercise. The performances of both of these functions on state-of-the-art databases were comparable if not better than most currently available scoring functions. Thus, analogously to interfacial residues of protein chains associated (docked) with specific geometry, amino acids found in the native interior have to satisfy fairly stringent constraints in terms of both Sm and Em. The functions were also found to be useful for correctly identifying the same fold for two sequences with low sequence identity. Finally, inspired by the Ramachandran plot, we developed a plot of Sm versus Em (referred to as the complementarity plot) that identifies residues with suboptimal packing and electrostatics which appear to be correlated to coordinate errors. PMID:22713576

Self-complementarity within proteins: bridging the gap between binding and folding.

PubMed

Basu, Sankar; Bhattacharyya, Dhananjay; Banerjee, Rahul

2012-06-06

Complementarity, in terms of both shape and electrostatic potential, has been quantitatively estimated at protein-protein interfaces and used extensively to predict the specific geometry of association between interacting proteins. In this work, we attempted to place both binding and folding on a common conceptual platform based on complementarity. To that end, we estimated (for the first time to our knowledge) electrostatic complementarity (Em) for residues buried within proteins. Em measures the correlation of surface electrostatic potential at protein interiors. The results show fairly uniform and significant values for all amino acids. Interestingly, hydrophobic side chains also attain appreciable complementarity primarily due to the trajectory of the main chain. Previous work from our laboratory characterized the surface (or shape) complementarity (Sm) of interior residues, and both of these measures have now been combined to derive two scoring functions to identify the native fold amid a set of decoys. These scoring functions are somewhat similar to functions that discriminate among multiple solutions in a protein-protein docking exercise. The performances of both of these functions on state-of-the-art databases were comparable if not better than most currently available scoring functions. Thus, analogously to interfacial residues of protein chains associated (docked) with specific geometry, amino acids found in the native interior have to satisfy fairly stringent constraints in terms of both Sm and Em. The functions were also found to be useful for correctly identifying the same fold for two sequences with low sequence identity. Finally, inspired by the Ramachandran plot, we developed a plot of Sm versus Em (referred to as the complementarity plot) that identifies residues with suboptimal packing and electrostatics which appear to be correlated to coordinate errors. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

From Ramachandran Maps to Tertiary Structures of Proteins.

PubMed

DasGupta, Debarati; Kaushik, Rahul; Jayaram, B

2015-08-27

Sequence to structure of proteins is an unsolved problem. A possible coarse grained resolution to this entails specification of all the torsional (Φ, Ψ) angles along the backbone of the polypeptide chain. The Ramachandran map quite elegantly depicts the allowed conformational (Φ, Ψ) space of proteins which is still very large for the purposes of accurate structure generation. We have divided the allowed (Φ, Ψ) space in Ramachandran maps into 27 distinct conformations sufficient to regenerate a structure to within 5 Å from the native, at least for small proteins, thus reducing the structure prediction problem to a specification of an alphanumeric string, i.e., the amino acid sequence together with one of the 27 conformations preferred by each amino acid residue. This still theoretically results in 27(n) conformations for a protein comprising "n" amino acids. We then investigated the spatial correlations at the two-residue (dipeptide) and three-residue (tripeptide) levels in what may be described as higher order Ramachandran maps, with the premise that the allowed conformational space starts to shrink as we introduce neighborhood effects. We found, for instance, for a tripeptide which potentially can exist in any of the 27(3) "allowed" conformations, three-fourths of these conformations are redundant to the 95% confidence level, suggesting sequence context dependent preferred conformations. We then created a look-up table of preferred conformations at the tripeptide level and correlated them with energetically favorable conformations. We found in particular that Boltzmann probabilities calculated from van der Waals energies for each conformation of tripeptides correlate well with the observed populations in the structural database (the average correlation coefficient is ∼0.8). An alpha-numeric string and hence the tertiary structure can be generated for any sequence from the look-up table within minutes on a single processor and to a higher level of accuracy if secondary structure can be specified. We tested the methodology on 100 small proteins, and in 90% of the cases, a structure within 5 Å is recovered. We thus believe that the method presented here provides the missing link between Ramachandran maps and tertiary structures of proteins. A Web server to convert a tertiary structure to an alphanumeric string and to predict the tertiary structure from the sequence of a protein using the above methodology is created and made freely accessible at http://www.scfbio-iitd.res.in/software/proteomics/rm2ts.jsp.

PeptideNavigator: An interactive tool for exploring large and complex data sets generated during peptide-based drug design projects.

PubMed

Diller, Kyle I; Bayden, Alexander S; Audie, Joseph; Diller, David J

2018-01-01

There is growing interest in peptide-based drug design and discovery. Due to their relatively large size, polymeric nature, and chemical complexity, the design of peptide-based drugs presents an interesting "big data" challenge. Here, we describe an interactive computational environment, PeptideNavigator, for naturally exploring the tremendous amount of information generated during a peptide drug design project. The purpose of PeptideNavigator is the presentation of large and complex experimental and computational data sets, particularly 3D data, so as to enable multidisciplinary scientists to make optimal decisions during a peptide drug discovery project. PeptideNavigator provides users with numerous viewing options, such as scatter plots, sequence views, and sequence frequency diagrams. These views allow for the collective visualization and exploration of many peptides and their properties, ultimately enabling the user to focus on a small number of peptides of interest. To drill down into the details of individual peptides, PeptideNavigator provides users with a Ramachandran plot viewer and a fully featured 3D visualization tool. Each view is linked, allowing the user to seamlessly navigate from collective views of large peptide data sets to the details of individual peptides with promising property profiles. Two case studies, based on MHC-1A activating peptides and MDM2 scaffold design, are presented to demonstrate the utility of PeptideNavigator in the context of disparate peptide-design projects. Copyright © 2017 Elsevier Ltd. All rights reserved.

Peptoids: a modular approach to drug discovery.

PubMed Central

Simon, R J; Kania, R S; Zuckermann, R N; Huebner, V D; Jewell, D A; Banville, S; Ng, S; Wang, L; Rosenberg, S; Marlowe, C K

1992-01-01

Peptoids, oligomers of N-substituted glycines, are described as a motif for the generation of chemically diverse libraries of novel molecules. Ramachandran-type plots were calculated and indicate a greater diversity of conformational states available for peptoids than for peptides. The monomers incorporate t-butyl-based side-chain and 9-fluorenylmethoxy-carbonyl alpha-amine protection. The controlled oligomerization of the peptoid monomers was performed manually and robotically with in situ activation by either benzotriazol-1-yloxytris(pyrrolidino)phosphonium hexafluorophosphate or bromotris(pyrrolidino)phosphonium hexaflurophosphate. Other steps were identical to peptide synthesis using alpha-(9-fluorenylmethoxycarbonyl)amino acids. A total of 15 monomers and 10 oligomers (peptoids) are described. Preliminary data are presented on the stability of a representative oligopeptoid to enzymatic hydrolysis. Peptoid versions of peptide ligands of three biological systems (bovine pancreatic alpha-amylase, hepatitis A virus 3C proteinase, and human immunodeficiency virus transactivator-responsive element RNA) were found with affinities comparable to those of the corresponding peptides. The potential use of libraries of these compounds in receptor- or enzyme-based assays is discussed. PMID:1409642

Protein modeling and molecular dynamics simulation of SlWRKY4 protein cloned from drought tolerant tomato (Solanum habrochaites) line EC520061.

PubMed

Karkute, Suhas G; Easwaran, Murugesh; Gujjar, Ranjit Singh; Piramanayagam, Shanmughavel; Singh, Major

2015-10-01

WRKY genes are members of one of the largest families of plant transcription factors and play an important role in response to biotic and abiotic stresses, and overall growth and development. Understanding the interaction of WRKY proteins with other proteins/ligands in plant cells is of utmost importance to develop plants having tolerance to biotic and abiotic stresses. The SlWRKY4 gene was cloned from a drought tolerant wild species of tomato (Solanum habrochaites) and the secondary structure and 3D modeling of this protein were predicted using Schrödinger Suite-Prime. Predicted structures were also subjected to plot against Ramachandran's conformation, and the modeled structure was minimized using Macromodel. Finally, the minimized structure was simulated in the water environment to check the protein stability. The behavior of the modeled structure was well-simulated and analyzed through RMSD and RMSF of the protein. The present work provides the modeled 3D structure of SlWRKY4 that will help in understanding the mechanism of gene regulation by further in silico interaction studies.

Isolation and in silico analysis of Fe-superoxide dismutase in the cyanobacterium Nostoc commune.

PubMed

Kesheri, Minu; Kanchan, Swarna; Richa; Sinha, Rajeshwar P

2014-12-15

Cyanobacteria are known to endure various stress conditions due to the inbuilt potential for oxidative stress alleviation owing to the presence of an array of antioxidants. The present study shows that Antarctic cyanobacterium Nostoc commune possesses two antioxidative enzymes viz., superoxide dismutase (SOD) and catalase that jointly cope with environmental stresses prevailing at its natural habitat. Native-PAGE analysis illustrates the presence of a single prominent isoform recognized as Fe-SOD and three distinct isoforms of catalase. The protein sequence of Fe-SOD in N. commune retrieved from NCBI protein sequence database was used for in silico analysis. 3D structure of N. commune was predicted by comparative modeling using MODELLER 9v11. Further, this model was validated for its quality by Ramachandran plot, ERRAT, Verify 3D and ProSA-web which revealed good structure quality of the model. Multiple sequence alignment showed high conservation in N and C-terminal domain regions along with all metal binding positions in Fe-SOD which were also found to be highly conserved in all 28 cyanobacterial species under study, including N. commune. In silico prediction of isoelectric point and molecular weight of Fe-SOD was found to be 5.48 and 22,342.98Da respectively. The phylogenetic tree revealed that among 28 cyanobacterial species, Fe-SOD in N. commune was the closest evolutionary homolog of Fe-SOD in Nostoc punctiforme as evident by strong bootstrap value. Thus, N. commune may serve as a good biological model for studies related to survival of life under extreme conditions prevailing at the Antarctic region. Moreover cyanobacteria may be exploited for biochemical and biotechnological applications of enzymatic antioxidants. Copyright © 2014 Elsevier B.V. All rights reserved.

Binding Patterns Associated Aß-HSP60 p458 Conjugate to HLA-DR-DRB Allele of Human in Alzheimer's Disease: An In Silico Approach.

PubMed

Padmadas, Naveen; Panda, Pritam Kumar; Durairaj, Sudarsanam

2018-03-01

Alzheimer's disease (AD) is a complex, irreversible, progressive brain disorder, which diminishes memory in a slow pace and thinking skills; ranked third by experts. It is a complex disorder that involves numerous cellular and subcellular alterations. The pathogenesis of AD is still unknown, but for better understanding, we proposed an in silico analysis to find out the binding patterns associated with HSP60. Several experimental conclusions have been drawn to understand the actual mechanism behind the forming of aggregation due to misfolding. Protein misfolding disorder is experimentally identified by the accumulation of protein aggregates at the intracellular or extracellular region of brain that adversely affects the cell functioning by disrupting the connection between the cells and ultimately leading to cell death. To unravel the mystery behind the mechanism of AD through computational approach, the current proposal shows the designing of Aß-HSP60 p458 conjugate followed by secondary structure analysis, which is further targeted to HLA-DR-DRB allele of human. The antigenicity of Aß (1-42) peptide is the major concern in our study predicted through PVS server, which provides an insight into the immunogenic behavior of Aß peptide. The mechanism involved in the interaction of HSP60-Aß conjugate with HLA-DR-DRB allele considering the fact that Aß (1-42) is highly immunogenic in human and interactions evoked highly robust T-cell response through MHC class II binding predictions. It was assisted by molecular dynamics simulation of predicted HSP60 structure followed by validation through Ramachandran plot analysis and protein-protein interaction of Aß (1-42) with HSP60.

Comparative analysis of amino acid composition in the active site of nirk gene encoding copper-containing nitrite reductase (CuNiR) in bacterial spp.

PubMed

Adhikari, Utpal Kumar; Rahman, M Mizanur

2017-04-01

The nirk gene encoding the copper-containing nitrite reductase (CuNiR), a key catalytic enzyme in the environmental denitrification process that helps to produce nitric oxide from nitrite. The molecular mechanism of denitrification process is definitely complex and in this case a theoretical investigation has been conducted to know the sequence information and amino acid composition of the active site of CuNiR enzyme using various Bioinformatics tools. 10 Fasta formatted sequences were retrieved from the NCBI database and the domain and disordered regions identification and phylogenetic analyses were done on these sequences. The comparative modeling of protein was performed through Modeller 9v14 program and visualized by PyMOL tools. Validated protein models were deposited in the Protein Model Database (PMDB) (PMDB id: PM0080150 to PM0080159). Active sites of nirk encoding CuNiR enzyme were identified by Castp server. The PROCHECK showed significant scores for four protein models in the most favored regions of the Ramachandran plot. Active sites and cavities prediction exhibited that the amino acid, namely Glycine, Alanine, Histidine, Aspartic acid, Glutamic acid, Threonine, and Glutamine were common in four predicted protein models. The present in silico study anticipates that active site analyses result will pave the way for further research on the complex denitrification mechanism of the selected species in the experimental laboratory. Copyright © 2016. Published by Elsevier Ltd.

TAP score: torsion angle propensity normalization applied to local protein structure evaluation

PubMed Central

Tosatto, Silvio CE; Battistutta, Roberto

2007-01-01

Background Experimentally determined protein structures may contain errors and require validation. Conformational criteria based on the Ramachandran plot are mainly used to distinguish between distorted and adequately refined models. While the readily available criteria are sufficient to detect totally wrong structures, establishing the more subtle differences between plausible structures remains more challenging. Results A new criterion, called TAP score, measuring local sequence to structure fitness based on torsion angle propensities normalized against the global minimum and maximum is introduced. It is shown to be more accurate than previous methods at estimating the validity of a protein model in terms of commonly used experimental quality parameters on two test sets representing the full PDB database and a subset of obsolete PDB structures. Highly selective TAP thresholds are derived to recognize over 90% of the top experimental structures in the absence of experimental information. Both a web server and an executable version of the TAP score are available at . Conclusion A novel procedure for energy normalization (TAP) has significantly improved the possibility to recognize the best experimental structures. It will allow the user to more reliably isolate problematic structures in the context of automated experimental structure determination. PMID:17504537

Protein Thermostability Is Owing to Their Preferences to Non-Polar Smaller Volume Amino Acids, Variations in Residual Physico-Chemical Properties and More Salt-Bridges.

PubMed

Panja, Anindya Sundar; Bandopadhyay, Bidyut; Maiti, Smarajit

2015-01-01

Protein thermostability is an important field for its evolutionary perspective of mesophilic versus thermophilic relationship and for its industrial/ therapeutic applications. Presently, a total 400 (200 thermophilic and 200 mesophilic homologue) proteins were studied utilizing several software/databases to evaluate their amino acid preferences. Randomly selected 50 homologous proteins with available PDB-structure of each group were explored for the understanding of the protein charges, isoelectric-points, hydrophilicity, hydrophobicity, tyrosine phosphorylation and salt-bridge occurrences. These 100 proteins were further probed to generate Ramachandran plot/data for the gross secondary structure prediction in and comparison between the thermophilic and mesophilic proteins. Present results strongly suggest that nonpolar smaller volume amino acids Ala (χ2 = 238.54, p<0.001) and Gly (χ2 = 73.35, p<0.001) are highly and Val moderately (χ2 = 144.43, p<0.001) occurring in the 85% of thermophilic proteins. Phospho-regulated Tyr and redox-sensitive Cys are also moderately distributed (χ2~20.0, p<0.01) in a larger number of thermophilic proteins. A consistent lower distribution of thermophilicity and discretely higher distribution of hydrophobicity is noticed in a large number of thermophilic versus their mesophilic protein homolog. The mean differences of isoelectric points and charges are found to be significantly less (7.11 vs. 6.39, p<0.05 and 1 vs. -0.6, p<0.01, respectively) in thermophilic proteins compared to their mesophilic counterpart. The possible sites for Tyr phosphorylation are noticed to be 25% higher (p<0.05) in thermophilic proteins. The 60% thermophiles are found with higher number of salt bridges in this study. The average percentage of salt-bridge of thermophiles is found to be higher by 20% than their mesophilic homologue. The GLU-HIS and GLU-LYS salt-bridge dyads are calculated to be significantly higher (p<0.05 and p<0.001, respectively) in thermophilic and GLU-ARG is higher in the mesophilic proteins. The Ramachandran plot/ data suggest a higher abundance of the helix, left-handed helix, sheet, nonplanar peptide and lower occurrence of cis peptide, loop/ turn and outlier in thermophiles. Pearson's correlation result suggests that the isoelectric points of mesophilic and thermophilic proteins are positively correlated (r = 0.93 and 0.84, respectively; p<0.001) to their corresponding charges. And their hydrophilicity is negatively associated with the corresponding hydrophobicity (r = -0.493, p<0.001 and r = -0.324, p<0.05) suggesting their reciprocal evolvement. Present results for the first time with this large amount of datasets and multiple contributing factors suggest the greater occurrence of hydrophobicity, salt-bridges and smaller volume nonpolar residues (Gly, Ala and Val) and lesser occurrence of bulky polar residues in the thermophilic proteins. A more stoichiometric relationship amongst these factors minimized the hindrance due to side chain burial and increased compactness and secondary structural stability in thermophilic proteins.

Bioinformatics analysis of ROP8 protein to improve vaccine design against Toxoplasma gondii.

PubMed

Foroutan, Masoud; Ghaffarifar, Fatemeh; Sharifi, Zohreh; Dalimi, Abdolhosein; Pirestani, Majid

2018-04-26

Rhoptry proteins (ROPs) are involved in the different stages of Toxoplasma gondii (T. gondii) invasion and are also critical for survival within host cells. ROP8 is expressed in the early stages of infection and have a key role in the parasitophorous vacuole (PV) formation. In this paper, we have combined several bioinformatics online servers for immunogenicity prediction of ROP8 protein. In this study, several bioinformatics approaches were used to analyze the different aspects of ROP8 protein, including the physico-chemical properties, transmembrane domain, subcellular localization, secondary and tertiary structure, B and T-cell potential epitopes, and other important characteristics of this protein. The findings showed that ROP8 protein had 60 potential post-translational modification sites. Also, only one transmembrane domain was recognized for this protein. The secondary structure of ROP8 protein comprises 33.04% alpha-helix, 18.26% extended strand, and 48.70% random coil. Moreover, several potential B and T-cell epitopes were identified for ROP8. In addition, the obtained findings from antigenicity and allergenicity evaluation remarked that this protein is immunogenic and non-allergen. Based on the results of Ramachandran plot, 94.8%, 4.1%, and 1.1% of amino acid residues were incorporated in the favored, allowed, and outlier regions, respectively. This paper provides a foundation for further investigations, and laid a theoretical basis for the development of an appropriate vaccine against toxoplasmosis. More studies are needed experimentally using the ROP8 alone or in combination with other antigens in the future. Copyright © 2018 Elsevier B.V. All rights reserved.

An algorithm for converting a virtual-bond chain into a complete polypeptide backbone chain

NASA Technical Reports Server (NTRS)

Luo, N.; Shibata, M.; Rein, R.

1991-01-01

A systematic analysis is presented of the algorithm for converting a virtual-bond chain, defined by the coordinates of the alpha-carbons of a given protein, into a complete polypeptide backbone. An alternative algorithm, based upon the same set of geometric parameters used in the Purisima-Scheraga algorithm but with a different "linkage map" of the algorithmic procedures, is proposed. The global virtual-bond chain geometric constraints are more easily separable from the loal peptide geometric and energetic constraints derived from, for example, the Ramachandran criterion, within the framework of this approach.

Protein structural similarity search by Ramachandran codes

PubMed Central

Lo, Wei-Cheng; Huang, Po-Jung; Chang, Chih-Hung; Lyu, Ping-Chiang

2007-01-01

Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation). SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE) and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era. PMID:17716377

JPRS Report, Near East & South Asia.

DTIC Science & Technology

1990-11-15

weapons and if war, should it break out, reaches a critical point. Recalling what Iraqi President Saddam Husayn said on several occasions, that...notwithstanding the contrary instances of M.G. Ramachandran and Chenna Reddy, any other person, incapacitated in the manner he was, would have on his

Redescription of the gonad-infecting nematode Philometra saltatrix Ramachandran, 1973 (Philometridae) based on specimens from the type host Pomatomus saltatrix (L.) (Osteichthyes) from the Tuscan Sea, Italy.

PubMed

Moravec, Frantisek; Magi, Marta; Macchioni, Fabio

2008-09-01

The philometrid nematode, Philometra saltatrix Ramachandran, 1973, is redescribed from male and female specimens collected from the ovaries of the marine fish (bluefish) Pomatomus saltatrix (L.) (Pomatomidae, Perciformes) from the Tuscan Sea, Italy. The light and scanning electron microscopical examination made it possible to study in detail the morphology of this so far little known species. For the first time, the actual structure of the male cephalic and caudal ends is described. The male possesses 14 small cephalic papillae arranged in two circles, the spicules are 84-111 microm long and the gubernaculum, 75-84 microm long, has its distal portion provided with dorsal transverse lamella-like structures. The caudal end of subgravid females bears two very small, hardly visible lateral papilla-like projections. This is the first record of P. saltatrix, a species originally described from the West Atlantic, from the Tuscan Sea and the second one in the Mediterranean region.

Active Transport of Nanomaterials Using Motor Proteins -Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hess, Henry

During the six months of funding we have focused first on the completion of the research begun at the University of Washington in the previous funding cycle. Specifically, we developed a method to polymerize oriented networks of microtubules on lithographically patterned surfaces (M.S. thesis Robert Doot). The properties of active transport have been studied detail, yielding insights into the dispersion mechanisms (Nitta et al.). The assembly of multifunctional structures with a microtubule core has been investigated (Ramachandran et al.). Isaac Luria (B.S. in physics, U. of Florida 2005) worked on the directed assembly of nanoscale, non-equilibrium structures as a summermore » intern. He is now a graduate student in my group at the University of Florida. T. Nitta and H. Hess: Dispersion in Active Transport by Kinesin-Powered Molecular Shuttles, Nano Letters, 5, 1337-1342 (2005) S. Ramachandran, K.-H. Ernst, G. D. Bachand, V. Vogel, H. Hess*: Selective Loading of Kinesin-Powered Molecular Shuttles with Protein Cargo and its Application to Biosensing, submitted to Small (2005)« less

Molecular Modeling and docking of Wheat Hydroquinone Glucosyl transferase by using Hydroquinone, Phenyl phosphorodiamate and n-(n butyl) Phosphorothiocic Triamide as Inhibitors

PubMed Central

Huma, Tayyaba; Maryam, Arooma; qamar, Tahir ul

2014-01-01

In agriculture high urease activity during urea fertilization causes substantial environmental and economical problems by releasing abnormally large amount of ammonia into the atmosphere which leads to plant damage as well as ammonia toxicity. All over the world, urea is the most widely applied nitrogen fertilizer. Due to the action of enzyme urease; urea nitrogen is lost as volatile ammonia. For efficient use of nitrogen fertilizer, urease inhibitor along with the urea fertilizer is one of the best promising strategies. Urease inhibitors also provide an insight in understanding the mechanism of enzyme catalyzed reaction, the role of various amino acids in catalytic activity present at the active site of enzyme and the importance of nickel to this metallo enzyme. By keeping it in view, the present study was designed to dock three urease inhibitors namely Hydroquinone (HQ), Phenyl Phosphorodiamate (PPD) and N-(n-butyl) Phosphorothiocic triamide (NBPT) against Hydroquinone glucosyltransferase using molecular docking approach. The 3D structure of Hydroquinone glucosyltransferase was predicted using homology modeling approach and quality of the structure was assured using Ramachandran plot. This study revealed important interactions among the urease inhibitors and Hydroquinone glucosyltransferase. Thus, it can be inferred that these inhibitors may serve as future anti toxic constituent against plant toxins. PMID:24748751

Homology modeling, binding site identification and docking study of human angiotensin II type I (Ang II-AT1) receptor.

PubMed

Vyas, Vivek K; Ghate, Manjunath; Patel, Kinjal; Qureshi, Gulamnizami; Shah, Surmil

2015-08-01

Ang II-AT1 receptors play an important role in mediating virtually all of the physiological actions of Ang II. Several drugs (SARTANs) are available, which can block the AT1 receptor effectively and lower the blood pressure in the patients with hypertension. Currently, there is no experimental Ang II-AT1 structure available; therefore, in this study we modeled Ang II-AT1 receptor structure using homology modeling followed by identification and characterization of binding sites and thereby assessing druggability of the receptor. Homology models were constructed using MODELLER and I-TASSER server, refined and validated using PROCHECK in which 96.9% of 318 residues were present in the favoured regions of the Ramachandran plots. Various Ang II-AT1 receptor antagonist drugs are available in the market as antihypertensive drug, so we have performed docking study with the binding site prediction algorithms to predict different binding pockets on the modeled proteins. The identification of 3D structures and binding sites for various known drugs will guide us for the structure-based drug design of novel compounds as Ang II-AT1 receptor antagonists for the treatment of hypertension. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

In silico structure prediction and inhibition mechanism studies of AtHDA14 as revealed by homology modeling, docking, molecular dynamics simulation.

PubMed

Zhao, Ming-Lang; Wang, Wang; Nie, Hu; Cao, Sha-Sha; Du, Lin-Fang

2018-05-06

Histone deacetylases (HDACs) play a significant role in the epigenetic mechanism by catalyzing deacetylation of lysine on histone in both animals and plants. HDACs involved in growth, development and response to stresses in plants. Arabidopsis thaliana histone deacetylase 14 (AtHDA14) is found to localize in the mitochondria and chloroplasts, and it involved in photosynthesis and melatonin biosynthesis. However, its mechanism of action was still unknowns so far. Therefore, in this study, we constructed AtHDA14 protein model using homology modeling method, validated using PROCHECK and presented using Ramachandran plots. We also performed virtual screening of AtHDA14 by docking with small molecule drugs and predicted their ADMET properties to select representative inhibitors. MD simulation for representative AtHDA14-ligand complexes was carried out to further research and reveal their stability and inhibition mechanism. Meanwhile, MM/PBSA method was utilized to obtain more valuable information about the residues energy contribution. Moreover, compared with four candidate inhibitors, we also found that compound 645533 and 6918837 might be a more potent AtHDA14 inhibitor than TSA (444732) and SAHA (5311). Therefore, compound 6445533 and 6918837 was anticipated to be a promising drug candidate for inhibition of AtHDA14. Copyright © 2018 Elsevier Ltd. All rights reserved.

Structural prediction and comparative docking studies of psychrophilic β- Galactosidase with lactose, ONPG and PNPG against its counter parts of mesophilic and thermophilic enzymes.

PubMed

Kumar, Ponnada Suresh; Pulicherla, Kk; Ghosh, Mrinmoy; Kumar, Anmol; Rao, Krs Sambasiva

2011-01-01

Enzymes from psychrophiles catalyze the reactions at low temperatures with higher specific activity. Among all the psychrophilic enzymes produced, cold active β-galactosidase from marine psychrophiles revalorizes a new arena in numerous areas at industrial level. The hydrolysis of lactose in to glucose and galactose by cold active β-galactosidase offers a new promising approach in removal of lactose from milk to overcome the problem of lactose intolerance. Herein we propose, a 3D structure of cold active β-galactosidase enzyme sourced from Pseudoalteromonas haloplanktis by using Modeler 9v8 and best model was developed having 88% of favourable region in ramachandran plot. Modelling was followed by docking studies with the help of Auto dock 4.0 against the three substrates lactose, ONPG and PNPG. In addition, comparative docking studies were also performed for the 3D model of psychrophilic β-galactosidase with mesophilic and thermophilic enzymes. Docking studies revealed that binding affinity of enzyme towards the three different substrates is more for psychrophilic enzyme when compared with mesophilic and thermophilic enzymes. It indicates that the enzyme has high specific activity at low temperature when compared with mesophilic and thermophilic enzymes.

Molecular Modeling and docking of Wheat Hydroquinone Glucosyl transferase by using Hydroquinone, Phenyl phosphorodiamate and n-(n butyl) Phosphorothiocic Triamide as Inhibitors.

PubMed

Huma, Tayyaba; Maryam, Arooma; Qamar, Tahir Ul

2014-01-01

In agriculture high urease activity during urea fertilization causes substantial environmental and economical problems by releasing abnormally large amount of ammonia into the atmosphere which leads to plant damage as well as ammonia toxicity. All over the world, urea is the most widely applied nitrogen fertilizer. Due to the action of enzyme urease; urea nitrogen is lost as volatile ammonia. For efficient use of nitrogen fertilizer, urease inhibitor along with the urea fertilizer is one of the best promising strategies. Urease inhibitors also provide an insight in understanding the mechanism of enzyme catalyzed reaction, the role of various amino acids in catalytic activity present at the active site of enzyme and the importance of nickel to this metallo enzyme. By keeping it in view, the present study was designed to dock three urease inhibitors namely Hydroquinone (HQ), Phenyl Phosphorodiamate (PPD) and N-(n-butyl) Phosphorothiocic triamide (NBPT) against Hydroquinone glucosyltransferase using molecular docking approach. The 3D structure of Hydroquinone glucosyltransferase was predicted using homology modeling approach and quality of the structure was assured using Ramachandran plot. This study revealed important interactions among the urease inhibitors and Hydroquinone glucosyltransferase. Thus, it can be inferred that these inhibitors may serve as future anti toxic constituent against plant toxins.

Protein Thermostability Is Owing to Their Preferences to Non-Polar Smaller Volume Amino Acids, Variations in Residual Physico-Chemical Properties and More Salt-Bridges

PubMed Central

Panja, Anindya Sundar; Bandopadhyay, Bidyut; Maiti, Smarajit

2015-01-01

Introduction Protein thermostability is an important field for its evolutionary perspective of mesophilic versus thermophilic relationship and for its industrial/ therapeutic applications. Methods Presently, a total 400 (200 thermophilic and 200 mesophilic homologue) proteins were studied utilizing several software/databases to evaluate their amino acid preferences. Randomly selected 50 homologous proteins with available PDB-structure of each group were explored for the understanding of the protein charges, isoelectric-points, hydrophilicity, hydrophobicity, tyrosine phosphorylation and salt-bridge occurrences. These 100 proteins were further probed to generate Ramachandran plot/data for the gross secondary structure prediction in and comparison between the thermophilic and mesophilic proteins. Results Present results strongly suggest that nonpolar smaller volume amino acids Ala (χ 2 = 238.54, p<0.001) and Gly (χ 2 = 73.35, p<0.001) are highly and Val moderately (χ 2 = 144.43, p<0.001) occurring in the 85% of thermophilic proteins. Phospho-regulated Tyr and redox-sensitive Cys are also moderately distributed (χ 2~20.0, p<0.01) in a larger number of thermophilic proteins. A consistent lower distribution of thermophilicity and discretely higher distribution of hydrophobicity is noticed in a large number of thermophilic versus their mesophilic protein homolog. The mean differences of isoelectric points and charges are found to be significantly less (7.11 vs. 6.39, p<0.05 and 1 vs. -0.6, p<0.01, respectively) in thermophilic proteins compared to their mesophilic counterpart. The possible sites for Tyr phosphorylation are noticed to be 25% higher (p<0.05) in thermophilic proteins. The 60% thermophiles are found with higher number of salt bridges in this study. The average percentage of salt-bridge of thermophiles is found to be higher by 20% than their mesophilic homologue. The GLU-HIS and GLU-LYS salt-bridge dyads are calculated to be significantly higher (p<0.05 and p<0.001, respectively) in thermophilic and GLU-ARG is higher in the mesophilic proteins. The Ramachandran plot/ data suggest a higher abundance of the helix, left-handed helix, sheet, nonplanar peptide and lower occurrence of cis peptide, loop/ turn and outlier in thermophiles. Pearson’s correlation result suggests that the isoelectric points of mesophilic and thermophilic proteins are positively correlated (r = 0.93 and 0.84, respectively; p<0.001) to their corresponding charges. And their hydrophilicity is negatively associated with the corresponding hydrophobicity (r = -0.493, p<0.001 and r = -0.324, p<0.05) suggesting their reciprocal evolvement. Conclusions Present results for the first time with this large amount of datasets and multiple contributing factors suggest the greater occurrence of hydrophobicity, salt-bridges and smaller volume nonpolar residues (Gly, Ala and Val) and lesser occurrence of bulky polar residues in the thermophilic proteins. A more stoichiometric relationship amongst these factors minimized the hindrance due to side chain burial and increased compactness and secondary structural stability in thermophilic proteins. PMID:26177372

Anomaly Detection in the Right Hemisphere: The Influence of Visuospatial Factors

ERIC Educational Resources Information Center

Smith, Stephen D.; Dixon, Michael J.; Tays, William J.; Bulman-Fleming, M. Barbara

2004-01-01

Previous research with both brain-damaged and neurologically intact populations has demonstrated that the right cerebral hemisphere (RH) is superior to the left cerebral hemisphere (LH) at detecting anomalies (or incongruities) in objects (Ramachandran, 1995; Smith, Tays, Dixon, & Bulman-Fleming, 2002). The current research assesses whether the RH…

Isolation, characterization and molecular three-dimensional structural predictions of metalloprotease from a phytopathogenic fungus, Alternaria solani (Ell. and Mart.) Sor.

PubMed

Chandrasekaran, Murugesan; Chandrasekar, Raman; Chun, Se-Chul; Sathiyabama, Muthukrishnan

2016-08-01

The present study aims at isolation, identification, characterization and prediction of three-dimensional molecular architecture of a proteolytic enzyme from the early blight pathogen, Alternaria solani which are hypothesized to be a marker of phytopathogenicity. Maximum enzyme production by A. solani was observed in Czapex's Dox broth amended with 2% (w/v) casein than other inducer amendments. Results indicate that the enzyme remained highly active in a pH range of 7.0-10.0 and a temperature range of 45-50°C. The enzyme was strongly inhibited by EDTA, whereas phenylmethylsulfonyl fluoride and monovalent cations (Na(+), K(+)) had little effect. Metal ions such as MgSO4, CaCl2, KCl at 10 mM concentration showed a stimulatory effect (>85%) on protease activity. Matrix-assisted laser desorption and ionization time of flight/mass spectrometry analysis of partially purified enzyme revealed the presence of protease belonging to a keratinolytic protein (metalloprotease) of exopeptidase nature. Putative A. solani keratinolytic enzyme (AsK) is made up of 216 amino acid residues with molecular weight (MW) 24.5 kDa, having a molecular formula of C1094H1704N290O342S4. Ramachandran plot analysis of the protein residues falling into the most favored secondary structures was observed at 84.2%. The major protein structural blocks, 2-β-sheets, and 9-α-helices have a greater tendency to be conserved during the evolutionary process than do mere sequences of amino acids. Besides, AsK, model prediction showed the presence of a Zinc atom at helix regions (Helix 3, 6, 7: His(57), His(130), His(169), and Cys(123)). Thus, it can be concluded that the major proteinases of AsK are divalent cation-requiring metalloproteinases and make them potential targets of protease inhibitors designing. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Identification of a key structural element for protein folding within beta-hairpin turns.

PubMed

Kim, Jaewon; Brych, Stephen R; Lee, Jihun; Logan, Timothy M; Blaber, Michael

2003-05-09

Specific residues in a polypeptide may be key contributors to the stability and foldability of the unique native structure. Identification and prediction of such residues is, therefore, an important area of investigation in solving the protein folding problem. Atypical main-chain conformations can help identify strains within a folded protein, and by inference, positions where unique amino acids may have a naturally high frequency of occurrence due to favorable contributions to stability and folding. Non-Gly residues located near the left-handed alpha-helical region (L-alpha) of the Ramachandran plot are a potential indicator of structural strain. Although many investigators have studied mutations at such positions, no consistent energetic or kinetic contributions to stability or folding have been elucidated. Here we report a study of the effects of Gly, Ala and Asn substitutions found within the L-alpha region at a characteristic position in defined beta-hairpin turns within human acidic fibroblast growth factor, and demonstrate consistent effects upon stability and folding kinetics. The thermodynamic and kinetic data are compared to available data for similar mutations in other proteins, with excellent agreement. The results have identified that Gly at the i+3 position within a subset of beta-hairpin turns is a key contributor towards increasing the rate of folding to the native state of the polypeptide while leaving the rate of unfolding largely unchanged.

Homology modelling, molecular docking, and molecular dynamics simulations reveal the inhibition of Leishmania donovani dihydrofolate reductase-thymidylate synthase enzyme by Withaferin-A.

PubMed

Vadloori, Bharadwaja; Sharath, A K; Prabhu, N Prakash; Maurya, Radheshyam

2018-04-16

Present in silico study was carried out to explore the mode of inhibition of Leishmania donovani dihydrofolate reductase-thymidylate synthase (Ld DHFR-TS) enzyme by Withaferin-A, a withanolide isolated from Withania somnifera. Withaferin-A (WA) is known for its profound multifaceted properties, but its antileishmanial activity is not well understood. The parasite's DHFR-TS enzyme is diverse from its mammalian host and could be a potential drug target in parasites. A 3D model of Ld DHFR-TS enzyme was built and verified using Ramachandran plot and SAVES tools. The protein was docked with WA-the ligand, methotrexate (MTX)-competitive inhibitor of DHFR, and dihydrofolic acid (DHFA)-substrate for DHFR-TS. Molecular docking studies reveal that WA competes for active sites of both Hu DHFR and TS enzymes whereas it binds to a site other than active site in Ld DHFR-TS. Moreover, Lys 173 residue of DHFR-TS forms a H-bond with WA and has higher binding affinity to Ld DHFR-TS than Hu DHFR and Hu TS. The MD simulations confirmed the H-bonding interactions were stable. The binding energies of WA with Ld DHFR-TS were calculated using MM-PBSA. Homology modelling, molecular docking and MD simulations of Ld DHFR-TS revealed that WA could be a potential anti-leishmanial drug.

Homology modeling of Homo sapiens lipoic acid synthase: Substrate docking and insights on its binding mode.

PubMed

Krishnamoorthy, Ezhilarasi; Hassan, Sameer; Hanna, Luke Elizabeth; Padmalayam, Indira; Rajaram, Rama; Viswanathan, Vijay

2017-05-07

Lipoic acid synthase (LIAS) is an iron-sulfur cluster mitochondrial enzyme which catalyzes the final step in the de novo pathway for the biosynthesis of lipoic acid, a potent antioxidant. Recently there has been significant interest in its role in metabolic diseases and its deficiency in LIAS expression has been linked to conditions such as diabetes, atherosclerosis and neonatal-onset epilepsy, suggesting a strong inverse correlation between LIAS reduction and disease status. In this study we use a bioinformatics approach to predict its structure, which would be helpful to understanding its role. A homology model for LIAS protein was generated using X-ray crystallographic structure of Thermosynechococcus elongatus BP-1 (PDB ID: 4U0P). The predicted structure has 93% of the residues in the most favour region of Ramachandran plot. The active site of LIAS protein was mapped and docked with S-Adenosyl Methionine (SAM) using GOLD software. The LIAS-SAM complex was further refined using molecular dynamics simulation within the subsite 1 and subsite 3 of the active site. To the best of our knowledge, this is the first study to report a reliable homology model of LIAS protein. This study will facilitate a better understanding mode of action of the enzyme-substrate complex for future studies in designing drugs that can target LIAS protein. Copyright © 2017 Elsevier Ltd. All rights reserved.

Homology modeling and virtual screening to discover potent inhibitors targeting the imidazole glycerophosphate dehydratase protein in Staphylococcus xylosus

NASA Astrophysics Data System (ADS)

Chen, Xing-Ru; Wang, Xiao-Ting; Hao, Mei-Qi; Zhou, Yong-Hui; Cui, Wen-Qiang; Xing, Xiao-Xu; Xu, Chang-Geng; Bai, Jing-Wen; Li, Yan-Hua

2017-11-01

The imidazole glycerophosphate dehydratase (IGPD) protein is a therapeutic target for herbicide discovery. It is also regarded as a possible target in Staphylococcus xylosus (S. xylosus) for solving mastitis in the dairy cow. The 3D structure of IGPD protein is essential for discovering novel inhibitors during high-throughput virtual screening. However, to date, the 3D structure of IGPD protein of S. xylosus has not been solved. In this study, a series of computational techniques including homology modeling, Ramachandran Plots, and Verify 3D were performed in order to construct an appropriate 3D model of IGPD protein of S. xylosus. Nine hits were identified from 2500 compounds by docking studies. Then, these 9 compounds were first tested in vitro in S. xylosus biofilm formation using crystal violet staining. One of the potential compounds, baicalin was shown to significantly inhibit S. xylosus biofilm formation. Finally, the baicalin was further evaluated, which showed better inhibition of biofilm formation capability in S. xylosus by scanning electron microscopy. Hence, we have predicted the structure of IGPD protein of S. xylosus using computational techniques. We further discovered the IGPD protein was targeted by baicalin compound which inhibited the biofilm formation in S. xylosus. Our findings here would provide implications for the further development of novel IGPD inhibitors for the treatment of dairy mastitis.

Homology Modeling and Virtual Screening to Discover Potent Inhibitors Targeting the Imidazole Glycerophosphate Dehydratase Protein in Staphylococcus xylosus.

PubMed

Chen, Xing-Ru; Wang, Xiao-Ting; Hao, Mei-Qi; Zhou, Yong-Hui; Cui, Wen-Qiang; Xing, Xiao-Xu; Xu, Chang-Geng; Bai, Jing-Wen; Li, Yan-Hua

2017-01-01

The imidazole glycerophosphate dehydratase (IGPD) protein is a therapeutic target for herbicide discovery. It is also regarded as a possible target in Staphylococcus xylosus ( S. xylosus ) for solving mastitis in the dairy cow. The 3D structure of IGPD protein is essential for discovering novel inhibitors during high-throughput virtual screening. However, to date, the 3D structure of IGPD protein of S. xylosus has not been solved. In this study, a series of computational techniques including homology modeling, Ramachandran Plots, and Verify 3D were performed in order to construct an appropriate 3D model of IGPD protein of S. xylosus . Nine hits were identified from 2,500 compounds by docking studies. Then, these nine compounds were first tested in vitro in S. xylosus biofilm formation using crystal violet staining. One of the potential compounds, baicalin was shown to significantly inhibit S. xylosus biofilm formation. Finally, the baicalin was further evaluated, which showed better inhibition of biofilm formation capability in S. xylosus by scanning electron microscopy. Hence, we have predicted the structure of IGPD protein of S. xylosus using computational techniques. We further discovered the IGPD protein was targeted by baicalin compound which inhibited the biofilm formation in S. xylosus . Our findings here would provide implications for the further development of novel IGPD inhibitors for the treatment of dairy mastitis.

Comparative analysis of CDPK family in maize, Arabidopsis, rice and sorghum revealed potential targets for drought tolerance improvement

NASA Astrophysics Data System (ADS)

Mittal, Shikha; Mallikarjuna, Mallana Gowdra; Rao, Atmakuri R.; Jain, Prashant A.; Dash, Prasanta K.; Thirunavukkarasu, Nepolean

2017-12-01

Calcium dependent protein kinases (CDPKs) play major role in regulation of plant growth and development in response to various stresses including drought. A set of 32 CDPK genes identified in maize were further used for searching of orthologs in the model plant Arabidopsis (72) and major food crops such as rice (78) and sorghum (91). We comprehensively investigated the phylogenetic relationship, annotations, gene duplications, gene structure, divergence time, 3-D protein structures and tissue-specific drought induced expression of CDPK genes in all four species. Variation in intron frequency among these species likely contributed to the functional diversity of CDPK genes to various stress responses. Protein kinase and protein kinase C phosphorylation site domains were the most conserved motifs identified in all species. Four groups were identified from the sequence-based phylogenetic analysis, in which maize CDPKs were clustered in group III. The time of divergence (Ka/Ks) analysis revealed that the CDPKs were evolved through stabilizing selection. Expression data showed that the CDPK genes were highly expressed in leaf of maize, rice, and sorghum whereas in Arabidopsis the maximum expression was observed in root. 3-D protein structure were predicted for the nine genes (Arabidopsis: 2, maize: 2, rice: 3 and sorghum: 2) showing differential expression in at least three species. The predicted 3-D structures were further evaluated and validated by Ramachandran plot, ANOLEA, ProSA and Verify-3D. The superimposed 3-D structure of drought-related orthologous proteins retained similar folding pattern owing to their conserved nature. Functional annotation revealed the involvement of CDPK genes in various pathways such as osmotic homeostasis, cell protection and root growth. The interactions of CDPK genes in various pathways play crucial role in imparting drought tolerance through different ABA and MAPK signalling cascades. Our studies suggest that these selected candidate genes could be targeted in development of drought tolerant cultivars in maize, rice and sorghum through appropriate breeding approaches. Our comparative experiments of CDPK genes could also be extended in the drought stress breeding programmes of the related species.

A Comparison of the Health Systems in China and India

DTIC Science & Technology

2008-01-01

some contagious diseases—such as hepatitis, pulmonary tuberculosis , and snail fever (schistosomiasis)—have revived; some endemic diseases, such as HIV... tuberculosis and malaria, have reemerged as greater public health concerns (Gupte, Ramachandran, and Mutatkar, 2001). Figure 2.2 Financial...diseases accounted for 77 percent of all deaths. Heart disease, chronic obstructive pulmonary disease, and cancer accounted for approximately 67 percent of

Using Molecular Models To Show Steric Clash in Peptides: An Illustration of Two Disallowed Regions in the Ramachandran Diagram

ERIC Educational Resources Information Center

Halkides, Christopher J.

2013-01-01

In this activity, students manipulate three-dimensional molecular models of the Ala-Ala-Ala tripeptide, where Ala is alanine. They rotate bonds to show that the pairs of dihedral angles phi = 0 degrees, psi = 180 degrees, and phi = 0 degrees, psi = 0 degrees lead to unfavorable interactions among the main chain atoms of the tripeptide. This…

Modeled structure of trypanothione reductase of Leishmania infantum.

PubMed

Singh, Bishal K; Sarkar, Nandini; Jagannadham, M V; Dubey, Vikash K

2008-06-30

Trypanothione reductase is an important target enzyme for structure-based drug design against Leishmania. We used homology modeling to construct a three-dimensional structure of the trypanothione reductase (TR) of Leishmania infantum. The structure shows acceptable Ramachandran statistics and a remarkably different active site from glutathione reductase(GR). Thus, a specific inhibitor against TR can be designed without interfering with host (human) GR activity.

An unconventional antimicrobial protein histone from freshwater prawn Macrobrachium rosenbergii: analysis of immune properties.

PubMed

Arockiaraj, Jesu; Gnanam, Annie J; Kumaresan, Venkatesh; Palanisamy, Rajesh; Bhatt, Prasanth; Thirumalai, Muthukumaresan Kuppusamy; Roy, Arpita; Pasupuleti, Mukesh; Kasi, Marimuthu

2013-11-01

In this study, we have reported the first histone characterized at molecular level from freshwater prawn Macrobrachium rosenbergii (MrHis). A full length cDNA of MrHis (751 base pairs) was identified from an established M. rosenbergii cDNA library using GS-FLX technique. It encodes 137 amino acid residues with a calculated molecular mass of 15 kDa and an isoelectric point of 10.5. MrHis peptide contains a histone H2A signature between 21 and 27 amino acids. Homologous analysis showed that MrHis had a significant sequence identity (99%) with other known histone H2A groups especially from Penaeus monodon. Phylogenetic analysis of MrHis showed a strong relationship with other amino acid sequences from histone H2A arthropod groups. Further phylogenetic analysis showed that the MrHis belongs to histone H2A superfamily and H2A1A sub-family. Secondary structure of MrHis showed that the protein contains 50.36% α-helical region and 49.64% coils. The 3D model of MrHis was predicted by I-Tasser program and the model was evaluated for quality analysis including C-score analysis, Ramachandran plot analysis and RMSD analysis. The surface view analysis of MrHis showed the active domain at the N terminal. The antimicrobial property of MrHis protein was confirmed by the helical structure and the total hydrophobic surface along with its net charge. The MFE of the predicted RNA structure of MrHis is -128.62 kcal/mol, shows its mRNA stability. Schiffer-Edmundson helical wheel analysis of the N-terminal of MrHis showed a perfect amphipathic nature of the peptide. Significantly (P < 0.05) highest gene expression was noticed in the hemocyte and is induced with viral (WSBV and MrNV) and bacteria (A eromonas hydrophila and Vibrio harveyi) infections. The coding sequence of recombinant MrHis protein was expressed in a pMAL vector and purified to study the antimicrobial properties. The recombinant product showed antimicrobial activity against both Gram negative and Gram positive bacteria. In this study, the recombinant MrHis protein displayed antimicrobial activity in its entirety. Hence, it is possible to suggest that the activity may be due to the direct defense role of histone or its N-terminal antimicrobial property. However, this remains to be verified by detailed investigations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Novel vascular endothelial growth factor blocker improves cellular viability and reduces hypobaric hypoxia-induced vascular leakage and oedema in rat brain.

PubMed

Saraswat, Deepika; Nehra, Sarita; Chaudhary, Kamal; CVS, Siva Prasad

2015-05-01

Vascular endothelial growth factor (VEGF) is an important cerebral angiogenic and permeability factor under hypoxia. There is a need to find effective molecules that may ameliorate hypoxia-induced cerebral oedema. In silico identification of novel candidate molecules that block VEGF-A site were identified and validated with a Ramachandran plot. The active site residues of VEGF-A were detected by Pocketfinder, CASTp, and DogSiteScorer. Based on in silico data, three VEGF-A blocker (VAB) candidate molecules (VAB1, VAB2, and VAB3) were checked for improvement in cellular viability and regulation of VEGF levels in N2a cells under hypoxia (0.5% O2 ). Additionally, the best candidate molecule's efficacy was assessed in male Sprague-Dawley rats for its ameliorative effect on cerebral oedema and vascular leakage under hypobaric hypoxia 7260 m. All experimental results were compared with the commercially available VEGF blocker sunitinib. Vascular endothelial growth factor-A blocker 1 was found most effective in increasing cellular viability and maintaining normal VEGF levels under hypoxia (0.5% oxygen) in N2a cells. Vascular endothelial growth factor-A blocker 1 effectively restored VEGF levels, decreased cerebral oedema, and reduced vascular leakage under hypobaric hypoxia when compared to sunitinib-treated rats. Vascular endothelial growth factor-A blocker 1 may be a promising candidate molecule for ameliorating hypobaric hypoxia-induced vasogenic oedema by regulating VEGF levels. © 2015 Wiley Publishing Asia Pty Ltd.

Interaction model of steviol glycosides from Stevia rebaudiana (Bertoni) with sweet taste receptors: A computational approach.

PubMed

Mayank; Jaitak, Vikas

2015-08-01

Docking studies were performed on natural sweeteners from Stevia rebaudiana by constructing homology models of T1R2 and T1R3 subunits of human sweet taste receptors. Ramachandran plot, PROCHECK results and ERRAT overall quality factor were used to validate the quality of models. Furthermore, docking results of steviol glycosides (SG's) were correlated significantly with data available in the literature which enabled to predict the exact sweetness rank order of SG's. The binding pattern indicated that Asn 44, Ans 52, Ala 345, Pro 343, Ile 352, Gly 346, Gly 47, Ala 354, Ser 336, Thr 326 and Ser 329 are the main interacting amino acid residues in case of T1R2 and Arg 56, Glu 105, Asp 215, Asp 216, Glu 148, Asp 258, Lys 255, Ser 104, Glu 217, Leu 51, Arg 52 for T1R3, respectively. Amino acids interact with SG's mainly by forming hydrogen bonds with the hydroxyl group of glucose moieties. Significant variation in docked poses of all the SG's were found. In this study, we have proposed the mechanism of the sweetness of the SG's in the form of multiple point stimulation model by considering the diverse binding patterns of various SG's, as well as their structural features. It will give further insight in understanding the differences in the quality of taste and will be used to improve the taste of SG's using semi-synthetic approaches. Copyright © 2015 Elsevier Ltd. All rights reserved.

Exploration of Structural and Functional Variations Owing to Point Mutations in α-NAGA.

PubMed

Meshach Paul, D; Rajasekaran, R

2018-03-01

Schindler disease is a lysosomal storage disorder caused due to deficiency or defective activity of alpha-N-acetylgalactosaminidase (α-NAGA). Mutations in gene encoding α-NAGA cause wide range of diseases, characterized with mild to severe clinical features. Molecular effects of these mutations are yet to be explored in detail. Therefore, this study was focused on four missense mutations of α-NAGA namely, S160C, E325K, R329Q and R329W. Native and mutant structures of α-NAGA were analysed to determine geometrical deviations such as the contours of root mean square deviation, root mean square fluctuation, percentage of residues in allowed regions of Ramachandran plot and solvent accessible surface area, using conformational sampling technique. Additionally, global energy-minimized structures of native and mutants were further analysed to compute their intra-molecular interactions, hydrogen bond dilution and distribution of secondary structure. In addition, docking studies were also performed to determine variations in binding energies between native and mutants. The deleterious effects of mutants were evident due to variations in their active site residues pertaining to spatial conformation and flexibility, comparatively. Hence, variations exhibited by mutants, namely S160C, E325K, R329Q and R329W to that of native, consequently, lead to the detrimental effects causing Schindler disease. This study computationally explains the underlying reasons for the pathogenesis of the disease, thereby aiding future researchers in drug development and disease management.

Comparative protein modeling of methionine S-adenosyltransferase (MAT) enzyme from Mycobacterium tuberculosis: a potential target for antituberculosis drug discovery.

PubMed

Khedkar, Santosh A; Malde, Alpeshkumar K; Coutinho, Evans C

2005-01-01

Mycobacterium tuberculosis (Mtb) is a successful pathogen that overcomes the numerous challenges presented by the immune system of the host. In the last 40 years few anti-TB drugs have been developed, while the drug-resistance problem is increasing; there is thus a pressing need to develop new anti-TB drugs active against both the acute and chronic growth phases of the mycobacterium. Methionine S-adenosyltransferase (MAT) is an enzyme involved in the synthesis of S-adenosylmethionine (SAM), a methyl donor essential for mycolipid biosynthesis. As an anti-TB drug target, Mtb-MAT has been well validated. A homology model of MAT has been constructed using the X-ray structures of E. coli MAT (PDB code: 1MXA) and rat MAT (PDB code: 1QM4) as templates, by comparative protein modeling principles. The resulting model has the correct stereochemistry as gauged from the Ramachandran plot and good three-dimensional (3D) structure compatibility as assessed by the Profiles-3D score. The structurally and functionally important residues (active site) of Mtb-MAT have been identified using the E. coli and rat MAT crystal structures and the reported point mutation data. The homology model conserves the topological and active site features of the MAT family of proteins. The differences in the molecular electrostatic potentials (MEP) of Mtb and human MAT provide evidences that selective and specific Mtb-MAT inhibitors can be designed using the homology model, by the structure-based drug design approaches.

Homology modelling of frequent HLA class-II alleles: A perspective to improve prediction of HLA binding peptide and understand the HLA associated disease susceptibility.

PubMed

Kashyap, Manju; Farooq, Umar; Jaiswal, Varun

2016-10-01

Human leukocyte antigen (HLA) plays significant role via the regulation of immune system and contribute in the progression and protection of many diseases. HLA molecules bind and present peptides to T- cell receptors which generate the immune response. HLA peptide interaction and molecular function of HLA molecule is the key to predict peptide binding and understanding its role in different diseases. The availability of accurate three dimensional (3D) structures is the initial step towards this direction. In the present work, homology modelling of important and frequent HLA-DRB1 alleles (07:01, 11:01 and 09:01) was done and acceptable models were generated. These modelled alleles were further refined and cross validated by using several methods including Ramachandran plot, Z-score, ERRAT analysis and root mean square deviation (RMSD) calculations. It is known that numbers of allelic variants are related to the susceptibility or protection of various infectious diseases. Difference in amino acid sequences and structures of alleles were also studied to understand the association of HLA with disease susceptibility and protection. Susceptible alleles showed more amino acid variations than protective alleles in three selected diseases caused by different pathogens. Amino acid variations at binding site were found to be more than other part of alleles. RMSD values were also higher at variable positions within binding site. Higher RMSD values indicate that mutations occurring at peptide binding site alter protein structure more than rest of the protein. Hence, these findings and modelled structures can be used to design HLA-DRB1 binding peptides to overcome low prediction accuracy of HLA class II binding peptides. Furthermore, it may help to understand the allele specific molecular mechanisms involved in susceptibility/resistance against pathogenic diseases. Copyright © 2016 Elsevier B.V. All rights reserved.

Development of a multi-epitope peptide vaccine inducing robust T cell responses against brucellosis using immunoinformatics based approaches.

PubMed

Saadi, Mahdiye; Karkhah, Ahmad; Nouri, Hamid Reza

2017-07-01

Current investigations have demonstrated that a multi-epitope peptide vaccine targeting multiple antigens could be considered as an ideal approach for prevention and treatment of brucellosis. According to the latest findings, the most effective immunogenic antigens of brucella to induce immune responses are included Omp31, BP26, BLS, DnaK and L7-L12. Therefore, in the present study, an in silico approach was used to design a novel multi-epitope vaccine to elicit a desirable immune response against brucellosis. First, five novel T-cell epitopes were selected from Omp31, BP26, BLS, DnaK and L7-L12 proteins using different servers. In addition, helper epitopes selected from Tetanus toxin fragment C (TTFrC) were applied to induce CD4+ helper T lymphocytes (HTLs) responses. Selected epitopes were fused together by GPGPG linkers to facilitate the immune processing and epitope presentation. Moreover, cholera toxin B (CTB) was linked to N terminal of vaccine construct as an adjuvant by using EAAAK linker. A multi-epitope vaccine was designed based on predicted epitopes which was 377 amino acid residues in length. Then, the physico-chemical properties, secondary and tertiary structures, stability, intrinsic protein disorder, solubility and allergenicity of this multi-epitope vaccine were assessed using immunoinformatics tools and servers. Based on obtained results, a soluble, and non-allergic protein with 40.59kDa molecular weight was constructed. Expasy ProtParam classified this chimeric protein as a stable protein and also 89.8% residues of constructed vaccine were located in favored regions of the Ramachandran plot. Furthermore, this multi-epitope peptide vaccine was able to strongly induce T cell and B-cell mediated immune responses. In conclusion, immunoinformatics analysis indicated that this multi-epitope peptide vaccine can be effectively expressed and potentially be used for prophylactic or therapeutic usages against brucellosis. Copyright © 2017 Elsevier B.V. All rights reserved.

The Spatiotemporal Characteristics of Visual Motion Priming

DTIC Science & Technology

1994-07-01

859. Barden, W. (1982, June). A general-purpose I/O board for the Color Computer. BYTE Magazine, pp. 260-281. B . ->,.. H . & Levick , W. (1965). The... B y ...... . ........ Distribution I Availability Codes Avail and i or Dist Special DTIC qU(A~ry niNPETEM 3 iii ABSTRACT THE...bistable diamond, apparent motion figure 52 (after Ramachandran & Anstis, 1983). ( b ) "Streaming" and "bouncing" percepts of apparent 52 motion dot

Monomeric Aβ1–40 and Aβ1–42 Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil

PubMed Central

2016-01-01

The pathogenesis of Alzheimer’s disease is characterized by the aggregation and fibrillation of amyloid peptides Aβ1–40 and Aβ1–42 into amyloid plaques. Despite strong potential therapeutic interest, the structural pathways associated with the conversion of monomeric Aβ peptides into oligomeric species remain largely unknown. In particular, the higher aggregation propensity and associated toxicity of Aβ1–42 compared to that of Aβ1–40 are poorly understood. To explore in detail the structural propensity of the monomeric Aβ1–40 and Aβ1–42 peptides in solution, we recorded a large set of nuclear magnetic resonance (NMR) parameters, including chemical shifts, nuclear Overhauser effects (NOEs), and J couplings. Systematic comparisons show that at neutral pH the Aβ1–40 and Aβ1–42 peptides populate almost indistinguishable coil-like conformations. Nuclear Overhauser effect spectra collected at very high resolution remove assignment ambiguities and show no long-range NOE contacts. Six sets of backbone J couplings (3JHNHα, 3JC′C′, 3JC′Hα, 1JHαCα, 2JNCα, and 1JNCα) recorded for Aβ1–40 were used as input for the recently developed MERA Ramachandran map analysis, yielding residue-specific backbone ϕ/ψ torsion angle distributions that closely resemble random coil distributions, the absence of a significantly elevated propensity for β-conformations in the C-terminal region of the peptide, and a small but distinct propensity for αL at K28. Our results suggest that the self-association of Aβ peptides into toxic oligomers is not driven by elevated propensities of the monomeric species to adopt β-strand-like conformations. Instead, the accelerated disappearance of Aβ NMR signals in D2O over H2O, particularly pronounced for Aβ1–42, suggests that intermolecular interactions between the hydrophobic regions of the peptide dominate the aggregation process. PMID:26780756

Monomeric Aβ(1-40) and Aβ(1-42) Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil.

PubMed

Roche, Julien; Shen, Yang; Lee, Jung Ho; Ying, Jinfa; Bax, Ad

2016-02-09

The pathogenesis of Alzheimer's disease is characterized by the aggregation and fibrillation of amyloid peptides Aβ(1-40) and Aβ(1-42) into amyloid plaques. Despite strong potential therapeutic interest, the structural pathways associated with the conversion of monomeric Aβ peptides into oligomeric species remain largely unknown. In particular, the higher aggregation propensity and associated toxicity of Aβ(1-42) compared to that of Aβ(1-40) are poorly understood. To explore in detail the structural propensity of the monomeric Aβ(1-40) and Aβ(1-42) peptides in solution, we recorded a large set of nuclear magnetic resonance (NMR) parameters, including chemical shifts, nuclear Overhauser effects (NOEs), and J couplings. Systematic comparisons show that at neutral pH the Aβ(1-40) and Aβ(1-42) peptides populate almost indistinguishable coil-like conformations. Nuclear Overhauser effect spectra collected at very high resolution remove assignment ambiguities and show no long-range NOE contacts. Six sets of backbone J couplings ((3)JHNHα, (3)JC'C', (3)JC'Hα, (1)JHαCα, (2)JNCα, and (1)JNCα) recorded for Aβ(1-40) were used as input for the recently developed MERA Ramachandran map analysis, yielding residue-specific backbone ϕ/ψ torsion angle distributions that closely resemble random coil distributions, the absence of a significantly elevated propensity for β-conformations in the C-terminal region of the peptide, and a small but distinct propensity for αL at K28. Our results suggest that the self-association of Aβ peptides into toxic oligomers is not driven by elevated propensities of the monomeric species to adopt β-strand-like conformations. Instead, the accelerated disappearance of Aβ NMR signals in D2O over H2O, particularly pronounced for Aβ(1-42), suggests that intermolecular interactions between the hydrophobic regions of the peptide dominate the aggregation process.

Backbone conformational preferences of an intrinsically disordered protein in solution.

PubMed

Espinoza-Fonseca, L Michel; Ilizaliturri-Flores, Ian; Correa-Basurto, José

2012-06-01

We have performed a 4-μs molecular dynamics simulation to investigate the native conformational preferences of the intrinsically disordered kinase-inducible domain (KID) of the transcription factor CREB in solution. There is solid experimental evidence showing that KID does not possess a bound-like structure in solution; however, it has been proposed that coil-to-helix transitions upon binding to its binding partner (CBP) are template-driven. While these studies indicate that IDPs possess a bias towards the bound structure, they do not provide direct evidence on the time-dependent conformational preferences of IDPs in atomic detail. Our simulation captured intrinsic conformational characteristics of KID that are in good agreement with experimental data such as a very small percentage of helical structure in its segment α(B) and structural disorder in solution. We used dihedral principal component analysis dPCA to map the conformations of KID in the microsecond timescale. By using principal components as reaction coordinates, we further constructed dPCA-based free energy landscapes of KID. Analysis of the free energy landscapes showed that KID is best characterized as a conformational ensemble of rapidly interconverting conformations. Interestingly, we found that despite the conformational heterogeneity of the backbone and the absence of substantial secondary structure, KID does not randomly sample the conformational space in solution: analysis of the (Φ, Ψ) dihedral angles showed that several individual residues of KID possess a strong bias toward the helical region of the Ramachandran plot. We suggest that the intrinsic conformational preferences of KID provide a bias toward the folded state without having to populate bound-like conformations before binding. Furthermore, we argue that these conformational preferences do not represent actual structural constraints which drive binding through a single pathway, which allows for specific interactions with multiple binding partners. Based on this evidence, we propose that the backbone conformational preferences of KID provide a thermodynamic advantage for folding and binding without negatively affecting the kinetics of binding. We further discuss the relation of our results to previous studies to rationalize the functional implications of the conformational preferences of IDPs, such as the optimization of structural disorder in protein-protein interactions. This study illustrates the importance in obtaining atomistic information of intrinsically disordered proteins in real time to reveal functional features arising from their complex conformational space.

The Use of R and S2 Charts Under Nonstandard Conditions.

DTIC Science & Technology

1980-03-01

and Krishnaiah (1964), David (1956), Finney (1941), Ghosh (1955), 5 Gupta (1963), Nair (1948), and Ramachandran (1956). Under Gaussian assumptions...the extensive tables of Armitage and Krishnaiah (1964) are tabulations of upper percentiles limited to the range 1 < t < 12 and thus are not suited to...REFERENCES Armitage, J.V. and Krishnaiah , P.R. (1964). "Tables for the Studentized largest chi-square distribution and their applications." Report ARL 64- 188

Electromagnetic Induction Spectroscopy for the Detection of Subsurface Targets

DTIC Science & Technology

2012-12-01

curves of the proposed method and that of Fails et al.. For the kNN ROC curve, k = 7. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81...et al. [6] and Ramachandran et al. [7] both demonstrated success in detecting mines using the k-nearest-neighbor ( kNN ) algorithm based on the EMI...error is also included in the feature vector. The kNN labels an unknown target based on the closest targets in a training set. Collins et al. [2] and

Renormalized Hamiltonian for a peptide chain: Digitalizing the protein folding problem

NASA Astrophysics Data System (ADS)

Fernández, Ariel; Colubri, Andrés

2000-05-01

A renormalized Hamiltonian for a flexible peptide chain is derived to generate the long-time limit dynamics compatible with a coarsening of torsional conformation space. The renormalization procedure is tailored taking into account the coarse graining imposed by the backbone torsional constraints due to the local steric hindrance and the local backbone-side-group interactions. Thus, the torsional degrees of freedom for each residue are resolved modulo basins of attraction in its so-called Ramachandran map. This Ramachandran renormalization (RR) procedure is implemented so that the chain is energetically driven to form contact patterns as their respective collective topological constraints are fulfilled within the coarse description. In this way, the torsional dynamics are digitalized and become codified as an evolving pattern in a binary matrix. Each accepted Monte Carlo step in a canonical ensemble simulation is correlated with the real mean first passage time it takes to reach the destination coarse topological state. This real-time correlation enables us to test the RR dynamics by comparison with experimentally probed kinetic bottlenecks along the dominant folding pathway. Such intermediates are scarcely populated at any given time, but they determine the kinetic funnel leading to the active structure. This landscape region is reached through kinetically controlled steps needed to overcome the conformational entropy of the random coil. The results are specialized for the bovine pancreatic trypsin inhibitor, corroborating the validity of our method.

The influence of solvent on conformational properties of peptides with Aib residue-a DFT study.

PubMed

Wałęsa, Roksana; Broda, Małgorzata A

2017-11-21

The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe 2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results, the available conformations of similar X-ray structures from the Cambridge Crystallographic Data Center (CCDC) were analyzed. The results of the calculations show that both derivatives with the Aib residue in the gas phase prefer structures stabilized by intramolecular N-H⋯O hydrogen bonds, i.e., C 5 and C 7 conformations, while polar solvent promotes helical conformation with φ, ψ values equal to +/-60°, +/-40°. In addition, in the case of molecule 2, the helical conformation is the only one available in the polar environment. This result is fully consistent with the X-ray data. Graphical abstract Effect of solvent on the Ramachandran maps of the model peptides with Aib residue.

Improvement on a simplified model for protein folding simulation.

PubMed

Zhang, Ming; Chen, Changjun; He, Yi; Xiao, Yi

2005-11-01

Improvements were made on a simplified protein model--the Ramachandran model-to achieve better computer simulation of protein folding. To check the validity of such improvements, we chose the ultrafast folding protein Engrailed Homeodomain as an example and explored several aspects of its folding. The engrailed homeodomain is a mainly alpha-helical protein of 61 residues from Drosophila melanogaster. We found that the simplified model of Engrailed Homeodomain can fold into a global minimum state with a tertiary structure in good agreement with its native structure.

User Guide for the Plotting Software for the Los Alamos National Laboratory Nuclear Weapons Analysis Tools Version 2.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cleland, Timothy James

The Los Alamos National Laboratory Plotting Software for the Nuclear Weapons Analysis Tools is a Java™ application based upon the open source library JFreeChart. The software provides a capability for plotting data on graphs with a rich variety of display options while allowing the viewer interaction via graph manipulation and scaling to best view the data. The graph types include XY plots, Date XY plots, Bar plots and Histogram plots.

A first look at measurement error on FIA plots using blind plots in the Pacific Northwest

Treesearch

Susanna Melson; David Azuma; Jeremy S. Fried

2002-01-01

Measurement error in the Forest Inventory and Analysis work of the Pacific Northwest Station was estimated with a recently implemented blind plot measurement protocol. A small subset of plots was revisited by a crew having limited knowledge of the first crew's measurements. This preliminary analysis of the first 18 months' blind plot data indicates that...

A density management diagram for even-aged ponderosa pine stands

Treesearch

James N. Long; John D. Shaw

2005-01-01

We developed a density management diagram (DMD) for ponderosa pine using Forest Inventory and Analysis (FIA) data. Analysis plots were drawn from all FIA plots in the western United States on which ponderosa pine occurred. A total of 766 plots met the criteria for analysis. Selection criteria were for purity, defined as ponderosa pine basal area 80% of plot basal area...

PET kinetic analysis --pitfalls and a solution for the Logan plot.

PubMed

Kimura, Yuichi; Naganawa, Mika; Shidahara, Miho; Ikoma, Yoko; Watabe, Hiroshi

2007-01-01

The Logan plot is a widely used algorithm for the quantitative analysis of neuroreceptors using PET because it is easy to use and simple to implement. The Logan plot is also suitable for receptor imaging because its algorithm is fast. However, use of the Logan plot, and interpretation of the formed receptor images should be regarded with caution, because noise in PET data causes bias in the Logan plot estimates. In this paper, we describe the basic concept of the Logan plot in detail and introduce three algorithms for the Logan plot. By comparing these algorithms, we demonstrate the pitfalls of the Logan plot and discuss the solution.

Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

PubMed Central

Hong, Mei

2016-01-01

We have determined refined multidimensional chemical shift ranges for intra-residue correlations (13C–13C, 15N–13C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 13C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ~94 % of the 13C NMR data and almost all 15N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the 13C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided command-line Python script (PLUQin), which should be useful in protein structure determination. The refined chemical shift distributions are utilized in a simple quality test (SQAT) that should be applied to new protein NMR data before deposition in a databank, and they could benefit many other chemical-shift based tools. PMID:26787537

[Heart rate variability study based on a novel RdR RR Intervals Scatter Plot].

PubMed

Lu, Hongwei; Lu, Xiuyun; Wang, Chunfang; Hua, Youyuan; Tian, Jiajia; Liu, Shihai

2014-08-01

On the basis of Poincare scatter plot and first order difference scatter plot, a novel heart rate variability (HRV) analysis method based on scatter plots of RR intervals and first order difference of RR intervals (namely, RdR) was proposed. The abscissa of the RdR scatter plot, the x-axis, is RR intervals and the ordinate, y-axis, is the difference between successive RR intervals. The RdR scatter plot includes the information of RR intervals and the difference between successive RR intervals, which captures more HRV information. By RdR scatter plot analysis of some records of MIT-BIH arrhythmias database, we found that the scatter plot of uncoupled premature ventricular contraction (PVC), coupled ventricular bigeminy and ventricular trigeminy PVC had specific graphic characteristics. The RdR scatter plot method has higher detecting performance than the Poincare scatter plot method, and simpler and more intuitive than the first order difference method.

True versus perturbed forest inventory plot locations for modeling: a simulation study

Treesearch

John W. Coulston; Kurt H. Riitters; Ronald E. McRoberts; William D. Smith

2006-01-01

USDA Forest Service Forest Inventory and Analysis plot information is widely used for timber inventories, forest health assessments, and environmental risk analyses. With few exceptions, true plot locations are not revealed; the plot coordinates are manipulated to obscure the location of field plots and thereby preserve plot integrity. The influence of perturbed plot...

Recurrence quantification analysis of electrically evoked surface EMG signal.

PubMed

Liu, Chunling; Wang, Xu

2005-01-01

Recurrence Plot is a quite useful tool used in time-series analysis, in particular for measuring unstable periodic orbits embedded in a chaotic dynamical system. This paper introduced the structures of the Recurrence Plot and the ways of the plot coming into being. Then the way of the quantification of the Recurrence Plot is defined. In this paper, one of the possible applications of Recurrence Quantification Analysis (RQA) strategy to the analysis of electrical stimulation evoked surface EMG. The result shows the percent determination is increased along with stimulation intensity.

Master plot analysis of microcracking in graphite/epoxy and graphite/PEEK laminates

NASA Technical Reports Server (NTRS)

Nairn, John A.; Hu, Shoufeng; Bark, Jong Song

1993-01-01

We used a variational stress analysis and an energy release rate failure criterion to construct a master plot analysis of matrix microcracking. In the master plot, the results for all laminates of a single material are predicted to fall on a single line whose slope gives the microcracking toughness of the material. Experimental results from 18 different layups of AS4/3501-6 laminates show that the master plot analysis can explain all observations. In particular, it can explain the differences between microcracking of central 90 deg plies and of free-surface 90 deg plies. Experimental results from two different AS4/PEEK laminates tested at different temperatures can be explained by a modified master plot that accounts for changes in the residual thermal stresses. Finally, we constructed similar master plot analyses for previous literature microcracking models. All microcracking theories that ignore the thickness dependence of the stresses gave poor results.

Analytical and experimental investigation of a 1/8-scale dynamic model of the shuttle orbiter. Volume 3B: Supporting data

NASA Technical Reports Server (NTRS)

Mason, P. W.; Harris, H. G.; Zalesak, J.; Bernstein, M.

1974-01-01

The NASA Structural Analysis System (NASTRAN) Model 1 finite element idealization, input data, and detailed analytical results are presented. The data presented include: substructuring analysis for normal modes, plots of member data, plots of symmetric free-free modes, plots of antisymmetric free-free modes, analysis of the wing, analysis of the cargo doors, analysis of the payload, and analysis of the orbiter.

Visual evaluation of kinetic characteristics of PET probe for neuroreceptors using a two-phase graphic plot analysis.

PubMed

Ito, Hiroshi; Ikoma, Yoko; Seki, Chie; Kimura, Yasuyuki; Kawaguchi, Hiroshi; Takuwa, Hiroyuki; Ichise, Masanori; Suhara, Tetsuya; Kanno, Iwao

2017-05-01

Objectives In PET studies for neuroreceptors, tracer kinetics are described by the two-tissue compartment model (2-TCM), and binding parameters, including the total distribution volume (V T ), non-displaceable distribution volume (V ND ), and binding potential (BP ND ), can be determined from model parameters estimated by kinetic analysis. The stability of binding parameter estimates depends on the kinetic characteristics of radioligands. To describe these kinetic characteristics, we previously developed a two-phase graphic plot analysis in which V ND and V T can be estimated from the x-intercept of regression lines for early and delayed phases, respectively. In this study, we applied this graphic plot analysis to visual evaluation of the kinetic characteristics of radioligands for neuroreceptors, and investigated a relationship between the shape of these graphic plots and the stability of binding parameters estimated by the kinetic analysis with 2-TCM in simulated brain tissue time-activity curves (TACs) with various binding parameters. Methods 90-min TACs were generated with the arterial input function and assumed kinetic parameters according to 2-TCM. Graphic plot analysis was applied to these simulated TACs, and the curvature of the plot for each TAC was evaluated visually. TACs with several noise levels were also generated with various kinetic parameters, and the bias and variation of binding parameters estimated by kinetic analysis were calculated in each TAC. These bias and variation were compared with the shape of graphic plots. Results The graphic plots showed larger curvature for TACs with higher specific binding and slower dissociation of specific binding. The quartile deviations of V ND and BP ND determined by kinetic analysis were smaller for radioligands with slow dissociation. Conclusions The larger curvature of graphic plots for radioligands with slow dissociation might indicate a stable determination of V ND and BP ND by kinetic analysis. For investigation of the kinetics of radioligands, such kinetic characteristics should be considered.

GRAFLAB 2.3 for UNIX - A MATLAB database, plotting, and analysis tool: User`s guide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunn, W.N.

1998-03-01

This report is a user`s manual for GRAFLAB, which is a new database, analysis, and plotting package that has been written entirely in the MATLAB programming language. GRAFLAB is currently used for data reduction, analysis, and archival. GRAFLAB was written to replace GRAFAID, which is a FORTRAN database, analysis, and plotting package that runs on VAX/VMS.

Plotting equation for gaussian percentiles and a spreadsheet program for generating probability plots

USGS Publications Warehouse

Balsillie, J.H.; Donoghue, J.F.; Butler, K.M.; Koch, J.L.

2002-01-01

Two-dimensional plotting tools can be of invaluable assistance in analytical scientific pursuits, and have been widely used in the analysis and interpretation of sedimentologic data. We consider, in this work, the use of arithmetic probability paper (APP). Most statistical computer applications do not allow for the generation of APP plots, because of apparent intractable nonlinearity of the percentile (or probability) axis of the plot. We have solved this problem by identifying an equation(s) for determining plotting positions of Gaussian percentiles (or probabilities), so that APP plots can easily be computer generated. An EXCEL example is presented, and a programmed, simple-to-use EXCEL application template is hereby made publicly available, whereby a complete granulometric analysis including data listing, moment measure calculations, and frequency and cumulative APP plots, is automatically produced.

Advancements in LiDAR-based registration of FIA field plots

Treesearch

Demetrios Gatziolis

2012-01-01

Meaningful integration of National Forest Inventory field plot information with spectral imagery acquired from satellite or airborne platforms requires precise plot registration. Global positioning system-based plot registration procedures, such as the one employed by the Forest Inventory and Analysis (FIA) Program, yield plot coordinates that, although adequate for...

Asymptotic solution of Fokker-Planck equation for plasma in Paul traps

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shah, Kushal

2010-05-15

An exact analytic solution of the Vlasov equation for the plasma distribution in a Paul trap is known to be a Maxwellian and thus, immune to collisions under the assumption of infinitely fast relaxation [K. Shah and H. S. Ramachandran, Phys. Plasmas 15, 062303 (2008)]. In this paper, it is shown that even for a more realistic situation of finite time relaxation, solutions of the Fokker-Planck equation lead to an equilibrium solution of the form of a Maxwellian with oscillatory temperature. This shows that the rf heating observed in Paul traps cannot be caused due to collisional effects alone.

Genetic engineering combined with deep UV resonance Raman spectroscopy for structural characterization of amyloid-like fibrils.

PubMed

Sikirzhytski, Vitali; Topilina, Natalya I; Higashiya, Seiichiro; Welch, John T; Lednev, Igor K

2008-05-07

Elucidating the structure of the cross-beta core in large amyloid fibrils is a challenging problem in modern structural biology. For the first time, a set of de novo polypeptides was genetically engineered to form amyloid-like fibrils with similar morphology and yet different strand length. Differential ultraviolet Raman spectroscopy allowed for separation of the spectroscopic signatures of the highly ordered beta-sheet strands and turns of the fibril core. The relationship between Raman frequencies and Ramachandran dihedral angles of the polypeptide backbone indicates the nature of the beta-sheet and turn structural elements.

A method for analyzing temporal patterns of variability of a time series from Poincare plots.

PubMed

Fishman, Mikkel; Jacono, Frank J; Park, Soojin; Jamasebi, Reza; Thungtong, Anurak; Loparo, Kenneth A; Dick, Thomas E

2012-07-01

The Poincaré plot is a popular two-dimensional, time series analysis tool because of its intuitive display of dynamic system behavior. Poincaré plots have been used to visualize heart rate and respiratory pattern variabilities. However, conventional quantitative analysis relies primarily on statistical measurements of the cumulative distribution of points, making it difficult to interpret irregular or complex plots. Moreover, the plots are constructed to reflect highly correlated regions of the time series, reducing the amount of nonlinear information that is presented and thereby hiding potentially relevant features. We propose temporal Poincaré variability (TPV), a novel analysis methodology that uses standard techniques to quantify the temporal distribution of points and to detect nonlinear sources responsible for physiological variability. In addition, the analysis is applied across multiple time delays, yielding a richer insight into system dynamics than the traditional circle return plot. The method is applied to data sets of R-R intervals and to synthetic point process data extracted from the Lorenz time series. The results demonstrate that TPV complements the traditional analysis and can be applied more generally, including Poincaré plots with multiple clusters, and more consistently than the conventional measures and can address questions regarding potential structure underlying the variability of a data set.

How To ... Guide

Treesearch

Duncan C. Lutes; Robert E. Keane; John F. Caratti; Carl H. Key; Nathan C. Benson

2006-01-01

This is probably the most critical phase of FIREMON sampling because this plot ID must be unique across all plots that will be entered in the FIREMON database. The plot identifier is made up of three parts: Registration Code, Project Code, and Plot Number.The FIREMON Analysis Tools program will allow summarization and comparison of plots only if...

Considerations in Forest Growth Estimation Between Two Measurements of Mapped Forest Inventory Plots

Treesearch

Michael T. Thompson

2006-01-01

Several aspects of the enhanced Forest Inventory and Analysis (FIA) program?s national plot design complicate change estimation. The design incorporates up to three separate plot sizes (microplot, subplot, and macroplot) to sample trees of different sizes. Because multiple plot sizes are involved, change estimators designed for polyareal plot sampling, such as those...

Applying an Empirical Hydropathic Forcefield in Refinement May Improve Low-Resolution Protein X-Ray Crystal Structures

PubMed Central

Koparde, Vishal N.; Scarsdale, J. Neel; Kellogg, Glen E.

2011-01-01

Background The quality of X-ray crystallographic models for biomacromolecules refined from data obtained at high-resolution is assured by the data itself. However, at low-resolution, >3.0 Å, additional information is supplied by a forcefield coupled with an associated refinement protocol. These resulting structures are often of lower quality and thus unsuitable for downstream activities like structure-based drug discovery. Methodology An X-ray crystallography refinement protocol that enhances standard methodology by incorporating energy terms from the HINT (Hydropathic INTeractions) empirical forcefield is described. This protocol was tested by refining synthetic low-resolution structural data derived from 25 diverse high-resolution structures, and referencing the resulting models to these structures. The models were also evaluated with global structural quality metrics, e.g., Ramachandran score and MolProbity clashscore. Three additional structures, for which only low-resolution data are available, were also re-refined with this methodology. Results The enhanced refinement protocol is most beneficial for reflection data at resolutions of 3.0 Å or worse. At the low-resolution limit, ≥4.0 Å, the new protocol generated models with Cα positions that have RMSDs that are 0.18 Å more similar to the reference high-resolution structure, Ramachandran scores improved by 13%, and clashscores improved by 51%, all in comparison to models generated with the standard refinement protocol. The hydropathic forcefield terms are at least as effective as Coulombic electrostatic terms in maintaining polar interaction networks, and significantly more effective in maintaining hydrophobic networks, as synthetic resolution is decremented. Even at resolutions ≥4.0 Å, these latter networks are generally native-like, as measured with a hydropathic interactions scoring tool. PMID:21246043

Perceived spatial displacement of motion-defined contours in peripheral vision.

PubMed

Fan, Zhao; Harris, John

2008-12-01

The perceived displacement of motion-defined contours in peripheral vision was examined in four experiments. In Experiment 1, in line with Ramachandran and Anstis' finding [Ramachandran, V. S., & Anstis, S. M. (1990). Illusory displacement of equiluminous kinetic edges. Perception, 19, 611-616], the border between a field of drifting dots and a static dot pattern was apparently displaced in the same direction as the movement of the dots. When a uniform dark area was substituted for the static dots, a similar displacement was found, but this was smaller and statistically insignificant. In Experiment 2, the border between two fields of dots moving in opposite directions was displaced in the direction of motion of the dots in the more eccentric field, so that the location of a boundary defined by a diverging pattern is perceived as more eccentric, and that defined by a converging as less eccentric. Two explanations for this effect (that the displacement reflects a greater weight given to the more eccentric motion, or that the region containing stronger centripetal motion components expands perceptually into that containing centrifugal motion) were tested in Experiment 3, by varying the velocity of the more eccentric region. The results favoured the explanation based on the expansion of an area in centripetal motion. Experiment 4 showed that the difference in perceived location was unlikely to be due to differences in the discriminability of contours in diverging and converging patterns, and confirmed that this effect is due to a difference between centripetal and centrifugal motion rather than motion components in other directions. Our result provides new evidence for a bias towards centripetal motion in human vision, and suggests that the direction of motion-induced displacement of edges is not always in the direction of an adjacent moving pattern.

Sampling saddle points on a free energy surface

NASA Astrophysics Data System (ADS)

Samanta, Amit; Chen, Ming; Yu, Tang-Qing; Tuckerman, Mark; E, Weinan

2014-04-01

Many problems in biology, chemistry, and materials science require knowledge of saddle points on free energy surfaces. These saddle points act as transition states and are the bottlenecks for transitions of the system between different metastable states. For simple systems in which the free energy depends on a few variables, the free energy surface can be precomputed, and saddle points can then be found using existing techniques. For complex systems, where the free energy depends on many degrees of freedom, this is not feasible. In this paper, we develop an algorithm for finding the saddle points on a high-dimensional free energy surface "on-the-fly" without requiring a priori knowledge the free energy function itself. This is done by using the general strategy of the heterogeneous multi-scale method by applying a macro-scale solver, here the gentlest ascent dynamics algorithm, with the needed force and Hessian values computed on-the-fly using a micro-scale model such as molecular dynamics. The algorithm is capable of dealing with problems involving many coarse-grained variables. The utility of the algorithm is illustrated by studying the saddle points associated with (a) the isomerization transition of the alanine dipeptide using two coarse-grained variables, specifically the Ramachandran dihedral angles, and (b) the beta-hairpin structure of the alanine decamer using 20 coarse-grained variables, specifically the full set of Ramachandran angle pairs associated with each residue. For the alanine decamer, we obtain a detailed network showing the connectivity of the minima obtained and the saddle-point structures that connect them, which provides a way to visualize the gross features of the high-dimensional surface.

On-Line 1D and 2D PLOT/LC-ESI-MS Using 10 μm i.d. Poly(styrene–divinylbenzene) Porous Layer Open Tubular (PLOT) Columns For Ultrasensitive Proteomic Analysis

PubMed Central

Luo, Quanzhou; Yue, Guihua; Valaskovic, Gary A; Gu, Ye; Wu, Shiaw-Lin; Karger, Barry L.

2008-01-01

Following on our recent work, on-line one dimensional (1D) and two dimensional (2D) PLOT/LC-ESI-MS platforms using 3.2 m × 10 μm i.d. poly(styrenedivinylbenzene) (PS-DVB) porous layer open tubular (PLOT) columns have been developed to provide robust, high performance and ultrasensitive proteomic analysis. Using a PicoClear tee, the dead volume connection between a 50 μm i.d. PS-DVB monolithic microSPE column and the PLOT column was minimized. The microSPE/PLOT column assembly provided a separation performance similar to that obtained with direct injection onto the PLOT column at a mobile phase flow rate of 20 nL/min. The trace analysis potential of the platform was evaluated using an in-gel tryptic digest sample of a gel fraction (15 to 40 kDa) of a cervical cancer (SiHa) cell line. As an example of the sensitivity of the system, ∼2.5 ng of protein in 2 μL solution, an amount corresponding to 20 SiHa cells, was subjected to on-line microSPE-PLOT/LC-ESIMS/MS analysis using a linear ion trap MS. 237 peptides associated with 163 unique proteins were identified from a single analysis when using stringent criteria associated with a false positive rate less than 1% . The number of identified peptides and proteins increased to 638 and 343, respectively, as the injection amount was raised to ∼45 ng of protein, an amount corresponding to 350 SiHa cells. In comparison, only 338 peptides and 231 unique proteins were identified (false positive rate again less than 1%) from 750 ng of protein from the identical gel fraction, an amount corresponding to 6000 SiHa cells, using a typical 15 cm × 75 μm i.d. packed capillary column. The greater sensitivity, higher recovery, and higher resolving power of the PLOT column resulted in the increased number of identifications from only ∼5% of the injected sample amount. The resolving power of the microSPE/PLOT assembly was further extended by 2D chromatography via combination of the high-efficiency reversed phase PLOT column with strong cation exchange chromatography (SCX). As an example, 1071 peptides associated with 536 unique proteins were identified from 75 ng of protein from the same gel fraction, an amount corresponding to 600 cells, using 5 ion exchange fractions in online 2D SCX-PLOT/LC-MS. The 2D system, implemented in an automated format, led to simple and robust operation for proteomic analysis. These promising results demonstrate the potential of the PLOT column for ultratrace analysis. PMID:17625912

Estimating the number of tree species in forest populations using current vegetation survey and forest inventory and analysis approximation plots and grid intensities

Treesearch

Hans T. Schreuder; Jin-Mann S. Lin; John Teply

2000-01-01

We estimate number of tree species in National Forest populations using the nonparametric estimator. Data from the Current Vegetation Survey (CVS) of Region 6 of the USDA Forest Service were used to estimate the number of tree species with a plot close in size to the Forest Inventory and Analysis (FIA) plot and the actual CVS plot for the 5.5 km FIA grid and the 2.7 km...

Round versus rectangular: Does the plot shape matter?

NASA Astrophysics Data System (ADS)

Iserloh, Thomas; Bäthke, Lars; Ries, Johannes B.

2016-04-01

Field rainfall simulators are designed to study soil erosion processes and provide urgently needed data for various geomorphological, hydrological and pedological issues. Due to the different conditions and technologies applied, there are several methodological aspects under review of the scientific community, particularly concerning design, procedures and conditions of measurement for infiltration, runoff and soil erosion. Extensive discussions at the Rainfall Simulator Workshop 2011 in Trier and the Splinter Meeting at EGU 2013 "Rainfall simulation: Big steps forward!" lead to the opinion that the rectangular shape is the more suitable plot shape compared to the round plot. A horizontally edging Gerlach trough is installed for sample collection without forming unnatural necks as is found at round or triangle plots. Since most research groups did and currently do work with round plots at the point scale (<1m²), a precise analysis of the differences between the output of round and square plots are necessary. Our hypotheses are: - Round plot shapes disturb surface runoff, unnatural fluvial dynamics for the given plot size such as pool development especially directly at the plot's outlet occur. - A square plot shape prevent these problems. A first comparison between round and rectangular plots (Iserloh et al., 2015) indicates that the rectangular plot could indeed be the more suitable, but the rather ambiguous results make a more elaborate test setup necessary. The laboratory test setup includes the two plot shapes (round, square), a standardised silty substrate and three inclinations (2°, 6°, 12°). The analysis of the laboratory test provide results on the best performance concerning undisturbed surface runoff and soil/water sampling at the plot's outlet. The analysis of the plot shape concerning its influence on runoff and erosion shows that clear methodological standards are necessary in order to make rainfall simulation experiments comparable. Reference: Iserloh, T., Pegoraro, D., Schlösser, A., Thesing, H., Seeger, M., Ries, J.B. (2015): Rainfall simulation experiments: Influence of water temperature, water quality and plot design on soil erosion and runoff. Geophysical Research Abstracts, Vol. 17, EGU2015-5817.

The poor man's Geographic Information System: plot expansion factors

Treesearch

Paul C. Van Deusen

2007-01-01

Plot expansion factors can serve as a crude Geographic Information System for users of Forest Inventory and Analysis (FIA) data. Each FIA plot has an associated expansion factor that is often interpreted as the number of forested acres that the plot represents. The derivation of expansion factors is discussed and it is shown that the mapped plot design requires a...

Sequence-structure correlations in silk: Poly-Ala repeat of N. clavipes MaSp1 is naturally optimized at a critical length scale.

PubMed

Bratzel, Graham; Buehler, Markus J

2012-03-01

Spider silk is a self-assembling biopolymer that outperforms many known materials in terms of its mechanical performance despite being constructed from simple and inferior building blocks. While experimental studies have shown that the molecular structure of silk has a direct influence on the stiffness, toughness, and failure strength of silk, few molecular-level analyses of the nanostructure of silk assemblies in particular under variations of genetic sequences have been reported. Here we report atomistic-level structures of the MaSp1 protein from the Nephila Clavipes spider dragline silk sequence, obtained using an in silico approach based on replica exchange molecular dynamics (REMD) and explicit water molecular dynamics. We apply this method to study the effects of a systematic variation of the poly-alanine repeat lengths, a parameter controlled by the genetic makeup of silk, on the resulting molecular structure of silk at the nanoscale. Confirming earlier experimental and computational work, a structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly β-sheet crystal domains while disorderly regions are formed by glycine-rich repeats that consist of 3(10)-helix type structures and β-turns. Our predictions are directly validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots combined with an analysis of the secondary structure content. The key result of our study is our finding of a strong dependence of the resulting silk nanostructure depending on the poly-alanine length. We observe that the wildtype poly-alanine repeat length of six residues defines a critical minimum length that consistently results in clearly defined β-sheet nanocrystals. For poly-alanine lengths below six, the β-sheet nanocrystals are not well-defined or not visible at all, while for poly-alanine lengths at and above six, the characteristic nanocomposite structure of silk emerges with no significant improvement of the quality of the β-sheet nanocrystal geometry. We present a simple biophysical model that explains these computational observations based on the mechanistic insight gained from the molecular simulations. Our findings set the stage for understanding how variations in the spidroin sequence can be used to engineer the structure and thereby functional properties of this biological superfiber, and present a design strategy for the genetic optimization of spidroins for enhanced mechanical properties. The approach used here may also find application in the design of other self-assembled molecular structures and fibers and in particular biologically inspired or completely synthetic systems. Copyright © 2011 Elsevier Ltd. All rights reserved.

Spatially Locating FIA Plots from Pixel Values

Treesearch

Greg C. Liknes; Geoffrey R. Holden; Mark D. Nelson; Ronald E. McRoberts

2005-01-01

The USDA Forest Service Forest Inventory and Analysis (FIA) program is required to ensure the confidentiality of the geographic locations of plots. To accommodate user requests for data without releasing actual plot coordinates, FIA creates overlays of plot locations on various geospatial data, including satellite imagery. Methods for reporting pixel values associated...

A density management diagram for even-aged Sierra Nevada mixed-conifer stands

Treesearch

James N. Long; John D. Shaw

2012-01-01

We have developed a density management diagram (DMD) for even-aged mixed-conifer stands in the Sierra Nevada Mountains using forest inventory and analysis (FIA) data. Analysis plots were drawn from FIA plots in California, southern Oregon, and western Nevada which included those conifer species associated with the mixed-conifer forest type. A total of 204 plots met the...

The status of accurately locating forest inventory and analysis plots using the Global Positioning System

Treesearch

Michael Hoppus; Andrew Lister

2007-01-01

Historically, field crews used Global Positioning System (GPS) coordinates to establish and relocate plots, as well as document their general location. During the past 5 years, the increase in Geographic Information System (GIS) capabilities and in customer requests to use the spatial relationships between Forest Inventory and Analysis (FIA) plot data and other GIS...

MolTalk – a programming library for protein structures and structure analysis

PubMed Central

Diemand, Alexander V; Scheib, Holger

2004-01-01

Background Two of the mostly unsolved but increasingly urgent problems for modern biologists are a) to quickly and easily analyse protein structures and b) to comprehensively mine the wealth of information, which is distributed along with the 3D co-ordinates by the Protein Data Bank (PDB). Tools which address this issue need to be highly flexible and powerful but at the same time must be freely available and easy to learn. Results We present MolTalk, an elaborate programming language, which consists of the programming library libmoltalk implemented in Objective-C and the Smalltalk-based interpreter MolTalk. MolTalk combines the advantages of an easy to learn and programmable procedural scripting with the flexibility and power of a full programming language. An overview of currently available applications of MolTalk is given and with PDBChainSaw one such application is described in more detail. PDBChainSaw is a MolTalk-based parser and information extraction utility of PDB files. Weekly updates of the PDB are synchronised with PDBChainSaw and are available for free download from the MolTalk project page following the link to PDBChainSaw. For each chain in a protein structure, PDBChainSaw extracts the sequence from its co-ordinates and provides additional information from the PDB-file header section, such as scientific organism, compound name, and EC code. Conclusion MolTalk provides a rich set of methods to analyse and even modify experimentally determined or modelled protein structures. These methods vary in complexity and are thus suitable for beginners and advanced programmers alike. We envision MolTalk to be most valuable in the following applications: 1) To analyse protein structures repetitively in large-scale, i.e. to benchmark protein structure prediction methods or to evaluate structural models. The quality of the resulting 3D-models can be assessed by e.g. calculating a Ramachandran-Sasisekharan plot. 2) To quickly retrieve information for (a limited number of) macro-molecular structures, i.e. H-bonds, salt bridges, contacts between amino acids and ligands or at the interface between two chains. 3) To programme more complex structural bioinformatics software and to implement demanding algorithms through its portability to Objective-C, e.g. iMolTalk. 4) To be used as a front end to databases, e.g. PDBChainSaw. PMID:15096277

Domain analyses of Usher syndrome causing Clarin-1 and GPR98 protein models.

PubMed

Khan, Sehrish Haider; Javed, Muhammad Rizwan; Qasim, Muhammad; Shahzadi, Samar; Jalil, Asma; Rehman, Shahid Ur

2014-01-01

Usher syndrome is an autosomal recessive disorder that causes hearing loss, Retinitis Pigmentosa (RP) and vestibular dysfunction. It is clinically and genetically heterogeneous disorder which is clinically divided into three types i.e. type I, type II and type III. To date, there are about twelve loci and ten identified genes which are associated with Usher syndrome. A mutation in any of these genes e.g. CDH23, CLRN1, GPR98, MYO7A, PCDH15, USH1C, USH1G, USH2A and DFNB31 can result in Usher syndrome or non-syndromic deafness. These genes provide instructions for making proteins that play important roles in normal hearing, balance and vision. Studies have shown that protein structures of only seven genes have been determined experimentally and there are still three genes whose structures are unavailable. These genes are Clarin-1, GPR98 and Usherin. In the absence of an experimentally determined structure, homology modeling and threading often provide a useful 3D model of a protein. Therefore in the current study Clarin-1 and GPR98 proteins have been analyzed for signal peptide, domains and motifs. Clarin-1 protein was found to be without any signal peptide and consists of prokar lipoprotein domain. Clarin-1 is classified within claudin 2 super family and consists of twelve motifs. Whereas, GPR98 has a 29 amino acids long signal peptide and classified within GPCR family 2 having Concanavalin A-like lectin/glucanase superfamily. It was found to be consists of GPS and G protein receptor F2 domains and twenty nine motifs. Their 3D structures have been predicted using I-TASSER server. The model of Clarin-1 showed only α-helix but no beta sheets while model of GPR98 showed both α-helix and β sheets. The predicted structures were then evaluated and validated by MolProbity and Ramachandran plot. The evaluation of the predicted structures showed 78.9% residues of Clarin-1 and 78.9% residues of GPR98 within favored regions. The findings of present study has resulted in the three dimensional structure prediction and conserved domain analysis which will be quite beneficial in better understanding of molecular components, protein-protein interaction, clinical heterogeneity and pathophysiology of Usher syndrome.

MolTalk--a programming library for protein structures and structure analysis.

PubMed

Diemand, Alexander V; Scheib, Holger

2004-04-19

Two of the mostly unsolved but increasingly urgent problems for modern biologists are a) to quickly and easily analyse protein structures and b) to comprehensively mine the wealth of information, which is distributed along with the 3D co-ordinates by the Protein Data Bank (PDB). Tools which address this issue need to be highly flexible and powerful but at the same time must be freely available and easy to learn. We present MolTalk, an elaborate programming language, which consists of the programming library libmoltalk implemented in Objective-C and the Smalltalk-based interpreter MolTalk. MolTalk combines the advantages of an easy to learn and programmable procedural scripting with the flexibility and power of a full programming language. An overview of currently available applications of MolTalk is given and with PDBChainSaw one such application is described in more detail. PDBChainSaw is a MolTalk-based parser and information extraction utility of PDB files. Weekly updates of the PDB are synchronised with PDBChainSaw and are available for free download from the MolTalk project page http://www.moltalk.org following the link to PDBChainSaw. For each chain in a protein structure, PDBChainSaw extracts the sequence from its co-ordinates and provides additional information from the PDB-file header section, such as scientific organism, compound name, and EC code. MolTalk provides a rich set of methods to analyse and even modify experimentally determined or modelled protein structures. These methods vary in complexity and are thus suitable for beginners and advanced programmers alike. We envision MolTalk to be most valuable in the following applications:1) To analyse protein structures repetitively in large-scale, i.e. to benchmark protein structure prediction methods or to evaluate structural models. The quality of the resulting 3D-models can be assessed by e.g. calculating a Ramachandran-Sasisekharan plot.2) To quickly retrieve information for (a limited number of) macro-molecular structures, i.e. H-bonds, salt bridges, contacts between amino acids and ligands or at the interface between two chains.3) To programme more complex structural bioinformatics software and to implement demanding algorithms through its portability to Objective-C, e.g. iMolTalk.4) To be used as a front end to databases, e.g. PDBChainSaw.

Domain analyses of Usher syndrome causing Clarin-1 and GPR98 protein models

PubMed Central

Khan, Sehrish Haider; Javed, Muhammad Rizwan; Qasim, Muhammad; Shahzadi, Samar; Jalil, Asma; Rehman, Shahid ur

2014-01-01

Usher syndrome is an autosomal recessive disorder that causes hearing loss, Retinitis Pigmentosa (RP) and vestibular dysfunction. It is clinically and genetically heterogeneous disorder which is clinically divided into three types i.e. type I, type II and type III. To date, there are about twelve loci and ten identified genes which are associated with Usher syndrome. A mutation in any of these genes e.g. CDH23, CLRN1, GPR98, MYO7A, PCDH15, USH1C, USH1G, USH2A and DFNB31 can result in Usher syndrome or non-syndromic deafness. These genes provide instructions for making proteins that play important roles in normal hearing, balance and vision. Studies have shown that protein structures of only seven genes have been determined experimentally and there are still three genes whose structures are unavailable. These genes are Clarin-1, GPR98 and Usherin. In the absence of an experimentally determined structure, homology modeling and threading often provide a useful 3D model of a protein. Therefore in the current study Clarin-1 and GPR98 proteins have been analyzed for signal peptide, domains and motifs. Clarin-1 protein was found to be without any signal peptide and consists of prokar lipoprotein domain. Clarin-1 is classified within claudin 2 super family and consists of twelve motifs. Whereas, GPR98 has a 29 amino acids long signal peptide and classified within GPCR family 2 having Concanavalin A-like lectin/glucanase superfamily. It was found to be consists of GPS and G protein receptor F2 domains and twenty nine motifs. Their 3D structures have been predicted using I-TASSER server. The model of Clarin-1 showed only α-helix but no beta sheets while model of GPR98 showed both α-helix and β sheets. The predicted structures were then evaluated and validated by MolProbity and Ramachandran plot. The evaluation of the predicted structures showed 78.9% residues of Clarin-1 and 78.9% residues of GPR98 within favored regions. The findings of present study has resulted in the three dimensional structure prediction and conserved domain analysis which will be quite beneficial in better understanding of molecular components, protein-protein interaction, clinical heterogeneity and pathophysiology of Usher syndrome. PMID:25258483

Computer routine adds plotting capabilities to existing programs

NASA Technical Reports Server (NTRS)

Harris, J. C.; Linnekin, J. S.

1966-01-01

PLOTAN, a generalized plot analysis routine written for the IBM 7094 computer, minimizes the difficulties in adding plot capabilities to large existing programs. PLOTAN is used in conjunction with a binary tape writing routine and has the ability to plot any variable on the intermediate binary tape as a function of any other.

NEMAR plotting computer program

NASA Technical Reports Server (NTRS)

Myler, T. R.

1981-01-01

A FORTRAN coded computer program which generates CalComp plots of trajectory parameters is examined. The trajectory parameters are calculated and placed on a data file by the Near Earth Mission Analysis Routine computer program. The plot program accesses the data file and generates the plots as defined by inputs to the plot program. Program theory, user instructions, output definitions, subroutine descriptions and detailed FORTRAN coding information are included. Although this plot program utilizes a random access data file, a data file of the same type and formatted in 102 numbers per record could be generated by any computer program and used by this plot program.

Mars Science Laboratory Launch-Arrival Space Study: A Pork Chop Plot Analysis

NASA Technical Reports Server (NTRS)

Cianciolo, Alicia Dwyer; Powell, Richard; Lockwood, Mary Kae

2006-01-01

Launch-Arrival, or "pork chop", plot analysis can provide mission designers with valuable information and insight into a specific launch and arrival space selected for a mission. The study begins with the array of entry states for each pair of selected Earth launch and Mars arrival dates, and nominal entry, descent and landing trajectories are simulated for each pair. Parameters of interest, such as maximum heat rate, are plotted in launch-arrival space. The plots help to quickly identify launch and arrival regions that are not feasible under current constraints or technology and also provide information as to what technologies may need to be developed to reach a desired region. This paper provides a discussion of the development, application, and results of a pork chop plot analysis to the Mars Science Laboratory mission. This technique is easily applicable to other missions at Mars and other destinations.

Using recurrence plot analysis for software execution interpretation and fault detection

NASA Astrophysics Data System (ADS)

Mosdorf, M.

2015-09-01

This paper shows a method targeted at software execution interpretation and fault detection using recurrence plot analysis. In in the proposed approach recurrence plot analysis is applied to software execution trace that contains executed assembly instructions. Results of this analysis are subject to further processing with PCA (Principal Component Analysis) method that simplifies number coefficients used for software execution classification. This method was used for the analysis of five algorithms: Bubble Sort, Quick Sort, Median Filter, FIR, SHA-1. Results show that some of the collected traces could be easily assigned to particular algorithms (logs from Bubble Sort and FIR algorithms) while others are more difficult to distinguish.

Relative equilibrium plot improves graphical analysis and allows bias correction of SUVR in quantitative [11C]PiB PET studies

PubMed Central

Zhou, Yun; Sojkova, Jitka; Resnick, Susan M.; Wong, Dean F.

2012-01-01

Both the standardized uptake value ratio (SUVR) and the Logan plot result in biased distribution volume ratios (DVR) in ligand-receptor dynamic PET studies. The objective of this study is to use a recently developed relative equilibrium-based graphical plot (RE plot) method to improve and simplify the two commonly used methods for quantification of [11C]PiB PET. Methods The overestimation of DVR in SUVR was analyzed theoretically using the Logan and the RE plots. A bias-corrected SUVR (bcSUVR) was derived from the RE plot. Seventy-eight [11C]PiB dynamic PET scans (66 from controls and 12 from mildly cognitively impaired participants (MCI) from the Baltimore Longitudinal Study of Aging (BLSA)) were acquired over 90 minutes. Regions of interest (ROIs) were defined on coregistered MRIs. Both the ROI and pixelwise time activity curves (TACs) were used to evaluate the estimates of DVR. DVRs obtained using the Logan plot applied to ROI TACs were used as a reference for comparison of DVR estimates. Results Results from the theoretical analysis were confirmed by human studies. ROI estimates from the RE plot and the bcSUVR were nearly identical to those from the Logan plot with ROI TACs. In contrast, ROI estimates from DVR images in frontal, temporal, parietal, cingulate regions, and the striatum were underestimated by the Logan plot (controls 4 – 12%; MCI 9 – 16%) and overestimated by the SUVR (controls 8 – 16%; MCI 16 – 24%). This bias was higher in the MCI group than in controls (p < 0.01) but was not present when data were analyzed using either the RE plot or the bcSUVR. Conclusion The RE plot improves pixel-wise quantification of [11C]PiB dynamic PET compared to the conventional Logan plot. The bcSUVR results in lower bias and higher consistency of DVR estimates compared to SUVR. The RE plot and the bcSUVR are practical quantitative approaches that improve the analysis of [11C]PiB studies. PMID:22414634

Recurrence plots and recurrence quantification analysis of human motion data

NASA Astrophysics Data System (ADS)

Josiński, Henryk; Michalczuk, Agnieszka; Świtoński, Adam; Szczesna, Agnieszka; Wojciechowski, Konrad

2016-06-01

The authors present exemplary application of recurrence plots, cross recurrence plots and recurrence quantification analysis for the purpose of exploration of experimental time series describing selected aspects of human motion. Time series were extracted from treadmill gait sequences which were recorded in the Human Motion Laboratory (HML) of the Polish-Japanese Academy of Information Technology in Bytom, Poland by means of the Vicon system. Analysis was focused on the time series representing movements of hip, knee, ankle and wrist joints in the sagittal plane.

The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides.

PubMed

Engin, Ozge; Sayar, Mehmet; Erman, Burak

2009-01-13

Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. The isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. The statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. These are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. A systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations.

The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides

NASA Astrophysics Data System (ADS)

Engin, Ozge; Sayar, Mehmet; Erman, Burak

2009-03-01

Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. The isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. The statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. These are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. A systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations.

Integrating P3 Data Into P2 Analyses: What is the Added Value

Treesearch

James R. Steinman

2001-01-01

The Forest Inventory and Analysis and Forest Health Monitoring Programs of the USDA Forest Service are integrating field procedures for measuring their networks of plots throughout the United States. These plots are now referred to as Phase 2 (P2) and Phase 3 (P3) plots, respectively, and 1 out of every 16 P2 plots will also be a P3 plot. Mensurational methods will be...

Flyby Error Analysis Based on Contour Plots for the Cassini Tour

NASA Technical Reports Server (NTRS)

Stumpf, P. W.; Gist, E. M.; Goodson, T. D.; Hahn, Y.; Wagner, S. V.; Williams, P. N.

2008-01-01

The maneuver cancellation analysis consists of cost contour plots employed by the Cassini maneuver team. The plots are two-dimensional linear representations of a larger six-dimensional solution to a multi-maneuver, multi-encounter mission at Saturn. By using contours plotted with the dot product of vectors B and R and the dot product of vectors B and T components, it is possible to view the effects delta V on for various encounter positions in the B-plane. The plot is used in operations to help determine if the Approach Maneuver (ensuing encounter minus three days) and/or the Cleanup Maneuver (ensuing encounter plus three days) can be cancelled and also is a linear check of an integrated solution.

Analysis of variance calculations for irregular experiments

Treesearch

Jonathan W. Wright

1977-01-01

Irregular experiments may be more useful than much smaller regular experiments and can be analyzed statistically without undue expenditure of time. For a few missing plots, standard methods of calculating missing-plot values can be used. For more missing plots (up to 10 percent), seedlot means or randomly chosen plot means of the same seedlot can be substituted for...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wackerbarth, David

Sandia National Laboratories has developed a computer program to review, reduce and manipulate waveform data. PlotData is designed for post-acquisition waveform data analysis. PlotData is both a post-acquisition and an advanced interactive data analysis environment. PlotData requires unidirectional waveform data with both uniform and discrete time-series measurements. PlotData operates on a National Instruments' LabVIEW™ software platform. Using PlotData, the user can capture waveform data from digitizing oscilloscopes over a GPIB, USB and Ethernet interface from Tektronix, Lecroy or Agilent scopes. PlotData can both import and export several types of binary waveform files including, but not limited to, Tektronix .wmf files,more » Lecroy.trc files and xy pair ASCIIfiles. Waveform manipulation includes numerous math functions, integration, differentiation, smoothing, truncation, and other specialized data reduction routines such as VISAR, POV, PVDF (Bauer) piezoelectric gauges, and piezoresistive gauges such as carbon manganin pressure gauges.« less

Molecular modeling of the human sperm associated antigen 11 B (SPAG11B) proteins.

PubMed

Narmadha, Ganapathy; Yenugu, Suresh

2015-04-01

Antimicrobial proteins and peptides are ubiquitous in nature with diverse structural and biological properties. Among them, the human beta-defensins are known to contribute to the innate immune response. Besides the defensins, a number of defensin-like proteins and peptides are expressed in many organ systems including the male reproductive system. Some of the protein isoforms encoded by the sperm associated antigen 11B (SPAG11) gene in humans are beta-defensin-like and exhibit structure dependent and salt tolerant antimicrobial activity, besides contributing to sperm maturation. Though some of the functional roles of these proteins are reported, the structural and molecular features that contribute to their antimicrobial activity is not yet reported. In this study, using in silico tools, we report the three dimensional structure of the human SPAG11B proteins and their C-terminal peptides. web-based hydropathy, amphipathicity, and topology (WHAT) analyses and grand average of hydropathy (GRAVY) indices show that these proteins and peptides are amphipathic and highly hydrophilic. Self-optimized prediction method with alignment (SOPMA) analyses and circular dichroism data suggest that the secondary structure of these proteins and peptides primarily contain beta-sheet and random coil structure and alpha-helix to a lesser extent. Ramachandran plots show that majority of the amino acids in these proteins and peptides fall in the permissible regions, thus indicating stable structures. The secondary structure of SPAG11B isoforms and their peptides were not perturbed with increasing NaCl concentration (0-300 mM) and at different pH (3, 7, and 10), thus reinforcing our previously reported observation that their antimicrobial activity is salt tolerant. To the best of our knowledge, for the first time, results of our study provide vital information on the structural features of SPAG11B protein isoforms and their contribution to antimicrobial activity.

Identification of B cell epitopes of alcohol dehydrogenase allergen of Curvularia lunata.

PubMed

Nair, Smitha; Kukreja, Neetu; Singh, Bhanu Pratap; Arora, Naveen

2011-01-01

Epitope identification assists in developing molecules for clinical applications and is useful in defining molecular features of allergens for understanding structure/function relationship. The present study was aimed to identify the B cell epitopes of alcohol dehydrogenase (ADH) allergen from Curvularia lunata using in-silico methods and immunoassay. B cell epitopes of ADH were predicted by sequence and structure based methods and protein-protein interaction tools while T cell epitopes by inhibitory concentration and binding score methods. The epitopes were superimposed on a three dimensional model of ADH generated by homology modeling and analyzed for antigenic characteristics. Peptides corresponding to predicted epitopes were synthesized and immunoreactivity assessed by ELISA using individual and pooled patients' sera. The homology model showed GroES like catalytic domain joined to Rossmann superfamily domain by an alpha helix. Stereochemical quality was confirmed by Procheck which showed 90% residues in most favorable region of Ramachandran plot while Errat gave a quality score of 92.733%. Six B cell (P1-P6) and four T cell (P7-P10) epitopes were predicted by a combination of methods. Peptide P2 (epitope P2) showed E(X)(2)GGP(X)(3)KKI conserved pattern among allergens of pathogenesis related family. It was predicted as high affinity binder based on electronegativity and low hydrophobicity. The computational methods employed were validated using Bet v 1 and Der p 2 allergens where 67% and 60% of the epitope residues were predicted correctly. Among B cell epitopes, Peptide P2 showed maximum IgE binding with individual and pooled patients' sera (mean OD 0.604±0.059 and 0.506±0.0035, respectively) followed by P1, P4 and P3 epitopes. All T cell epitopes showed lower IgE binding. Four B cell epitopes of C. lunata ADH were identified. Peptide P2 can serve as a potential candidate for diagnosis of allergic diseases.

Relative equilibrium plot improves graphical analysis and allows bias correction of standardized uptake value ratio in quantitative 11C-PiB PET studies.

PubMed

Zhou, Yun; Sojkova, Jitka; Resnick, Susan M; Wong, Dean F

2012-04-01

Both the standardized uptake value ratio (SUVR) and the Logan plot result in biased distribution volume ratios (DVRs) in ligand-receptor dynamic PET studies. The objective of this study was to use a recently developed relative equilibrium-based graphical (RE) plot method to improve and simplify the 2 commonly used methods for quantification of (11)C-Pittsburgh compound B ((11)C-PiB) PET. The overestimation of DVR in SUVR was analyzed theoretically using the Logan and the RE plots. A bias-corrected SUVR (bcSUVR) was derived from the RE plot. Seventy-eight (11)C-PiB dynamic PET scans (66 from controls and 12 from participants with mild cognitive impaired [MCI] from the Baltimore Longitudinal Study of Aging) were acquired over 90 min. Regions of interest (ROIs) were defined on coregistered MR images. Both the ROI and the pixelwise time-activity curves were used to evaluate the estimates of DVR. DVRs obtained using the Logan plot applied to ROI time-activity curves were used as a reference for comparison of DVR estimates. Results from the theoretic analysis were confirmed by human studies. ROI estimates from the RE plot and the bcSUVR were nearly identical to those from the Logan plot with ROI time-activity curves. In contrast, ROI estimates from DVR images in frontal, temporal, parietal, and cingulate regions and the striatum were underestimated by the Logan plot (controls, 4%-12%; MCI, 9%-16%) and overestimated by the SUVR (controls, 8%-16%; MCI, 16%-24%). This bias was higher in the MCI group than in controls (P < 0.01) but was not present when data were analyzed using either the RE plot or the bcSUVR. The RE plot improves pixelwise quantification of (11)C-PiB dynamic PET, compared with the conventional Logan plot. The bcSUVR results in lower bias and higher consistency of DVR estimates than of SUVR. The RE plot and the bcSUVR are practical quantitative approaches that improve the analysis of (11)C-PiB studies.

A tool to determine crown and plot canopy transparency for forest inventory and analysis phase 3 plots using digital photographs

Treesearch

Matthew F. Winn; Philip A. Araman

2012-01-01

The USDA Forest Service Forest Inventory and Analysis (FIA) program collects crown foliage transparency estimates for individual trees on Phase 3 (P3) inventory plots. The FIA crown foliage estimate is obtained from a pair of perpendicular side views of the tree. Researchers with the USDA Forest Service Southern Research Station have developed a computer program that...

An urban forest-inventory-and-analysis investigation in Oregon and Washington

Treesearch

Jacob L. Strunk; John R. Mills; Paul Ries; Hailemariam Temesgen; Lacey Jeroue

2016-01-01

The U.S. Department of Agriculture (USDA) Forest Service, Forest Inventory and Analysis program recently inventoried trees on 257 sample plots in the urbanized areas of Oregon and Washington. Plots were located on the standard grid (≈1 plot/2428 ha) and installed with the 4-subplot footprint (≈.067 ha with 4 circular subplots). Using these data, we examined: 1) use of...

iCanPlot: Visual Exploration of High-Throughput Omics Data Using Interactive Canvas Plotting

PubMed Central

Sinha, Amit U.; Armstrong, Scott A.

2012-01-01

Increasing use of high throughput genomic scale assays requires effective visualization and analysis techniques to facilitate data interpretation. Moreover, existing tools often require programming skills, which discourages bench scientists from examining their own data. We have created iCanPlot, a compelling platform for visual data exploration based on the latest technologies. Using the recently adopted HTML5 Canvas element, we have developed a highly interactive tool to visualize tabular data and identify interesting patterns in an intuitive fashion without the need of any specialized computing skills. A module for geneset overlap analysis has been implemented on the Google App Engine platform: when the user selects a region of interest in the plot, the genes in the region are analyzed on the fly. The visualization and analysis are amalgamated for a seamless experience. Further, users can easily upload their data for analysis—which also makes it simple to share the analysis with collaborators. We illustrate the power of iCanPlot by showing an example of how it can be used to interpret histone modifications in the context of gene expression. PMID:22393367

Modeling post-fire woody carbon dynamics with data from remeasured inventory plots

Treesearch

Bianca N.I. Eskelson; Jeremy Fried; Vicente Monleon

2015-01-01

In California, the Forest Inventory and Analysis (FIA) plots within large fires were visited one year after the fire occurred resulting in a time series of measurements before and after fire. During this additional plot visit, the standard inventory measurements were augmented for these burned plots to assess fire effects. One example of the additional measurements is...

Practical Considerations When Using Perturbed Forest Inventory Plot Locations To Develop Spatial Models: A Case Study

Treesearch

John W. Coulston; Gregory A. Reams; Ronald E. McRoberts; William D. Smith

2006-01-01

U.S. Department of Agriculture Forest Service Forest Inventory and Analysis plot information is used in many capacities including timber inventories, forest health assessments, and environmental risk analyses. With few exceptions, actual plot locations cannot be revealed to the general public. The public does, however, have access to perturbed plot coordinates. The...

Variable Selection Strategies for Small-area Estimation Using FIA Plots and Remotely Sensed Data

Treesearch

Andrew Lister; Rachel Riemann; James Westfall; Mike Hoppus

2005-01-01

The USDA Forest Service's Forest Inventory and Analysis (FIA) unit maintains a network of tens of thousands of georeferenced forest inventory plots distributed across the United States. Data collected on these plots include direct measurements of tree diameter and height and other variables. We present a technique by which FIA plot data and coregistered...

Runoff and soil erosion plot-scale studies under natural rainfall: A meta-analysis of the Brazilian experience

USDA-ARS?s Scientific Manuscript database

Research to measure soil erosion rates in the United States from natural rainfall runoff plots began in the early 1900’s. In Brazil, the first experimental study at the plot-scale was conducted in the 1940’s; however, the monitoring process and the creation of new experimental field plots have not c...

Using T-Z plots as a graphical method to infer lithological variations from growth strata

NASA Astrophysics Data System (ADS)

Castelltort, Sébastien; Pochat, Stéphane; Van Den Driessche, Jean

2004-08-01

The 'T-Z plot' method consists of plotting the throw of sedimentary horizons across a growth fault versus their depth in the hanging wall. This method has been initially developed for the analysis of growth fault kinematics from seismic data. A brief analytical examination of such plots shows that they can also provide valuable information about the evolution of fault topography. When growth is a continuous process, stages of topography creation (fault scarp) and filling (of the space available in the hanging-wall) are related to non-dynamic (draping, mud-prone pelagic settling) and dynamic (sand-prone, dynamically deposited) sedimentation, respectively. In this case, the T-Z plot analysis becomes a powerful tool to predict major lithological variations on seismic profiles in faulted settings.

Using variance components to estimate power in a hierarchically nested sampling design improving monitoring of larval Devils Hole pupfish

USGS Publications Warehouse

Dzul, Maria C.; Dixon, Philip M.; Quist, Michael C.; Dinsomore, Stephen J.; Bower, Michael R.; Wilson, Kevin P.; Gaines, D. Bailey

2013-01-01

We used variance components to assess allocation of sampling effort in a hierarchically nested sampling design for ongoing monitoring of early life history stages of the federally endangered Devils Hole pupfish (DHP) (Cyprinodon diabolis). Sampling design for larval DHP included surveys (5 days each spring 2007–2009), events, and plots. Each survey was comprised of three counting events, where DHP larvae on nine plots were counted plot by plot. Statistical analysis of larval abundance included three components: (1) evaluation of power from various sample size combinations, (2) comparison of power in fixed and random plot designs, and (3) assessment of yearly differences in the power of the survey. Results indicated that increasing the sample size at the lowest level of sampling represented the most realistic option to increase the survey's power, fixed plot designs had greater power than random plot designs, and the power of the larval survey varied by year. This study provides an example of how monitoring efforts may benefit from coupling variance components estimation with power analysis to assess sampling design.

Detecting small-study effects and funnel plot asymmetry in meta-analysis of survival data: A comparison of new and existing tests.

PubMed

Debray, Thomas P A; Moons, Karel G M; Riley, Richard D

2018-03-01

Small-study effects are a common threat in systematic reviews and may indicate publication bias. Their existence is often verified by visual inspection of the funnel plot. Formal tests to assess the presence of funnel plot asymmetry typically estimate the association between the reported effect size and their standard error, the total sample size, or the inverse of the total sample size. In this paper, we demonstrate that the application of these tests may be less appropriate in meta-analysis of survival data, where censoring influences statistical significance of the hazard ratio. We subsequently propose 2 new tests that are based on the total number of observed events and adopt a multiplicative variance component. We compare the performance of the various funnel plot asymmetry tests in an extensive simulation study where we varied the true hazard ratio (0.5 to 1), the number of published trials (N=10 to 100), the degree of censoring within trials (0% to 90%), and the mechanism leading to participant dropout (noninformative versus informative). Results demonstrate that previous well-known tests for detecting funnel plot asymmetry suffer from low power or excessive type-I error rates in meta-analysis of survival data, particularly when trials are affected by participant dropout. Because our novel test (adopting estimates of the asymptotic precision as study weights) yields reasonable power and maintains appropriate type-I error rates, we recommend its use to evaluate funnel plot asymmetry in meta-analysis of survival data. The use of funnel plot asymmetry tests should, however, be avoided when there are few trials available for any meta-analysis. © 2017 The Authors. Research Synthesis Methods Published by John Wiley & Sons, Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steed, Chad Allen

EDENx is a multivariate data visualization tool that allows interactive user driven analysis of large-scale data sets with high dimensionality. EDENx builds on our earlier system, called EDEN to enable analysis of more dimensions and larger scale data sets. EDENx provides an initial overview of summary statistics for each variable in the data set under investigation. EDENx allows the user to interact with graphical summary plots of the data to investigate subsets and their statistical associations. These plots include histograms, binned scatterplots, binned parallel coordinate plots, timeline plots, and graphical correlation indicators. From the EDENx interface, a user can selectmore » a subsample of interest and launch a more detailed data visualization via the EDEN system. EDENx is best suited for high-level, aggregate analysis tasks while EDEN is more appropriate for detail data investigations.« less

Interactive computer programs for the graphic analysis of nucleotide sequence data.

PubMed Central

Luckow, V A; Littlewood, R K; Rownd, R H

1984-01-01

A group of interactive computer programs have been developed which aid in the collection and graphical analysis of nucleotide and protein sequence data. The programs perform the following basic functions: a) enter, edit, list, and rearrange sequence data; b) permit automatic entry of nucleotide sequence data directly from an autoradiograph into the computer; c) search for restriction sites or other specified patterns and plot a linear or circular restriction map, or print their locations; d) plot base composition; e) analyze homology between sequences by plotting a two-dimensional graphic matrix; and f) aid in plotting predicted secondary structures of RNA molecules. PMID:6546437

Determination of variability in leaf biomass densities of conifers and mixed conifers under different environmental conditions in the San Joaquin Valley air basin. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Temple, P.J.; Mutters, R.J.; Adams, C.

1995-06-01

Biomass sampling plots were established at 29 locations within the dominant vegetation zones of the study area. Estimates of foliar biomass were made for each plot by three independent methods: regression analysis on the basis of tree diameter, calculation of the amount of light intercepted by the leaf canopy, and extrapolation from branch leaf area. Multivariate regression analysis was used to relate these foliar biomass estimates for oak plots and conifer plots to several independent predictor variables, including elevation, slope, aspect, temperature, precipitation, and soil chemical characteristics.

On spectral techniques in analysis of Boolean networks

NASA Astrophysics Data System (ADS)

Kesseli, Juha; Rämö, Pauli; Yli-Harja, Olli

2005-06-01

In this work we present results that can be used for analysis of Boolean networks. The results utilize Fourier spectra of the functions in the network. An accurate formula is given for Derrida plots of networks of finite size N based on a result on Boolean functions presented in another context. Derrida plots are widely used to examine the stability issues of Boolean networks. For the limit N→∞, we give a computationally simple form that can be used as a good approximation for rather small networks as well. A formula for Derrida plots of random Boolean networks (RBNs) presented earlier in the literature is given an alternative derivation. It is shown that the information contained in the Derrida plot is equal to the average Fourier spectrum of the functions in the network. In the case of random networks the mean Derrida plot can be obtained from the mean spectrum of the functions. The method is applied to real data by using the Boolean functions found in genetic regulatory networks of eukaryotic cells in an earlier study. Conventionally, Derrida plots and stability analysis have been computed with statistical sampling resulting in poorer accuracy.

Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot.

PubMed

Loh, Yong-Hwee Eddie; Shen, Li

2016-01-01

The continual maturation and increasing applications of next-generation sequencing technology in scientific research have yielded ever-increasing amounts of data that need to be effectively and efficiently analyzed and innovatively mined for new biological insights. We have developed ngs.plot-a quick and easy-to-use bioinformatics tool that performs visualizations of the spatial relationships between sequencing alignment enrichment and specific genomic features or regions. More importantly, ngs.plot is customizable beyond the use of standard genomic feature databases to allow the analysis and visualization of user-specified regions of interest generated by the user's own hypotheses. In this protocol, we demonstrate and explain the use of ngs.plot using command line executions, as well as a web-based workflow on the Galaxy framework. We replicate the underlying commands used in the analysis of a true biological dataset that we had reported and published earlier and demonstrate how ngs.plot can easily generate publication-ready figures. With ngs.plot, users would be able to efficiently and innovatively mine their own datasets without having to be involved in the technical aspects of sequence coverage calculations and genomic databases.

Oscillating two-stream instability in a magnetized electron-positron-ion plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tinakiche, Nouara; Faculty of Physics, U.S.T.H.B, Algiers 16111; Annou, R.

2015-04-15

Oscillating two-stream instability (OTSI) in a magnetized electron-ion plasma has been thoroughly studied, e.g., in ionospheric heating experiments [C. S. Liu and V. K. Tripathi, Interaction of Electromagnetic Waves With Electron Beams and Plasmas (World Scientific, 1994); V. K. Tripathi and P. V. Siva Rama Prasad, J. Plasma Phys. 41, 13 (1989); K. Ramachandran and V. K. Tripathi, IEEE Trans. Plasma Sci. 25, 423 (1997)]. In this paper, OTSI is investigated in a magnetized electron-positron-ion plasma. The dispersion relation of the process is established. The pump field threshold, along with the maximum growth rate of the instability is assessed usingmore » the Arecibo and HAARP parameters.« less

Oscillating two-stream instability in a magnetized electron-positron-ion plasma

NASA Astrophysics Data System (ADS)

Tinakiche, Nouara; Annou, R.

2015-04-01

Oscillating two-stream instability (OTSI) in a magnetized electron-ion plasma has been thoroughly studied, e.g., in ionospheric heating experiments [C. S. Liu and V. K. Tripathi, Interaction of Electromagnetic Waves With Electron Beams and Plasmas (World Scientific, 1994); V. K. Tripathi and P. V. Siva Rama Prasad, J. Plasma Phys. 41, 13 (1989); K. Ramachandran and V. K. Tripathi, IEEE Trans. Plasma Sci. 25, 423 (1997)]. In this paper, OTSI is investigated in a magnetized electron-positron-ion plasma. The dispersion relation of the process is established. The pump field threshold, along with the maximum growth rate of the instability is assessed using the Arecibo and HAARP parameters.

What determines the spectrum of protein native state structures?

PubMed

Lezon, Timothy R; Banavar, Jayanth R; Lesk, Arthur M; Maritan, Amos

2006-05-01

We present a brief summary of the key factors underlying protein structure, as developed in the investigations of Pauling, Ramachandran, and Rose. We then outline a simplified physical model of proteins that focuses on geometry and symmetry. Although this model superficially appears unrelated to the detailed chemical descriptions commonly applied to proteins, we show that it captures the essential elements of the chemistry and provides a unified framework for understanding the common characteristics of folded proteins. We suggest that the spectrum of protein native state structures is determined by geometry and symmetry and the role of the sequence is to choose its native state structure from this predetermined menu. 2006 Wiley-Liss, Inc.

Mapping U.S. forest biomass using nationwide forest inventory data and moderate resolution information

Treesearch

J. A. Blackard; M. V. Finco; E. H. Helmer; G. R. Holden; M. L. Hoppus; D.M. Jacobs; A. J. Lister; G. G. Moisen; M. D. Nelson; R. Riemann; B. Ruefenacht; D. Salajanu; D. L. Weyermann; K. C. Winterberger; T. J. Brandeis; R. L. Czaplewski; R. E. McRoberts; P. L. Patterson; R. P. Tymcio

2008-01-01

A spatially explicit dataset of aboveground live forest biomass was made from ground measured inventory plots for the conterminous U.S., Alaska and Puerto Rico. The plot data are from the USDA Forest Service Forest Inventory and Analysis (FIA) program. To scale these plot data to maps, we developed models relating field-measured response variables to plot attributes...

ANALYSIS/PLOT: a graphics package for use with the SORT/ANALYSIS data bases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sady, C.A.

1983-08-01

This report describes a graphics package that is used with the SORT/ANALYSIS data bases. The data listed by the SORT/ANALYSIS program can be presented in pie, bar, line, or Gantt chart form. Instructions for the use of the plotting program and descriptions of the subroutines are given in the report.

GOplot: an R package for visually combining expression data with functional analysis.

PubMed

Walter, Wencke; Sánchez-Cabo, Fátima; Ricote, Mercedes

2015-09-01

Despite the plethora of methods available for the functional analysis of omics data, obtaining comprehensive-yet detailed understanding of the results remains challenging. This is mainly due to the lack of publicly available tools for the visualization of this type of information. Here we present an R package called GOplot, based on ggplot2, for enhanced graphical representation. Our package takes the output of any general enrichment analysis and generates plots at different levels of detail: from a general overview to identify the most enriched categories (bar plot, bubble plot) to a more detailed view displaying different types of information for molecules in a given set of categories (circle plot, chord plot, cluster plot). The package provides a deeper insight into omics data and allows scientists to generate insightful plots with only a few lines of code to easily communicate the findings. The R package GOplot is available via CRAN-The Comprehensive R Archive Network: http://cran.r-project.org/web/packages/GOplot. The shiny web application of the Venn diagram can be found at: https://wwalter.shinyapps.io/Venn/. A detailed manual of the package with sample figures can be found at https://wencke.github.io/ fscabo@cnic.es or mricote@cnic.es. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The isometric log-ratio (ilr)-ion plot: A proposed alternative to the Piper diagram

USGS Publications Warehouse

Shelton, Jenna L.; Engle, Mark A.; Buccianti, Antonella; Blondes, Madalyn S.

2018-01-01

The Piper diagram has been a staple for the analysis of water chemistry data since its introduction in 1944. It was conceived to be a method for water classification, determination of potential water mixing between end-members, and to aid in the identification of chemical reactions controlling a sample set. This study uses the information gleaned over the years since the release of the Piper diagram and proposes an alternative to it, capturing the strengths of the original diagram while adding new ideas to increase its robustness. The new method uses compositional data analysis to create 4 isometric log-ratio coordinates for the 6 major chemical species analyzed in the Piper diagram and transforms the data to a 4-field bi-plot, the ilr-ion plot. This ilr-ion plot conveys all of the information in the Piper diagram (water mixing, water types, and chemical reactions) while also visualizing additional data, the ability to examine Ca2+/Mg2+ versus Cl-/SO42−. The Piper and the ilr-ion plot were also compared using multiple synthetic and real datasets in order to illustrate the caveats and the advantages of using either diagram to analyze water chemistry data. Although there are challenges with using the ilr-ion plot (e.g., missing or zero values zeros in the dataset must be imputed by positive real numbers), it appears that the use of compositional data analysis coupled with the ilr-ion plot provides a more in-depth and complete analysis of water quality data compared to the original Piper diagram.

User's manual for the coupled rotor/airframe vibration analysis graphic package

NASA Technical Reports Server (NTRS)

Studwell, R. E.

1982-01-01

User instructions for a graphics package for coupled rotor/airframe vibration analysis are presented. Responses to plot package messages which the user must make to activate plot package operations and options are described. Installation instructions required to set up the program on the CDC system are included. The plot package overlay structure and subroutines which have to be modified for the CDC system are also described. Operating instructions for CDC applications are included.

An analysis of mortality inventory tally using large plots compared to tally using small plot clusters

Treesearch

Vernon J. LaBau; John W. Hazard

2000-01-01

During an inventory to assess spruce bark beetle impact on the Kenai Peninsula in south-central Alaska, 5-year mortality estimates were made for all growing-stock trees on 0.6 ha areas, on 0.4 ha areas, and on a cluster of four 1/60-ha subplots. The analysis of the results of the comparison between cluster data and the larger plot data highlighted some of the problems...

Simpson's paradox visualized: The example of the Rosiglitazone meta-analysis

PubMed Central

Rücker, Gerta; Schumacher, Martin

2008-01-01

Background Simpson's paradox is sometimes referred to in the areas of epidemiology and clinical research. It can also be found in meta-analysis of randomized clinical trials. However, though readers are able to recalculate examples from hypothetical as well as real data, they may have problems to easily figure where it emerges from. Method First, two kinds of plots are proposed to illustrate the phenomenon graphically, a scatter plot and a line graph. Subsequently, these can be overlaid, resulting in a overlay plot. The plots are applied to the recent large meta-analysis of adverse effects of rosiglitazone on myocardial infarction and to an example from the literature. A large set of meta-analyses is screened for further examples. Results As noted earlier by others, occurrence of Simpson's paradox in the meta-analytic setting, if present, is associated with imbalance of treatment arm size. This is well illustrated by the proposed plots. The rosiglitazone meta-analysis shows an effect reversion if all trials are pooled. In a sample of 157 meta-analyses, nine showed an effect reversion after pooling, though non-significant in all cases. Conclusion The plots give insight on how the imbalance of trial arm size works as a confounder, thus producing Simpson's paradox. Readers can see why meta-analytic methods must be used and what is wrong with simple pooling. PMID:18513392

Cross-Scale Analysis of the Region Effect on Vascular Plant Species Diversity in Southern and Northern European Mountain Ranges

PubMed Central

Lenoir, Jonathan; Gégout, Jean-Claude; Guisan, Antoine; Vittoz, Pascal; Wohlgemuth, Thomas; Zimmermann, Niklaus E.; Dullinger, Stefan; Pauli, Harald; Willner, Wolfgang; Grytnes, John-Arvid; Virtanen, Risto; Svenning, Jens-Christian

2010-01-01

Background The divergent glacial histories of southern and northern Europe affect present-day species diversity at coarse-grained scales in these two regions, but do these effects also penetrate to the more fine-grained scales of local communities? Methodology/Principal Findings We carried out a cross-scale analysis to address this question for vascular plants in two mountain regions, the Alps in southern Europe and the Scandes in northern Europe, using environmentally paired vegetation plots in the two regions (n = 403 in each region) to quantify four diversity components: (i) total number of species occurring in a region (total γ-diversity), (ii) number of species that could occur in a target plot after environmental filtering (habitat-specific γ-diversity), (iii) pair-wise species compositional turnover between plots (plot-to-plot β-diversity) and (iv) number of species present per plot (plot α-diversity). We found strong region effects on total γ-diversity, habitat-specific γ-diversity and plot-to-plot β-diversity, with a greater diversity in the Alps even towards distances smaller than 50 m between plots. In contrast, there was a slightly greater plot α-diversity in the Scandes, but with a tendency towards contrasting region effects on high and low soil-acidity plots. Conclusions/Significance We conclude that there are strong regional differences between coarse-grained (landscape- to regional-scale) diversity components of the flora in the Alps and the Scandes mountain ranges, but that these differences do not necessarily penetrate to the finest-grained (plot-scale) diversity component, at least not on acidic soils. Our findings are consistent with the contrasting regional Quaternary histories, but we also consider alternative explanatory models. Notably, ecological sorting and habitat connectivity may play a role in the unexpected limited or reversed region effect on plot α-diversity, and may also affect the larger-scale diversity components. For instance, plot connectivity and/or selection for high dispersal ability may increase plot α-diversity and compensate for low total γ-diversity. PMID:21203521

Maintaining the confidentiality of plot locations by exploiting the low sensitivity of forest structure models to different spectral extraction kernels

Treesearch

Sean P. Healey; Elizabeth Lapoint; Gretchen G. Moisen; Scott L. Powell

2011-01-01

The United States Forest Service Forest Inventory and Analysis (FIA) unit maintains a large national network of inventory plots.While the consistency and extent of this network make FIA data attractive for ecological modelling, the FIA is charged by statute not to publicly reveal inventory plot locations. However, use of FIA plot data by the remote sensing community...

Fuzzy recurrence plots

NASA Astrophysics Data System (ADS)

Pham, T. D.

2016-12-01

Recurrence plots display binary texture of time series from dynamical systems with single dots and line structures. Using fuzzy recurrence plots, recurrences of the phase-space states can be visualized as grayscale texture, which is more informative for pattern analysis. The proposed method replaces the crucial similarity threshold required by symmetrical recurrence plots with the number of cluster centers, where the estimate of the latter parameter is less critical than the estimate of the former.

PuffinPlot: A versatile, user-friendly program for paleomagnetic analysis

NASA Astrophysics Data System (ADS)

Lurcock, P. C.; Wilson, G. S.

2012-06-01

PuffinPlot is a user-friendly desktop application for analysis of paleomagnetic data, offering a unique combination of features. It runs on several operating systems, including Windows, Mac OS X, and Linux; supports both discrete and long core data; and facilitates analysis of very weakly magnetic samples. As well as interactive graphical operation, PuffinPlot offers batch analysis for large volumes of data, and a Python scripting interface for programmatic control of its features. Available data displays include demagnetization/intensity, Zijderveld, equal-area (for sample, site, and suite level demagnetization data, and for magnetic susceptibility anisotropy data), a demagnetization data table, and a natural remanent magnetization intensity histogram. Analysis types include principal component analysis, Fisherian statistics, and great-circle path intersections. The results of calculations can be exported as CSV (comma-separated value) files; graphs can be printed, and can also be saved as publication-quality vector files in SVG or PDF format. PuffinPlot is free, and the program, user manual, and fully documented source code may be downloaded from http://code.google.com/p/puffinplot/.

From fuzzy recurrence plots to scalable recurrence networks of time series

NASA Astrophysics Data System (ADS)

Pham, Tuan D.

2017-04-01

Recurrence networks, which are derived from recurrence plots of nonlinear time series, enable the extraction of hidden features of complex dynamical systems. Because fuzzy recurrence plots are represented as grayscale images, this paper presents a variety of texture features that can be extracted from fuzzy recurrence plots. Based on the notion of fuzzy recurrence plots, defuzzified, undirected, and unweighted recurrence networks are introduced. Network measures can be computed for defuzzified recurrence networks that are scalable to meet the demand for the network-based analysis of big data.

Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots.

PubMed

Hirata, Yoshito; Oda, Arisa; Ohta, Kunihiro; Aihara, Kazuyuki

2016-10-11

Single-cell analysis of the three-dimensional (3D) chromosome structure can reveal cell-to-cell variability in genome activities. Here, we propose to apply recurrence plots, a mathematical method of nonlinear time series analysis, to reconstruct the 3D chromosome structure of a single cell based on information of chromosomal contacts from genome-wide chromosome conformation capture (Hi-C) data. This recurrence plot-based reconstruction (RPR) method enables rapid reconstruction of a unique structure in single cells, even from incomplete Hi-C information.

Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots

NASA Astrophysics Data System (ADS)

Hirata, Yoshito; Oda, Arisa; Ohta, Kunihiro; Aihara, Kazuyuki

2016-10-01

Single-cell analysis of the three-dimensional (3D) chromosome structure can reveal cell-to-cell variability in genome activities. Here, we propose to apply recurrence plots, a mathematical method of nonlinear time series analysis, to reconstruct the 3D chromosome structure of a single cell based on information of chromosomal contacts from genome-wide chromosome conformation capture (Hi-C) data. This recurrence plot-based reconstruction (RPR) method enables rapid reconstruction of a unique structure in single cells, even from incomplete Hi-C information.

Graphical Data Analysis on the Circle: Wrap-Around Time Series Plots for (Interrupted) Time Series Designs.

PubMed

Rodgers, Joseph Lee; Beasley, William Howard; Schuelke, Matthew

2014-01-01

Many data structures, particularly time series data, are naturally seasonal, cyclical, or otherwise circular. Past graphical methods for time series have focused on linear plots. In this article, we move graphical analysis onto the circle. We focus on 2 particular methods, one old and one new. Rose diagrams are circular histograms and can be produced in several different forms using the RRose software system. In addition, we propose, develop, illustrate, and provide software support for a new circular graphical method, called Wrap-Around Time Series Plots (WATS Plots), which is a graphical method useful to support time series analyses in general but in particular in relation to interrupted time series designs. We illustrate the use of WATS Plots with an interrupted time series design evaluating the effect of the Oklahoma City bombing on birthrates in Oklahoma County during the 10 years surrounding the bombing of the Murrah Building in Oklahoma City. We compare WATS Plots with linear time series representations and overlay them with smoothing and error bands. Each method is shown to have advantages in relation to the other; in our example, the WATS Plots more clearly show the existence and effect size of the fertility differential.

Analysis of Cost Growth and Cost Composition in the Defense Aerospace Industry

DTIC Science & Technology

1988-09-01

Making. New York: Harcourt Brace Jovanovich, Inc., 1977. 16. Horngren , Charles T. Cost Accounting , A Managerial Emphasis. Englewood Cliffs NJ: Prentice...58 7. Scatter Plot of Cost /DL Hour Ratio, Data Set C ................ .................. 59 8. Scatter Plot of Cost /DL S Ratio, Data Set...C 62 9. Scatter Plot of Cost /DL S Ratio, Then-Year Dollars ................... .................... 63 10. Scatter Plot of OH/TC Ratio, Data Set C

Analysis of arson fire debris by low temperature dynamic headspace adsorption porous layer open tubular columns.

PubMed

Nichols, Jessica E; Harries, Megan E; Lovestead, Tara M; Bruno, Thomas J

2014-03-21

In this paper we present results of the application of PLOT-cryoadsorption (PLOT-cryo) to the analysis of ignitable liquids in fire debris. We tested ignitable liquids, broadly divided into fuels and solvents (although the majority of the results presented here were obtained with gasoline and diesel fuel) on three substrates: Douglas fir, oak plywood and Nylon carpet. We determined that PLOT-cryo allows the analyst to distinguish all of the ignitable liquids tested by use of a very rapid sampling protocol, and performs better (more recovered components, higher efficiency, lower elution solvent volumes) than a conventional purge and trap method. We also tested the effect of latency (the time period between applying the ignitable liquid and ignition), and we tested a variety of sampling times and a variety of PLOT capillary lengths. Reliable results can be obtained with sampling time periods as short as 3min, and on PLOT capillaries as short as 20cm. The variability of separate samples was also assessed, a study made possible by the high throughput nature of the PLOT-cryo method. We also determined that the method performs better than the conventional carbon strip method that is commonly used in fire debris analysis. Published by Elsevier B.V.

Dalitz plot analysis of the D+→K-π+π+ decay in the FOCUS experiment

NASA Astrophysics Data System (ADS)

Link, J. M.; Yager, P. M.; Anjos, J. C.; Bediaga, I.; Castromonte, C.; Machado, A. A.; Magnin, J.; Massafferri, A.; de Miranda, J. M.; Pepe, I. M.; Polycarpo, E.; Dos Reis, A. C.; Carrillo, S.; Casimiro, E.; Cuautle, E.; Sánchez-Hernández, A.; Uribe, C.; Vázquez, F.; Agostino, L.; Cinquini, L.; Cumalat, J. P.; Frisullo, V.; O'Reilly, B.; Segoni, I.; Stenson, K.; Butler, J. N.; Cheung, H. W. K.; Chiodini, G.; Gaines, I.; Garbincius, P. H.; Garren, L. A.; Gottschalk, E.; Kasper, P. H.; Kreymer, A. E.; Kutschke, R.; Wang, M.; Benussi, L.; Bianco, S.; Fabbri, F. L.; Zallo, A.; Reyes, M.; Cawlfield, C.; Kim, D. Y.; Rahimi, A.; Wiss, J.; Gardner, R.; Kryemadhi, A.; Chung, Y. S.; Kang, J. S.; Ko, B. R.; Kwak, J. W.; Lee, K. B.; Cho, K.; Park, H.; Alimonti, G.; Barberis, S.; Boschini, M.; Cerutti, A.; D'Angelo, P.; Dicorato, M.; Dini, P.; Edera, L.; Erba, S.; Inzani, P.; Leveraro, F.; Malvezzi, S.; Menasce, D.; Mezzadri, M.; Moroni, L.; Pedrini, D.; Pontoglio, C.; Prelz, F.; Rovere, M.; Sala, S.; Davenport, T. F.; Arena, V.; Boca, G.; Bonomi, G.; Gianini, G.; Liguori, G.; Lopes Pegna, D.; Merlo, M. M.; Pantea, D.; Ratti, S. P.; Riccardi, C.; Vitulo, P.; Göbel, C.; Otalora, J.; Hernandez, H.; Lopez, A. M.; Mendez, H.; Paris, A.; Quinones, J.; Ramirez, J. E.; Zhang, Y.; Wilson, J. R.; Handler, T.; Mitchell, R.; Engh, D.; Hosack, M.; Johns, W. E.; Luiggi, E.; Nehring, M.; Sheldon, P. D.; Vaandering, E. W.; Webster, M.; Sheaff, M.; Pennington, M. R.; Focus Collaboration

2007-09-01

Using data collected by the high-energy photoproduction experiment FOCUS at Fermilab we performed a Dalitz plot analysis of the Cabibbo favored decay D+ →K-π+π+. This study uses 53653 Dalitz-plot events with a signal fraction of ∼ 97%, and represents the highest statistics, most complete Dalitz plot analysis for this channel. Results are presented and discussed using two different formalisms. The first is a simple sum of Breit-Wigner functions with freely fitted masses and widths. It is the model traditionally adopted and serves as comparison with the already published analyses. The second uses a K-matrix approach for the dominant S-wave, in which the parameters are fixed by first fitting Kπ scattering data and continued to threshold by Chiral Perturbation Theory. We show that the Dalitz plot distribution for this decay is consistent with the assumption of two-body dominance of the final state interactions and the description of these interactions is in agreement with other data on the Kπ final state.

Quantitative chemical exchange saturation transfer (qCEST) MRI--RF spillover effect-corrected omega plot for simultaneous determination of labile proton fraction ratio and exchange rate.

PubMed

Sun, Phillip Zhe; Wang, Yu; Dai, ZhuoZhi; Xiao, Gang; Wu, Renhua

2014-01-01

Chemical exchange saturation transfer (CEST) MRI is sensitive to dilute proteins and peptides as well as microenvironmental properties. However, the complexity of the CEST MRI effect, which varies with the labile proton content, exchange rate and experimental conditions, underscores the need for developing quantitative CEST (qCEST) analysis. Towards this goal, it has been shown that omega plot is capable of quantifying paramagnetic CEST MRI. However, the use of the omega plot is somewhat limited for diamagnetic CEST (DIACEST) MRI because it is more susceptible to direct radio frequency (RF) saturation (spillover) owing to the relatively small chemical shift. Recently, it has been found that, for dilute DIACEST agents that undergo slow to intermediate chemical exchange, the spillover effect varies little with the labile proton ratio and exchange rate. Therefore, we postulated that the omega plot analysis can be improved if RF spillover effect could be estimated and taken into account. Specifically, simulation showed that both labile proton ratio and exchange rate derived using the spillover effect-corrected omega plot were in good agreement with simulated values. In addition, the modified omega plot was confirmed experimentally, and we showed that the derived labile proton ratio increased linearly with creatine concentration (p < 0.01), with little difference in their exchange rate (p = 0.32). In summary, our study extends the conventional omega plot for quantitative analysis of DIACEST MRI. Copyright © 2014 John Wiley & Sons, Ltd.

F-15 inlet/engine test techniques and distortion methodologies studies. Volume 2: Time variant data quality analysis plots

NASA Technical Reports Server (NTRS)

Stevens, C. H.; Spong, E. D.; Hammock, M. S.

1978-01-01

Time variant data quality analysis plots were used to determine if peak distortion data taken from a subscale inlet model can be used to predict peak distortion levels for a full scale flight test vehicle.

Weighted analysis methods for mapped plot forest inventory data: Tables, regressions, maps and graphs

Treesearch

Paul C. Van Deusen; Linda S. Heath

2010-01-01

Weighted estimation methods for analysis of mapped plot forest inventory data are discussed. The appropriate weighting scheme can vary depending on the type of analysis and graphical display. Both statistical issues and user expectations need to be considered in these methods. A weighting scheme is proposed that balances statistical considerations and the logical...

[Application of Stata software to test heterogeneity in meta-analysis method].

PubMed

Wang, Dan; Mou, Zhen-yun; Zhai, Jun-xia; Zong, Hong-xia; Zhao, Xiao-dong

2008-07-01

To introduce the application of Stata software to heterogeneity test in meta-analysis. A data set was set up according to the example in the study, and the corresponding commands of the methods in Stata 9 software were applied to test the example. The methods used were Q-test and I2 statistic attached to the fixed effect model forest plot, H statistic and Galbraith plot. The existence of the heterogeneity among studies could be detected by Q-test and H statistic and the degree of the heterogeneity could be detected by I2 statistic. The outliers which were the sources of the heterogeneity could be spotted from the Galbraith plot. Heterogeneity test in meta-analysis can be completed by the four methods in Stata software simply and quickly. H and I2 statistics are more robust, and the outliers of the heterogeneity can be clearly seen in the Galbraith plot among the four methods.

Segmented Poincaré plot analysis for risk stratification in patients with dilated cardiomyopathy.

PubMed

Voss, A; Fischer, C; Schroeder, R; Figulla, H R; Goernig, M

2010-01-01

The prognostic value of heart rate variability in patients with dilated cardiomyopathy (DCM) is limited and does not contribute to risk stratification although the dynamics of ventricular repolarization differs considerably between DCM patients and healthy subjects. Neither linear nor nonlinear methods of heart rate variability analysis could discriminate between patients at high and low risk for sudden cardiac death. The aim of this study was to analyze the suitability of the new developed segmented Poincaré plot analysis (SPPA) to enhance risk stratification in DCM. In contrast to the usual applied Poincaré plot analysis the SPPA retains nonlinear features from investigated beat-to-beat interval time series. Main features of SPPA are the rotation of cloud of points and their succeeded variability depended segmentation. Significant row and column probabilities were calculated from the segments and led to discrimination (up to p<0.005) between low and high risk in DCM patients. For the first time an index from Poincaré plot analysis of heart rate variability was able to contribute to risk stratification in patients suffering from DCM.

Myth Structure and Media Fiction Plot: An Exploration.

ERIC Educational Resources Information Center

Harless, James D.

Based on the general research of Joseph Campbell in adventure plots from mythology, the author explores the simplified monomyth plots currently in frequent use in mass media programing. The close relationship of media fiction to mythic stories is established through the analysis of more than 25 stories resulting from media broadcasting. The media…

Precise FIA plot registration using field and dense LIDAR data

Treesearch

Demetrios Gatziolis

2009-01-01

Precise registration of forest inventory and analysis (FIA) plots is a prerequisite for an effective fusion of field data with ancillary spatial information, which is an approach commonly employed in the mapping of various forest parameters. Although the adoption of Global Positioning System technology has improved the precision of plot coordinates obtained during...

Comparison of Imputation Procedures for Replacing Denied-access Plots

Treesearch

Susan L. King

2005-01-01

In forest inventories, missing plots are caused by hazardous terrain, inaccessible locations, or denied access. Maryland had a large number of denied-access plots in the latest periodic inventory conducted by the Northeastern Forest Inventory and Analysis unit. The denial pattern, which can introduce error into the estimates, was investigated by dropping the 1999...

Refining FIA plot locations using LiDAR point clouds

Treesearch

Charlie Schrader-Patton; Greg C. Liknes; Demetrios Gatziolis; Brian M. Wing; Mark D. Nelson; Patrick D. Miles; Josh Bixby; Daniel G. Wendt; Dennis Kepler; Abbey Schaaf

2015-01-01

Forest Inventory and Analysis (FIA) plot location coordinate precision is often insufficient for use with high resolution remotely sensed data, thereby limiting the use of these plots for geospatial applications and reducing the validity of models that assume the locations are precise. A practical and efficient method is needed to improve coordinate precision. To...

National FIA plot intensification procedure report

Treesearch

Jock A. Blackard; Paul L. Patterson

2014-01-01

The Forest Inventory and Analysis (FIA) program of the U.S. Forest Service (USFS) measures a spatially distributed base grid of forest inventory plots across the United States. The sampling intensity of plots may be increased in some regions when warranted by specific inventory objectives. Several intensification methods have been developed within FIA and USFS National...

An investigation of condition mapping and plot proportion calculation issues

Treesearch

Demetrios Gatziolis

2007-01-01

A systematic examination of Forest Inventory and Analysis condition data collected under the annual inventory protocol in the Pacific Northwest region between 2000 and 2004 revealed the presence of errors both in condition topology and plot proportion computations. When plots were compiled to generate population estimates, proportion errors were found to cause...

The Role of Recurrence Plots in Characterizing the Output-Unemployment Relationship: An Analysis

PubMed Central

Caraiani, Petre; Haven, Emmanuel

2013-01-01

We analyse the output-unemployment relationship using an approach based on cross-recurrence plots and quantitative recurrence analysis. We use post-war period quarterly U.S. data. The results obtained show the emergence of a complex and interesting relationship. PMID:23460814

Calibration of multivariate scatter plots for exploratory analysis of relations within and between sets of variables in genomic research.

PubMed

Graffelman, Jan; van Eeuwijk, Fred

2005-12-01

The scatter plot is a well known and easily applicable graphical tool to explore relationships between two quantitative variables. For the exploration of relations between multiple variables, generalisations of the scatter plot are useful. We present an overview of multivariate scatter plots focussing on the following situations. Firstly, we look at a scatter plot for portraying relations between quantitative variables within one data matrix. Secondly, we discuss a similar plot for the case of qualitative variables. Thirdly, we describe scatter plots for the relationships between two sets of variables where we focus on correlations. Finally, we treat plots of the relationships between multiple response and predictor variables, focussing on the matrix of regression coefficients. We will present both known and new results, where an important original contribution concerns a procedure for the inclusion of scales for the variables in multivariate scatter plots. We provide software for drawing such scales. We illustrate the construction and interpretation of the plots by means of examples on data collected in a genomic research program on taste in tomato.

[Recurrence plot analysis of HRV for brain ischemia and asphyxia].

PubMed

Chen, Xiaoming; Qiu, Yihong; Zhu, Yisheng

2008-02-01

Heart rate variability (HRV) is the tiny variability existing in the cycles of the heart beats, which reflects the corresponding balance between sympathetic and vagus nerves. Since the nonlinear characteristic of HRV is confirmed, the Recurrence Plot method, a nonlinear dynamic analysis method based on the complexity, could be used to analyze HRV. The results showed the recurrence plot structures and some quantitative indices (L-Mean, L-Entr) during asphyxia insult vary significantly as compared to those in normal conditions, which offer a new method to monitor brain asphyxia injury.

Numerical flow analysis of axial flow compressor for steady and unsteady flow cases

NASA Astrophysics Data System (ADS)

Prabhudev, B. M.; Satish kumar, S.; Rajanna, D.

2017-07-01

Performance of jet engine is dependent on the performance of compressor. This paper gives numerical study of performance characteristics for axial compressor. The test rig is present at CSIR LAB Bangalore. Flow domains are meshed and fluid dynamic equations are solved using ANSYS package. Analysis is done for six different speeds and for operating conditions like choke, maximum efficiency & before stall point. Different plots are compared and results are discussed. Shock displacement, vortex flows, leakage patterns are presented along with unsteady FFT plot and time step plot.

Missed opportunities in crystallography.

PubMed

Dauter, Zbigniew; Jaskolski, Mariusz

2014-09-01

Scrutinized from the perspective of time, the giants in the history of crystallography more than once missed a nearly obvious chance to make another great discovery, or went in the wrong direction. This review analyzes such missed opportunities focusing on macromolecular crystallographers (using Perutz, Pauling, Franklin as examples), although cases of particular historical (Kepler), methodological (Laue, Patterson) or structural (Pauling, Ramachandran) relevance are also described. Linus Pauling, in particular, is presented several times in different circumstances, as a man of vision, oversight, or even blindness. His example underscores the simple truth that also in science incessant creativity is inevitably connected with some probability of fault. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Sound Symbolism Facilitates Word Learning in 14-Month-Olds

PubMed Central

Imai, Mutsumi; Miyazaki, Michiko; Yeung, H. Henny; Hidaka, Shohei; Kantartzis, Katerina; Okada, Hiroyuki; Kita, Sotaro

2015-01-01

Sound symbolism, or the nonarbitrary link between linguistic sound and meaning, has often been discussed in connection with language evolution, where the oral imitation of external events links phonetic forms with their referents (e.g., Ramachandran & Hubbard, 2001). In this research, we explore whether sound symbolism may also facilitate synchronic language learning in human infants. Sound symbolism may be a useful cue particularly at the earliest developmental stages of word learning, because it potentially provides a way of bootstrapping word meaning from perceptual information. Using an associative word learning paradigm, we demonstrated that 14-month-old infants could detect Köhler-type (1947) shape-sound symbolism, and could use this sensitivity in their effort to establish a word-referent association. PMID:25695741

Representing Uncertainty on Model Analysis Plots

ERIC Educational Resources Information Center

Smith, Trevor I.

2016-01-01

Model analysis provides a mechanism for representing student learning as measured by standard multiple-choice surveys. The model plot contains information regarding both how likely students in a particular class are to choose the correct answer and how likely they are to choose an answer consistent with a well-documented conceptual model.…

Conformational Entropy of Intrinsically Disordered Proteins from Amino Acid Triads

PubMed Central

Baruah, Anupaul; Rani, Pooja; Biswas, Parbati

2015-01-01

This work quantitatively characterizes intrinsic disorder in proteins in terms of sequence composition and backbone conformational entropy. Analysis of the normalized relative composition of the amino acid triads highlights a distinct boundary between globular and disordered proteins. The conformational entropy is calculated from the dihedral angles of the middle amino acid in the amino acid triad for the conformational ensemble of the globular, partially and completely disordered proteins relative to the non-redundant database. Both Monte Carlo (MC) and Molecular Dynamics (MD) simulations are used to characterize the conformational ensemble of the representative proteins of each group. The results show that the globular proteins span approximately half of the allowed conformational states in the Ramachandran space, while the amino acid triads in disordered proteins sample the entire range of the allowed dihedral angle space following Flory’s isolated-pair hypothesis. Therefore, only the sequence information in terms of the relative amino acid triad composition may be sufficient to predict protein disorder and the backbone conformational entropy, even in the absence of well-defined structure. The predicted entropies are found to agree with those calculated using mutual information expansion and the histogram method. PMID:26138206

Model-independent plot of dynamic PET data facilitates data interpretation and model selection.

PubMed

Munk, Ole Lajord

2012-02-21

When testing new PET radiotracers or new applications of existing tracers, the blood-tissue exchange and the metabolism need to be examined. However, conventional plots of measured time-activity curves from dynamic PET do not reveal the inherent kinetic information. A novel model-independent volume-influx plot (vi-plot) was developed and validated. The new vi-plot shows the time course of the instantaneous distribution volume and the instantaneous influx rate. The vi-plot visualises physiological information that facilitates model selection and it reveals when a quasi-steady state is reached, which is a prerequisite for the use of the graphical analyses by Logan and Gjedde-Patlak. Both axes of the vi-plot have direct physiological interpretation, and the plot shows kinetic parameter in close agreement with estimates obtained by non-linear kinetic modelling. The vi-plot is equally useful for analyses of PET data based on a plasma input function or a reference region input function. The vi-plot is a model-independent and informative plot for data exploration that facilitates the selection of an appropriate method for data analysis. Copyright © 2011 Elsevier Ltd. All rights reserved.

PETRO.CALC.PLOT, Microsoft Excel macros to aid petrologic interpretation

USGS Publications Warehouse

Sidder, G.B.

1994-01-01

PETRO.CALC.PLOT is a package of macros which normalizes whole-rock oxide data to 100%, calculates the cation percentages and molecular proportions used for normative mineral calculations, computes the apices for ternary diagrams, determines sums and ratios of specific elements of petrologic interest, and plots 33 X-Y graphs and five ternary diagrams. PETRO.CALC.PLOT also may be used to create other diagrams as desired by the user. The macros run in Microsoft Excel 3.0 and 4.0 for Macintosh computers and in Microsoft Excel 3.0 and 4.0 for Windows. Macros provided in PETRO.CALC.PLOT minimize repetition and time required to recalculate and plot whole-rock oxide data for petrologic analysis. ?? 1994.

User manual for two simple postscript output FORTRAN plotting routines

NASA Technical Reports Server (NTRS)

Nguyen, T. X.

1991-01-01

Graphics is one of the important tools in engineering analysis and design. However, plotting routines that generate output on high quality laser printers normally come in graphics packages, which tend to be expensive and system dependent. These factors become important for small computer systems or desktop computers, especially when only some form of a simple plotting routine is sufficient. With the Postscript language becoming popular, there are more and more Postscript laser printers now available. Simple, versatile, low cost plotting routines that can generate output on high quality laser printers are needed and standard FORTRAN language plotting routines using output in Postscript language seems logical. The purpose here is to explain two simple FORTRAN plotting routines that generate output in Postscript language.

The Zombie Plot: A Simple Graphic Method for Visualizing the Efficacy of a Diagnostic Test.

PubMed

Richardson, Michael L

2016-08-09

One of the most important jobs of a radiologist is to pick the most appropriate imaging test for a particular clinical situation. Making a proper selection sometimes requires statistical analysis. The objective of this article is to introduce a simple graphic technique, an ROC plot that has been divided into zones of mostly bad imaging efficacy (ZOMBIE, hereafter referred to as the "zombie plot"), that transforms information about imaging efficacy from the numeric domain into the visual domain. The numeric rationale for the use of zombie plots is given, as are several examples of the clinical use of these plots. Two online calculators are described that simplify the process of producing a zombie plot.

Corrections for Cluster-Plot Slop

Treesearch

Harry T. Valentine; Mark J. Ducey; Jeffery H. Gove; Adrian Lanz; David L.R. Affleck

2006-01-01

Cluster-plot designs, including the design used by the Forest Inventory and Analysis program of the USDA Forest Service (FIA), are attended by a complicated boundary slopover problem. Slopover occurs where inclusion zones of objects of interest cross the boundary of the area of interest. The dispersed nature of inclusion zones that arise from the use of cluster plots...

Analysis issues due to mapped conditions changing over time

Treesearch

Paul. Van Deusen

2015-01-01

Plot mapping is one of the innovations that were implemented when FIA moved to the annual forest inventory system. Mapped plots can improve the precision of estimates if the mapped conditions are carefully chosen and used judiciously. However, after plots are remeasured multiple times, it can be difficult to properly track changes in conditions and incorporate this...

Compensating for missing plot observations inforest inventory estimation

Treesearch

Ronald E. McRoberts

2003-01-01

The Enhanced Forest Inventory and Analysis program of the U.S. Forest Service has established a nationwide array of permanent field plots, each representing approximately 2400 ha. Each plot has been assigned to one of five interpenetrating, nonoverlapping panels, with one panel selected for measurement on a rotating basis each year. As with most large surveys,...

Estimating number and size of forest patches from FIA plot data

Treesearch

Mark D. Nelson; Andrew J. Lister; Mark H. Hansen

2009-01-01

Forest inventory and analysis (FIA) annual plot data provide for estimates of forest area, type, volume, growth, and other attributes. Estimates of forest landscape metrics, such as those describing abundance, size, and shape of forest patches, however, typically are not derived from FIA plot data but from satellite image-based land cover maps. Associating image-based...

The hexagon/panel system for selecting FIA plots under an annual inventory

Treesearch

Gary J. Brand; Mark D. Nelson; Daniel G. Wendt; Kevin K. Nimerfro

2000-01-01

Forest Inventory and Analysis (FIA) is changing to an annual nationwide forest inventory. This paper describes the sampling grid used to distribute FIA plots across the landscape and to allocate them to a particular measurement year. We also describe the integration of the F1A and Forest Health Monitoring (FHM) plot networks.

Effects of plot size on forest-type algorithm accuracy

Treesearch

James A. Westfall

2009-01-01

The Forest Inventory and Analysis (FIA) program utilizes an algorithm to consistently determine the forest type for forested conditions on sample plots. Forest type is determined from tree size and species information. Thus, the accuracy of results is often dependent on the number of trees present, which is highly correlated with plot area. This research examines the...

Estimating mapped-plot forest attributes with ratios of means

Treesearch

S.J. Zarnoch; W.A. Bechtold

2000-01-01

The mapped-plot design utilized by the U.S. Department of Agriculture (USDA) Forest Inventory and Analysis and the National Forest Health Monitoring Programs is described. Data from 2458 forested mapped plots systematically spread across 25 States reveal that 35 percent straddle multiple conditions. The ratio-of-means estimator is developed as a method to obtain...

The Gran Plot Analysis of an Acid Mixture. An Undergraduate Experiment to Highlight this Alternate Method.

ERIC Educational Resources Information Center

Boiani, James A.

1986-01-01

Describes an experiment which uses the Gran plot for analyzing free ions as well as those involved in an equilibrium. Discusses the benefits of using Gran plots in the study of acids, as well as other analytes in solutions. Presents background theory along with a description of the experimental procedures. (TW)

An Intuitive Graphical Approach to Understanding the Split-Plot Experiment

ERIC Educational Resources Information Center

Robinson, Timothy J.; Brenneman, William A.; Myers, William R.

2009-01-01

While split-plot designs have received considerable attention in the literature over the past decade, there seems to be a general lack of intuitive understanding of the error structure of these designs and the resulting statistical analysis. Typically, students learn the proper error terms for testing factors of a split-plot design via "expected…

Adding uncertainty to forest inventory plot locations: effects on analyses using geospatial data

Treesearch

Alexia A. Sabor; Volker C. Radeloff; Ronald E. McRoberts; Murray Clayton; Susan I. Stewart

2007-01-01

The Forest Inventory and Analysis (FIA) program of the USDA Forest Service alters plot locations before releasing data to the public to ensure landowner confidentiality and sample integrity, but using data with altered plot locations in conjunction with other spatially explicit data layers produces analytical results with unknown amounts of error. We calculated the...

magicaxis: Pretty scientific plotting with minor-tick and log minor-tick support

NASA Astrophysics Data System (ADS)

Robotham, Aaron S. G.

2016-04-01

The R suite magicaxis makes useful and pretty plots for scientific plotting and includes functions for base plotting, with particular emphasis on pretty axis labelling in a number of circumstances that are often used in scientific plotting. It also includes functions for generating images and contours that reflect the 2D quantile levels of the data designed particularly for output of MCMC posteriors where visualizing the location of the 68% and 95% 2D quantiles for covariant parameters is a necessary part of the post MCMC analysis, can generate low and high error bars, and allows clipping of values, rejection of bad values, and log stretching.

Structural Analysis Of CD59 Of Chinese Tree Shrew: A New Reference Molecule For Human Immune System Specific CD59 Drug Discovery.

PubMed

Panda, Subhamay; Kumari, Leena; Panda, Santamay

2017-11-17

Chinese tree shrews (Tupaia belangeri chinensis) bear several characteristics that are considered to be very crucial for utilizing in animal experimental models in biomedical research. Subsequent to the identification of key aspects and signaling pathways in nervous and immune systems, it is revealed that tree shrews acquires shared common as well as unique characteristics, and hence offers a genetic basis for employing this animal as a prospective model for biomedical research. CD59 glycoprotein, commonly referred to as MAC-inhibitory protein (MAC-IP), membrane inhibitor of reactive lysis (MIRL), or protectin, is encoded by the CD59 gene in human beings. It is the member of the LY6/uPAR/alpha-neurotoxin protein family. With this initial point the objective of this study was to determine a comparative composite based structure of CD59 of Chinese tree shrew. The additional objective of this study was to examine the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis with the assistance of several bioinformatical analytical tools. CD59 Amino acid sequence of Chinese tree shrew collected from the online database system of National Centre for Biotechnology Information. SignalP 4.0 online server was employed for detection of signal peptide instance within the protein sequence of CD59. Molecular model structure of CD59 protein was generated by the Iterative Threading ASSEmbly Refinement (I-TASSER) suite. The confirmation for three-dimensional structural model was evaluated by structure validation tools. Location of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, and hydrophobicity molecular surface analysis was performed with the help of Chimera tool. Electrostatic potential analysis was carried out with the adaptive Poisson-Boltzmann solver package. Subsequently validated model was used for the functionally critical amino acids and active site prediction. The functionally critical amino acids and ligand- binding site (LBS) of the proteins (modeled) was determined using the COACH program. Analysis of Ramachandran plot for Chinese tree shrew depicted that overall, 100% of the residues in homology model were observed in allowed and favored regions, sequentially leading to the validation of the standard of generated protein structural model. In case of CD59 of Chinese tree shrew, the total score of G-factor was found to be -0.66 that was generally larger than the acceptable value. This approach suggests the significance and acceptability of the modeled structure of CD59 of Chinese tree shrew. The molecular model data in cooperation to other relevant post model analysis data put forward molecular insight to protecting activity of CD59 protein molecule of Chinese tree shrew. In the present study, we have proposed the first molecular model structure of uncharted CD59 of Chinese tree shrew by significantly utilizing the comparative composite modeling approach. Therefore, the development of a structural model of the CD59 protein was carried out and analyzed further for deducing molecular enrichment technique. The collaborative effort of molecular model and other relevant data of post model analysis carry forward molecular understanding to protecting activity of CD59 functions towards better insight of features of this natural lead compound. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Graphical augmentations to the funnel plot assess the impact of additional evidence on a meta-analysis.

PubMed

Langan, Dean; Higgins, Julian P T; Gregory, Walter; Sutton, Alexander J

2012-05-01

We aim to illustrate the potential impact of a new study on a meta-analysis, which gives an indication of the robustness of the meta-analysis. A number of augmentations are proposed to one of the most widely used of graphical displays, the funnel plot. Namely, 1) statistical significance contours, which define regions of the funnel plot in which a new study would have to be located to change the statistical significance of the meta-analysis; and 2) heterogeneity contours, which show how a new study would affect the extent of heterogeneity in a given meta-analysis. Several other features are also described, and the use of multiple features simultaneously is considered. The statistical significance contours suggest that one additional study, no matter how large, may have a very limited impact on the statistical significance of a meta-analysis. The heterogeneity contours illustrate that one outlying study can increase the level of heterogeneity dramatically. The additional features of the funnel plot have applications including 1) informing sample size calculations for the design of future studies eligible for inclusion in the meta-analysis; and 2) informing the updating prioritization of a portfolio of meta-analyses such as those prepared by the Cochrane Collaboration. Copyright © 2012 Elsevier Inc. All rights reserved.

Visual Data Analysis for Satellites

NASA Technical Reports Server (NTRS)

Lau, Yee; Bhate, Sachin; Fitzpatrick, Patrick

2008-01-01

The Visual Data Analysis Package is a collection of programs and scripts that facilitate visual analysis of data available from NASA and NOAA satellites, as well as dropsonde, buoy, and conventional in-situ observations. The package features utilities for data extraction, data quality control, statistical analysis, and data visualization. The Hierarchical Data Format (HDF) satellite data extraction routines from NASA's Jet Propulsion Laboratory were customized for specific spatial coverage and file input/output. Statistical analysis includes the calculation of the relative error, the absolute error, and the root mean square error. Other capabilities include curve fitting through the data points to fill in missing data points between satellite passes or where clouds obscure satellite data. For data visualization, the software provides customizable Generic Mapping Tool (GMT) scripts to generate difference maps, scatter plots, line plots, vector plots, histograms, timeseries, and color fill images.

A method for developing design diagrams for ceramic and glass materials using fatigue data

NASA Technical Reports Server (NTRS)

Heslin, T. M.; Magida, M. B.; Forrest, K. A.

1986-01-01

The service lifetime of glass and ceramic materials can be expressed as a plot of time-to-failure versus applied stress whose plot is parametric in percent probability of failure. This type of plot is called a design diagram. Confidence interval estimates for such plots depend on the type of test that is used to generate the data, on assumptions made concerning the statistical distribution of the test results, and on the type of analysis used. This report outlines the development of design diagrams for glass and ceramic materials in engineering terms using static or dynamic fatigue tests, assuming either no particular statistical distribution of test results or a Weibull distribution and using either median value or homologous ratio analysis of the test results.

An investigation of wing buffeting response at subsonic and transonic speeds. Phase 2: F-111A flight data analysis. Volume 2: Plotted power spectra

NASA Technical Reports Server (NTRS)

Benepe, D. B.; Cunningham, A. M., Jr.; Traylor, S., Jr.; Dunmyer, W. D.

1978-01-01

Plotted power spectra for all of the flight points examined during the Phase 2 flight data analysis are presented. Detailed descriptions of the aircraft, the flight instrumentation and the analysis techniques are given. Measured and calculated vibration mode frequencies are also presented to assist in further interpretation of the PSD data.

Igloo-Plot: a tool for visualization of multidimensional datasets.

PubMed

Kuntal, Bhusan K; Ghosh, Tarini Shankar; Mande, Sharmila S

2014-01-01

Advances in science and technology have resulted in an exponential growth of multivariate (or multi-dimensional) datasets which are being generated from various research areas especially in the domain of biological sciences. Visualization and analysis of such data (with the objective of uncovering the hidden patterns therein) is an important and challenging task. We present a tool, called Igloo-Plot, for efficient visualization of multidimensional datasets. The tool addresses some of the key limitations of contemporary multivariate visualization and analysis tools. The visualization layout, not only facilitates an easy identification of clusters of data-points having similar feature compositions, but also the 'marker features' specific to each of these clusters. The applicability of the various functionalities implemented herein is demonstrated using several well studied multi-dimensional datasets. Igloo-Plot is expected to be a valuable resource for researchers working in multivariate data mining studies. Igloo-Plot is available for download from: http://metagenomics.atc.tcs.com/IglooPlot/. Copyright © 2014 Elsevier Inc. All rights reserved.

Split-plot microarray experiments: issues of design, power and sample size.

PubMed

Tsai, Pi-Wen; Lee, Mei-Ling Ting

2005-01-01

This article focuses on microarray experiments with two or more factors in which treatment combinations of the factors corresponding to the samples paired together onto arrays are not completely random. A main effect of one (or more) factor(s) is confounded with arrays (the experimental blocks). This is called a split-plot microarray experiment. We utilise an analysis of variance (ANOVA) model to assess differentially expressed genes for between-array and within-array comparisons that are generic under a split-plot microarray experiment. Instead of standard t- or F-test statistics that rely on mean square errors of the ANOVA model, we use a robust method, referred to as 'a pooled percentile estimator', to identify genes that are differentially expressed across different treatment conditions. We illustrate the design and analysis of split-plot microarray experiments based on a case application described by Jin et al. A brief discussion of power and sample size for split-plot microarray experiments is also presented.

Analysis Tools (AT)

Treesearch

Larry J. Gangi

2006-01-01

The FIREMON Analysis Tools program is designed to let the user perform grouped or ungrouped summary calculations of single measurement plot data, or statistical comparisons of grouped or ungrouped plot data taken at different sampling periods. The program allows the user to create reports and graphs, save and print them, or cut and paste them into a word processor....

Omitted Variable Sensitivity Analysis with the Annotated Love Plot

ERIC Educational Resources Information Center

Hansen, Ben B.; Fredrickson, Mark M.

2014-01-01

The goal of this research is to make sensitivity analysis accessible not only to empirical researchers but also to the various stakeholders for whom educational evaluations are conducted. To do this it derives anchors for the omitted variable (OV)-program participation association intrinsically, using the Love plot to present a wide range of…

Technologies for Teaching and Learning about Box Plots and Statistical Analysis

ERIC Educational Resources Information Center

Forster, Patricia A.

2007-01-01

This paper analyses technology-based instruction on data-analysis with box plots. Examples of instruction taken from the research literature inform a study of two classes of 17 year-old students (upper secondary) in which the mathematical relationships that their teachers targeted are distinguished as being, or not being, relevant to statistical…

Importance of the Correlation between Width and Length in the Shape Analysis of Nanorods: Use of a 2D Size Plot To Probe Such a Correlation.

PubMed

Zhao, Zhihua; Zheng, Zhiqin; Roux, Clément; Delmas, Céline; Marty, Jean-Daniel; Kahn, Myrtil L; Mingotaud, Christophe

2016-08-22

Analysis of nanoparticle size through a simple 2D plot is proposed in order to extract the correlation between length and width in a collection or a mixture of anisotropic particles. Compared to the usual statistics on the length associated with a second and independent statistical analysis of the width, this simple plot easily points out the various types of nanoparticles and their (an)isotropy. For each class of nano-objects, the relationship between width and length (i.e., the strong or weak correlations between these two parameters) may suggest information concerning the nucleation/growth processes. It allows one to follow the effect on the shape and size distribution of physical or chemical processes such as simple ripening. Various electron microscopy pictures from the literature or from the authors' own syntheses are used as examples to demonstrate the efficiency and simplicity of the proposed 2D plot combined with a multivariate analysis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Amplitude Analysis of the Decay $$D_s^+ \\to \\pi^+ \\pi^- \\pi^+$$ in the Experiment E831/FOCUS (in Portuguese)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schilithz, Anderson Correa; /Rio de Janeiro, CBPF

We present in this thesis the Dalitz Plot analysis of the D{sub s}{sup +} {yields} {pi}{sup +}{pi}{sup -}{pi}{sup +} decay, with the data of the E831/FOCUS, that took data in 1996 and 1997. The masses and widhts of f{sub 0}(980) and f{sub 0}(1370) are free parametres of the fit on Dalitz Plot, objectiving to study in detail these resonances. After this analysis we present the Spectator Model study on the S wave in this decay. For this study we used the formalism developed by M. Svec [2] for scattering. We present the comparison between the Isobar Model, frequently used inmore » Dalitz Plot analysis, and this formalism.« less

Landscape complexity and soil moisture variation in south Georgia, USA, for remote sensing applications

NASA Astrophysics Data System (ADS)

Giraldo, Mario A.; Bosch, David; Madden, Marguerite; Usery, Lynn; Kvien, Craig

2008-08-01

SummaryThis research addressed the temporal and spatial variation of soil moisture (SM) in a heterogeneous landscape. The research objective was to investigate soil moisture variation in eight homogeneous 30 by 30 m plots, similar to the pixel size of a Landsat Thematic Mapper (TM) or Enhanced Thematic Mapper plus (ETM+) image. The plots were adjacent to eight stations of an in situ soil moisture network operated by the United States Department of Agriculture-Agriculture Research Service USDA-ARS in Tifton, GA. We also studied five adjacent agricultural fields to examine the effect of different landuses/land covers (LULC) (grass, orchard, peanuts, cotton and bare soil) on the temporal and spatial variation of soil moisture. Soil moisture field data were collected on eight occasions throughout 2005 and January 2006 to establish comparisons within and among eight homogeneous plots. Consistently throughout time, analysis of variance (ANOVA) showed high variation in the soil moisture behavior among the plots and high homogeneity in the soil moisture behavior within them. A precipitation analysis for the eight sampling dates throughout the year 2005 showed similar rainfall conditions for the eight study plots. Therefore, soil moisture variation among locations was explained by in situ local conditions. Temporal stability geostatistical analysis showed that soil moisture has high temporal stability within the small plots and that a single point reading can be used to monitor soil moisture status for the plot within a maximum 3% volume/volume (v/v) soil moisture variation. Similarly, t-statistic analysis showed that soil moisture status in the upper soil layer changes within 24 h. We found statistical differences in the soil moisture between the different LULC in the agricultural fields as well as statistical differences between these fields and the adjacent 30 by 30 m plots. From this analysis, it was demonstrated that spatial proximity is not enough to produce similar soil moisture, since t-test's among adjacent plots with different LULCs showed significant differences. These results confirm that a remote sensing approach that considers homogeneous LULC landscape fragments can be used to identify landscape units of similar soil moisture behavior under heterogeneous landscapes. In addition, the in situ USDA-ARS network will serve better in remote sensing studies in which sensors with fine spatial resolution are evaluated. This study is a first step towards identifying landscape units that can be monitored using the single point reading of the USDA-ARS stations network.

Landscape complexity and soil moisture variation in south Georgia, USA, for remote sensing applications

USGS Publications Warehouse

Giraldo, M.A.; Bosch, D.; Madden, M.; Usery, L.; Kvien, Craig

2008-01-01

This research addressed the temporal and spatial variation of soil moisture (SM) in a heterogeneous landscape. The research objective was to investigate soil moisture variation in eight homogeneous 30 by 30 m plots, similar to the pixel size of a Landsat Thematic Mapper (TM) or Enhanced Thematic Mapper plus (ETM+) image. The plots were adjacent to eight stations of an in situ soil moisture network operated by the United States Department of Agriculture-Agriculture Research Service USDA-ARS in Tifton, GA. We also studied five adjacent agricultural fields to examine the effect of different landuses/land covers (LULC) (grass, orchard, peanuts, cotton and bare soil) on the temporal and spatial variation of soil moisture. Soil moisture field data were collected on eight occasions throughout 2005 and January 2006 to establish comparisons within and among eight homogeneous plots. Consistently throughout time, analysis of variance (ANOVA) showed high variation in the soil moisture behavior among the plots and high homogeneity in the soil moisture behavior within them. A precipitation analysis for the eight sampling dates throughout the year 2005 showed similar rainfall conditions for the eight study plots. Therefore, soil moisture variation among locations was explained by in situ local conditions. Temporal stability geostatistical analysis showed that soil moisture has high temporal stability within the small plots and that a single point reading can be used to monitor soil moisture status for the plot within a maximum 3% volume/volume (v/v) soil moisture variation. Similarly, t-statistic analysis showed that soil moisture status in the upper soil layer changes within 24 h. We found statistical differences in the soil moisture between the different LULC in the agricultural fields as well as statistical differences between these fields and the adjacent 30 by 30 m plots. From this analysis, it was demonstrated that spatial proximity is not enough to produce similar soil moisture, since t-test's among adjacent plots with different LULCs showed significant differences. These results confirm that a remote sensing approach that considers homogeneous LULC landscape fragments can be used to identify landscape units of similar soil moisture behavior under heterogeneous landscapes. In addition, the in situ USDA-ARS network will serve better in remote sensing studies in which sensors with fine spatial resolution are evaluated. This study is a first step towards identifying landscape units that can be monitored using the single point reading of the USDA-ARS stations network. ?? 2008 Elsevier B.V.

Automated mesostructural analyses using GIS, Beta test: Paleozoic structures from the New Jersey Great Valley region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herman, G.C.; French, M.A.; Monteverde, D.H.

1993-03-01

An automated method has been developed for representing outcrop data on geologic structures on maps. Using a MS-DOS custom database management system in conjunction with the ARC/INFO Geographic Information System (GIS), trends of geologic structures are plotted with user-specific symbols. The length of structural symbols can be frequency-weighted based on collective values from structural domains. The PC-based data manager is the NJGS Field data Management System (FMS) Version 2.0 which includes sort, output, and analysis functions for structural data input in either azimuth or quadrant form. Program options include lineament sorting, data output to other data management and analysis software,more » and a circular histogram (rose diagram) routine for trend frequency analysis. Trends can be displayed with either half-or full-rose diagrams using either 10[degree] sectors or one degree spikes for strike, trend, or dip azimuth readings. Scalar and vector statistics are both included. For the mesostructural analysis, ASCII files containing the station number, structural trend and inclination, and plot-symbol-length value are downloaded from FMS and uploaded into an ARC/INFO macro which sequentially plots the information. Plots can be generated in conjunction with any complimentary GIS coverage for various types of spatial analyses. Mesostructural plots can be used for regional tectonic analyses, for hydrogeologic analysis of fractured bedrock aquifers, or for ground-truthing data from fracture-trace or lineament analyses.« less

A technique for identifying treatment opportunities from western Oregon and Washington forest survey plots.

Treesearch

Colin D. MacLean

1980-01-01

Identification of opportunities for silvicultural treatment from inventory data is an important objective of Renewable Resources Evaluation in the Pacific Northwest. This paper describes the field plot design and data analysis procedure used by what used to be known as Forest Survey to determine the treatment opportunity associated with each inventory plot in western...

Field methods and data processing techniques associated with mapped inventory plots

Treesearch

William A. Bechtold; Stanley J. Zarnoch

1999-01-01

The U.S. Forest Inventory and Analysis (FIA) and Forest Health Monitoring (FHM) programs utilize a fixed-area mapped-plot design as the national standard for extensive forest inventories. The mapped-plot design is explained, as well as the rationale for its selection as the national standard. Ratio-of-means estimators am presented as a method to process data from...

Access and Use of FIA Data Through FIA Spatial Data Services

Treesearch

Elizabeth LaPoint

2005-01-01

Forest Inventory and Analysis (FIA) Spatial Data Services (SDS) was established in May 2002 to facilitate outside access to FIA data and allow use of georeferenced plot data while protecting the confidentiality of plot locations. Modification of the Food Security Act of 1985 legislated the protection of information on plot location and ownership. Penalties were put in...

Development of carbon response trajectories using FIA plot data and FVS growth simulator: challenges of a large scale simulation project

Treesearch

James B. McCarter; Sean Healey

2015-01-01

The Forest Carbon Management Framework (ForCaMF) integrates Forest Inventory and Analysis (FIA) plot inventory data, disturbance histories, and carbon response trajectories to develop estimates of disturbance and management effects on carbon pools for the National Forest System. All appropriate FIA inventory plots are simulated using the Forest Vegetation Simulator (...

Accuracy assessment of the vegetation continuous field tree cover product using 3954 ground plots in the southwestern USA

Treesearch

M. A. White; J. D. Shaw; R. D. Ramsey

2005-01-01

An accuracy assessment of the Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation continuous field (VCF) tree cover product using two independent ground-based tree cover databases was conducted. Ground data included 1176 Forest Inventory and Analysis (FIA) plots for Arizona and 2778 Southwest Regional GAP (SWReGAP) plots for Utah and western Colorado....

Comparative study of Poincaré plot analysis using short electroencephalogram signals during anaesthesia with spectral edge frequency 95 and bispectral index.

PubMed

Hayashi, K; Yamada, T; Sawa, T

2015-03-01

The return or Poincaré plot is a non-linear analytical approach in a two-dimensional plane, where a timed signal is plotted against itself after a time delay. Its scatter pattern reflects the randomness and variability in the signals. Quantification of a Poincaré plot of the electroencephalogram has potential to determine anaesthesia depth. We quantified the degree of dispersion (i.e. standard deviation, SD) along the diagonal line of the electroencephalogram-Poincaré plot (named as SD1/SD2), and compared SD1/SD2 values with spectral edge frequency 95 (SEF95) and bispectral index values. The regression analysis showed a tight linear regression equation with a coefficient of determination (R(2) ) value of 0.904 (p < 0.0001) between the Poincaré index (SD1/SD2) and SEF95, and a moderate linear regression equation between SD1/SD2 and bispectral index (R(2)  = 0.346, p < 0.0001). Quantification of the Poincaré plot tightly correlates with SEF95, reflecting anaesthesia-dependent changes in electroencephalogram oscillation. © 2014 The Association of Anaesthetists of Great Britain and Ireland.

Intelligence Constraints on Terrorist Network Plots

NASA Astrophysics Data System (ADS)

Woo, Gordon

Since 9/11, the western intelligence and law enforcement services have managed to interdict the great majority of planned attacks against their home countries. Network analysis shows that there are important intelligence constraints on the number and complexity of terrorist plots. If two many terrorists are involved in plots at a given time, a tipping point is reached whereby it becomes progressively easier for the dots to be joined and for the conspirators to be arrested, and for the aggregate evidence to secure convictions. Implications of this analysis are presented for the campaign to win hearts and minds.

Grassland degradation caused by tourism activities in Hulunbuir, Inner Mongolia, China

NASA Astrophysics Data System (ADS)

Le, C.; Ikazaki, K.; Siriguleng; Kadono, A.; Kosaki, T.

2014-02-01

The recent increase in the number of tourists has raised serious concerns about grassland degradation by tourism activities in Inner Mongolia. Thus, we evaluated the effects of tourism activities on the vegetation and soil in Hulunbuir grassland. We identified all the plant species, measured the number and height of plant and plant coverage rate, and calculated species diversity, estimated above-ground biomass in use plot and non-use plot. We also measured soil hardness, and collected soil samples for physical and chemical analysis in both plots. The obtained results were as follows: a) the height of the dominant plants, plant coverage rate, species diversity, and above-ground biomass were significantly lower in use plot than in non-use plot, b) Carex duriuscula C.A.Mey., indicator plant for soil degradation, was dominant in use plot, c) soil hardness was significantly higher in use plot than in non-use plot, and spatial dependence of soil hardness was only found in the use plot, d) CEC, TC, TN and pH in the topsoil were significantly lower in use plot than non-use plot. On the basis of the results, we concluded that the tourism activities can be another major cause of the grassland degradation in Inner Mongolia.

Using Data Analysis to Explore Class Enrollment.

ERIC Educational Resources Information Center

Davis, Gretchen

1990-01-01

Describes classroom activities and shows that statistics is a practical tool for solving real problems. Presents a histogram, a stem plot, and a box plot to compare data involving class enrollments. (YP)

Visualizing the deep end of sound: plotting multi-parameter results from infrasound data analysis

NASA Astrophysics Data System (ADS)

Perttu, A. B.; Taisne, B.

2016-12-01

Infrasound is sound below the threshold of human hearing: approximately 20 Hz. The field of infrasound research, like other waveform based fields relies on several standard processing methods and data visualizations, including waveform plots and spectrograms. The installation of the International Monitoring System (IMS) global network of infrasound arrays, contributed to the resurgence of infrasound research. Array processing is an important method used in infrasound research, however, this method produces data sets with a large number of parameters, and requires innovative plotting techniques. The goal in designing new figures is to be able to present easily comprehendible, and information-rich plots by careful selection of data density and plotting methods.

Parallel line analysis: multifunctional software for the biomedical sciences

NASA Technical Reports Server (NTRS)

Swank, P. R.; Lewis, M. L.; Damron, K. L.; Morrison, D. R.

1990-01-01

An easy to use, interactive FORTRAN program for analyzing the results of parallel line assays is described. The program is menu driven and consists of five major components: data entry, data editing, manual analysis, manual plotting, and automatic analysis and plotting. Data can be entered from the terminal or from previously created data files. The data editing portion of the program is used to inspect and modify data and to statistically identify outliers. The manual analysis component is used to test the assumptions necessary for parallel line assays using analysis of covariance techniques and to determine potency ratios with confidence limits. The manual plotting component provides a graphic display of the data on the terminal screen or on a standard line printer. The automatic portion runs through multiple analyses without operator input. Data may be saved in a special file to expedite input at a future time.

A statistical data analysis and plotting program for cloud microphysics experiments

NASA Technical Reports Server (NTRS)

Jordan, A. J.

1981-01-01

The analysis software developed for atmospheric cloud microphysics experiments conducted in the laboratory as well as aboard a KC-135 aircraft is described. A group of four programs was developed and implemented on a Hewlett Packard 1000 series F minicomputer running under HP's RTE-IVB operating system. The programs control and read data from a MEMODYNE Model 3765-8BV cassette recorder, format the data on the Hewlett Packard disk subsystem, and generate statistical data (mean, variance, standard deviation) and voltage and engineering unit plots on a user selected plotting device. The programs are written in HP FORTRAN IV and HP ASSEMBLY Language with the graphics software using the HP 1000 Graphics. The supported plotting devices are the HP 2647A graphics terminal, the HP 9872B four color pen plotter, and the HP 2608A matrix line printer.

Metaplot: a novel stata graph for assessing heterogeneity at a glance.

PubMed

Poorolajal, J; Mahmoodi, M; Majdzadeh, R; Fotouhi, A

2010-01-01

Heterogeneity is usually a major concern in meta-analysis. Although there are some statistical approaches for assessing variability across studies, here we present a new approach to heterogeneity using "MetaPlot" that investigate the influence of a single study on the overall heterogeneity. MetaPlot is a two-way (x, y) graph, which can be considered as a complementary graphical approach for testing heterogeneity. This method shows graphically as well as numerically the results of an influence analysis, in which Higgins' I(2) statistic with 95% (Confidence interval) CI are computed omitting one study in each turn and then are plotted against reciprocal of standard error (1/SE) or "precision". In this graph, "1/SE" lies on x axis and "I(2) results" lies on y axe. Having a first glance at MetaPlot, one can predict to what extent omission of a single study may influence the overall heterogeneity. The precision on x-axis enables us to distinguish the size of each trial. The graph describes I(2) statistic with 95% CI graphically as well as numerically in one view for prompt comparison. It is possible to implement MetaPlot for meta-analysis of different types of outcome data and summary measures. This method presents a simple graphical approach to identify an outlier and its effect on overall heterogeneity at a glance. We wish to suggest MetaPlot to Stata experts to prepare its module for the software.

Forest Inventory and Analysis and Forest Health Monitoring: Piecing the Quilt

Treesearch

Joseph M. McCollum; Jamie K. Cochran

2005-01-01

Against the backdrop of a discussion about patchwork quilt assembly, the authors present background information on global grids. They show how to compose hexagons, an important task in systematically developing a subset of Forest Health Monitoring (FHM) Program plots from Forest Inventory and Analysis (FIA) plots. Finally, they outline the FHM and FIA grids, along with...

Graphical and Numerical Descriptive Analysis: Exploratory Tools Applied to Vietnamese Data

ERIC Educational Resources Information Center

Haughton, Dominique; Phong, Nguyen

2004-01-01

This case study covers several exploratory data analysis ideas, the histogram and boxplot, kernel density estimates, the recently introduced bagplot--a two-dimensional extension of the boxplot--as well as the violin plot, which combines a boxplot with a density shape plot. We apply these ideas and demonstrate how to interpret the output from these…

South Carolina, 2010 forest inventory and analysis factsheet

Treesearch

Roger C. Conner

2011-01-01

The Forest Inventory and Analysis (FIA) Program implemented a nationally consistent annual inventory system in 1998. Under the new design, one-fifth of all inventory plots in South Carolina are visited each year. The southern FIA unit, working cooperatively with South Carolina Forestry Commission crews, established the State’s initial annual inventory plots during the...

Path Analysis and Residual Plotting as Methods of Environmental Scanning in Higher Education: An Illustration with Applications and Enrollments.

ERIC Educational Resources Information Center

Morcol, Goktug; McLaughlin, Gerald W.

1990-01-01

The study proposes using path analysis and residual plotting as methods supporting environmental scanning in strategic planning for higher education institutions. Path models of three levels of independent variables are developed. Dependent variables measuring applications and enrollments at Virginia Polytechnic Institute and State University are…

Florida, 2011-forest inventory and analysis factsheet

Treesearch

Mark J. Brown; Jarek Nowak

2013-01-01

Forest Inventory and Analysis (FIA) factsheets are produced periodically to keep the public up to date on the extent and condition of the forest lands in each State. The forestrelated estimates in the factsheets are based upon data collected from thousands of sample plots distributed across the landscape in a systematic manner. The total number of these plots is...

Presenting simulation results in a nested loop plot.

PubMed

Rücker, Gerta; Schwarzer, Guido

2014-12-12

Statisticians investigate new methods in simulations to evaluate their properties for future real data applications. Results are often presented in a number of figures, e.g., Trellis plots. We had conducted a simulation study on six statistical methods for estimating the treatment effect in binary outcome meta-analyses, where selection bias (e.g., publication bias) was suspected because of apparent funnel plot asymmetry. We varied five simulation parameters: true treatment effect, extent of selection, event proportion in control group, heterogeneity parameter, and number of studies in meta-analysis. In combination, this yielded a total number of 768 scenarios. To present all results using Trellis plots, 12 figures were needed. Choosing bias as criterion of interest, we present a 'nested loop plot', a diagram type that aims to have all simulation results in one plot. The idea was to bring all scenarios into a lexicographical order and arrange them consecutively on the horizontal axis of a plot, whereas the treatment effect estimate is presented on the vertical axis. The plot illustrates how parameters simultaneously influenced the estimate. It can be combined with a Trellis plot in a so-called hybrid plot. Nested loop plots may also be applied to other criteria such as the variance of estimation. The nested loop plot, similar to a time series graph, summarizes all information about the results of a simulation study with respect to a chosen criterion in one picture and provides a suitable alternative or an addition to Trellis plots.

Graphical analysis of power systems for mobile robotics

NASA Astrophysics Data System (ADS)

Raade, Justin William

The field of mobile robotics places stringent demands on the power system. Energetic autonomy, or the ability to function for a useful operation time independent of any tether, refueling, or recharging, is a driving force in a robot designed for a field application. The focus of this dissertation is the development of two graphical analysis tools, namely Ragone plots and optimal hybridization plots, for the design of human scale mobile robotic power systems. These tools contribute to the intuitive understanding of the performance of a power system and expand the toolbox of the design engineer. Ragone plots are useful for graphically comparing the merits of different power systems for a wide range of operation times. They plot the specific power versus the specific energy of a system on logarithmic scales. The driving equations in the creation of a Ragone plot are derived in terms of several important system parameters. Trends at extreme operation times (both very short and very long) are examined. Ragone plot analysis is applied to the design of several power systems for high-power human exoskeletons. Power systems examined include a monopropellant-powered free piston hydraulic pump, a gasoline-powered internal combustion engine with hydraulic actuators, and a fuel cell with electric actuators. Hybrid power systems consist of two or more distinct energy sources that are used together to meet a single load. They can often outperform non-hybrid power systems in low duty-cycle applications or those with widely varying load profiles and long operation times. Two types of energy sources are defined: engine-like and capacitive. The hybridization rules for different combinations of energy sources are derived using graphical plots of hybrid power system mass versus the primary system power. Optimal hybridization analysis is applied to several power systems for low-power human exoskeletons. Hybrid power systems examined include a fuel cell and a solar panel coupled with lithium polymer batteries. In summary, this dissertation describes the development and application of two graphical analysis tools for the intuitive design of mobile robotic power systems. Several design examples are discussed involving human exoskeleton power systems.

Texture Analysis of Recurrence Plots Based on Wavelets and PSO for Laryngeal Pathologies Detection.

PubMed

Souza, Taciana A; Vieira, Vinícius J D; Correia, Suzete E N; Costa, Silvana L N C; de A Costa, Washington C; Souza, Micael A

2015-01-01

This paper deals with the discrimination between healthy and pathological speech signals using recurrence plots and wavelet transform with texture features. Approximation and detail coefficients are obtained from the recurrence plots using Haar wavelet transform, considering one decomposition level. The considered laryngeal pathologies are: paralysis, Reinke's edema and nodules. Accuracy rates above 86% were obtained by means of the employed method.

Finding Your Way out of the Forest without a Trail of Bread Crumbs: Development and Evaluation of Two Novel Displays of Forest Plots

ERIC Educational Resources Information Center

Schild, Anne H. E.; Voracek, Martin

2015-01-01

Research has shown that forest plots are a gold standard in the visualization of meta-analytic results. However, research on the general interpretation of forest plots and the role of researchers' meta-analysis experience and field of study is still unavailable. Additionally, the traditional display of effect sizes, confidence intervals, and…

Using publically available forest inventory data in climate-based modes of tree species distribution: Examining effects of true versus altered location coordinates

Treesearch

Jacob Gibson; Gretchen Moisen; Tracey Frescino; Thomas C. Edwards

2013-01-01

Species distribution models (SDMs) were built with US Forest Inventory and Analysis (FIA) publicly available plot coordinates, which are altered for plot security purposes, and compared with SDMs built with true plot coordinates. Six species endemic to the western US, including four junipers (Juniperus deppeana var. deppeana, J. monosperma, J. occidentalis, J....

Analysis of the Korean Navy Selection Process for the Naval Post Graduate School

DTIC Science & Technology

1988-06-01

OUTCOME OF ECL TESTING SCORE..........................54 C. OUTCOME OF TOEFL TESTING SCORE.......................55 D. PLOT OF NPS GRADE WITH ECL...TESTING SCORE..............55 E. PLOT OF NPS GRADE WIHT NA GRADE......................56 F. PLOT OF NPS GRADE WITH TOEFL TESTING SCORE............56...OF ECL TESTING SCORE ............. 30 Table S. EXPECTANCY TABLE OF NAG ............................ 31 Table 9. EXPECTANCY TABLE OF TOEFL TESTING SCORE

Redrawing the baseline: a method for adjusting biased historical forest estimates using a spatial and temporally representative plot network

Treesearch

Sara A. Goeking; Paul L. Patterson

2015-01-01

Users of Forest Inventory and Analysis (FIA) data sometimes compare historic and current forest inventory estimates, despite warnings that such comparisons may be tenuous. The purpose of this study was to demonstrate a method for obtaining a more accurate and representative reference dataset using data collected at co-located plots (i.e., plots that were measured...

Effects of low intensity prescribed fires on ponderosa pine forests in wilderness areas of Zion National Park, Utah

Treesearch

Henry V. Bastian

2001-01-01

Vegetation and fuel loading plots were monitored and sampled in wilderness areas treated with prescribed fire. Changes in ponderosa pine (Pinus ponderosa) forest structure tree species and fuel loading are presented. Plots were randomly stratified and established in burn units in 1995. Preliminary analysis of nine plots 2 years after burning show litter was reduced 54....

Pilot Inventory of FIA plots traditionally called `nonforest'

Treesearch

Rachel Riemann

2003-01-01

Forest-inventory data were collected on plots defined as ?nonforest? by the USDA Forest Service?s Forest Inventory and Analysis (FIA) unit. Nonforest plots may have trees on them, but they do not fit FIA?s definition of forest because the area covered by trees is too small, too sparsely populated by trees, too narrow (e.g., trees between fields or in the middle of a...

Aquifer test interpretation using derivative analysis and diagnostic plots

NASA Astrophysics Data System (ADS)

Hernández-Espriú, Antonio; Real-Rangel, Roberto; Cortés-Salazar, Iván; Castro-Herrera, Israel; Luna-Izazaga, Gabriela; Sánchez-León, Emilio

2017-04-01

Pumping tests remain a method of choice to deduce fundamental aquifer properties and to assess well condition. In the oil and gas (O&G) industry, well testing has been the core technique in examining reservoir behavior over the last 50 years. The pressure derivative by Bourdet, it is perhaps, the most significant single development in the history of well test analysis. Recently, the so-called diagnostics plots (e.g. drawdown and drawdown derivative in a log-log plot) have been successfully tested in aquifers. However, this procedure is still underutilized by groundwater professionals. This research illustrates the applicability range, advantages and drawbacks (e.g. smoothing procedures) of diagnostic plots using field examples from a wide spectrum of tests (short/long tests, constant/variable flow rates, drawdown/buildup stages, pumping well/observation well) in dissimilar geological conditions. We analyze new and pre-existent aquifer tests in Mexico, USA, Canada, Germany, France and Saudi Arabia. In constant flow rate tests, our results show that derivative analysis is an easy, robust and powerful tool to assess near-borehole damage effects, formation heterogeneity, boundaries, flow regimes, infinite-acting radial stages, i.e., valid Theisian framework, and fracture-driven flow. In step tests, the effectiveness relies on high-frequency drawdown measurements. Moreover, we adapt O&G analytical solutions to cater for the conditions in groundwater systems. In this context, further parameters can be computed analytically from the plots, such as skin factor, head losses, wellbore storage, distance to the boundary, channel-aquifer and/or fracture zone width, among others. Therefore, diagnostic plots should be considered a mandatory tool for pumping tests analysis among hydrogeologists. This project has been supported by DGAPA (UNAM) under the research project PAPIIT IN-112815.

The rainfall plot: its motivation, characteristics and pitfalls.

PubMed

Domanska, Diana; Vodák, Daniel; Lund-Andersen, Christin; Salvatore, Stefania; Hovig, Eivind; Sandve, Geir Kjetil

2017-05-18

A visualization referred to as rainfall plot has recently gained popularity in genome data analysis. The plot is mostly used for illustrating the distribution of somatic cancer mutations along a reference genome, typically aiming to identify mutation hotspots. In general terms, the rainfall plot can be seen as a scatter plot showing the location of events on the x-axis versus the distance between consecutive events on the y-axis. Despite its frequent use, the motivation for applying this particular visualization and the appropriateness of its usage have never been critically addressed in detail. We show that the rainfall plot allows visual detection even for events occurring at high frequency over very short distances. In addition, event clustering at multiple scales may be detected as distinct horizontal bands in rainfall plots. At the same time, due to the limited size of standard figures, rainfall plots might suffer from inability to distinguish overlapping events, especially when multiple datasets are plotted in the same figure. We demonstrate the consequences of plot congestion, which results in obscured visual data interpretations. This work provides the first comprehensive survey of the characteristics and proper usage of rainfall plots. We find that the rainfall plot is able to convey a large amount of information without any need for parameterization or tuning. However, we also demonstrate how plot congestion and the use of a logarithmic y-axis may result in obscured visual data interpretations. To aid the productive utilization of rainfall plots, we demonstrate their characteristics and potential pitfalls using both simulated and real data, and provide a set of practical guidelines for their proper interpretation and usage.

Dalitz plot analysis of three-body charmonium decays at BABAR

NASA Astrophysics Data System (ADS)

Palano, Antimo

2016-05-01

We present preliminary results on the measurement of the I=1/2 Kπ S-wave through a model independent partial wave analysis of ηc decays to KS0 K+π- and K+ K-π0 produced in two-photon interactions. We also perform a Dalitz plot analysis of the J/ψ decays to π+π-π0 and K+ K-π0 produced in the initial state radiation process.

On-Line Pattern Analysis and Recognition System. OLPARS VI. Software Reference Manual,

DTIC Science & Technology

1982-06-18

Discriminant Analysis Data Transformation, Feature Extraction, Feature Evaluation Cluster Analysis, Classification Computer Software 20Z. ABSTRACT... cluster /scatter cut-off value, (2) change the one-space bin factor, (3) change from long prompts to short prompts or vice versa, (4) change the...value, a cluster plot is displayed, otherwise a scatter plot is shown. if option 1 is selected, the program requests that a new value be input

A further use for the Harvest plot: a novel method for the presentation of data synthesis.

PubMed

Crowther, Mark; Avenell, Alison; MacLennan, Graeme; Mowatt, Graham

2011-06-01

When performing a systematic review, whether or not a meta-analysis is performed, graphical displays can be useful. Data do still need to be described, ideally in graphical form. The Harvest plot has been developed to display combined data from several studies that allows demonstration of not only effect but also study quality. We describe a modification to the Harvest plot that allows the presentation of data that normally could not be included in a forest plot meta-analysis and allows extra information to be displayed. Using specific examples, we describe how the arrangement of studies, height of the bars and additional information can be used to enhance the plot. This is an important development, which by fulfilling Tufte's nine requirements for graphical presentation, allows researchers to display evidence in a flexible way. This means readers can follow an argument in a clear and efficient manner without the need for large volumes of descriptive text. Copyright © 2011 John Wiley & Sons, Ltd. Copyright © 2011 John Wiley & Sons, Ltd.

Q-mode versus R-mode principal component analysis for linear discriminant analysis (LDA)

NASA Astrophysics Data System (ADS)

Lee, Loong Chuen; Liong, Choong-Yeun; Jemain, Abdul Aziz

2017-05-01

Many literature apply Principal Component Analysis (PCA) as either preliminary visualization or variable con-struction methods or both. Focus of PCA can be on the samples (R-mode PCA) or variables (Q-mode PCA). Traditionally, R-mode PCA has been the usual approach to reduce high-dimensionality data before the application of Linear Discriminant Analysis (LDA), to solve classification problems. Output from PCA composed of two new matrices known as loadings and scores matrices. Each matrix can then be used to produce a plot, i.e. loadings plot aids identification of important variables whereas scores plot presents spatial distribution of samples on new axes that are also known as Principal Components (PCs). Fundamentally, the scores matrix always be the input variables for building classification model. A recent paper uses Q-mode PCA but the focus of analysis was not on the variables but instead on the samples. As a result, the authors have exchanged the use of both loadings and scores plots in which clustering of samples was studied using loadings plot whereas scores plot has been used to identify important manifest variables. Therefore, the aim of this study is to statistically validate the proposed practice. Evaluation is based on performance of external error obtained from LDA models according to number of PCs. On top of that, bootstrapping was also conducted to evaluate the external error of each of the LDA models. Results show that LDA models produced by PCs from R-mode PCA give logical performance and the matched external error are also unbiased whereas the ones produced with Q-mode PCA show the opposites. With that, we concluded that PCs produced from Q-mode is not statistically stable and thus should not be applied to problems of classifying samples, but variables. We hope this paper will provide some insights on the disputable issues.

Insights into gait disorders: walking variability using phase plot analysis, Huntington's disease.

PubMed

Collett, Johnny; Esser, Patrick; Khalil, Hanan; Busse, Monica; Quinn, Lori; DeBono, Katy; Rosser, Anne; Nemeth, Andrea H; Dawes, Helen

2014-09-01

Huntington's disease (HD) is a progressive inherited neurodegenerative disorder. Identifying sensitive methodologies to quantitatively measure early motor changes have been difficult to develop. This exploratory observational study investigated gait variability and symmetry in HD using phase plot analysis. We measured the walking of 22 controls and 35 HD gene carriers (7 premanifest (PreHD)), 16 early/mid (HD1) and 12 late stage (HD2) in Oxford and Cardiff, UK. The unified Huntington's disease rating scale-total motor scores (UHDRS-TMS) and disease burden scores (DBS) were used to quantify disease severity. Data was collected during a clinical walk test (8.8 or 10 m) using an inertial measurement unit attached to the trunk. The 6 middle strides were used to calculate gait variability determined by spatiotemporal parameters (co-efficient of variation (CoV)) and phase plot analysis. Phase plots considered the variability in consecutive wave forms from vertical movement and were quantified by SDA (spatiotemporal variability), SDB (temporal variability), ratio ∀ (ratio SDA:SDB) and Δangleβ (symmetry). Step time CoV was greater in manifest HD (p<0.01, both manifest groups) than controls, as was stride length CoV for HD2 (p<0.01). No differences were found in spatiotemporal variability between PreHD and controls (p>0.05). Phase plot analysis identified differences between manifest HD and controls for SDB, Ratio ∀ and Δangle (all p<0.01, both manifest groups). Furthermore Ratio ∀ was smaller in PreHD compared with controls (p<0.01). Ratio ∀ also produced the strongest correlation with UHDRS-TMS (r=-0.61, p<0.01) and was correlated with DBS (r=-0.42, p=0.02). Phase plot analysis may be a sensitive method of detecting gait changes in HD and can be performed quickly during clinical walking tests. Copyright © 2014 Elsevier B.V. All rights reserved.

Patterns of exotic plant invasions in Pennsylvania's Allegheny National Forest using intensive Forest Inventory and Analysis plots

Treesearch

Cynthia D. Huebner; Randall S. Morin; Ann Zurbriggen; Robert L. White

2009-01-01

Intensive Forest Inventory and Analysis (FIA) plot data collected in the Allegheny National Forest (ANF), Pennsylvania, between 1999 and 2006 were evaluated for their ability to predict ANF's vulnerability to invasion by exotic plants. A total of 26 variables classified by biotic, abiotic, or disturbance characteristics were examined. Likelihood of colonization by...

TrackPlot Enhancements: Support for Multiple Animal Tracks and Gyros

DTIC Science & Technology

2015-09-30

visualization and kinematic analysis of marine animal movements derived from archival tag data. Tags are supported that have sensors for pressure, acceleration...1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. TrackPlot Enhancements: Support for Multiple Animal ...in combination with accelerometer and magnetometer data. 2) the extraction and frequency analysis of accelerations and rotation in animal

Potential applications of prefield land use and canopy cover data: Examples from nonforest and nonsampled forest inventory plots

Treesearch

Sara A. Goeking

2012-01-01

The Forest Inventory and Analysis (FIA) prefield workflow involves interpreting aerial imagery to determine whether each plot in a given inventory year may meet FIA’s definition of forest land. The primary purpose of this determination is to minimize inventory costs by avoiding unnecessary ground surveys of plots that are obviously in nonforest areas. Since the...

Volcano plots in analyzing differential expressions with mRNA microarrays.

PubMed

Li, Wentian

2012-12-01

A volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log(10)(p-value) from the t-test). We review the basic and interactive use of the volcano plot and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide a unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility of applying volcano plots to other fields beyond microarray.

Homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8

PubMed Central

Garba, Lawal; Mohamad Yussoff, Mohamad Ariff; Abd Halim, Khairul Bariyyah; Ishak, Siti Nor Hasmah; Mohamad Ali, Mohd Shukuri; Oslan, Siti Nurbaya

2018-01-01

Membrane-bound fatty acid desaturases perform oxygenated desaturation reactions to insert double bonds within fatty acyl chains in regioselective and stereoselective manners. The Δ9-fatty acid desaturase strictly creates the first double bond between C9 and 10 positions of most saturated substrates. As the three-dimensional structures of the bacterial membrane fatty acid desaturases are not available, relevant information about the enzymes are derived from their amino acid sequences, site-directed mutagenesis and domain swapping in similar membrane-bound desaturases. The cold-tolerant Pseudomonas sp. AMS8 was found to produce high amount of monounsaturated fatty acids at low temperature. Subsequently, an active Δ9-fatty acid desaturase was isolated and functionally expressed in Escherichia coli. In this paper we report homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8 for the first time to the best of our knowledge. Three dimensional structure of the enzyme was built using MODELLER version 9.18 using a suitable template. The protein model contained the three conserved-histidine residues typical for all membrane-bound desaturase catalytic activity. The structure was subjected to energy minimization and checked for correctness using Ramachandran plots and ERRAT, which showed a good quality model of 91.6 and 65.0%, respectively. The protein model was used to preform MD simulation and docking of palmitic acid using CHARMM36 force field in GROMACS Version 5 and Autodock tool Version 4.2, respectively. The docking simulation with the lowest binding energy, −6.8 kcal/mol had a number of residues in close contact with the docked palmitic acid namely, Ile26, Tyr95, Val179, Gly180, Pro64, Glu203, His34, His206, His71, Arg182, Thr85, Lys98 and His177. Interestingly, among the binding residues are His34, His71 and His206 from the first, second, and third conserved histidine motif, respectively, which constitute the active site of the enzyme. The results obtained are in compliance with the in vivo activity of the Δ9-fatty acid desaturase on the membrane phospholipids. PMID:29576935

In silico designing of therapeutic protein enriched with branched-chain amino acids for the dietary treatment of chronic liver disease.

PubMed

L, Sunil; Vasu, Prasanna

2017-09-01

Leucine, isoleucine, and valine are three essential branched-chain amino acids (BCAA) account for 40-45% of total essential amino acids. BCAA stimulates protein synthesis primarily in skeletal muscles, and it can directly transport to circulatory blood stream bypassing the liver. Hence, a protein enriched with BCAA is an important therapeutic target for the dietary treatment of chronic liver disease. The present study is to design a synthetic protein enriched with BCAA and the challenge is to maximize the BCAA content, keeping the balanced ratio of leucine, isoleucine, valine - 2: 1: 1.2 as specified by WHO/UNU/FAO. Here, we turned the general concept of homology modeling and tried to find a suitable scaffold (α-helix) to host an excess amount of BCAA for increased stability and digestibility. A total of 50 protein models were constructed by using SWISS-MODEL, Modeller 9.17, ProtParam tool, and allergen online tools. Out of 50 different protein models, protein model-50 was found to be best, which had a well-defined 3D structure, good in silico digestibility, balanced ratio of BCAA and showed 65.57% structure identity to the template apo-bovine α-lactalbumin (1F6R). Templates search was performed against PDB using PSI-BLAST, SWISS-MODEL, PROFUNC, I-TASSER, and ConSurf. The secondary structure was predicted by PSSPred, PSIPRED, I-TASSER, PORTER, and SPIDER2. The modeled structure of protein Model-50 was validated by PROCHECK, ERRAT, ProSA, and QMEAN. COACH and ProFUNC tools were performed to determine the functional effects of protein model-50. Overall, the BCAA was enriched from 22 to 56.4% with the balanced ratio of Leu: Ile: Val (2: 1: 1.2). The Ramachandran plot showed 97.7% of the amino acid residues in allowed regions with ERRAT score of 86.05. We have successfully modeled the complete three-dimensional structure of the target protein model-50 using highly reputed computational tools. Copyright © 2017 Elsevier Inc. All rights reserved.

Structural characterization and mutational assessment of podocin - a novel drug target to nephrotic syndrome - an in silico approach.

PubMed

Tabassum, Asra; Rajeshwari, Tadigadapa; Soni, Nidhi; Raju, D S B; Yadav, Mukesh; Nayarisseri, Anuraj; Jahan, Parveen

2014-03-01

Non-synonymous single nucleotide changes (nSNC) are coding variants that introduce amino acid changes in their corresponding proteins. They can affect protein function; they are believed to have the largest impact on human health compared with SNCs in other regions of the genome. Such a sequence alteration directly affects their structural stability through conformational changes. Presence of these conformational changes near catalytic site or active site may alter protein function and as a consequence receptor-ligand complex interactions. The present investigation includes assessment of human podocin mutations (G92C, P118L, R138Q, and D160G) on its structure. Podocin is an important glomerular integral membrane protein thought to play a key role in steroid resistant nephrotic syndrome. Podocin has a hairpin like structure with 383 amino acids, it is an integral protein homologous to stomatin, and acts as a molecular link in a stretch-sensitive system. We modeled 3D structure of podocin by means of Modeller and validated via PROCHECK to get a Ramachandran plot (88.5% in most favored region), main chain, side chain, bad contacts, gauche and pooled standard deviation. Further, a protein engineering tool Triton was used to induce mutagenesis corresponding to four variants G92C, P118L, R138Q and D160G in the wild type. Perusal of energies of wild and mutated type of podocin structures confirmed that mutated structures were thermodynamically more stable than wild type and therefore biological events favored synthesis of mutated forms of podocin than wild type. As a conclusive part, two mutations G92C (-8179.272 kJ/mol) and P118L (-8136.685 kJ/mol) are more stable and probable to take place in podocin structure over wild podocin structure (-8105.622 kJ/mol). Though there is lesser difference in mutated and wild type (approximately, 74 and 35 kJ/mol), it may play a crucial role in deciding why mutations are favored and occur at the genetic level.

scraps: An open-source Python-based analysis package for analyzing and plotting superconducting resonator data

DOE PAGES

Carter, Faustin Wirkus; Khaire, Trupti S.; Novosad, Valentyn; ...

2016-11-07

We present "scraps" (SuperConducting Analysis and Plotting Software), a Python package designed to aid in the analysis and visualization of large amounts of superconducting resonator data, specifically complex transmission as a function of frequency, acquired at many different temperatures and driving powers. The package includes a least-squares fitting engine as well as a Monte-Carlo Markov Chain sampler for sampling the posterior distribution given priors, marginalizing over nuisance parameters, and estimating covariances. A set of plotting tools for generating publication-quality figures is also provided in the package. Lastly, we discuss the functionality of the software and provide some examples of itsmore » utility on data collected from a niobium-nitride coplanar waveguide resonator fabricated at Argonne National Laboratory.« less

Analysis of a Split-Plot Experimental Design Applied to a Low-Speed Wind Tunnel Investigation

NASA Technical Reports Server (NTRS)

Erickson, Gary E.

2013-01-01

A procedure to analyze a split-plot experimental design featuring two input factors, two levels of randomization, and two error structures in a low-speed wind tunnel investigation of a small-scale model of a fighter airplane configuration is described in this report. Standard commercially-available statistical software was used to analyze the test results obtained in a randomization-restricted environment often encountered in wind tunnel testing. The input factors were differential horizontal stabilizer incidence and the angle of attack. The response variables were the aerodynamic coefficients of lift, drag, and pitching moment. Using split-plot terminology, the whole plot, or difficult-to-change, factor was the differential horizontal stabilizer incidence, and the subplot, or easy-to-change, factor was the angle of attack. The whole plot and subplot factors were both tested at three levels. Degrees of freedom for the whole plot error were provided by replication in the form of three blocks, or replicates, which were intended to simulate three consecutive days of wind tunnel facility operation. The analysis was conducted in three stages, which yielded the estimated mean squares, multiple regression function coefficients, and corresponding tests of significance for all individual terms at the whole plot and subplot levels for the three aerodynamic response variables. The estimated regression functions included main effects and two-factor interaction for the lift coefficient, main effects, two-factor interaction, and quadratic effects for the drag coefficient, and only main effects for the pitching moment coefficient.

A new graphic plot analysis for determination of neuroreceptor binding in positron emission tomography studies.

PubMed

Ito, Hiroshi; Yokoi, Takashi; Ikoma, Yoko; Shidahara, Miho; Seki, Chie; Naganawa, Mika; Takahashi, Hidehiko; Takano, Harumasa; Kimura, Yuichi; Ichise, Masanori; Suhara, Tetsuya

2010-01-01

In positron emission tomography (PET) studies with radioligands for neuroreceptors, tracer kinetics have been described by the standard two-tissue compartment model that includes the compartments of nondisplaceable binding and specific binding to receptors. In the present study, we have developed a new graphic plot analysis to determine the total distribution volume (V(T)) and nondisplaceable distribution volume (V(ND)) independently, and therefore the binding potential (BP(ND)). In this plot, Y(t) is the ratio of brain tissue activity to time-integrated arterial input function, and X(t) is the ratio of time-integrated brain tissue activity to time-integrated arterial input function. The x-intercept of linear regression of the plots for early phase represents V(ND), and the x-intercept of linear regression of the plots for delayed phase after the equilibrium time represents V(T). BP(ND) can be calculated by BP(ND)=V(T)/V(ND)-1. Dynamic PET scanning with measurement of arterial input function was performed on six healthy men after intravenous rapid bolus injection of [(11)C]FLB457. The plot yielded a curve in regions with specific binding while it yielded a straight line through all plot data in regions with no specific binding. V(ND), V(T), and BP(ND) values calculated by the present method were in good agreement with those by conventional non-linear least-squares fitting procedure. This method can be used to distinguish graphically whether the radioligand binding includes specific binding or not.

Central sleep apnea detection from ECG-derived respiratory signals. Application of multivariate recurrence plot analysis.

PubMed

Maier, C; Dickhaus, H

2010-01-01

This study examines the suitability of recurrence plot analysis for the problem of central sleep apnea (CSA) detection and delineation from ECG-derived respiratory (EDR) signals. A parameter describing the average length of vertical line structures in recurrence plots is calculated at a time resolution of 1 s as 'instantaneous trapping time'. Threshold comparison of this parameter is used to detect ongoing CSA. In data from 26 patients (duration 208 h) we assessed sensitivity for detection of CSA and mixed apnea (MSA) events by comparing the results obtained from 8-channel Holter ECGs to the annotations (860 CSA, 480 MSA) of simultaneously registered polysomnograms. Multivariate combination of the EDR from different ECG leads improved the detection accuracy significantly. When all eight leads were considered, an average instantaneous vertical line length above 5 correctly identified 1126 of the 1340 events (sensitivity 84%) with a total number of 1881 positive detections. We conclude that recurrence plot analysis is a promising tool for detection and delineation of CSA epochs from EDR signals with high time resolution. Moreover, the approach is likewise applicable to directly measured respiratory signals.

Low-Cost Insulator

DTIC Science & Technology

1984-02-01

propellants. This type of propellant produces an erosive exhaust gas,/ whlch is the best condition for evaluating the ablative coating formula - tions. Other...RFCOMMFNDATrIONS 93 i. I Finail Formula lions 93 -..-.... ,.-...... ., ..... .’-.’.....,. .,.,. .. I ... .% " , 4.2 Cost Analysis of Toscanite 95 4.3...ing Pedestal 15 7 Density Plot, Sand, NCO/OH Ratio 1.0 18 P, Density Plot, Glass feads, NCO/OH Ratio 1.0 18 9 Density Plot, Sand, NCO/OH Ratio 0.9 19 10

Cycles till failure of silver-zinc cells with competing failure modes - Preliminary data analysis

NASA Technical Reports Server (NTRS)

Sidik, S. M.; Leibecki, H. F.; Bozek, J. M.

1980-01-01

The data analysis of cycles to failure of silver-zinc electrochemical cells with competing failure modes is presented. The test ran 129 cells through charge-discharge cycles until failure; preliminary data analysis consisted of response surface estimate of life. Batteries fail through low voltage condition and an internal shorting condition; a competing failure modes analysis was made using maximum likelihood estimation for the extreme value life distribution. Extensive residual plotting and probability plotting were used to verify data quality and selection of model.

Analysis and test for space shuttle propellant dynamics (1/10th scale model test results). Volume 2: 1/10th scale model test data

NASA Technical Reports Server (NTRS)

Berry, R. L.; Tegart, J. R.; Demchak, L. J.

1979-01-01

Thirty sets of test data selected from the 89 low-g aircraft tests flown by NASA KC-135 zero-g aircraft are listed in tables with their accompanying test conditions. The data for each test consists of the time history plots of digitalized data (in engineering units) and the time history plots of the load cell data transformed to the tank axis system. The transformed load cell data was developed for future analytical comparisons; therefore, these data were transformed and plotted from the time at which the aircraft Z axis acceleration passed through l-g. There are 14 time history plots per test condition. The contents of each plot is shown in a table.

Application of remote sensing for fishery resource assessment and monitoring. [analysis of fish catch relative to water rips

NASA Technical Reports Server (NTRS)

Savastano, K. J. (Principal Investigator)

1974-01-01

The author has identified the following significant results. A plot was drawn of the dolphin catch and the water discontinuities observed in the aerial photography. This plot was similar in format to the one made earlier on the white marlin catch relative to the water rips. Neither plot substantiates (as far as white marlin and dolphin are concerned) an opinion held by fishermen that better fishing may be found in the vicinity of the rips. Remotely inferred values for sea surface temperature, chlorophyll-a and turbidity were substituted for sea truth measurements in prediction models developed in previous analysis. Model performance, using the new values, was disappointing.

Evaluation of glioblastomas and lymphomas with whole-brain CT perfusion: Comparison between a delay-invariant singular-value decomposition algorithm and a Patlak plot.

PubMed

Hiwatashi, Akio; Togao, Osamu; Yamashita, Koji; Kikuchi, Kazufumi; Yoshimoto, Koji; Mizoguchi, Masahiro; Suzuki, Satoshi O; Yoshiura, Takashi; Honda, Hiroshi

2016-07-01

Correction of contrast leakage is recommended when enhancing lesions during perfusion analysis. The purpose of this study was to assess the diagnostic performance of computed tomography perfusion (CTP) with a delay-invariant singular-value decomposition algorithm (SVD+) and a Patlak plot in differentiating glioblastomas from lymphomas. This prospective study included 17 adult patients (12 men and 5 women) with pathologically proven glioblastomas (n=10) and lymphomas (n=7). CTP data were analyzed using SVD+ and a Patlak plot. The relative tumor blood volume and flow compared to contralateral normal-appearing gray matter (rCBV and rCBF derived from SVD+, and rBV and rFlow derived from the Patlak plot) were used to differentiate between glioblastomas and lymphomas. The Mann-Whitney U test and receiver operating characteristic (ROC) analyses were used for statistical analysis. Glioblastomas showed significantly higher rFlow (3.05±0.49, mean±standard deviation) than lymphomas (1.56±0.53; P<0.05). There were no statistically significant differences between glioblastomas and lymphomas in rBV (2.52±1.57 vs. 1.03±0.51; P>0.05), rCBF (1.38±0.41 vs. 1.29±0.47; P>0.05), or rCBV (1.78±0.47 vs. 1.87±0.66; P>0.05). ROC analysis showed the best diagnostic performance with rFlow (Az=0.871), followed by rBV (Az=0.771), rCBF (Az=0.614), and rCBV (Az=0.529). CTP analysis with a Patlak plot was helpful in differentiating between glioblastomas and lymphomas, but CTP analysis with SVD+ was not. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Dalitz plot analysis of Ds+→K+K-π+

NASA Astrophysics Data System (ADS)

Del Amo Sanchez, P.; Lees, J. P.; Poireau, V.; Prencipe, E.; Tisserand, V.; Garra Tico, J.; Grauges, E.; Martinelli, M.; Milanes, D. A.; Palano, A.; Pappagallo, M.; Eigen, G.; Stugu, B.; Sun, L.; Brown, D. N.; Kerth, L. T.; Kolomensky, Yu. G.; Lynch, G.; Osipenkov, I. L.; Koch, H.; Schroeder, T.; Asgeirsson, D. J.; Hearty, C.; Mattison, T. S.; McKenna, J. A.; Khan, A.; Blinov, V. E.; Buzykaev, A. R.; Druzhinin, V. P.; Golubev, V. B.; Kravchenko, E. A.; Onuchin, A. P.; Serednyakov, S. I.; Skovpen, Yu. I.; Solodov, E. P.; Todyshev, K. Yu.; Yushkov, A. N.; Bondioli, M.; Curry, S.; Kirkby, D.; Lankford, A. J.; Mandelkern, M.; Martin, E. C.; Stoker, D. P.; Atmacan, H.; Gary, J. W.; Liu, F.; Long, O.; Vitug, G. M.; Campagnari, C.; Hong, T. M.; Kovalskyi, D.; Richman, J. D.; West, C.; Eisner, A. M.; Heusch, C. A.; Kroseberg, J.; Lockman, W. S.; Martinez, A. J.; Schalk, T.; Schumm, B. A.; Seiden, A.; Winstrom, L. O.; Cheng, C. H.; Doll, D. A.; Echenard, B.; Hitlin, D. G.; Ongmongkolkul, P.; Porter, F. C.; Rakitin, A. Y.; Andreassen, R.; Dubrovin, M. S.; Mancinelli, G.; Meadows, B. T.; Sokoloff, M. D.; Bloom, P. C.; Ford, W. T.; Gaz, A.; Nagel, M.; Nauenberg, U.; Smith, J. G.; Wagner, S. R.; Ayad, R.; Toki, W. H.; Jasper, H.; Karbach, T. M.; Petzold, A.; Spaan, B.; Kobel, M. J.; Schubert, K. R.; Schwierz, R.; Bernard, D.; Verderi, M.; Clark, P. J.; Playfer, S.; Watson, J. E.; Andreotti, M.; Bettoni, D.; Bozzi, C.; Calabrese, R.; Cecchi, A.; Cibinetto, G.; Fioravanti, E.; Franchini, P.; Garzia, I.; Luppi, E.; Munerato, M.; Negrini, M.; Petrella, A.; Piemontese, L.; Baldini-Ferroli, R.; Calcaterra, A.; de Sangro, R.; Finocchiaro, G.; Nicolaci, M.; Pacetti, S.; Patteri, P.; Peruzzi, I. M.; Piccolo, M.; Rama, M.; Zallo, A.; Contri, R.; Guido, E.; Lo Vetere, M.; Monge, M. R.; Passaggio, S.; Patrignani, C.; Robutti, E.; Tosi, S.; Bhuyan, B.; Prasad, V.; Lee, C. L.; Morii, M.; Edwards, A. J.; Adametz, A.; Marks, J.; Uwer, U.; Bernlochner, F. U.; Ebert, M.; Lacker, H. M.; Lueck, T.; Volk, A.; Dauncey, P. D.; Tibbetts, M.; Behera, P. K.; Mallik, U.; Chen, C.; Cochran, J.; Crawley, H. B.; Dong, L.; Meyer, W. T.; Prell, S.; Rosenberg, E. I.; Rubin, A. E.; Gritsan, A. V.; Guo, Z. J.; Arnaud, N.; Davier, M.; Derkach, D.; Firmino da Costa, J.; Grosdidier, G.; Le Diberder, F.; Lutz, A. M.; Malaescu, B.; Perez, A.; Roudeau, P.; Schune, M. H.; Serrano, J.; Sordini, V.; Stocchi, A.; Wang, L.; Wormser, G.; Lange, D. J.; Wright, D. M.; Bingham, I.; Chavez, C. A.; Coleman, J. P.; Fry, J. R.; Gabathuler, E.; Gamet, R.; Hutchcroft, D. E.; Payne, D. J.; Touramanis, C.; Bevan, A. J.; di Lodovico, F.; Sacco, R.; Sigamani, M.; Cowan, G.; Paramesvaran, S.; Wren, A. C.; Brown, D. N.; Davis, C. L.; Denig, A. G.; Fritsch, M.; Gradl, W.; Hafner, A.; Alwyn, K. E.; Bailey, D.; Barlow, R. J.; Jackson, G.; Lafferty, G. D.; Anderson, J.; Cenci, R.; Jawahery, A.; Roberts, D. A.; Simi, G.; Tuggle, J. M.; Dallapiccola, C.; Salvati, E.; Cowan, R.; Dujmic, D.; Sciolla, G.; Zhao, M.; Lindemann, D.; Patel, P. M.; Robertson, S. H.; Schram, M.; Biassoni, P.; Lazzaro, A.; Lombardo, V.; Palombo, F.; Stracka, S.; Cremaldi, L.; Godang, R.; Kroeger, R.; Sonnek, P.; Summers, D. J.; Nguyen, X.; Simard, M.; Taras, P.; de Nardo, G.; Monorchio, D.; Onorato, G.; Sciacca, C.; Raven, G.; Snoek, H. L.; Jessop, C. P.; Knoepfel, K. J.; Losecco, J. M.; Wang, W. F.; Corwin, L. A.; Honscheid, K.; Kass, R.; Morris, J. P.; Blount, N. L.; Brau, J.; Frey, R.; Igonkina, O.; Kolb, J. A.; Rahmat, R.; Sinev, N. B.; Strom, D.; Strube, J.; Torrence, E.; Castelli, G.; Feltresi, E.; Gagliardi, N.; Margoni, M.; Morandin, M.; Posocco, M.; Rotondo, M.; Simonetto, F.; Stroili, R.; Ben-Haim, E.; Bonneaud, G. R.; Briand, H.; Calderini, G.; Chauveau, J.; Hamon, O.; Leruste, Ph.; Marchiori, G.; Ocariz, J.; Prendki, J.; Sitt, S.; Biasini, M.; Manoni, E.; Rossi, A.; Angelini, C.; Batignani, G.; Bettarini, S.; Carpinelli, M.; Casarosa, G.; Cervelli, A.; Forti, F.; Giorgi, M. A.; Lusiani, A.; Neri, N.; Paoloni, E.; Rizzo, G.; Walsh, J. J.; Lopes Pegna, D.; Lu, C.; Olsen, J.; Smith, A. J. S.; Telnov, A. V.; Anulli, F.; Baracchini, E.; Cavoto, G.; Faccini, R.; Ferrarotto, F.; Ferroni, F.; Gaspero, M.; Li Gioi, L.; Mazzoni, M. A.; Piredda, G.; Renga, F.; Hartmann, T.; Leddig, T.; Schröder, H.; Waldi, R.; Adye, T.; Franek, B.; Olaiya, E. O.; Wilson, F. F.; Emery, S.; Hamel de Monchenault, G.; Vasseur, G.; Yèche, Ch.; Zito, M.; Allen, M. T.; Aston, D.; Bard, D. J.; Bartoldus, R.; Benitez, J. F.; Cartaro, C.; Convery, M. R.; Dorfan, J.; Dubois-Felsmann, G. P.; Dunwoodie, W.; Field, R. C.; Franco Sevilla, M.; Fulsom, B. G.; Gabareen, A. M.; Graham, M. T.; Grenier, P.; Hast, C.; Innes, W. R.; Kelsey, M. H.; Kim, H.; Kim, P.; Kocian, M. L.; Leith, D. W. G. S.; Li, S.; Lindquist, B.; Luitz, S.; Luth, V.; Lynch, H. L.; Macfarlane, D. B.; Marsiske, H.; Muller, D. R.; Neal, H.; Nelson, S.; O'Grady, C. P.; Ofte, I.; Perl, M.; Pulliam, T.; Ratcliff, B. N.; Roodman, A.; Salnikov, A. A.; Santoro, V.; Schindler, R. H.; Schwiening, J.; Snyder, A.; Su, D.; Sullivan, M. K.; Sun, S.; Suzuki, K.; Thompson, J. M.; Va'Vra, J.; Wagner, A. P.; Weaver, M.; Wisniewski, W. J.; Wittgen, M.; Wright, D. H.; Wulsin, H. W.; Yarritu, A. K.; Young, C. C.; Ziegler, V.; Chen, X. R.; Park, W.; Purohit, M. V.; White, R. M.; Wilson, J. R.; Randle-Conde, A.; Sekula, S. J.; Bellis, M.; Burchat, P. R.; Miyashita, T. S.; Ahmed, S.; Alam, M. S.; Ernst, J. A.; Pan, B.; Saeed, M. A.; Zain, S. B.; Guttman, N.; Soffer, A.; Lund, P.; Spanier, S. M.; Eckmann, R.; Ritchie, J. L.; Ruland, A. M.; Schilling, C. J.; Schwitters, R. F.; Wray, B. C.; Izen, J. M.; Lou, X. C.; Bianchi, F.; Gamba, D.; Pelliccioni, M.; Bomben, M.; Lanceri, L.; Vitale, L.; Lopez-March, N.; Martinez-Vidal, F.; Oyanguren, A.; Albert, J.; Banerjee, Sw.; Choi, H. H. F.; Hamano, K.; King, G. J.; Kowalewski, R.; Lewczuk, M. J.; Lindsay, C.; Nugent, I. M.; Roney, J. M.; Sobie, R. J.; Gershon, T. J.; Harrison, P. F.; Latham, T. E.; Pennington, M. R.; Puccio, E. M. T.; Band, H. R.; Dasu, S.; Flood, K. T.; Pan, Y.; Prepost, R.; Vuosalo, C. O.; Wu, S. L.

2011-03-01

We perform a Dalitz plot analysis of about 100 000 Ds+ decays to K+K-π+ and measure the complex amplitudes of the intermediate resonances which contribute to this decay mode. We also measure the relative branching fractions of Ds+→K+K+π- and Ds+→K+K+K-. For this analysis we use a 384 fb-1 data sample, recorded by the BABAR detector at the PEP-II asymmetric-energy e+e- collider running at center-of-mass energies near 10.58 GeV.

Clouds and the Earth's Radiant Energy System (CERES) Visualization Single Satellite Footprint (SSF) Plot Generator

NASA Technical Reports Server (NTRS)

Barsi, Julia A.

1995-01-01

The first Clouds and the Earth's Radiant Energy System (CERES) instrument will be launched in 1997 to collect data on the Earth's radiation budget. The data retrieved from the satellite will be processed through twelve subsystems. The Single Satellite Footprint (SSF) plot generator software was written to assist scientists in the early stages of CERES data analysis, producing two-dimensional plots of the footprint radiation and cloud data generated by one of the subsystems. Until the satellite is launched, however, software developers need verification tools to check their code. This plot generator will aid programmers by geolocating algorithm result on a global map.

Why fibrous proteins are romantic.

PubMed

Cohen, C

1998-01-01

Here I give a personal account of the great history of fibrous protein structure. I describe how Astbury first recognized the essential simplicity of fibrous proteins and their paradigmatic role in protein structure. The poor diffraction patterns yielded by these proteins were then deciphered by Pauling, Crick, Ramachandran and others (in part by model building) to reveal alpha-helical coiled coils, beta-sheets, and the collagen triple helical coiled coil-all characterized by different local sequence periodicities. Longer-range sequence periodicities (or "magic numbers") present in diverse fibrous proteins, such as collagen, tropomyosin, paramyosin, myosin, and were then shown to account for the characteristic axial repeats observed in filaments of these proteins. More recently, analysis of fibrous protein structure has been extended in many cases to atomic resolution, and some systems, such as "leucine zippers," are providing a deeper understanding of protein design than similar studies of globular proteins. In the last sections, I provide some dramatic examples of fibrous protein dynamics. One example is the so-called "spring-loaded" mechanism for viral fusion by the hemagglutinin protein of influenza. Another is the possible conformational changes in prion proteins, implicated in "mad cow disease," which may be related to similar transitions in a variety of globular and fibrous proteins. Copyright 1998 Academic Press.

PPII propensity of multiple-guest amino acids in a proline-rich environment.

PubMed

Moradi, Mahmoud; Babin, Volodymyr; Sagui, Celeste; Roland, Christopher

2011-07-07

There has been considerable debate about the intrinsic PPII propensity of amino acid residues in denatured polypeptides. Experimentally, this scale is based on the behavior of guest amino acid residues placed in the middle of proline-based hosts. We have used classical molecular dynamics simulations combined with replica-exchange methods to carry out a comprehensive analysis of the conformational equilibria of proline-based host oligopeptides with multiple guest amino acids including alanine, glutamine, valine, and asparagine. The tracked structural characteristics include the secondary structural motifs based on the Ramachandran angles and the cis/trans isomerization of the prolyl bonds. In agreement with our recent study of single amino acid guests, we did not observe an intrinsic PPII propensity in any of the guest amino acids in a multiple-guest setting. Instead, the experimental results can be explained in terms of (i) the steric restrictions imposed on the C-terminal guest amino acid that is immediately followed by a proline residue and (ii) an increase in the trans content of the prolyl bonds due to the presence of guest residues. In terms of the latter, we found that the more guests added to the system, the larger the increase in the trans content of the prolyl bonds, which results in an effective increase in the PPII content of the peptide.

Protocol for statistical analysis of vegetation changes at Catoctin Mountain Park

USGS Publications Warehouse

Hatfield, Jeff S.; Krafft, Cairn

2010-01-01

Vegetation data collected at Catoctin Mountain Park, Maryland, in a split-panel rotation design during 2004-2009 were analyzed for differences among three regions within the park and among years. Six plots were paired with plots fenced to exclude white-tailed deer (Odocoileus virginianus), and differences between open and exclosed plots were also investigated. Repeated measures analysis of variance (ANOVA) was used to test for differences in the following variables: percentage of twigs browsed, percentage of canopy cover, and number of tree and shrub seedlings in each of five height classes. Except for some differences in numbers of tree and shrub seedlings among height classes among the regions, no differences (P > 0.05) were found among the regions or over time in the variables measured. Recommendations for future sampling and analysis are discussed.

Investigation into the Use of Normal and Half-Normal Plots for Interpreting Results from Screening Experiments.

DTIC Science & Technology

1987-03-25

by Lloyd (1952) using generalized least squares instead of ordinary least squares, and by Wilk, % 20 Gnanadesikan , and Freeny (1963) using a maximum...plot. The half-normal distribution is a special case of the gamma distribution proposed by Wilk, Gnanadesikan , and Huyett (1962). VARIATIONS ON THE... Gnanadesikan , R. Probability plotting methods for the analysis of data. Biometrika, 1968, 55, 1-17. This paper describes and discusses graphical techniques

TEMPEST. Transient 3-D Thermal-Hydraulic

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eyler, L.L.

TEMPEST is a transient, three-dimensional, hydrothermal program that is designed to analyze a range of coupled fluid dynamic and heat transfer systems of particular interest to the Fast Breeder Reactor (FBR) thermal-hydraulic design community. The full three-dimensional, time-dependent equations of motion, continuity, and heat transport are solved for either laminar or turbulent fluid flow, including heat diffusion and generation in both solid and liquid materials. The equations governing mass, momentum, and energy conservation for incompressible flows and small density variations (Boussinesq approximation) are solved using finite-difference techniques. Analyses may be conducted in either cylindrical or Cartesian coordinate systems. Turbulence ismore » treated using a two-equation model. Two auxiliary plotting programs, SEQUEL and MANPLOT, for use with TEMPEST output are included. SEQUEL may be operated in batch or interactive mode; it generates data required for vector plots, contour plots of scalar quantities, line plots, grid and boundary plots, and time-history plots. MANPLOT reads the SEQUEL-generated data and creates the hardcopy plots. TEMPEST can be a valuable hydrothermal design analysis tool in areas outside the intended FBR thermal-hydraulic design community.« less

Response to commercial thinning in a 110-year-old Douglas-fir stand.

Treesearch

Richard L. Williamson

1982-01-01

During a 19-year period after a 110-year-old Douglas-fir stand was thinned, both standard plot compilations and stem analysis showed that growth of heavily and lightly thinned stands equaled growth of stands in control plots.

Use of recurrence plots in the analysis of pupil diameter dynamics in narcoleptics

NASA Astrophysics Data System (ADS)

Keegan, Andrew P.; Zbilut, J. P.; Merritt, S. L.; Mercer, P. J.

1993-11-01

Recurrence plots were used to evaluate pupil dynamics of subjects with narcolepsy. Preliminary data indicate that this nonlinear method of analyses may be more useful in revealing underlying deterministic differences than traditional methods like FFT and counting statistics.

Stocking, Forest Type, and Stand Size Class - The Southern Forest Inventory and Analysis Unit's Calculation of Three Important Stand Descriptors

Treesearch

Dennis M. May

1990-01-01

The procedures by which the Southern Forest Inventory and Analysis unit calculates stocking from tree data collected on inventory sample plots are described in this report. Stocking is then used to ascertain two other important stand descriptors: forest type and stand size class. Inventory data for three plots from the recently completed 1989 Tennessee survey are used...

Opinions on Suicide and Perceived Barriers to Care in a Sample of United States Marine Non-Commissioned Officers: Implications for Future Frontline Supervisors’ Suicide Prevention Training Programs

DTIC Science & Technology

2013-11-06

the Scree plot (Figure 3) and the analysis was repeated saving these four factors. The Kaiser - Meyer - Olkin measure of sampling adequacy was .95...the Scree plot (Figure 4) and the analysis was repeated saving these three factors. The Kaiser - Meyer - Olkin measure of sampling adequacy was .90, above

Gene features selection for three-class disease classification via multiple orthogonal partial least square discriminant analysis and S-plot using microarray data.

PubMed

Yang, Mingxing; Li, Xiumin; Li, Zhibin; Ou, Zhimin; Liu, Ming; Liu, Suhuan; Li, Xuejun; Yang, Shuyu

2013-01-01

DNA microarray analysis is characterized by obtaining a large number of gene variables from a small number of observations. Cluster analysis is widely used to analyze DNA microarray data to make classification and diagnosis of disease. Because there are so many irrelevant and insignificant genes in a dataset, a feature selection approach must be employed in data analysis. The performance of cluster analysis of this high-throughput data depends on whether the feature selection approach chooses the most relevant genes associated with disease classes. Here we proposed a new method using multiple Orthogonal Partial Least Squares-Discriminant Analysis (mOPLS-DA) models and S-plots to select the most relevant genes to conduct three-class disease classification and prediction. We tested our method using Golub's leukemia microarray data. For three classes with subtypes, we proposed hierarchical orthogonal partial least squares-discriminant analysis (OPLS-DA) models and S-plots to select features for two main classes and their subtypes. For three classes in parallel, we employed three OPLS-DA models and S-plots to choose marker genes for each class. The power of feature selection to classify and predict three-class disease was evaluated using cluster analysis. Further, the general performance of our method was tested using four public datasets and compared with those of four other feature selection methods. The results revealed that our method effectively selected the most relevant features for disease classification and prediction, and its performance was better than that of the other methods.

Using volcano plots and regularized-chi statistics in genetic association studies.

PubMed

Li, Wentian; Freudenberg, Jan; Suh, Young Ju; Yang, Yaning

2014-02-01

Labor intensive experiments are typically required to identify the causal disease variants from a list of disease associated variants in the genome. For designing such experiments, candidate variants are ranked by their strength of genetic association with the disease. However, the two commonly used measures of genetic association, the odds-ratio (OR) and p-value may rank variants in different order. To integrate these two measures into a single analysis, here we transfer the volcano plot methodology from gene expression analysis to genetic association studies. In its original setting, volcano plots are scatter plots of fold-change and t-test statistic (or -log of the p-value), with the latter being more sensitive to sample size. In genetic association studies, the OR and Pearson's chi-square statistic (or equivalently its square root, chi; or the standardized log(OR)) can be analogously used in a volcano plot, allowing for their visual inspection. Moreover, the geometric interpretation of these plots leads to an intuitive method for filtering results by a combination of both OR and chi-square statistic, which we term "regularized-chi". This method selects associated markers by a smooth curve in the volcano plot instead of the right-angled lines which corresponds to independent cutoffs for OR and chi-square statistic. The regularized-chi incorporates relatively more signals from variants with lower minor-allele-frequencies than chi-square test statistic. As rare variants tend to have stronger functional effects, regularized-chi is better suited to the task of prioritization of candidate genes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Quadrantal multi-scale distribution entropy analysis of heartbeat interval series based on a modified Poincaré plot

NASA Astrophysics Data System (ADS)

Huo, Chengyu; Huang, Xiaolin; Zhuang, Jianjun; Hou, Fengzhen; Ni, Huangjing; Ning, Xinbao

2013-09-01

The Poincaré plot is one of the most important approaches in human cardiac rhythm analysis. However, further investigations are still needed to concentrate on techniques that can characterize the dispersion of the points displayed by a Poincaré plot. Based on a modified Poincaré plot, we provide a novel measurement named distribution entropy (DE) and propose a quadrantal multi-scale distribution entropy analysis (QMDE) for the quantitative descriptions of the scatter distribution patterns in various regions and temporal scales. We apply this method to the heartbeat interval series derived from healthy subjects and congestive heart failure (CHF) sufferers, respectively, and find that the discriminations between them are most significant in the first quadrant, which implies significant impacts on vagal regulation brought about by CHF. We also investigate the day-night differences of young healthy people, and it is shown that the results present a clearly circadian rhythm, especially in the first quadrant. In addition, the multi-scale analysis indicates that the results of healthy subjects and CHF sufferers fluctuate in different trends with variation of the scale factor. The same phenomenon also appears in circadian rhythm investigations of young healthy subjects, which implies that the cardiac dynamic system is affected differently in various temporal scales by physiological or pathological factors.

Automatic contouring of geologic fabric and finite strain data on the unit hyperboloid

NASA Astrophysics Data System (ADS)

Vollmer, Frederick W.

2018-06-01

Fabric and finite strain analysis, an integral part of studies of geologic structures and orogenic belts, is commonly done by the analysis of particles whose shapes can be approximated as ellipses. Given a sample of such particles, the mean and confidence intervals of particular parameters can be calculated, however, taking the extra step of plotting and contouring the density distribution can identify asymmetries or modes related to sedimentary fabrics or other factors. A common graphical strain analysis technique is to plot final ellipse ratios, Rf , versus orientations, ϕf on polar Elliott or Rf / ϕ plots to examine the density distribution. The plot may be contoured, however, it is desirable to have a contouring method that is rapid, reproducible, and based on the underlying geometry of the data. The unit hyperboloid, H2 , gives a natural parameter space for two-dimensional strain, and various projections, including equal-area and stereographic, have useful properties for examining density distributions for anisotropy. An index, Ia , is given to quantify the magnitude and direction of anisotropy. Elliott and Rf / ϕ plots can be understood by applying hyperbolic geometry and recognizing them as projections of H2 . These both distort area, however, so the equal-area projection is preferred for examining density distributions. The algorithm presented here gives fast, accurate, and reproducible contours of density distributions calculated directly on H2 . The algorithm back-projects the data onto H2 , where the density calculation is done at regular nodes using a weighting value based on the hyperboloid distribution, which is then contoured. It is implemented as an Octave compatible MATLAB function that plots ellipse data using a variety of projections, and calculates and displays contours of their density distribution on H2 .

Scaling and the frequency dependence of Nyquist plot maxima of the electrical impedance of the human thigh.

PubMed

Shiffman, Carl

2017-11-30

To define and elucidate the properties of reduced-variable Nyquist plots. Non-invasive measurements of the electrical impedance of the human thigh. A retrospective analysis of the electrical impedances of 154 normal subjects measured over the past decade shows that 'scaling' of the Nyquist plots for human thigh muscles is a property shared by healthy thigh musculature, irrespective of subject and the length of muscle segment. Here the term scaling signifies the near and sometimes 'perfect' coalescence of the separate X versus R plots into one 'reduced' Nyquist plot by the simple expedient of dividing R and X by X m , the value of X at the reactance maximum. To the extent allowed by noise levels one can say that there is one 'universal' reduced Nyquist plot for the thigh musculature of healthy subjects. There is one feature of the Nyquist curves which is not 'universal', however, namely the frequency f m at which the maximum in X is observed. That is found to vary from 10 to 100 kHz. depending on subject and segment length. Analysis shows, however, that the mean value of 1/f m is an accurately linear function of segment length, though there is a small subject-to-subject random element as well. Also, following the recovery of an otherwise healthy victim of ankle fracture demonstrates the clear superiority of measurements above about 800 kHz, where scaling is not observed, in contrast to measurements below about 400 kHz, where scaling is accurately obeyed. The ubiquity of 'scaling' casts new light on the interpretation of impedance results as they are used in electrical impedance myography and bioelectric impedance analysis.

US army land condition-trend analysis (LCTA) program

NASA Astrophysics Data System (ADS)

Diersing, Victor E.; Shaw, Robert B.; Tazik, David J.

1992-05-01

The US Army Land Condition-Trend Analysis (LCTA) program is a standardized method of data collection, analysis, and reporting designed to meet multiple goals and objectives. The method utilizes vascular plant inventories, permanent field plot data, and wildlife inventories. Vascular plant inventories are used for environmental documentation, training of personnel, species identification during LCTA implementation, and as a survey for state and federal endangered or threatened species. The permanent field plot data documents the vegetational, edaphic, topographic, and disturbance characteristics of the installation. Inventory plots are allocated in a stratified random fashion across the installation utilizing a geographic information system that integrates satellite imagery and soil survey information. Ground cover, canopy cover, woody plant density, slope length, slope gradient, soil information, and disturbance data are collected at each plot. Plot data are used to: (1) describe plant communities, (2) characterize wildlife and threatened and endangered species habitat, (3) document amount and kind of military and nonmilitary disturbance, (4) determine the impact of military training on vegetation and soil resources, (5) estimate soil erosion potential, (6) classify land as to the kind and amount of use it can support, (7) determine allowable use estimates for tracked vehicle training, (8) document concealment resources, (9) identify lands that require restoration and evaluate the effectiveness of restorative techniques, and (10) evaluate potential acquisition property. Wildlife inventories survey small and midsize mammals, birds, bats, amphibians, and reptiles. Data from these surveys can be used for environmental documentation, to identify state and federal endangered and threatened species, and to evaluate the impact of military activities on wildlife populations. Short- and long-term monitoring of permanent field plots is used to evaluate and adjust land management decisions.

Music-colour synaesthesia: Concept, context and qualia.

PubMed

Curwen, Caroline

2018-05-01

This review provides a commentary on coloured-hearing arising on hearing music: music-colour synaesthesia. Although traditionally explained by the hyperconnectivity theory (Ramachandran & Hubbard, 2001a) and the disinhibited feedback theory (Grossenbacher & Lovelace, 2001) as a purely perceptual phenomenon, the review of eight coloured-hearing neuroimaging studies shows that it may not be assumed that these explanations are directly translatable to music-colour synaesthesia. The concept of 'ideaesthesia' (Nikolić, 2009) and the role of conceptual and semantic inducers challenge the likelihood of a single mechanism underlying the cause of synaesthesia and argue for a move away from a purely sensory to sensory explanation. Finally, music-colour synaesthesia forms a challenge for established philosophical theories and the position of synaesthesia is considered within the larger context of musical qualia. Copyright © 2018 Elsevier Inc. All rights reserved.

Quantum calculations of the rate constant for the O(3P)+HCl reaction on new ab initio 3A″ and 3A' surfaces

NASA Astrophysics Data System (ADS)

Xie, Tiao; Bowman, Joel M.; Peterson, K. A.; Ramachandran, B.

2003-11-01

We report the thermal rate constant of the O(3P)+HCl→OH+Cl reaction calculated from 200 to 3200 K, using new fits to extensive ab initio calculations [B. Ramachandran and K. A. Peterson, J. Chem. Phys. 119, 9590 (2003), preceding paper]. The rate constants are obtained for both the 3A″ and 3A' surfaces using exact quantum reactive scattering calculations for selected values of the total angular momentum and the J-shifting approximation for both the 3A″ and 3A' surfaces. The results are compared with the ICVT/μOMT rate constants calculated by the POLYRATE program and all available experimental data. Other related high-energy reaction channels are also studied qualitatively for their contribution to the total thermal rate constant at high temperature.

Carnage interrupted : an analysis of fifteen terrorist plots against public surface transportation.

DOT National Transportation Integrated Search

2012-04-01

This report examines 13 terrorist plots against public surface transportation that were uncovered and foiled by authorities between 1997 and 2010 and two failed attempts to carry out attacks. Certainly, this is not the total universe of foiled or fai...

The Tendril Plot-a novel visual summary of the incidence, significance and temporal aspects of adverse events in clinical trials.

PubMed

Karpefors, Martin; Weatherall, James

2018-03-21

In contrast to efficacy, safety hypotheses of clinical trials are not always pre-specified, and therefore, the safety interpretation work of a trial tends to be more exploratory, often reactive, and the analysis more statistically and graphically challenging. We introduce a new means of visualizing the adverse event data across an entire clinical trial. The approach overcomes some of the current limitations of adverse event analysis and streamlines the way safety data can be explored, interpreted and analyzed. Using a phase II study, we describe and exemplify how the tendril plot effectively summarizes the time-resolved safety profile of two treatment arms in a single plot and how that can provide scientists with a trial safety overview that can support medical decision making. To our knowledge, the tendril plot is the only way to graphically show important treatment differences with preserved temporal information, across an entire clinical trial, in a single view.

An investigation of wing buffeting response at subsonic and transonic speeds. Phase 1: F-111A flight data analysis. Volume 2: Plotted power spectra

NASA Technical Reports Server (NTRS)

Benepe, D. B.; Cunningham, A. M., Jr.; Dunmyer, W. D.

1978-01-01

Volume 2 of this three volume report is presented. This volume presents plotted variations of power spectral density data with frequency for each structural response item for each data sampled and analyzed during the course of the investigation. Some of the information contained in Volume 1 are repeated to allow the reader to identify the specific conditions appropriate to each plot presented and to interpret the data.

Recurrence Density Enhanced Complex Networks for Nonlinear Time Series Analysis

NASA Astrophysics Data System (ADS)

Costa, Diego G. De B.; Reis, Barbara M. Da F.; Zou, Yong; Quiles, Marcos G.; Macau, Elbert E. N.

We introduce a new method, which is entitled Recurrence Density Enhanced Complex Network (RDE-CN), to properly analyze nonlinear time series. Our method first transforms a recurrence plot into a figure of a reduced number of points yet preserving the main and fundamental recurrence properties of the original plot. This resulting figure is then reinterpreted as a complex network, which is further characterized by network statistical measures. We illustrate the computational power of RDE-CN approach by time series by both the logistic map and experimental fluid flows, which show that our method distinguishes different dynamics sufficiently well as the traditional recurrence analysis. Therefore, the proposed methodology characterizes the recurrence matrix adequately, while using a reduced set of points from the original recurrence plots.

Cu, Zn and Mn uptake and redistribution in Cabernet Sauvignon grapes and wine: effect of soil metal content and plant vigor

NASA Astrophysics Data System (ADS)

Concepción Ramos, Maria; Romero, María Paz

2015-04-01

This study investigated the influence of leaf thinning on micronutrient (Cu, Zn and Mn) uptake and distribution in grape tissues, in a 16 year-old Cabernet Sauvignon vineyard. The analysis was carried out in two plots with differences in vigor (P1- high and P2-low) grown in calcareous soils. Vigour was analysed by the NDVI values. In each plot, two treatments (with and without leaf thinning after bloom) were applied. Total and the CaCl2-DTPA extractable fraction of these micronutrients were evaluated. Nutrient concentration in petiole were evaluated from veraison to harvest as well as the concentration of those elements in seeds and skins at ripening and in wines elaborated with grapes grown in each plot and treatment in 2013. Their relationships were evaluated. The soil extractable fraction did not give a good correlation with petiole concentrations. However, Mn in petiole was strongly correlated with soil total Mn. Cu and Zn had higher concentration at veraison than at harvest, while for Mn it was the opposite. Cu concentration in petiole and seeds was greater in the most vigorous plots, but there were not clear differences between treatments. Cu in seeds and skins correlated significantly but there was not correlation with Cu in petiole. Zn concentration in skins was quite similar in both plots, but with higher values in vines without leaf thinning. Zn concentrations in skins were correlated with Zn in petiole but no significant correlation was found with Zn in seeds. Higher concentrations were found in the no thinning treatment in skins. For Mn, petiole concentrations were greater in the high vigorous plot and in the leaf thinning treatment. However, petiole Zn concentrations were greater in the less vigorous plot and without clear effect of leaf thinning. Mn concentration in skins was greater in the less vigorous vines in both treatments and it was inversely correlated with Mn in seeds, but there were no significant correlation between them and Mn in petiole. In wine, significant differences between both plots were found for Cu and Zn, with greater values in the most vigorous vines and with some differences in the wines elaborated with grapes from the leaf thinning treatment and without it. Cu levels in wine ranged between 0.78 and 0.96 mg/l in plot 1 and between 0.28 and 0.44 mg/L in plot 2, respectively for the areas with and without leaf thinning. For Zn, levels ranged between 0.76 and 0.74 in plot 1and between 0.24 and 0.22 mg/L in plot 2. However, no differences were found between plots for Mn. Mn levels in wine ranged between 1 and 1.9 mg/L in plot 1 and between 1.12 and 1.2 mg/L in plot 2. This behavior was similar to that found in the skins and seed analysis.

Software Aids In Graphical Depiction Of Flow Data

NASA Technical Reports Server (NTRS)

Stegeman, J. D.

1995-01-01

Interactive Data Display System (IDDS) computer program is graphical-display program designed to assist in visualization of three-dimensional flow in turbomachinery. Grid and simulation data files in PLOT3D format required for input. Able to unwrap volumetric data cone associated with centrifugal compressor and display results in easy-to-understand two- or three-dimensional plots. IDDS provides majority of visualization and analysis capability for Integrated Computational Fluid Dynamics and Experiment (ICE) system. IDDS invoked from any subsystem, or used as stand-alone package of display software. Generates contour, vector, shaded, x-y, and carpet plots. Written in C language. Input file format used by IDDS is that of PLOT3D (COSMIC item ARC-12782).

Generic Space Science Visualization in 2D/3D using SDDAS

NASA Astrophysics Data System (ADS)

Mukherjee, J.; Murphy, Z. B.; Gonzalez, C. A.; Muller, M.; Ybarra, S.

2017-12-01

The Southwest Data Display and Analysis System (SDDAS) is a flexible multi-mission / multi-instrument software system intended to support space physics data analysis, and has been in active development for over 20 years. For the Magnetospheric Multi-Scale (MMS), Juno, Cluster, and Mars Express missions, we have modified these generic tools for visualizing data in two and three dimensions. The SDDAS software is open source and makes use of various other open source packages, including VTK and Qwt. The software offers interactive plotting as well as a Python and Lua module to modify the data before plotting. In theory, by writing a Lua or Python module to read the data, any data could be used. Currently, the software can natively read data in IDFS, CEF, CDF, FITS, SEG-Y, ASCII, and XLS formats. We have integrated the software with other Python packages such as SPICE and SpacePy. Included with the visualization software is a database application and other utilities for managing data that can retrieve data from the Cluster Active Archive and Space Physics Data Facility at Goddard, as well as other local archives. Line plots, spectrograms, geographic, volume plots, strip charts, etc. are just some of the types of plots one can generate with SDDAS. Furthermore, due to the design, output is not limited to strictly visualization as SDDAS can also be used to generate stand-alone IDL or Python visualization code.. Lastly, SDDAS has been successfully used as a backend for several web based analysis systems as well.

Metaplot: A Novel Stata Graph for Assessing Heterogeneity at a Glance

PubMed Central

Poorolajal, J; Mahmoodi, M; Majdzadeh, R; Fotouhi, A

2010-01-01

Background: Heterogeneity is usually a major concern in meta-analysis. Although there are some statistical approaches for assessing variability across studies, here we present a new approach to heterogeneity using “MetaPlot” that investigate the influence of a single study on the overall heterogeneity. Methods: MetaPlot is a two-way (x, y) graph, which can be considered as a complementary graphical approach for testing heterogeneity. This method shows graphically as well as numerically the results of an influence analysis, in which Higgins’ I2 statistic with 95% (Confidence interval) CI are computed omitting one study in each turn and then are plotted against reciprocal of standard error (1/SE) or “precision”. In this graph, “1/SE” lies on x axis and “I2 results” lies on y axe. Results: Having a first glance at MetaPlot, one can predict to what extent omission of a single study may influence the overall heterogeneity. The precision on x-axis enables us to distinguish the size of each trial. The graph describes I2 statistic with 95% CI graphically as well as numerically in one view for prompt comparison. It is possible to implement MetaPlot for meta-analysis of different types of outcome data and summary measures. Conclusion: This method presents a simple graphical approach to identify an outlier and its effect on overall heterogeneity at a glance. We wish to suggest MetaPlot to Stata experts to prepare its module for the software. PMID:23113013

Polar plot representation of time-resolved fluorescence.

PubMed

Eichorst, John Paul; Wen Teng, Kai; Clegg, Robert M

2014-01-01

Measuring changes in a molecule's fluorescence emission is a common technique to study complex biological systems such as cells and tissues. Although the steady-state fluorescence intensity is frequently used, measuring the average amount of time that a molecule spends in the excited state (the fluorescence lifetime) reveals more detailed information about its local environment. The lifetime is measured in the time domain by detecting directly the decay of fluorescence following excitation by short pulse of light. The lifetime can also be measured in the frequency domain by recording the phase and amplitude of oscillation in the emitted fluorescence of the sample in response to repetitively modulated excitation light. In either the time or frequency domain, the analysis of data to extract lifetimes can be computationally intensive. For example, a variety of iterative fitting algorithms already exist to determine lifetimes from samples that contain multiple fluorescing species. However, recently a method of analysis referred to as the polar plot (or phasor plot) is a graphical tool that projects the time-dependent features of the sample's fluorescence in either the time or frequency domain into the Cartesian plane to characterize the sample's lifetime. The coordinate transformations of the polar plot require only the raw data, and hence, there are no uncertainties from extensive corrections or time-consuming fitting in this analysis. In this chapter, the history and mathematical background of the polar plot will be presented along with examples that highlight how it can be used in both cuvette-based and imaging applications.

Carnage interrupted : an analysis of fifteen terrorist plots against public surface transportation [research brief].

DOT National Transportation Integrated Search

2012-04-01

Since 1997, terrorists have focused much attention on public surface transportation as a target for attacks. Many of the plots have failed or been foiled, but those that have succeeded have resulted in large numbers of casualties and caused widesprea...

Cycles till failure of silver-zinc cells with completing failures modes: Preliminary data analysis

NASA Technical Reports Server (NTRS)

Sidik, S. M.; Leibecki, H. F.; Bozek, J. M.

1980-01-01

One hundred and twenty nine cells were run through charge-discharge cycles until failure. The experiment design was a variant of a central composite factorial in five factors. Preliminary data analysis consisted of response surface estimation of life. Batteries fail under two basic modes; a low voltage condition and an internal shorting condition. A competing failure modes analysis using maximum likelihood estimation for the extreme value life distribution was performed. Extensive diagnostics such as residual plotting and probability plotting were employed to verify data quality and choice of model.

An improved multiple linear regression and data analysis computer program package

NASA Technical Reports Server (NTRS)

Sidik, S. M.

1972-01-01

NEWRAP, an improved version of a previous multiple linear regression program called RAPIER, CREDUC, and CRSPLT, allows for a complete regression analysis including cross plots of the independent and dependent variables, correlation coefficients, regression coefficients, analysis of variance tables, t-statistics and their probability levels, rejection of independent variables, plots of residuals against the independent and dependent variables, and a canonical reduction of quadratic response functions useful in optimum seeking experimentation. A major improvement over RAPIER is that all regression calculations are done in double precision arithmetic.

A Review on the Nonlinear Dynamical System Analysis of Electrocardiogram Signal

PubMed Central

Mohapatra, Biswajit

2018-01-01

Electrocardiogram (ECG) signal analysis has received special attention of the researchers in the recent past because of its ability to divulge crucial information about the electrophysiology of the heart and the autonomic nervous system activity in a noninvasive manner. Analysis of the ECG signals has been explored using both linear and nonlinear methods. However, the nonlinear methods of ECG signal analysis are gaining popularity because of their robustness in feature extraction and classification. The current study presents a review of the nonlinear signal analysis methods, namely, reconstructed phase space analysis, Lyapunov exponents, correlation dimension, detrended fluctuation analysis (DFA), recurrence plot, Poincaré plot, approximate entropy, and sample entropy along with their recent applications in the ECG signal analysis. PMID:29854361

A Review on the Nonlinear Dynamical System Analysis of Electrocardiogram Signal.

PubMed

Nayak, Suraj K; Bit, Arindam; Dey, Anilesh; Mohapatra, Biswajit; Pal, Kunal

2018-01-01

Electrocardiogram (ECG) signal analysis has received special attention of the researchers in the recent past because of its ability to divulge crucial information about the electrophysiology of the heart and the autonomic nervous system activity in a noninvasive manner. Analysis of the ECG signals has been explored using both linear and nonlinear methods. However, the nonlinear methods of ECG signal analysis are gaining popularity because of their robustness in feature extraction and classification. The current study presents a review of the nonlinear signal analysis methods, namely, reconstructed phase space analysis, Lyapunov exponents, correlation dimension, detrended fluctuation analysis (DFA), recurrence plot, Poincaré plot, approximate entropy, and sample entropy along with their recent applications in the ECG signal analysis.

A new improved graphical and quantitative method for detecting bias in meta-analysis.

PubMed

Furuya-Kanamori, Luis; Barendregt, Jan J; Doi, Suhail A R

2018-04-04

Detection of publication and related biases remains suboptimal and threatens the validity and interpretation of meta-analytical findings. When bias is present, it usually differentially affects small and large studies manifesting as an association between precision and effect size and therefore visual asymmetry of conventional funnel plots. This asymmetry can be quantified and Egger's regression is, by far, the most widely used statistical measure for quantifying funnel plot asymmetry. However, concerns have been raised about both the visual appearance of funnel plots and the sensitivity of Egger's regression to detect such asymmetry, particularly when the number of studies is small. In this article, we propose a new graphical method, the Doi plot, to visualize asymmetry and also a new measure, the LFK index, to detect and quantify asymmetry of study effects in Doi plots. We demonstrate that the visual representation of asymmetry was better for the Doi plot when compared with the funnel plot. We also show that the diagnostic accuracy of the LFK index in discriminating between asymmetry due to simulated publication bias versus chance or no asymmetry was also better with the LFK index which had areas under the receiver operating characteristic curve of 0.74-0.88 with simulations of meta-analyses with five, 10, 15, and 20 studies. The Egger's regression result had lower areas under the receiver operating characteristic curve values of 0.58-0.75 across the same simulations. The LFK index also had a higher sensitivity (71.3-72.1%) than the Egger's regression result (18.5-43.0%). We conclude that the methods proposed in this article can markedly improve the ability of researchers to detect bias in meta-analysis.

Poincaré plot indexes of heart rate variability detect dynamic autonomic modulation during general anesthesia induction.

PubMed

Hsu, Che-Hao; Tsai, Ming-Ya; Huang, Go-Shine; Lin, Tso-Chou; Chen, Kuen-Pao; Ho, Shung-Tai; Shyu, Liang-Yu; Li, Chi-Yuan

2012-03-01

Beat-to-beat heart rate variability (HRV) is caused by the fluctuating balance of sympathetic and parasympathetic tone. The Poincaré plot has been used to evaluate HRV. In this study, we validate that this new method may qualitatively and quantitatively assess the sympathovagal fluctuation in patients during induction of anesthesia with sevoflurane. Twenty-eight young patients were allocated for the study. The patients received a tilt test and on the next day they sustained anesthesia induced with inhaled anesthetics. Electrocardiography signals from the patients were relayed to an analogue-digital converter. The Poincaré plot is quantified by measuring SD1, SD2, and SD1/SD2. Power spectral analyses were performed and LF, HF and HF/LF were calculated. The LF power and the SD2 of the Poincaré plot increased while subjects were tilt-up from the supine position. Additionally, a significant correlation were found between LF and SD2, HF and SD1 (p < 0.05), and LF/HF and SD2/SD1 (p < 0.01). Sevoflurane inhalation for 10 minutes had no effect on heart rate, but diminished LF, total power and SD1, SD2 of the Poincaré plot respectively. However, the LF, SD2 and LF/HF increased; the HF, SD1 and SD1/SD2 ratio decreased after intubation stimulation. Poincaré plot and power spectral analysis of HRV during tilt test and sevoflurane induction significantly correlate. Poincaré plot analysis is easier and more sensitive at evaluating the sympathovagal balance and observing the beat-to-beat HRV. Copyright © 2012. Published by Elsevier B.V.

How Does Gender Affect Sustainable Intensification of Cereal Production in the West African Sahel? Evidence from Burkina Faso.

PubMed

Theriault, Veronique; Smale, Melinda; Haider, Hamza

2017-04-01

Better understanding of gender differences in the adoption of agricultural intensification strategies is crucial for designing effective policies to close the gender gap while sustainably enhancing farm productivity. We examine gender differences in adoption rates, likelihood and determinants of adopting strategy sets that enhance yields, protect crops, and restore soils in the West African Sahel, based on analysis of cereal production in Burkina Faso. Applying a multivariate probit model to a nationally representative household panel, we exploit the individual plot as unit of analysis and control for plot manager characteristics along with other covariates. Reflecting the socio-cultural context of farming combined with the economic attributes of inputs, we find that female managers of individual cereal fields are less likely than their male counterparts to adopt yield-enhancing and soil-restoring strategies, although no differential is apparent for yield-protecting strategies. More broadly, gender-disaggregated regressions demonstrate that adoption determinants differ by gender. Plot manager characteristics, including age, marital status, and access to credit or extension services do influence adoption decisions. Furthermore, household resources influence the probability of adopting intensification strategy sets differently by gender of the plot manager. Variables expressing the availability of household labor strongly influence the adoption of soil-restoring strategies by female plot managers. By contrast, household resources such as extent of livestock owned, value of non-farm income, and area planted to cotton affect the adoption choices of male plot managers. Rectifying the male bias in extension services along with improving access to credit, income, and equipment to female plot managers could contribute to sustainable agricultural intensification.

Does tree diversity increase wood production in pine forests?

PubMed

Vilà, Montserrat; Vayreda, Jordi; Gracia, Carles; Ibáñez, Joan Josep

2003-04-01

Recent experimental advances on the positive effect of species richness on ecosystem productivity highlight the need to explore this relationship in communities other than grasslands and using non-synthetic experiments. We investigated whether wood production in forests dominated by Aleppo pine (Pinus halepensis) and Pyrenean Scots pine (Pinus sylvestris) differed between monospecific and mixed forests (2-5 species) using the Ecological and Forest Inventory of Catalonia (IEFC) database which contains biotic and environmental characteristics for 10,644 field plots distributed within a 31,944 km(2) area in Catalonia (NE Spain). We found that in Pyrenean Scots pine forests wood production was not significantly different between monospecific and mixed plots. In contrast, in Aleppo pine forests wood production was greater in mixed plots than in monospecific plots. However, when climate, bedrock types, radiation and successional stage per plot were included in the analysis, species richness was no longer a significant factor. Aleppo pine forests had the highest productivity in plots located in humid climates and on marls and sandstone bedrocks. Climate did not influence wood production in Pyrenean Scots pine forests, but it was highest on sandstone and consolidated alluvial materials. For both pine forests wood production was negatively correlated with successional stage. Radiation did not influence wood production. Our analysis emphasizes the influence of macroenvironmental factors and temporal variation on tree productivity at the regional scale. Well-conducted forest surveys are an excellent source of data to test for the association between diversity and productivity driven by large-scale environmental factors.

Problems with sampling desert tortoises: A simulation analysis based on field data

USGS Publications Warehouse

Freilich, J.E.; Camp, R.J.; Duda, J.J.; Karl, A.E.

2005-01-01

The desert tortoise (Gopherus agassizii) was listed as a U.S. threatened species in 1990 based largely on population declines inferred from mark-recapture surveys of 2.59-km2 (1-mi2) plots. Since then, several census methods have been proposed and tested, but all methods still pose logistical or statistical difficulties. We conducted computer simulations using actual tortoise location data from 2 1-mi2 plot surveys in southern California, USA, to identify strengths and weaknesses of current sampling strategies. We considered tortoise population estimates based on these plots as "truth" and then tested various sampling methods based on sampling smaller plots or transect lines passing through the mile squares. Data were analyzed using Schnabel's mark-recapture estimate and program CAPTURE. Experimental subsampling with replacement of the 1-mi2 data using 1-km2 and 0.25-km2 plot boundaries produced data sets of smaller plot sizes, which we compared to estimates from the 1-mi 2 plots. We also tested distance sampling by saturating a 1-mi 2 site with computer simulated transect lines, once again evaluating bias in density estimates. Subsampling estimates from 1-km2 plots did not differ significantly from the estimates derived at 1-mi2. The 0.25-km2 subsamples significantly overestimated population sizes, chiefly because too few recaptures were made. Distance sampling simulations were biased 80% of the time and had high coefficient of variation to density ratios. Furthermore, a prospective power analysis suggested limited ability to detect population declines as high as 50%. We concluded that poor performance and bias of both sampling procedures was driven by insufficient sample size, suggesting that all efforts must be directed to increasing numbers found in order to produce reliable results. Our results suggest that present methods may not be capable of accurately estimating desert tortoise populations.

FIAMODEL: Users Guide Version 3.0.

Treesearch

Scott A. Pugh; David D. Reed; Kurt S. Pregitzer; Patrick D. Miles

2002-01-01

FIAMODEL is a geographic information system (GIS program used to summarize Forest Inventory and Analysis (FIA, USDA Forest Service) data such as volume. The model runs in ArcView and allows users to select FIA plots with heads-up-digitizing, overlays of digital map layers, or queries based on specific plot attributes.

Narrative Performance in Verbally Gifted Children.

ERIC Educational Resources Information Center

Porath, Marion

1996-01-01

Comparison of 14 verbally gifted 6-year olds with equal numbers of chronological-age and mental-age controls using a structural-developmental analysis found that the gifted children organized story plots in ways typical of children 2 years older, elaborated on basic plot structures more than control groups, and demonstrated advanced language…

Computer Programs for Calculating and Plotting the Stability Characteristics of a Balloon Tethered in a Wind

NASA Technical Reports Server (NTRS)

Bennett, R. M.; Bland, S. R.; Redd, L. T.

1973-01-01

Computer programs for calculating the stability characteristics of a balloon tethered in a steady wind are presented. Equilibrium conditions, characteristic roots, and modal ratios are calculated for a range of discrete values of velocity for a fixed tether-line length. Separate programs are used: (1) to calculate longitudinal stability characteristics, (2) to calculate lateral stability characteristics, (3) to plot the characteristic roots versus velocity, (4) to plot the characteristic roots in root-locus form, (5) to plot the longitudinal modes of motion, and (6) to plot the lateral modes for motion. The basic equations, program listings, and the input and output data for sample cases are presented, with a brief discussion of the overall operation and limitations. The programs are based on a linearized, stability-derivative type of analysis, including balloon aerodynamics, apparent mass, buoyancy effects, and static forces which result from the tether line.

Toward a clearer portrayal of confounding bias in instrumental variable applications.

PubMed

Jackson, John W; Swanson, Sonja A

2015-07-01

Recommendations for reporting instrumental variable analyses often include presenting the balance of covariates across levels of the proposed instrument and levels of the treatment. However, such presentation can be misleading as relatively small imbalances among covariates across levels of the instrument can result in greater bias because of bias amplification. We introduce bias plots and bias component plots as alternative tools for understanding biases in instrumental variable analyses. Using previously published data on proposed preference-based, geography-based, and distance-based instruments, we demonstrate why presenting covariate balance alone can be problematic, and how bias component plots can provide more accurate context for bias from omitting a covariate from an instrumental variable versus non-instrumental variable analysis. These plots can also provide relevant comparisons of different proposed instruments considered in the same data. Adaptable code is provided for creating the plots.

MID Plot: a new lithology technique. [Matrix identification plot

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clavier, C.; Rust, D.H.

1976-01-01

Lithology interpretation by the Litho-Porosity (M-N) method has been used for years, but is evidently too cumbersome and ambiguous for widespread acceptance as a field technique. To set aside these objections, another method has been devised. Instead of the log-derived parameters M and N, the MID Plot uses quasi-physical quantities, (rho/sub ma/)/sub a/ and (..delta..t/sub ma/)/sub a/, as its porosity-independent variables. These parameters, taken from suitably scaled Neutron-Density and Sonic-Neutron crossplots, define a unique matrix mineral or mixture for each point on the logs. The matrix points on the MID Plot thus remain constant in spite of changes in mudmore » filtrate, porosity, or neutron tool types (all of which significantly affect the M-N Plot). This new development is expected to bring welcome relief in areas where lithology identification is a routine part of log analysis.« less

SpectraPLOT, Visualization Package with a User-Friendly Graphical Interface

NASA Astrophysics Data System (ADS)

Sebald, James; Macfarlane, Joseph; Golovkin, Igor

2017-10-01

SPECT3D is a collisional-radiative spectral analysis package designed to compute detailed emission, absorption, or x-ray scattering spectra, filtered images, XRD signals, and other synthetic diagnostics. The spectra and images are computed for virtual detectors by post-processing the results of hydrodynamics simulations in 1D, 2D, and 3D geometries. SPECT3D can account for a variety of instrumental response effects so that direct comparisons between simulations and experimental measurements can be made. SpectraPLOT is a user-friendly graphical interface for viewing a wide variety of results from SPECT3D simulations, and applying various instrumental effects to the simulated images and spectra. We will present SpectraPLOT's ability to display a variety of data, including spectra, images, light curves, streaked spectra, space-resolved spectra, and drilldown plasma property plots, for an argon-doped capsule implosion experiment example. Future SpectraPLOT features and enhancements will also be discussed.

Identifying treatment effect heterogeneity in clinical trials using subpopulations of events: STEPP.

PubMed

Lazar, Ann A; Bonetti, Marco; Cole, Bernard F; Yip, Wai-Ki; Gelber, Richard D

2016-04-01

Investigators conducting randomized clinical trials often explore treatment effect heterogeneity to assess whether treatment efficacy varies according to patient characteristics. Identifying heterogeneity is central to making informed personalized healthcare decisions. Treatment effect heterogeneity can be investigated using subpopulation treatment effect pattern plot (STEPP), a non-parametric graphical approach that constructs overlapping patient subpopulations with varying values of a characteristic. Procedures for statistical testing using subpopulation treatment effect pattern plot when the endpoint of interest is survival remain an area of active investigation. A STEPP analysis was used to explore patterns of absolute and relative treatment effects for varying levels of a breast cancer biomarker, Ki-67, in the phase III Breast International Group 1-98 randomized clinical trial, comparing letrozole to tamoxifen as adjuvant therapy for postmenopausal women with hormone receptor-positive breast cancer. Absolute treatment effects were measured by differences in 4-year cumulative incidence of breast cancer recurrence, while relative effects were measured by the subdistribution hazard ratio in the presence of competing risks using O-E (observed-minus-expected) methodology, an intuitive non-parametric method. While estimation of hazard ratio values based on O-E methodology has been shown, a similar development for the subdistribution hazard ratio has not. Furthermore, we observed that the subpopulation treatment effect pattern plot analysis may not produce results, even with 100 patients within each subpopulation. After further investigation through simulation studies, we observed inflation of the type I error rate of the traditional test statistic and sometimes singular variance-covariance matrix estimates that may lead to results not being produced. This is due to the lack of sufficient number of events within the subpopulations, which we refer to as instability of the subpopulation treatment effect pattern plot analysis. We introduce methodology designed to improve stability of the subpopulation treatment effect pattern plot analysis and generalize O-E methodology to the competing risks setting. Simulation studies were designed to assess the type I error rate of the tests for a variety of treatment effect measures, including subdistribution hazard ratio based on O-E estimation. This subpopulation treatment effect pattern plot methodology and standard regression modeling were used to evaluate heterogeneity of Ki-67 in the Breast International Group 1-98 randomized clinical trial. We introduce methodology that generalizes O-E methodology to the competing risks setting and that improves stability of the STEPP analysis by pre-specifying the number of events across subpopulations while controlling the type I error rate. The subpopulation treatment effect pattern plot analysis of the Breast International Group 1-98 randomized clinical trial showed that patients with high Ki-67 percentages may benefit most from letrozole, while heterogeneity was not detected using standard regression modeling. The STEPP methodology can be used to study complex patterns of treatment effect heterogeneity, as illustrated in the Breast International Group 1-98 randomized clinical trial. For the subpopulation treatment effect pattern plot analysis, we recommend a minimum of 20 events within each subpopulation. © The Author(s) 2015.

Reproducible research in palaeomagnetism

NASA Astrophysics Data System (ADS)

Lurcock, Pontus; Florindo, Fabio

2015-04-01

The reproducibility of research findings is attracting increasing attention across all scientific disciplines. In palaeomagnetism as elsewhere, computer-based analysis techniques are becoming more commonplace, complex, and diverse. Analyses can often be difficult to reproduce from scratch, both for the original researchers and for others seeking to build on the work. We present a palaeomagnetic plotting and analysis program designed to make reproducibility easier. Part of the problem is the divide between interactive and scripted (batch) analysis programs. An interactive desktop program with a graphical interface is a powerful tool for exploring data and iteratively refining analyses, but usually cannot operate without human interaction. This makes it impossible to re-run an analysis automatically, or to integrate it into a larger automated scientific workflow - for example, a script to generate figures and tables for a paper. In some cases the parameters of the analysis process itself are not saved explicitly, making it hard to repeat or improve the analysis even with human interaction. Conversely, non-interactive batch tools can be controlled by pre-written scripts and configuration files, allowing an analysis to be 'replayed' automatically from the raw data. However, this advantage comes at the expense of exploratory capability: iteratively improving an analysis entails a time-consuming cycle of editing scripts, running them, and viewing the output. Batch tools also tend to require more computer expertise from their users. PuffinPlot is a palaeomagnetic plotting and analysis program which aims to bridge this gap. First released in 2012, it offers both an interactive, user-friendly desktop interface and a batch scripting interface, both making use of the same core library of palaeomagnetic functions. We present new improvements to the program that help to integrate the interactive and batch approaches, allowing an analysis to be interactively explored and refined, then saved as a self-contained configuration which can be re-run without human interaction. PuffinPlot can thus be used as a component of a larger scientific workflow, integrated with workflow management tools such as Kepler, without compromising its capabilities as an exploratory tool. Since both PuffinPlot and the platform it runs on (Java) are Free/Open Source software, even the most fundamental components of an analysis can be verified and reproduced.

MDplot: Visualise Molecular Dynamics.

PubMed

Margreitter, Christian; Oostenbrink, Chris

2017-05-10

The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.

The Application of TD/GC/NICI-MS with an Al2O3-PLOT-S Column for the Determination of Perfluoroalkylcycloalkanes in the Atmosphere.

PubMed

Ren, Yu; Schlager, Hans; Martin, Damien

2014-01-01

A modified method for the quantitative determination of atmospheric perfluoroalkylcycloalkanes (PFCs) using thermal desorption coupled with gas chromatography and detection by negative ion chemical ionization-mass spectrometry was developed. Using an optimized analytical system, a commercially available Al 2 O 3 porous layer open tubular (PLOT) capillary column (30 m × 0.25 mm) deactivated with Na 2 SO 4 was used for separation of PFCs. Improvements in the separation of PFCs, the corresponding identification and the limit of detection of PFCs using this method and column are presented. The method was successfully applied to determine the atmospheric background concentrations of a range of PFCs from a number of samples collected at a rural site in Germany. The results of this study suggest that the method outlined using the Al 2 O 3 -PLOT-S capillary column has good sensitivity and selectivity, and that it can be deployed in a routine laboratory process for the analysis of PFCs in the future research work. In addition, the ability of this column to separate the isomers of one of the lower boiling PFCs (perfluorodimethylcyclobutane) and its ability to resolve perfluoroethylcyclohexane offer the opportunity for single-column analysis for multiple PFCs.

Multi-Scale Morphological Analysis of Conductance Signals in Vertical Upward Gas-Liquid Two-Phase Flow

NASA Astrophysics Data System (ADS)

Lian, Enyang; Ren, Yingyu; Han, Yunfeng; Liu, Weixin; Jin, Ningde; Zhao, Junying

2016-11-01

The multi-scale analysis is an important method for detecting nonlinear systems. In this study, we carry out experiments and measure the fluctuation signals from a rotating electric field conductance sensor with eight electrodes. We first use a recurrence plot to recognise flow patterns in vertical upward gas-liquid two-phase pipe flow from measured signals. Then we apply a multi-scale morphological analysis based on the first-order difference scatter plot to investigate the signals captured from the vertical upward gas-liquid two-phase flow loop test. We find that the invariant scaling exponent extracted from the multi-scale first-order difference scatter plot with the bisector of the second-fourth quadrant as the reference line is sensitive to the inhomogeneous distribution characteristics of the flow structure, and the variation trend of the exponent is helpful to understand the process of breakup and coalescence of the gas phase. In addition, we explore the dynamic mechanism influencing the inhomogeneous distribution of the gas phase in terms of adaptive optimal kernel time-frequency representation. The research indicates that the system energy is a factor influencing the distribution of the gas phase and the multi-scale morphological analysis based on the first-order difference scatter plot is an effective method for indicating the inhomogeneous distribution of the gas phase in gas-liquid two-phase flow.

Multi-Sensor Distributive On-line Processing, Visualization, and Analysis Infrastructure for an Agricultural Information System at the NASA Goddard Earth Sciences DAAC

NASA Astrophysics Data System (ADS)

Teng, W.; Berrick, S.; Leptoukh, G.; Liu, Z.; Rui, H.; Pham, L.; Shen, S.; Zhu, T.

2004-12-01

The Goddard Space Flight Center Earth Sciences Data and Information Services Center (GES DISC) Distributed Active Archive Center (DAAC) is developing an Agricultural Information System (AIS), evolved from an existing TRMM Online Visualization and Analysis System (TOVAS), which will operationally provide precipitation and other satellite data products and services. AIS outputs will be integrated into existing operational decision support systems for global crop monitoring, such as that of the U.N. World Food Program. The ability to use the raw data stored in the GES DAAC archives is highly dependent on having a detailed understanding of the data's internal structure and physical implementation. To gain this understanding is a time-consuming process and not a productive investment of the user's time. This is an especially difficult challenge when users need to deal with multi-sensor data that usually are of different structures and resolutions. The AIS has taken a major step towards meeting this challenge by incorporating an underlying infrastructure, called the GES-DISC Interactive Online Visualization and Analysis Infrastructure or "Giovanni," that integrates various components to support web interfaces that allow users to perform interactive analysis on-line without downloading any data. Several instances of the Giovanni-based interface have been or are being created to serve users of TRMM precipitation, MODIS aerosol, and SeaWiFS ocean color data, as well as agricultural applications users. Giovanni-based interfaces are simple to use but powerful. The user selects geophysical parameters, area of interest, and time period; and the system generates an output on screen in a matter of seconds. The currently available output options are (1) area plot - averaged or accumulated over any available data period for any rectangular area; (2) time plot - time series averaged over any rectangular area; (3) Hovmoller plots - longitude-time and latitude-time plots; (4) ASCII output - for all plot types; and (5) image animation - for area plot. Planned output options for the near-future include correlation plots and GIS-compatible outputs. The AIS will enable the remote, interoperable access to distributed data, because the current Giovanni implementation incorporates the GrADS-DODS Server (GDS), a stable, secure data server that provides subsetting and analysis services across the Internet, for any GrADS-readable data set. The subsetting capability allows users to retrieve a specified spatial region from a large data set, eliminating the need to first download the entire data set. The analysis capability allows users to retrieve the results of an operation applied to one or more data sets on the server. The Giovanni-GDS technology allows the serving of data, through convenient on-line analysis tools, from any location where GDS and a few GrADS scripts are installed. The GES-DISC implementation of this technology is unique in the way it enables multi-sensor processing and analysis.

A MS-lesion pattern discrimination plot based on geostatistics.

PubMed

Marschallinger, Robert; Schmidt, Paul; Hofmann, Peter; Zimmer, Claus; Atkinson, Peter M; Sellner, Johann; Trinka, Eugen; Mühlau, Mark

2016-03-01

A geostatistical approach to characterize MS-lesion patterns based on their geometrical properties is presented. A dataset of 259 binary MS-lesion masks in MNI space was subjected to directional variography. A model function was fit to express the observed spatial variability in x, y, z directions by the geostatistical parameters Range and Sill. Parameters Range and Sill correlate with MS-lesion pattern surface complexity and total lesion volume. A scatter plot of ln(Range) versus ln(Sill), classified by pattern anisotropy, enables a consistent and clearly arranged presentation of MS-lesion patterns based on geometry: the so-called MS-Lesion Pattern Discrimination Plot. The geostatistical approach and the graphical representation of results are considered efficient exploratory data analysis tools for cross-sectional, follow-up, and medication impact analysis.

Recurrence plot analysis of nonstationary data: the understanding of curved patterns.

PubMed

Facchini, A; Kantz, H; Tiezzi, E

2005-08-01

Recurrence plots of the calls of the Nomascus concolor (Western black crested gibbon) and Hylobates lar (White-handed gibbon) show characteristic circular, curved, and hyperbolic patterns superimposed to the main temporal scale of the signal. It is shown that these patterns are related to particular nonstationarities in the signal. Some of them can be reproduced by artificial signals like frequency modulated sinusoids and sinusoids with time divergent frequency. These modulations are too faint to be resolved by conventional time-frequency analysis with similar precision. Therefore, recurrence plots act as a magnifying glass for the detection of multiple temporal scales in slightly modulated signals. The detected phenomena in these acoustic signals can be explained in the biomechanical context by taking in account the role of the muscles controlling the vocal folds.

Plotting program for aerodynamic lifting surface theory. [user manual for FORTRAN computer program

NASA Technical Reports Server (NTRS)

Medan, R. T.; Ray, K. S.

1973-01-01

A description of and users manual for a USA FORTRAN IV computer program which plots the planform and control points of a wing are presented. The program also plots some of the configuration data such as the aspect ratio. The planform data is stored on a disc file which is created by a geometry program. This program, the geometry program, and several other programs are used together in the analysis of lifting, thin wings in steady, subsonic flow according to a kernel function lifting surface theory.

Mayday - integrative analytics for expression data

PubMed Central

2010-01-01

Background DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files. Results We have rewritten large parts of Mayday's core to make it more efficient and ready for future developments. Among the large number of new plugins are an automated processing framework, dynamic filtering, new and efficient clustering methods, a machine learning module and database connectivity. Extensive manual data analysis can be done using an inbuilt R terminal and an integrated SQL querying interface. Our visualization framework has become more powerful, new plot types have been added and existing plots improved. Conclusions We present a major extension of Mayday, a very versatile open-source framework for efficient micro array data analysis designed for biologists and bioinformaticians. Most everyday tasks are already covered. The large number of available plugins as well as the extension possibilities using compiled plugins and ad-hoc scripting allow for the rapid adaption of Mayday also to very specialized data exploration. Mayday is available at http://microarray-analysis.org. PMID:20214778

Detection of variations in aspen forest habitat from LANDSAT digital data: Bear River Range, Utah

NASA Technical Reports Server (NTRS)

Merola, J. A.; Jaynes, R. A. (Principal Investigator)

1982-01-01

The aspen forests of the Bear River Range were analyzed and mapped using data recorded on July 2, 1979 by the LANDSAT III satellite; study efforts yielded sixty-seven light signatures for the study area, of which three groups were identified as aspen and mapped at a scale of 1:24,000. Analysis and verification of the three groups were accomplished by random location of twenty-six field study plots within the LANDSAT-defined aspen areas. All study plots are included within the Cache portion of the Wasatch-Cache National Forest. The following selected site characteristics were recorded for each study plot: a list of understory species present; average percent cover density for understory species; aspen canopy cover estimates and stem measurements; and general site topographic characteristics. The study plot data were then analyzed with respect to corresponding Landsat spectral signatures. Field studies show that all twenty-six study plots are associated with one of the three aspen groups. Further study efforts concentration on characterizing the differences between the site characteristics of plots falling into each of the three aspen groups.

Using Discursis to enhance the qualitative analysis of hospital pharmacist-patient interactions.

PubMed

Chevalier, Bernadette A M; Watson, Bernadette M; Barras, Michael A; Cottrell, William N; Angus, Daniel J

2018-01-01

Pharmacist-patient communication during medication counselling has been successfully investigated using Communication Accommodation Theory (CAT). Communication researchers in other healthcare professions have utilised Discursis software as an adjunct to their manual qualitative analysis processes. Discursis provides a visual, chronological representation of communication exchanges and identifies patterns of interactant engagement. The aim of this study was to describe how Discursis software was used to enhance previously conducted qualitative analysis of pharmacist-patient interactions (by visualising pharmacist-patient speech patterns, episodes of engagement, and identifying CAT strategies employed by pharmacists within these episodes). Visual plots from 48 transcribed audio recordings of pharmacist-patient exchanges were generated by Discursis. Representative plots were selected to show moderate-high and low- level speaker engagement. Details of engagement were investigated for pharmacist application of CAT strategies (approximation, interpretability, discourse management, emotional expression, and interpersonal control). Discursis plots allowed for identification of distinct patterns occurring within pharmacist-patient exchanges. Moderate-high pharmacist-patient engagement was characterised by multiple off-diagonal squares while alternating single coloured squares depicted low engagement. Engagement episodes were associated with multiple CAT strategies such as discourse management (open-ended questions). Patterns reflecting pharmacist or patient speaker dominance were dependant on clinical setting. Discursis analysis of pharmacist-patient interactions, a novel application of the technology in health communication, was found to be an effective visualisation tool to pin-point episodes for CAT analysis. Discursis has numerous practical and theoretical applications for future health communication research and training. Researchers can use the software to support qualitative analysis where large data sets can be quickly reviewed to identify key areas for concentrated analysis. Because Discursis plots are easily generated from audio recorded transcripts, they are conducive as teaching tools for both students and practitioners to assess and develop their communication skills.

Correlation analysis of respiratory signals by using parallel coordinate plots.

PubMed

Saatci, Esra

2018-01-01

The understanding of the bonds and the relationships between the respiratory signals, i.e. the airflow, the mouth pressure, the relative temperature and the relative humidity during breathing may provide the improvement on the measurement methods of respiratory mechanics and sensor designs or the exploration of the several possible applications in the analysis of respiratory disorders. Therefore, the main objective of this study was to propose a new combination of methods in order to determine the relationship between respiratory signals as a multidimensional data. In order to reveal the coupling between the processes two very different methods were used: the well-known statistical correlation analysis (i.e. Pearson's correlation and cross-correlation coefficient) and parallel coordinate plots (PCPs). Curve bundling with the number intersections for the correlation analysis, Least Mean Square Time Delay Estimator (LMS-TDE) for the point delay detection and visual metrics for the recognition of the visual structures were proposed and utilized in PCP. The number of intersections was increased when the correlation coefficient changed from high positive to high negative correlation between the respiratory signals, especially if whole breath was processed. LMS-TDE coefficients plotted in PCP indicated well-matched point delay results to the findings in the correlation analysis. Visual inspection of PCB by visual metrics showed range, dispersions, entropy comparisons and linear and sinusoidal-like relationships between the respiratory signals. It is demonstrated that the basic correlation analysis together with the parallel coordinate plots perceptually motivates the visual metrics in the display and thus can be considered as an aid to the user analysis by providing meaningful views of the data. Copyright © 2017 Elsevier B.V. All rights reserved.

Using Functional Languages and Declarative Programming to analyze ROOT data: LINQtoROOT

NASA Astrophysics Data System (ADS)

Watts, Gordon

2015-05-01

Modern high energy physics analysis is complex. It typically requires multiple passes over different datasets, and is often held together with a series of scripts and programs. For example, one has to first reweight the jet energy spectrum in Monte Carlo to match data before plots of any other jet related variable can be made. This requires a pass over the Monte Carlo and the Data to derive the reweighting, and then another pass over the Monte Carlo to plot the variables the analyser is really interested in. With most modern ROOT based tools this requires separate analysis loops for each pass, and script files to glue to the results of the two analysis loops together. A framework has been developed that uses the functional and declarative features of the C# language and its Language Integrated Query (LINQ) extensions to declare the analysis. The framework uses language tools to convert the analysis into C++ and runs ROOT or PROOF as a backend to get the results. This gives the analyser the full power of an object-oriented programming language to put together the analysis and at the same time the speed of C++ for the analysis loop. The tool allows one to incorporate C++ algorithms written for ROOT by others. A by-product of the design is the ability to cache results between runs, dramatically reducing the cost of adding one-more-plot and also to keep a complete record associated with each plot for data preservation reasons. The code is mature enough to have been used in ATLAS analyses. The package is open source and available on the open source site CodePlex.

Avoiding treatment bias of REDD+ monitoring by sampling with partial replacement.

PubMed

Köhl, Michael; Scott, Charles T; Lister, Andrew J; Demon, Inez; Plugge, Daniel

2015-12-01

Implementing REDD+ renders the development of a measurement, reporting and verification (MRV) system necessary to monitor carbon stock changes. MRV systems generally apply a combination of remote sensing techniques and in-situ field assessments. In-situ assessments can be based on 1) permanent plots, which are assessed on all successive occasions, 2) temporary plots, which are assessed only once, and 3) a combination of both. The current study focuses on in-situ assessments and addresses the effect of treatment bias, which is introduced by managing permanent sampling plots differently than the surrounding forests. Temporary plots are not subject to treatment bias, but are associated with large sampling errors and low cost-efficiency. Sampling with partial replacement (SPR) utilizes both permanent and temporary plots. We apply a scenario analysis with different intensities of deforestation and forest degradation to show that SPR combines cost-efficiency with the handling of treatment bias. Without treatment bias permanent plots generally provide lower sampling errors for change estimates than SPR and temporary plots, but do not provide reliable estimates, if treatment bias occurs, SPR allows for change estimates that are comparable to those provided by permanent plots, offers the flexibility to adjust sample sizes in the course of time, and allows to compare data on permanent versus temporary plots for detecting treatment bias. Equivalence of biomass or carbon stock estimates between permanent and temporary plots serves as an indication for the absence of treatment bias while differences suggest that there is evidence for treatment bias. SPR is a flexible tool for estimating emission factors from successive measurements. It does not entirely depend on sample plots that are installed at the first occasion but allows for the adjustment of sample sizes and placement of new plots at any occasion. This ensures that in-situ samples provide representative estimates over time. SPR offers the possibility to increase sampling intensity in areas with high degradation intensities or to establish new plots in areas where permanent plots are lost due to deforestation. SPR is also an ideal approach to mitigate concerns about treatment bias.

Effect of removal of hesperis matronalis (Dame's rocket) on species cover of forest understory vegetation in NW indiana

USGS Publications Warehouse

Pavlovic, N.B.; Leicht-Young, S. A.; Frohnapple, K.J.; Grundel, R.

2009-01-01

Exotic invasive plant species differ in their effects on indigenous vegetation as evidenced by research evaluating community response to their removal. We used a removal approach to quantify the response of a mesic woodland to the removal versus retention of an invasive plant, Hesperis matronalis (dame's rocket) from paired treatment plots over 3 y. Cover of H. matronalis did not differ between control and treatment plots prior to removal, declined in the removal plots and remained significantly lower in cover compared to the control plots. Removal did not significantly affect species richness and species diversity (evenness, Shannon and Simpson) at the plot scale, but did result in increased species richness overall in the removal plots in the last sampling year when compared to control plots. Non-metric multidimensional scaling ordination analysis indicated a significant compositional change in the spring plant composition of plots over the 3 y, reflecting an increase in exotic woody species. Exotic woody plants, especially Rosa multiflora and Euonymus alatus, increased in cover in response to H. matronalis removal. In the 3 y, neither native nor exotic forbs, nor native woody plants responded to the removal of H. matronalis in a statistically significant manner. The increasing cover of woody invasive plants in response to the removal of H. matronalis has important management implications for restoration of degraded communities.

Characterising infant inter-breath interval patterns during active and quiet sleep using recurrence plot analysis.

PubMed

Terrill, Philip I; Wilson, Stephen J; Suresh, Sadasivam; Cooper, David M

2009-01-01

Breathing patterns are characteristically different between active and quiet sleep states in infants. It has been previously identified that breathing dynamics are governed by a non-linear controller which implies the need for a nonlinear analytical tool. Further, it has been shown that quantified nonlinear variables are different between adult sleep states. This study aims to determine whether a nonlinear analytical tool known as recurrence plot analysis can characterize breath intervals of active and quiet sleep states in infants. Overnight polysomnograms were obtained from 32 healthy infants. The 6 longest periods each of active and quiet sleep were identified and a software routine extracted inter-breath interval data for recurrence plot analysis. Determinism (DET), laminarity (LAM) and radius (RAD) values were calculated for an embedding dimension of 4, 6, 8 and 16, and fixed recurrence of 0.5, 1, 2, 3.5 and 5%. Recurrence plots exhibited characteristically different patterns for active and quiet sleep. Active sleep periods typically had higher values of RAD, DET and LAM than for quiet sleep, and this trend was invariant to a specific choice of embedding dimension or fixed recurrence. These differences may provide a basis for automated sleep state classification, and the quantitative investigation of pathological breathing patterns.

Multi-reader ROC studies with split-plot designs: a comparison of statistical methods.

PubMed

Obuchowski, Nancy A; Gallas, Brandon D; Hillis, Stephen L

2012-12-01

Multireader imaging trials often use a factorial design, in which study patients undergo testing with all imaging modalities and readers interpret the results of all tests for all patients. A drawback of this design is the large number of interpretations required of each reader. Split-plot designs have been proposed as an alternative, in which one or a subset of readers interprets all images of a sample of patients, while other readers interpret the images of other samples of patients. In this paper, the authors compare three methods of analysis for the split-plot design. Three statistical methods are presented: the Obuchowski-Rockette method modified for the split-plot design, a newly proposed marginal-mean analysis-of-variance approach, and an extension of the three-sample U-statistic method. A simulation study using the Roe-Metz model was performed to compare the type I error rate, power, and confidence interval coverage of the three test statistics. The type I error rates for all three methods are close to the nominal level but tend to be slightly conservative. The statistical power is nearly identical for the three methods. The coverage of 95% confidence intervals falls close to the nominal coverage for small and large sample sizes. The split-plot multireader, multicase study design can be statistically efficient compared to the factorial design, reducing the number of interpretations required per reader. Three methods of analysis, shown to have nominal type I error rates, similar power, and nominal confidence interval coverage, are available for this study design. Copyright © 2012 AUR. All rights reserved.

Prefield methods: streamlining forest or nonforest determinations to increase inventory efficiency

Treesearch

Sara Goeking; Gretchen Moisen; Kevin Megown; Jason Toombs

2009-01-01

Interior West Forest Inventory and Analysis has developed prefield protocols to distinguish forested plots that require field visits from nonforested plots that do not require field visits. Recent innovations have increased the efficiency of the prefield process. First, the incorporation of periodic inventory data into a prefield database increased the amount of...

Models for estimation and simulation of crown and canopy cover

Treesearch

John D. Shaw

2005-01-01

Crown width measurements collected during Forest Inventory and Analysis and Forest Health Monitoring surveys are being used to develop individual tree crown width models and plot-level canopy cover models for species and forest types in the Intermountain West. Several model applications are considered in the development process, including remote sensing of plot...

Nebraska's forests, 2005: statistics, methods, and quality assurance

Treesearch

Patrick D. Miles; Dacia M. Meneguzzo; Charles J. Barnett

2011-01-01

The first full annual inventory of Nebraska's forests was completed in 2005 after 8,335 plots were selected and 274 forested plots were visited and measured. This report includes detailed information on forest inventory methods, and data quality estimates. Tables of various important resource statistics are presented. Detailed analysis of the inventory data are...

Kansas's forests, 2005: statistics, methods, and quality assurance

Treesearch

Patrick D. Miles; W. Keith Moser; Charles J. Barnett

2011-01-01

The first full annual inventory of Kansas's forests was completed in 2005 after 8,868 plots were selected and 468 forested plots were visited and measured. This report includes detailed information on forest inventory methods and data quality estimates. Important resource statistics are included in the tables. A detailed analysis of Kansas inventory is presented...

Continuum of risk analysis methods to assess tillage system sustainability at the experimental plot level

USDA-ARS?s Scientific Manuscript database

The primary goal of this study was to evaluate the efficacy of stochastic dominance and stochastic efficiency with respect to a function (SERF) methodology for ranking conventional and conservation tillage systems using 14 years (1990-2003) of economic budget data collected from 36 plots at the Iowa...

FIA forest inventory data for wildlife habitat assessment

Treesearch

David C. Chojnacky

2000-01-01

The Forest Inventory and Analysis (FIA) program of the USDA Forest Service maintains a network of permanent plots to monitor changing forest conditions. These plots were originally established to monitor the nation's timber supply; however, these data have great potential for evaluating other forest resources. To demonstrate a wildlife application, an assessment...

Soil and Nutrient Loss Following Site Preparation Burning

Treesearch

J.P. Field; E.A. Carter

2000-01-01

Sediment loss and nutrient cpncentrations in runoff were evaluated to determine the effects of site preparation burning on a recently harvested loblolly pine (Pinus taeda L.) site in east Texas. Sediment and nutrient losses prior to treatment were approximately the same from control plots and pretreatment burn plots. Nutrient analysis of runoff...

Soil and nutrient loss following site preparation burning

Treesearch

J.P. Field; K.W. Farrish; E.A. Carter

2000-01-01

Sediment loss and nutrient cpncentrations in runoff were evaluated to determine the effects of site preparation burning on a recently harvested loblolly pine (Pinur taeda L.) site in east Texas. Sediment and nutrient losses prior to treatment were approximately the same from control plots and pretreatment burn plots. Nutrient analysis of runoff...

Using Forest Service multiple species inventory and monitoring protocols to count birds at forest inventory and analysis plots on the Caribbean landscape: results, observations, and challenges from year 1 of a 2-year study

Treesearch

Sonja N. Oswalt; Thomas J. Brandeis; David W. Steadman; Scott K. Robinson

2009-01-01

We conducted double-observer point counts of birds from December 3 to December 31, 2005, on preestablished permanent Forest Inventory and Analysis (FIA) plots and National Park Service System trails within the Virgin Islands National Park, St. John, U.S. Virgin Islands. We had three objectives: (1) to collect abundance and distribution data for wintering land birds,...

Sine ars scientia nihil est: Leonardo da Vinci and beyond.

PubMed

Kickhöfel, Eduardo H P

2009-01-01

The aim of this article is to reflect on the relationship between art and science so far as it concerns a symposium on neurosciences. We undertake a historical overview of that relationship, paying particular attention to the sui generis case of Leonardo da Vinci, who very often is regarded as the man who worked on art and science with equal ease. We then explain why his idea of merging these two forms of knowledge failed, considering the clear-cut distinction between art and science in his time. With this clarification, we explore the matter today. We look at Raphael's The Transfiguration, in which the representation of the possessed boy is seen by neuroscientists as indicative of an epileptic seizure. We also look at the ideas of neuroscientists Semir Zeki and Vilayanur Ramachandran, who study particular aspects of brain function and suggest a new merging of art and science.

Earth science research

NASA Technical Reports Server (NTRS)

Botkin, Daniel B.

1987-01-01

The analysis of ground-truth data from the boreal forest plots in the Superior National Forest, Minnesota, was completed. Development of statistical methods was completed for dimension analysis (equations to estimate the biomass of trees from measurements of diameter and height). The dimension-analysis equations were applied to the data obtained from ground-truth plots, to estimate the biomass. Classification and analyses of remote sensing images of the Superior National Forest were done as a test of the technique to determine forest biomass and ecological state by remote sensing. Data was archived on diskette and tape and transferred to UCSB to be used in subsequent research.

Developing robust recurrence plot analysis techniques for investigating infant respiratory patterns.

PubMed

Terrill, Philip I; Wilson, Stephen; Suresh, Sadasivam; Cooper, David M

2007-01-01

Recurrence plot analysis is a useful non-linear analysis tool. There are still no well formalised procedures for carrying out this analysis on measured physiological data, and systemising analysis is often difficult. In this paper, the recurrence based embedding is compared to radius based embedding by studying a logistic attractor and measured breathing data collected from sleeping human infants. Recurrence based embedding appears to be a more robust method of carrying out a recurrence analysis when attractor size is likely to be different between datasets. In the infant breathing data, the radius measure calculated at a fixed recurrence, scaled by average respiratory period, allows the accurate discrimination of active sleep from quiet sleep states (AUC=0.975, Sn=098, Sp=0.94).

Encounters with neighbours : current developments of concepts based on recurrence plots and their applications

NASA Astrophysics Data System (ADS)

Marwan, Norbert

2003-09-01

In this work, different aspects and applications of the recurrence plot analysis are presented. First, a comprehensive overview of recurrence plots and their quantification possibilities is given. New measures of complexity are defined by using geometrical structures of recurrence plots. These measures are capable to find chaos-chaos transitions in processes. Furthermore, a bivariate extension to cross recurrence plots is studied. Cross recurrence plots exhibit characteristic structures which can be used for the study of differences between two processes or for the alignment and search for matching sequences of two data series. The selected applications of the introduced techniques to various kind of data demonstrate their ability. Analysis of recurrence plots can be adopted to the specific problem and thus opens a wide field of potential applications. Regarding the quantification of recurrence plots, chaos-chaos transitions can be found in heart rate variability data before the onset of life threatening cardiac arrhythmias. This may be of importance for the therapy of such cardiac arrhythmias. The quantification of recurrence plots allows to study transitions in brain during cognitive experiments on the base of single trials. Traditionally, for the finding of these transitions the averaging of a collection of single trials is needed. Using cross recurrence plots, the existence of an El Niño/Southern Oscillation-like oscillation is traced in northwestern Argentina 34,000 yrs. ago. In further applications to geological data, cross recurrence plots are used for time scale alignment of different borehole data and for dating a geological profile with a reference data set. Additional examples from molecular biology and speech recognition emphasize the suitability of cross recurrence plots. Diese Arbeit beschäftigt sich mit verschiedenen Aspekten und Anwendungen von Recurrence Plots. Nach einer Übersicht über Methoden, die auf Recurrence Plots basieren, werden neue Komplexitätsmaße eingeführt, die geometrische Strukturen in den Recurrence Plots beschreiben. Diese neuen Maße erlauben die Identifikation von Chaos-Chaos-Übergängen in dynamischen Prozessen. In einem weiteren Schritt werden Cross Recurrence Plots eingeführt, mit denen zwei verschiedene Prozesse untersucht werden. Diese bivariate Analyse ermöglicht die Bewertung von Unterschieden zwischen zwei Prozessen oder das Anpassen der Zeitskalen von zwei Zeitreihen. Diese Technik kann auch genutzt werden, um ähnliche Abschnitte in zwei verschiedenen Datenreihen zu finden. Im Anschluß werden diese neuen Entwicklungen auf Daten verschiedener Art angewendet. Methoden, die auf Recurrence Plots basieren, können an die speziellen Probleme angepaßt werden, so daß viele weitere Anwendungen möglich sind. Durch die Anwendung der neu eingeführten Komplexitätsmaße können Chaos-Chaos-Übergänge in Herzschlagdaten vor dem Auftreten einer lebensbedrohlichen Herzrhythmusstörung festgestellt werden, was für die Entwicklung neuer Therapien dieser Herzrhythmusstörungen von Bedeutung sein könnte. In einem weiteren Beispiel, in dem EEG-Daten aus einem kognitiv orientierten Experiment untersucht werden, ermöglichen diese Komplexitätsmaße das Erkennen von spezifischen Reaktionen im Gehirn bereits in Einzeltests. Normalerweise können diese Reaktionen erst durch die Auswertung von vielen Einzeltests erkannt werden. Mit der Hilfe von Cross Recurrence Plots wird die Existenz einer klimatischen Zirkulation, die der heutigen El Niño/ Southern Oscillation sehr ähnlich ist, im Nordwesten Argentiniens vor etwa 34000 Jahren nachgewiesen. Außerdem können mit Cross Recurrence Plots die Zeitskalen verschiedener Bohrlochdaten aufeinander abgeglichen werden. Diese Methode kann auch dazu genutzt werden, ein geologisches Profil mit Hilfe eines Referenzprofiles mit bekannter Zeitskala zu datieren. Weitere Beispiele aus den Gebieten der Molekularbiologie und der Spracherkennung unterstreichen das Potential dieser Methode.

Invasion of Impatiens glandulifera affects terrestrial gastropods by altering microclimate

NASA Astrophysics Data System (ADS)

Ruckli, Regina; Rusterholz, Hans-Peter; Baur, Bruno

2013-02-01

Invasive species can have far-reaching impacts on ecosystems. Invasive plants may be able to change habitat structure and quality. We conducted a field experiment to examine whether the invasive plant Impatiens glandulifera affects native terrestrial gastropods. We also evaluated whether the invasive plant alters forest soil characteristics and microclimate which in turn may influence gastropod abundance. We sampled gastropods in plots installed in patches of I. glandulifera, in plots in which I. glandulifera was regularly removed by hand, and in control plots which were not yet colonized by the invasive plant. The three types of plots were equally distributed over three mixed deciduous forest areas that were slightly, moderately or heavily affected by a wind throw 11 years ago. A total of 33 gastropod species were recorded. Gastropod species richness was not affected by delayed effects of the wind throw, but it was significantly higher in invaded plots than in uninvaded plots. Similarly, gastropod abundance was higher in invaded plots than in the two types of control plots. Canonical correspondence analysis revealed marginally significant shifts of gastropod communities between the three types of plots and indicated that soil moisture, presence of I. glandulifera and cover of woody debris affected gastropod species composition. Field measurements showed that soil moisture was higher and daily soil temperature was more damped in patches of I. glandulifera than in the native ground vegetation. The changed microclimatic conditions may favour certain gastropod species. In particular, ubiquitous species and species with a high inundation tolerance increased in abundance in plots invaded by I. glandulifera. Our field experiment demonstrated that an invasive plant can indirectly affect native organisms by changing soil characteristics and microclimate.

Serum hepcidin-25 may replace the ferritin index in the Thomas plot in assessing iron status in anemic patients.

PubMed

Thomas, C; Kobold, U; Balan, S; Roeddiger, R; Thomas, L

2011-04-01

Biochemical markers of iron deficiency do not distinguish iron-deficient anemia (IDA) from the anemia of chronic disease (ACD) and the combined state of ACD/IDA. Serum hepcidin-25 might be a marker resolving this problem. We investigated the extent to which serum hepcidin-25 enables the differentiation of the states above in comparison with the ferritin index plot, the so-called Thomas plot [soluble transferrin receptor (sTfR)/log ferritin and the reticulocyte hemoglobin content (CHr)]. Serum hepcidin-25 was determined in 155 anemic patients who were classified as having latent iron deficiency (latent ID), IDA, ACD, or ACD/IDA using the ferritin index plot (Thomas plot). Hepcidin-25 was determined using an isotope-dilution micro-HPLC-tandem mass spectrometry method. The ability to discriminate among these states based on serum hepcidin-25 alone or in combination with the CHr was evaluated in a receiver operating characteristic curve analysis and a comparison with the recently established ferritin index plot. Serum hepcidin-25 correlated with ferritin and the ferritin index. Use of a hepcidin-25 cutoff level of ≤4 nmol/l allowed the differentiation of IDA from ACD and ACD/IDA. Furthermore, the discrimination of ACD/IDA from ACD required combination with CHr in a new plot (hepcidin-25 and the CHr). The hepcidin-25 plot and the ferritin index plot showed a good correspondence in the differentiation of iron states in patients with anemia. Patients with IDA can be differentiated from ACD and ACD/IDA but not ACD from ACD/IDA based on hepcidin-25 alone. The combination of hepcidin-25 with CHr in the hepcidin-25 plot was useful for the differentiation of the states above. © 2010 Blackwell Publishing Ltd.

FERMI/GLAST Integrated Trending and Plotting System Release 5.0

NASA Technical Reports Server (NTRS)

Ritter, Sheila; Brumer, Haim; Reitan, Denise

2012-01-01

An Integrated Trending and Plotting System (ITPS) is a trending, analysis, and plotting system used by space missions to determine performance and status of spacecraft and its instruments. ITPS supports several NASA mission operational control centers providing engineers, ground controllers, and scientists with access to the entire spacecraft telemetry data archive for the life of the mission, and includes a secure Web component for remote access. FERMI/GLAST ITPS Release 5.0 features include the option to display dates (yyyy/ddd) instead of orbit numbers along orbital Long-Term Trend (LTT) plot axis, the ability to save statistics from daily production plots as image files, and removal of redundant edit/create Input Definition File (IDF) screens. Other features are a fix to address invalid packet lengths, a change in naming convention of image files in order to use in script, the ability to save all ITPS plot images (from Windows or the Web) as GIF or PNG format, the ability to specify ymin and ymax on plots where previously only the desired range could be specified, Web interface capability to plot IDFs that contain out-oforder page and plot numbers, and a fix to change all default file names to show yyyydddhhmmss time stamps instead of hhmmssdddyyyy. A Web interface capability sorts files based on modification date (with newest one at top), and the statistics block can be displayed via a Web interface. Via the Web, users can graphically view the volume of telemetry data from each day contained in the ITPS archive in the Web digest. The ITPS could be also used in nonspace fields that need to plot data or trend data, including financial and banking systems, aviation and transportation systems, healthcare and educational systems, sales and marketing, and housing and construction.

Use of first derivative of displacement vs. force profiles to determine deformation behavior of compressed powders.

PubMed

Gharaibeh, Shadi F; Aburub, Aktham

2013-03-01

Displacement (D) vs. force (F) profiles obtained during compaction of powders have been reported by several researchers. These profiles are usually used to obtain mechanical energies associated with the compaction of powders. In this work, we obtained displacement-force data associated with the compression of six powders; Avicel PH101, Avicel PH301, pregelatinized corn starch, anhydrous lactose, dicalcium phosphate, and mannitol. The first three powders are known to deform predominantly by plastic behavior while the later ones are known to deform predominantly by brittle fracture. Displacement-force data was utilized to perform in-die Heckel analysis and to calculate the first derivative (dD/dF) of displacement-force plots. First derivative results were then plotted against mean force (F') at each point and against 1/F' at compression forces between 1 and 20 kN. Results of the in-die Heckle analysis are in very good agreement with the known deformation behavior of the compressed materials. First derivative plots show that materials that deform predominantly by plastic behavior have first derivative values (0.0006-0.0016 mm/ N) larger than those of brittle materials (0.0004 mm/N). Moreover, when dD/dF is plotted against 1/F' for each powder, a linear correlation can be obtained (R2=>0.98). The slopes of the dD/dF vs. 1/F' plots for plastically deforming materials are relatively larger than those for materials that deform by brittle behavior. It is concluded that first derivative plots of displacement-force profiles can be used to determine deformation behavior of powders.

Land Reclamation in Brazilian Amazônia: A chronosequence study of floristic development in the national forest of Jamiri-RO mined areas

NASA Astrophysics Data System (ADS)

Fengler, Felipe; Ribeiro, Admilson; Longo, Regina; Merides, Marcela; Soares, Herlon; Melo, Wanderley

2017-04-01

Although reclamation techniques for forest ecosystems recovery have been developed over the past decades, there is still a great difficulty in the establishment on environment assessment, especially when compared to the non-disturbed ecosystems. This work evaluated the results and limitations on cassiterite-mined areas in reclamation, at Brazilian Amazônia. Floristic variables from 29 plots located on 15-year-old native species reforestation sites and two plots from preserved open/closed canopy forests were analyzed in a chronosequece way (2010-2015). Regeneration density, species richness, average girth, and average height were evaluated every year, by means of cluster analysis (Euclidian distance, Ward method) and submitted to multiscale bootstrap resampling (a=5%). It was conduced the regression analysis for each identified group in 2015 in order to verify differences between the chronosequece development. The results showed the existence of two main groups in 2010, one witch all mined plots were allocated and other with open/closed canopy plots. After 2011 some mined areas became allocated in the open/closed canopy plots group. From 2013 and on open/closed canopy plots appeared shuffled in the formed groups, indicating the reclamation sites conditions became similar to natural areas. Finally, in 2015 three main groups were formed. The regression analysis showed that group three had a higher trend of development for regeneration density, with higher angular coefficient and higher values. For species richness all the groups had a similar trend, with values lower than open/closed canopy forest. In average girth higher trends were observed in group one and all values were near to open canopy forest in 2015. Average height showed better trends and higher values in group two. It was concluded that all mined sites had a forest recovery process. However, different responses to reclamation process were observed due to the differences in the degraded soils characteristics. Keywords: Recovery, Restoration, Forest, Chronosequece, Cassiterite.

Real Data and Rapid Results: Ocean Color Data Analysis with Giovanni (GES DISC Interactive Online Visualization and ANalysis Infrastructure)

NASA Technical Reports Server (NTRS)

Acker, J. G.; Leptoukh, G.; Kempler, S.; Gregg, W.; Berrick, S.; Zhu, T.; Liu, Z.; Rui, H.; Shen, S.

2004-01-01

The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) has taken a major step addressing the challenge of using archived Earth Observing System (EOS) data for regional or global studies by developing an infrastructure with a World Wide Web interface which allows online, interactive, data analysis: the GES DISC Interactive Online Visualization and ANalysis Infrastructure, or "Giovanni." Giovanni provides a data analysis environment that is largely independent of underlying data file format. The Ocean Color Time-Series Project has created an initial implementation of Giovanni using monthly Standard Mapped Image (SMI) data products from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) mission. Giovanni users select geophysical parameters, and the geographical region and time period of interest. The system rapidly generates a graphical or ASCII numerical data output. Currently available output options are: Area plot (averaged or accumulated over any available data period for any rectangular area); Time plot (time series averaged over any rectangular area); Hovmeller plots (image view of any longitude-time and latitude-time cross sections); ASCII output for all plot types; and area plot animations. Future plans include correlation plots, output formats compatible with Geographical Information Systems (GIs), and higher temporal resolution data. The Ocean Color Time-Series Project will produce sensor-independent ocean color data beginning with the Coastal Zone Color Scanner (CZCS) mission and extending through SeaWiFS and Moderate Resolution Imaging Spectroradiometer (MODIS) data sets, and will enable incorporation of Visible/lnfrared Imaging Radiometer Suite (VIIRS) data, which will be added to Giovanni. The first phase of Giovanni will also include tutorials demonstrating the use of Giovanni and collaborative assistance in the development of research projects using the SeaWiFS and Ocean Color Time-Series Project data in the online Laboratory for Ocean Color Users (LOCUS). The synergy of Giovanni with high-quality ocean color data provides users with the ability to investigate a variety of important oceanic phenomena, such as coastal primary productivity related to pelagic fisheries, seasonal patterns and interannual variability, interdependence of atmospheric dust aerosols and harmful algal blooms, and the potential effects of climate change on oceanic productivity.

Similarity-dissimilarity plot for visualization of high dimensional data in biomedical pattern classification.

PubMed

Arif, Muhammad

2012-06-01

In pattern classification problems, feature extraction is an important step. Quality of features in discriminating different classes plays an important role in pattern classification problems. In real life, pattern classification may require high dimensional feature space and it is impossible to visualize the feature space if the dimension of feature space is greater than four. In this paper, we have proposed a Similarity-Dissimilarity plot which can project high dimensional space to a two dimensional space while retaining important characteristics required to assess the discrimination quality of the features. Similarity-dissimilarity plot can reveal information about the amount of overlap of features of different classes. Separable data points of different classes will also be visible on the plot which can be classified correctly using appropriate classifier. Hence, approximate classification accuracy can be predicted. Moreover, it is possible to know about whom class the misclassified data points will be confused by the classifier. Outlier data points can also be located on the similarity-dissimilarity plot. Various examples of synthetic data are used to highlight important characteristics of the proposed plot. Some real life examples from biomedical data are also used for the analysis. The proposed plot is independent of number of dimensions of the feature space.

New User-Friendly Approach to Obtain an Eisenberg Plot and Its Use as a Practical Tool in Protein Sequence Analysis

PubMed Central

Keller, Rob C.A.

2011-01-01

The Eisenberg plot or hydrophobic moment plot methodology is one of the most frequently used methods of bioinformatics. Bioinformatics is more and more recognized as a helpful tool in Life Sciences in general, and recent developments in approaches recognizing lipid binding regions in proteins are promising in this respect. In this study a bioinformatics approach specialized in identifying lipid binding helical regions in proteins was used to obtain an Eisenberg plot. The validity of the Heliquest generated hydrophobic moment plot was checked and exemplified. This study indicates that the Eisenberg plot methodology can be transferred to another hydrophobicity scale and renders a user-friendly approach which can be utilized in routine checks in protein–lipid interaction and in protein and peptide lipid binding characterization studies. A combined approach seems to be advantageous and results in a powerful tool in the search of helical lipid-binding regions in proteins and peptides. The strength and limitations of the Eisenberg plot approach itself are discussed as well. The presented approach not only leads to a better understanding of the nature of the protein–lipid interactions but also provides a user-friendly tool for the search of lipid-binding regions in proteins and peptides. PMID:22016610

New user-friendly approach to obtain an Eisenberg plot and its use as a practical tool in protein sequence analysis.

PubMed

Keller, Rob C A

2011-01-01

The Eisenberg plot or hydrophobic moment plot methodology is one of the most frequently used methods of bioinformatics. Bioinformatics is more and more recognized as a helpful tool in Life Sciences in general, and recent developments in approaches recognizing lipid binding regions in proteins are promising in this respect. In this study a bioinformatics approach specialized in identifying lipid binding helical regions in proteins was used to obtain an Eisenberg plot. The validity of the Heliquest generated hydrophobic moment plot was checked and exemplified. This study indicates that the Eisenberg plot methodology can be transferred to another hydrophobicity scale and renders a user-friendly approach which can be utilized in routine checks in protein-lipid interaction and in protein and peptide lipid binding characterization studies. A combined approach seems to be advantageous and results in a powerful tool in the search of helical lipid-binding regions in proteins and peptides. The strength and limitations of the Eisenberg plot approach itself are discussed as well. The presented approach not only leads to a better understanding of the nature of the protein-lipid interactions but also provides a user-friendly tool for the search of lipid-binding regions in proteins and peptides.

Recurrence quantification analysis of heart rate variability and respiratory flow series in patients on weaning trials.

PubMed

Arcentales, Andrés; Giraldo, Beatriz F; Caminal, Pere; Benito, Salvador; Voss, Andreas

2011-01-01

Autonomic nervous system regulates the behavior of cardiac and respiratory systems. Its assessment during the ventilator weaning can provide information about physio-pathological imbalances. This work proposes a non linear analysis of the complexity of the heart rate variability (HRV) and breathing duration (T(Tot)) applying recurrence plot (RP) and their interaction joint recurrence plot (JRP). A total of 131 patients on weaning trials from mechanical ventilation were analyzed: 92 patients with successful weaning (group S) and 39 patients that failed to maintain spontaneous breathing (group F). The results show that parameters as determinism (DET), average diagonal line length (L), and entropy (ENTR), are statistically significant with RP for T(Tot) series, but not with HRV. When comparing the groups with JRP, all parameters have been relevant. In all cases, mean values of recurrence quantification analysis are higher in the group S than in the group F. The main differences between groups were found on the diagonal and vertical structures of the joint recurrence plot.

Effect of support flexibilty and damping on the dynamic response of a single mass flexible rotor in elastic bearings

NASA Technical Reports Server (NTRS)

Kirk, R. G.; Gunter, E. J.

1972-01-01

A steady state analysis of the shaft and the bearing housing motion was made by assuming synchronous precession of the system. The conditions under which the support system would act as a dynamic vibration absorber at the rotor critical speed were studied; plots of the rotor and support amplitudes, phase angles, and forces transmitted were evaluated by the computer, and the performance curves were automatically plotted by a CalComp plotter unit. Curves are presented on the optimization of the support housing characteristics to attenuate the rotor unbalance response over the entire rotor speed range. The complete transient motion including rotor unbalance was examined by integrating the equations of motion numerically using a modified fourth order Runge-Kutta procedure, and the resulting whirl orbits were plotted by the CalComp plotter unit. The results of the transient analysis are discussed with regards to the design optimization procedure derived from the steady-state analysis.

CADDIS Volume 4. Data Analysis: Exploratory Data Analysis

EPA Pesticide Factsheets

Intro to exploratory data analysis. Overview of variable distributions, scatter plots, correlation analysis, GIS datasets. Use of conditional probability to examine stressor levels and impairment. Exploring correlations among multiple stressors.

Tides, and tidal and residual currents in Suisun and San Pablo bays, California; results of measurements, 1986

USGS Publications Warehouse

Gartner, J.W.; Yost, B.T.

1988-01-01

Current meter data collected at 11 stations and water level data collected at one station in Suisun and San Pablo Bays, California, in 1986 are compiled in this report. Current-meter measurements include current speed and direction, and water temperature and salinity (computed from temperature and conductivity). For each of the 19 current-meter records, data are presented in two forms. These are: (1) results of harmonic analysis; and (2) plots of tidal current speed and direction versus time and plots of temperature and salinity versus time. Spatial distribution of the properties of tidal currents are given in graphic form. In addition, Eulerian residual currents have been compiled by using a vector-averaging technique. Water level data are presented in the form of a time-series plot and the results of harmonic analysis. (USGS)

Critical behavior near the ferromagnetic phase transition in double perovskite Nd2NiMnO6

NASA Astrophysics Data System (ADS)

Ali, Anzar; Sharma, G.; Singh, Yogesh

2018-05-01

The knowledge of critical exponents plays a crucial role in trying to understand the interaction mechanism near a phase transition. In this report, we present a detailed study of the critical behaviour near the ferromagnetic (FM) transition (TC ˜ 193 K) in Nd2NiMnO6 using the temperature and magnetic field dependent isothermal magnetisation measurements. We used various analysis methods such as Arrott plot, modified Arrott plot, and Kouvel-Fisher plot to estimate the critical parameters. The magnetic critical parameters β = 0.49±0.02, γ = 1.05±0.04 and critical isothermal parameter δ = 3.05±0.02 are in excellent agreement with Widom scaling. The critical parameters analysis emphasizes that mean field interaction is the mechanism driving the FM transition in Nd2NiMnO6.

Analysis of vegetation in an Imperata grassland of Barak valley, Assam.

PubMed

Astapati, Ashim Das; Das, Ashesh Kumar

2012-09-01

Imperata grassland at Dorgakona, Barak valley, North Eastern India was analyzed for species composition and diversity pattern in relation to traditional management practices. 19 families were in the burnt and unburnt plots of the study site with Poaceae as the most dominant one. 29 species occurred in the burnt plot and 28 in the unburnt plot. Most of the species were common in both the plots. The pattern of frequency diagrams indicated that the vegetation was homogeneous. Imperata cylindrica, a rhizomatous grass was the dominant species based on density (318.75 and 304.18 nos. m(-2)), basal cover (158.22 and 148.34 cm2 m(-2)) and Importance value index (IVI) (132.64 and 138.74) for the burnt and unburnt plots respectively. Borreria pusilla was the co-dominant species constituting Imperata-Borreria assemblage of the studied grassland. It was observed that B. pusilla (162.25 nos. m(-2) and 50.37 nos. m(-2), I. cylindrica (318.75 nos. m(-2) and 304.18 nos. m(-2)) and Setaria glauca (24.70 nos. m(-2) and 16.46 nos. m(-2) were benefited from burning as shown by the values sequentially placed for burnt and unburnt plots. Certain grasses like Chrysopogon aciculatus and Sacciolepis indica were restricted to burnt plot while Oxalis corniculata showed its presence to unburnt plot. Grasses dominated the grassland as revealed by their contribution to the mean percentage cover of 72% in burnt plot and 76% in umburnt plot. The dominance-diversity curves in the study site approaches a log normal series distribution suggesting that the resources are shared by the constituent species. Seasonal pattern in diversity index suggested definite influence of climatic seasonality on species diversity; rainy season was conducive for maximum diversity (1.40 and 1.38 in the burnt and unburnt plots, respectively). Dominance increased with concentration of fewer species (0.0021 in burnt plot and 0.0055 in unbumt plot) in summer and behaves inversely to index of diversity. This study showed that the traditional management practices benefits the farmers as it promote grassland regeneration with I. cylindrica as the dominant grass.

MDplot: Visualise Molecular Dynamics

PubMed Central

Margreitter, Christian; Oostenbrink, Chris

2017-01-01

The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package′s functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. Availability The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project′s GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license. PMID:28845302

NASA GES DISC On-line Visualization and Analysis System for Gridded Remote Sensing Data

NASA Technical Reports Server (NTRS)

Leptoukh, Gregory G.; Berrick, S.; Rui, H.; Liu, Z.; Zhu, T.; Teng, W.; Shen, S.; Qin, J.

2005-01-01

The ability to use data stored in the current NASA Earth Observing System (EOS) archives for studying regional or global phenomena is highly dependent on having a detailed understanding of the data's internal structure and physical implementation. Gaining this understanding and applying it to data reduction is a time-consuming task that must be undertaken before the core investigation can begin. This is an especially difficult challenge when science objectives require users to deal with large multi-sensor data sets that are usually of different formats, structures, and resolutions. The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) has taken a major step towards meeting this challenge by developing an infrastructure with a Web interface that allows users to perform interactive analysis online without downloading any data, the GES-DISC Interactive Online Visualization and Analysis Infrastructure or "Giovanni." Giovanni provides interactive, online, analysis tools for data users to facilitate their research. There have been several instances of this interface created to serve TRMM users, Aerosol scientists, Ocean Color and Agriculture applications users. The first generation of these tools support gridded data only. The user selects geophysical parameters, area of interest, time period; and the system generates an output on screen in a matter of seconds. The currently available output options are: Area plot averaged or accumulated over any available data period for any rectangular area; Time plot time series averaged over any rectangular area; Hovmoller plots image view of any longitude-time and latitude-time cross sections; ASCII output for all plot types; Image animation for area plot. Another analysis suite deals with parameter intercomparison: scatter plots, temporal correlation maps, GIs-compatible outputs, etc. This allow user to focus on data content (i.e. science parameters) and eliminate the need for expensive learning, development and processing tasks that are redundantly incurred by an archive's user community. The current implementation utilizes the GrADS-DODS Server (GDS), and provides subsetting and analysis services across the Internet for any GrADS-readable dataset. The subsetting capability allows users to retrieve a specified temporal and/or spatial subdomain from a large dataset, eliminating the need to download everything simply to access a small relevant portion of a dataset. The analysis capability allows users to retrieve the results of an operation applied to one or more datasets on the server. We use this approach to read pre-processed binary files and/or to read and extract the needed parts directly from HDF or HDF-EOS files. These subsets then serve as inputs into GrADS analysis scripts. It can be used in a wide variety of Earth science applications: climate and weather events study and monitoring; modeling. It can be easily configured for new applications.

SnagPRO: snag and tree sampling and analysis methods for wildlife

Treesearch

Lisa J. Bate; Michael J. Wisdom; Edward O. Garton; Shawn C. Clabough

2008-01-01

We describe sampling methods and provide software to accurately and efficiently estimate snag and tree densities at desired scales to meet a variety of research and management objectives. The methods optimize sampling effort by choosing a plot size appropriate for the specified forest conditions and sampling goals. Plot selection and data analyses are supported by...

Comparison of three annual inventory designs, a periodic design, and a midcycle design

Treesearch

Stanford L. Arner

2000-01-01

Three annual inventory designs, a periodic design, and a periodic measurement with midcycle update design are compared using a population created from 14,754 remeasured Forest Inventory and Analysis plots. Two of the annual designs and the midcycle update design allow updating of plots using sampling with partial replacement procedures. Individual year and moving...

Forest Resources of East Oklahoma, 2008

Treesearch

Richard A. Harper; Tony G. Johnson

2012-01-01

The Forest Inventory and Analysis Program conducted the seventh survey of east Oklahoma forests. This was the establishment of the annual plot methodology and closeout of the prism remeasurement plots. Forest land area remained stable at 5.7 million acres and covered almost 57 percent of the land area. About 5.1 million acres of forest land was considered timberland...

Regional variation in Caribbean dry forest tree species composition

Treesearch

Janet Franklin; Julie Ripplinger; Ethan H. Freid; Humfredo Marcano-Vega; David W. Steadman

2015-01-01

How does tree species composition vary in relation to geographical and environmental gradients in a globally rare tropical/subtropical broadleaf dry forest community in the Caribbean? We analyzed data from 153 Forest Inventory and Analysis (FIA) plots from Puerto Rico and the U.S. Virgin Islands (USVI), along with 42 plots that we sampled in the Bahamian Archipelago (...

Hyperspectral remote sensing analysis of short rotation woody crops grown with controlled nutrient and irrigation treatments

Treesearch

Jungho Im; John R. Jensen; Mark Coleman; Eric Nelson

2009-01-01

Hyperspectral remote sensing research was conducted to document the biophysical and biochemical characteristics of controlled forest plots subjected to various nutrient and irrigation treatments. The experimental plots were located on the Savannah River Site near Aiken, SC. AISA hyperspectral imagery were analysed using three approaches, including: (1) normalized...

Estimating two-way tables based on forest surveys

Treesearch

Charles T. Scott

2000-01-01

Forest survey analysts usually are interested in tables of values rather than single point estimates. A common error is to include only plots on which nonzero values of the attribute were observed when computing the variance of a mean. Similarly, analysts often exclude nonforest plots from the analysis. The development of the correct estimates of forest area, attribute...

Detection of the fracture zone by the method of recurrence plot

NASA Astrophysics Data System (ADS)

Hilarov, V. L.

2017-12-01

Recurrence plots (RPs) and recurrence quantification analysis (RQA) characteristics for the normal component of the displacement vector upon excitation of a defect steel plate by a sound pulse are analyzed. Different cases of spatial distribution of defects (uniform and normal) are considered, and a difference in the RQA parameters in these cases is revealed.

Land Use, Recreation, and Wildlife Habitats: GIS Applications Using FIA Plot Data

Treesearch

Victor A. Rudis

2001-01-01

Spatial contexts govern whether and how land is used. Forest surveys inventory land uses from sampled plots and provide common forest resource summaries with limited information about associated nearby uses, or the landscape context. I used the USDA Forest Service's Forest Inventory and Analysis program of the South-Central States survey region (Alabama, Arkansas...

Vision for the Future of FIA: Paean to Progress, Possibilities, and Partners

Treesearch

Susan L. King; Charles T. Scott

2006-01-01

The Forest Inventory and Analysis (FIA) program of the U.S. Department of Agriculture Forest Service has made significant progress implementing the annualized inventory in 46 States in 2004. Major increases in program performance included the availability of plot data and the plots? corresponding approximate coordinates. A mill site study and biomass models were used...

Abundance and characteristics of snags in western Montana forests

Treesearch

Richard B. Harris

1999-01-01

Plot data from the U.S. Forest Service's Forest Inventory and Analysis program was used to characterize the abundance and selected characteristics of snags from forests in western Montana. Plots were grouped by whether they had a history of timber harvest, and the U.S. Forest Service classifications of forest type, habitat type, and potential vegetation group were...

North Dakota's forests, 2005: statistics, methods, and quality assurance

Treesearch

Patrick D. Miles; David E. Haugen; Charles J. Barnett

2011-01-01

The first full annual inventory of North Dakota's forests was completed in 2005 after 7,622 plots were selected and 164 forested plots were visited and measured. This report includes detailed information on forest inventory methods and data quality estimates. Important resource statistics are included in the tables. A detailed analysis of the North Dakota...

South Dakota's forests, 2005: statistics, methods, and quality assurance

Treesearch

Patrick D. Miles; Ronald J. Piva; Charles J. Barnett

2011-01-01

The first full annual inventory of South Dakota's forests was completed in 2005 after 8,302 plots were selected and 325 forested plots were visited and measured. This report includes detailed information on forest inventory methods and data quality estimates. Important resource statistics are included in the tables. A detailed analysis of the South Dakota...

Compariative analysis of strawberry total phenolics via fast blue BB vs. folin-ciocalteu: assay interference by ascorbic acid

USDA-ARS?s Scientific Manuscript database

Strawberry (Fragaria ×ananassa Duchesne ex Rozier) fruit were harvested from two field plots of five day-neutral cultivars: Albion, Monterey, Portola, San Andreas and Seacape. Marketable (salable) berries were harvested from each plot on 22 and 25 August, and unblemished fully ripe fruit were selec...

FIADB vegetation diversity and structure indicator (VEG)

Treesearch

Bethany K. Schulz; Kevin Dobelbower

2012-01-01

The Vegetation Diversity and Structure (VEG) Indicator is a suite of measurements including an inventory of vascular plants on an extensive systematic network of forest plots across the United States. This network is a subset of the standard forest inventory plots established by the U.S. Forest Service Forest Inventory and Analysis program. The VEG indicator provides...

Soil an-d nutrient loss following site preparation burning

Treesearch

E.A. Carter; J.P. Field; K.W. Farrish

2000-01-01

Sediment loss and nutrient cpncentrations in runoff were evaluated to determine the effects of site preparation burning on a recently harvested loblolly pine (Pinur taeda L.) site in east Texas. Sediment and nutrient losses prior to treatment were approximately the same from control plots and pretreatment burn plots. Nutrient analysis of runoff samples indicated that...

Dispersion-theoretical analysis of the D + → K - π + π + Dalitz plot

NASA Astrophysics Data System (ADS)

Niecknig, Franz; Kubis, Bastian

2015-10-01

We study the Dalitz plot of the Cabibbo-favored charmed-meson decay D + → K -π+π+ using dispersion theory. The formalism respects all constraints from analyticity and unitarity, and consistently describes final-state interactions between all three decay products. We employ pion-pion and pion-kaon phase shifts as input, and fit the pertinent subtraction constants to Dalitz plot data by the CLEO and FOCUS collaborations. Phase motions of resonant as well as nonresonant amplitudes are discussed, which should provide crucial input for future studies of CP violation in similar three-body charm decays.

Impact of animal waste application on runoff water quality in field experimental plots.

PubMed

Hill, Dagne D; Owens, William E; Tchoounwou, Paul B

2005-08-01

Animal waste from dairy and poultry operations is an economical and commonly used fertilizer in the state of Louisiana. The application of animal waste to pasture lands not only is a source of fertilizer, but also allows for a convenient method of waste disposal. The disposal of animal wastes on land is a potential nonpoint source of water degradation. Water degradation and human health is a major concern when considering the disposal of large quantities of animal waste. The objective of this research was to determine the effect of animal waste application on biological (fecal coliform, Enterobacter spp. and Escherichia coli) and physical/chemical (temperature, pH, nitrate nitrogen, ammonia nitrogen, phosphate, copper, zinc, and sulfate) characteristics of runoff water in experimental plots. The effects of the application of animal waste have been evaluated by utilizing experimental plots and simulated rainfall events. Samples of runoff water were collected and analyzed for fecal coliforms. Fecal coliforms isolated from these samples were identified to the species level. Chemical analysis was performed following standard test protocols. An analysis of temperature, ammonia nitrogen, nitrate nitrogen, iron, copper, phosphate, potassium, sulfate, zinc and bacterial levels was performed following standard test protocols as presented in Standard Methods for the Examination of Water and Wastewater [1]. In the experimental plots, less time was required in the tilled broiler litter plots for the measured chemicals to decrease below the initial pre-treatment levels. A decrease of over 50% was noted between the first and second rainfall events for sulfate levels. This decrease was seen after only four simulated rainfall events in tilled broiler litter plots whereas broiler litter plots required eight simulated rainfall events to show this same type of reduction. A reverse trend was seen in the broiler litter plots and the tilled broiler plots for potassium. Bacteria numbers present after the simulated rainfall events were above 200/100 ml of sample water. It can be concluded that: 1) non-point source pollution has a significant effect on bacterial and nutrients levels in runoff water and in water resources; 2) land application of animal waste for soil fertilization makes a significant contribution to water pollution; 3) the use of tilling can significantly reduce the amount of nutrients available in runoff water.

Impact of Animal Waste Application on Runoff Water Quality in Field Experimental Plots

PubMed Central

Hill, Dagne D.; Owens, William E.; Tchounwou, Paul B.

2005-01-01

Animal waste from dairy and poultry operations is an economical and commonly used fertilizer in the state of Louisiana. The application of animal waste to pasture lands not only is a source of fertilizer, but also allows for a convenient method of waste disposal. The disposal of animal wastes on land is a potential nonpoint source of water degradation. Water degradation and human health is a major concern when considering the disposal of large quantities of animal waste. The objective of this research was to determine the effect of animal waste application on biological (fecal coliform, Enterobacter spp. and Escherichia coli) and physical/chemical (temperature, pH, nitrate nitrogen, ammonia nitrogen, phosphate, copper, zinc, and sulfate) characteristics of runoff water in experimental plots. The effects of the application of animal waste have been evaluated by utilizing experimental plots and simulated rainfall events. Samples of runoff water were collected and analyzed for fecal coliforms. Fecal coliforms isolated from these samples were identified to the species level. Chemical analysis was performed following standard test protocols. An analysis of temperature, ammonia nitrogen, nitrate nitrogen, iron, copper, phosphate, potassium, sulfate, zinc and bacterial levels was performed following standard test protocols as presented in Standard Methods for the Examination of Water and Wastewater [1]. In the experimental plots, less time was required in the tilled broiler litter plots for the measured chemicals to decrease below the initial pre-treatment levels. A decrease of over 50% was noted between the first and second rainfall events for sulfate levels. This decrease was seen after only four simulated rainfall events in tilled broiler litter plots whereas broiler litter plots required eight simulated rainfall events to show this same type of reduction. A reverse trend was seen in the broiler litter plots and the tilled broiler plots for potassium. Bacteria numbers present after the simulated rainfall events were above 200/100 ml of sample water. It can be concluded that: 1) non-point source pollution has a significant effect on bacterial and nutrients levels in runoff water and in water resources; 2) land application of animal waste for soil fertilization makes a significant contribution to water pollution; 3) the use of tilling can significantly reduce the amount of nutrients available in runoff water. PMID:16705834

Parametric-Studies and Data-Plotting Modules for the SOAP

NASA Technical Reports Server (NTRS)

2008-01-01

"Parametric Studies" and "Data Table Plot View" are the names of software modules in the Satellite Orbit Analysis Program (SOAP). Parametric Studies enables parameterization of as many as three satellite or ground-station attributes across a range of values and computes the average, minimum, and maximum of a specified metric, the revisit time, or 21 other functions at each point in the parameter space. This computation produces a one-, two-, or three-dimensional table of data representing statistical results across the parameter space. Inasmuch as the output of a parametric study in three dimensions can be a very large data set, visualization is a paramount means of discovering trends in the data (see figure). Data Table Plot View enables visualization of the data table created by Parametric Studies or by another data source: this module quickly generates a display of the data in the form of a rotatable three-dimensional-appearing plot, making it unnecessary to load the SOAP output data into a separate plotting program. The rotatable three-dimensionalappearing plot makes it easy to determine which points in the parameter space are most desirable. Both modules provide intuitive user interfaces for ease of use.

Multiscale Poincaré plots for visualizing the structure of heartbeat time series.

PubMed

Henriques, Teresa S; Mariani, Sara; Burykin, Anton; Rodrigues, Filipa; Silva, Tiago F; Goldberger, Ary L

2016-02-09

Poincaré delay maps are widely used in the analysis of cardiac interbeat interval (RR) dynamics. To facilitate visualization of the structure of these time series, we introduce multiscale Poincaré (MSP) plots. Starting with the original RR time series, the method employs a coarse-graining procedure to create a family of time series, each of which represents the system's dynamics in a different time scale. Next, the Poincaré plots are constructed for the original and the coarse-grained time series. Finally, as an optional adjunct, color can be added to each point to represent its normalized frequency. We illustrate the MSP method on simulated Gaussian white and 1/f noise time series. The MSP plots of 1/f noise time series reveal relative conservation of the phase space area over multiple time scales, while those of white noise show a marked reduction in area. We also show how MSP plots can be used to illustrate the loss of complexity when heartbeat time series from healthy subjects are compared with those from patients with chronic (congestive) heart failure syndrome or with atrial fibrillation. This generalized multiscale approach to Poincaré plots may be useful in visualizing other types of time series.

Light attenuation versus evolved carbon (AVEC) - A new way to look at elemental and organic carbon analysis

NASA Astrophysics Data System (ADS)

Nicolosi, E. M. G.; Quincey, P.; Font, A.; Fuller, G. W.

2018-02-01

The Attenuation Versus Evolved Carbon (AVEC) plot is a new way to represent thermal-optical organic carbon/elemental carbon (OC/EC) analysis data. The accumulated carbon concentration is plotted against the attenuation (ln (I0/I)). Unlike the thermogram, it provides information about the sample properties rather than the instantaneous instrument sensor status. The plot can be used to refine the determination of OC and EC split point, either from consideration of laser instability or transit time within the instrument; to investigate the optical properties of the particles; and to spot the early evolution of pyrolysed carbon (PC) and/or EC during the inert phase. 168 samples from three sites were studied. The gradient of the AVEC plot curve in the oxygenated phase provides information about the mass absorption cross section (σ) of the particles leaving the filter. The σ of the PC generated in the higher temperature Quartz protocol was greater than the PC generated in the lower temperature EUSAAR_2 protocol. Also, in both cases the PC evolved at a lower temperature in the oxygenated phase than the native EC. To minimise the shadowing effect, σ was also measured for the particles leaving the filter at the end of the analysis. These σ values, which are expected to be a combination of inherent σ together with fixed instrumental factors, were consistent between the different sites (45 ± 10 m2 g-1 in rural samples, 42 ± 8 m2 g-1 in urban samples and 35 ± 14 m2 g-1 in roadside samples). The AVEC plot can be generated from the data routinely produced by the analytical instrument using the R-code supplied in the supplementary material.

A 43-year systematic review and meta-analysis: case-fatality and risk of death among adults with tuberculous meningitis in Africa.

PubMed

Woldeamanuel, Yohannes W; Girma, Belaineh

2014-05-01

Tuberculous meningitis (TBM) is a preventable and curable common health problem among African adults. Poor nutrition, poverty, household crowding, drug resistant tuberculosis (TB) strains, AIDS, and malfunctioning TB control programs are important risk factors. We conducted a systematic review and meta-analysis of published literature reporting case-fatalities of TBM among adults in African countries from 1970 till date. A PubMed search identified relevant papers. Employed terms include 'adult tuberculous meningitis' AND 'tuberculosis Africa'. PRISMA review guidelines were applied. Adult TBM case-fatalities, odds ratio (OR), relative risk (RR), forest-plot meta-analysis for weighted OR and RR, funnel plots, L'Abbé plots, meta-regressed bubble plots, and inter-study homogeneity were computed. Among 15 studies included, adult TBM occurred in up to 28 % of all meningitis forms with case-fatality of 60 % (inverse-variance weighted 54 %). Fixed-effect meta-analysis revealed weighted OR and RR of adult TBM fatalities to be 4.37 (95 % CI 3.92, 4.88) and 2.53 (95 % CI 2.38, 2.69), respectively. Inter-study homogeneity was reliable, regional representativeness was adequate allowing generalizability, and funnel-plots behaved symmetrically with insignificant inconsistency. All cases were initiated with anti-TB medication, while some had 'breakthrough' TBM. In Africa, adult TBM has a significant public health importance with a very high fatality which has remained stagnant for the past half-century. This reflects ongoing low quality of medical care at facilities where lengthy referrals end up. Community-based studies can reveal higher unaccounted morbidity, accrued disability, and larger mortality. Improving access points for early TB management at community-level, developing health infra-structure for comprehensive case management at facility-level, and poverty reduction can help combat this multi-faceted problem--whose reduction can in return help fight poverty.

The incorporation of plotting capability into the Unified Subsonic Supersonic Aerodynamic Analysis program, version B

NASA Technical Reports Server (NTRS)

Winter, O. A.

1980-01-01

The B01 version of the United Subsonic Supersonic Aerodynamic Analysis program is the result of numerous modifications and additions made to the B00 version. These modifications and additions affect the program input, its computational options, the code readability, and the overlay structure. The following are described: (1) the revised input; (2) the plotting overlay programs which were also modified, and their associated subroutines, (3) the auxillary files used by the program, the revised output data; and (4) the program overlay structure.

Modal Analysis of MARS Solar Panel and Planar Vibrations

NASA Technical Reports Server (NTRS)

Simonyan, Andranik; Williams, R. Brett

2007-01-01

This slide presentation reviews the modal analysis of MARS solar panels and the planar vibrations. Included are views of the solar panels mock-up assembly, a view of the test seup,a view of the plot from the test, with the raw numbers of the frequencies in Hz values with the mode number, the spatial acceleration plots of Center sub panel at resonant frequencies, predictions from the Finite element models, an explanation of the two test that were done on the plate and the results from both tests,

Correlation signatures of wet soils and snows. [algorithm development and computer programming

NASA Technical Reports Server (NTRS)

Phillips, M. R.

1972-01-01

Interpretation, analysis, and development of algorithms have provided the necessary computational programming tools for soil data processing, data handling and analysis. Algorithms that have been developed thus far, are adequate and have been proven successful for several preliminary and fundamental applications such as software interfacing capabilities, probability distributions, grey level print plotting, contour plotting, isometric data displays, joint probability distributions, boundary mapping, channel registration and ground scene classification. A description of an Earth Resources Flight Data Processor, (ERFDP), which handles and processes earth resources data under a users control is provided.

Accurate determination of Brillouin frequency based on cross recurrence plot analysis in Brillouin distributed fiber sensor

NASA Astrophysics Data System (ADS)

Haneef, Shahna M.; Srijith, K.; Venkitesh, D.; Srinivasan, B.

2017-04-01

We propose and demonstrate the use of cross recurrence plot analysis (CRPA) to accurately determine the Brillouin shift due to strain and temperature in a Brillouin distributed fiber sensor. This signal processing technique, which is implemented in Brillouin sensors for the first time relies on apriori data i.e, the lineshape of the Brillouin gain spectrum and its similarity with the spectral features measured at different locations along the fiber. Analytical and experimental investigation of the proposed scheme is presented in this paper.

Impacts of deer herbivory on vegetation in Rock Creek Park, 2001-2009

USGS Publications Warehouse

Kraft, Cairn C.; Hatfield, Jeff S.

2011-01-01

Starting in 2001, vegetation data have been collected annually in 16 study modules consisting of paired (1x4 m) fenced plots and unfenced control plots located in the upland forests of Rock Creek Park, Washington, D.C. Vegetation data collected from 2001-2009 have been analyzed to determine impacts of deer herbivory on vegetation in the park. Differences between fenced plots and unfenced control plots were analyzed for the following variables: cover provided by various groups of species (woody, herbaceous, native, non-native, trees, shrubs, and woody vines), as well as by individual dominant species, vegetation thickness (a measure of percent cover projected horizontally that provides information on the vertical distribution of vegetation), and species richness overall and for groups of species (woody, herbaceous, native, non-native, trees, shrubs, and woody vines). The analyses were performed using repeated measures analysis of variance (ANOVA) and associated tests. Vegetation in plots protected from deer herbivory for 9 years showed significantly greater vegetative cover compared to plots not protected from deer herbivory. This effect was most pronounced for woody and shrub cover. Cover by the dominant species was not significantly greater in the fenced plots compared to the unfenced control plots, indicating that the significant differences observed for groups were not driven by single species within those groups. With respect to vegetation thickness, results indicate that protection from deer herbivory produced significantly higher levels of vegetation in the fenced plots compared to the unfenced control plots for both the Low (0-30 cm) and Middle (30-110 cm) height classes. Protection from deer herbivory has led to higher overall species richness and higher species richness for woody species, natives, and shrubs compared to plots not receiving protection. There is also evidence that plots protected from deer herbivory and those not receiving this protection are diverging over time with respect to a number of variables such as cover by woody and shrub species, cover in the lowest height class, and species richness of woody and native species. Recommendations were made regarding future sampling.

Analysis of flexible aircraft longitudinal dynamics and handling qualities. Volume 2: Data

NASA Technical Reports Server (NTRS)

Waszak, M. R.; Schmidt, D. K.

1985-01-01

Two analysis methods are applied to a family of flexible aircraft in order to investigate how and when structural (especially dynamic aeroelastic) effects affect the dynamic characteristics of aircraft. The first type of analysis is an open loop modal analysis technique. This method considers the effect of modal residue magnitudes on determining vehicle handling qualities. The second method is a pilot in the loop analysis procedure that considers several closed loop system characteristics. Both analyses indicated that dynamic aeroelastic effects caused a degradation in vehicle tracking performance, based on the evaluation of some simulation results. Volume 2 consists of the presentation of the state variable models of the flexible aircraft configurations used in the analysis applications mode shape plots for the structural modes, numerical results from the modal analysis frequency response plots from the pilot in the loop analysis and a listing of the modal analysis computer program.

Convex Arrhenius plots and their interpretation

PubMed Central

Truhlar, Donald G.; Kohen, Amnon

2001-01-01

This paper draws attention to selected experiments on enzyme-catalyzed reactions that show convex Arrhenius plots, which are very rare, and points out that Tolman's interpretation of the activation energy places a fundamental model-independent constraint on any detailed explanation of these reactions. The analysis presented here shows that in such systems, the rate coefficient as a function of energy is not just increasing more slowly than expected, it is actually decreasing. This interpretation of the data provides a constraint on proposed microscopic models, i.e., it requires that any successful model of a reaction with a convex Arrhenius plot should be consistent with the microcanonical rate coefficient being a decreasing function of energy. The implications and limitations of this analysis to interpreting enzyme mechanisms are discussed. This model-independent conclusion has broad applicability to all fields of kinetics, and we also draw attention to an analogy with diffusion in metastable fluids and glasses. PMID:11158559

An assessment of autumn olive in northern U.S. forests

Treesearch

Cassandra M. Kurtz; Mark H. Hansen

2016-01-01

This publication is part of a series of research notes that provide an overview of the invasive plant species monitored on an extensive systematic network of plots measured by the Forest Inventory and Analysis (FIA) program of the U.S. Forest Service, Northern Research Station (NRS). Each research note features one of the invasive plants monitored on forested plots by...

Rapid classification of landsat TM imagery for phase 1 stratification using the automated NDVI threshold supervised classification (ANTSC) methodology

Treesearch

William H. Cooke; Dennis M. Jacobs

2002-01-01

FIA annual inventories require rapid updating of pixel-based Phase 1 estimates. Scientists at the Southern Research Station are developing an automated methodology that uses a Normalized Difference Vegetation Index (NDVI) for identifying and eliminating problem FIA plots from the analysis. Problem plots are those that have questionable land useiland cover information....

Estimating and circumventing the effects of perturbing and swapping inventory plot locations

Treesearch

Ronald E. McRoberts; Geoffrey R. Holden; Mark D. Nelson; Greg C. Liknes; Warren K. Moser; Andrew J. Lister; Susan L. King; Elizabeth B. LaPoint; John W. Coulston; W. Brad Smith; Gregory A. Reams

2005-01-01

The Forest Inventory and Analysis (FIA) program of the USDA Forest Service reports data and information about the Nation's forest resources. Increasingly, users request that FIA data and information be reported and distributed in a geospatial context, and they request access to exact plot locations for their own analyses. However, the FIA program is constrained by...

New Method for Determining the Relative Stand Density of Forest Inventory Plots

Treesearch

Christopher W. Woodall; Patrick D. Miles

2006-01-01

Determining the relative density of Forest Inventory and Analysis plots is complicated by the various species and tree size combinations in the Nation?s forested ecosystems. Stand density index (SDI), although developed for use in even-aged monocultures, has been used for stand density assessment in largescale forest inventories. To improve application of SDI in uneven...

An assessment of nonnative bush honeysuckle in northern U.S. forests

Treesearch

Cassandra Kurtz; M.H. Hansen

2015-01-01

This publication is part of a series that provides an overview of the presence of invasive plant species monitored on an extensive systematic network of plots measured by the Forest Inventory and Analysis (FIA) program of the U.S. Forest Service, Northern Research Station (NRS). Each research note features one of the invasive plants monitored on forested plots by NRS...

Evaluating the potential of structure from motion technology for forest inventory data collection

Treesearch

Demetrios Gatziolis

2015-01-01

Since the inception of its annual plot design, the Forest Inventory and Analysis (FIA) Program of the USDA Forest Service has integrated into its data collection operations elements of digital technology, including data loggers, laser distance recorders and clinometers, and GPS devices. Data collected with the assistance of this technology during a typical plot visit...

The use of VIEWIT and perspective plot to assist in determining the landscape's visual absorption capability

Treesearch

Wayne Tlusty

1979-01-01

The concept of Visual Absorption Capability (VAC) is widely used by Forest Service Landscape Architects. The use of computer generated graphics can aid in combining times an area is seen, distance from observer and land aspect relative viewer; to determine visual magnitude. Perspective Plot allows both fast and inexpensive graphic analysis of VAC allocations, for...

An assessment of common buckthorn in northern U.S. forests

Treesearch

Cassandra M. Kurtz; Mark H. Hansen

2018-01-01

This publication is part of a series of that provides an overview of the presence of invasive plant species monitored on an extensive systematic network of plots measured by the Forest Inventory and Analysis (FIA) program of the USDA Forest Service, Northern Research Station (NRS). Each research note features one of the invasive plants monitored on forested plots by...

A comparison of FIA plot data derived from image pixels and image objects

Treesearch

Charles E. Werstak

2012-01-01

The use of Forest Inventory and Analysis (FIA) plot data for producing continuous and thematic maps of forest attributes (e.g., forest type, canopy cover, volume, and biomass) at the regional level from satellite imagery can be challenging due to differences in scale. Specifically, classification errors that may result from assumptions made between what the field data...

Managing data from remeasured plots: An evaluation of existing systems

Treesearch

John C. Byrne; Michael D. Sweet

1992-01-01

Proper management of the valuable data from remeasured (or permanent) forest growth plots with data base management systems (DBMS) can greatly add to their utility. Twelve desired features for such a system (activities that facilitate the storage, accuracy, and use of the data for analysis) are described and used to evaluate the 36 systems found by a survey conducted...

An assessment of Japanese honeysuckle in northern U.S. forests

Treesearch

Cassandra M. Kurtz; Mark H. Hansen

2015-01-01

This publication is part of a series that provides an overview of the presence of invasive plant species monitored on an extensive systematic network of plots measured by the Forest Inventory and Analysis (FIA) program of the U.S. Forest Service, Northern Research Station (NRS). Each research note features one of the invasive plants monitored on forested plots by NRS...

An assessment of garlic mustard in northern U.S. forests

Treesearch

Cassandra M. Kurtz; Mark H. Hansen

2014-01-01

This publication is part of a series that provides an overview of the presence of invasive plant species monitored on an extensive systematic network of plots measured by the Forest Inventory and Analysis (FIA) program of the U.S. Forest Service, Northern Research Station (NRS). Each research note features one of the invasive plants monitored on forested plots by FIA...

A prototype for forest health monitoring in Indiana state parks

Treesearch

Rachel Morse; KaDonna Randolph; John W., Jr. Moser

2000-01-01

In 1997, 25 Forest Health Monitoring (FHM) plots were established in two Indiana state parks and a nearby parcel of privately owned land using a new protocol that differs from the systematic grid of the national program. All plots were reassessed in 1998. Data analysis focuses upon establishing baseline conditions for the study sites and providing relevant information...

Java Radar Analysis Tool

NASA Technical Reports Server (NTRS)

Zaczek, Mariusz P.

2005-01-01

Java Radar Analysis Tool (JRAT) is a computer program for analyzing two-dimensional (2D) scatter plots derived from radar returns showing pieces of the disintegrating Space Shuttle Columbia. JRAT can also be applied to similar plots representing radar returns showing aviation accidents, and to scatter plots in general. The 2D scatter plots include overhead map views and side altitude views. The superposition of points in these views makes searching difficult. JRAT enables three-dimensional (3D) viewing: by use of a mouse and keyboard, the user can rotate to any desired viewing angle. The 3D view can include overlaid trajectories and search footprints to enhance situational awareness in searching for pieces. JRAT also enables playback: time-tagged radar-return data can be displayed in time order and an animated 3D model can be moved through the scene to show the locations of the Columbia (or other vehicle) at the times of the corresponding radar events. The combination of overlays and playback enables the user to correlate a radar return with a position of the vehicle to determine whether the return is valid. JRAT can optionally filter single radar returns, enabling the user to selectively hide or highlight a desired radar return.

Dimensional analysis yields the general second-order differential equation underlying many natural phenomena: the mathematical properties of a phenomenon's data plot then specify a unique differential equation for it.

PubMed

Kepner, Gordon R

2014-08-27

This study uses dimensional analysis to derive the general second-order differential equation that underlies numerous physical and natural phenomena described by common mathematical functions. It eschews assumptions about empirical constants and mechanisms. It relies only on the data plot's mathematical properties to provide the conditions and constraints needed to specify a second-order differential equation that is free of empirical constants for each phenomenon. A practical example of each function is analyzed using the general form of the underlying differential equation and the observable unique mathematical properties of each data plot, including boundary conditions. This yields a differential equation that describes the relationship among the physical variables governing the phenomenon's behavior. Complex phenomena such as the Standard Normal Distribution, the Logistic Growth Function, and Hill Ligand binding, which are characterized by data plots of distinctly different sigmoidal character, are readily analyzed by this approach. It provides an alternative, simple, unifying basis for analyzing each of these varied phenomena from a common perspective that ties them together and offers new insights into the appropriate empirical constants for describing each phenomenon.

Ab-initio conformational epitope structure prediction using genetic algorithm and SVM for vaccine design.

PubMed

Moghram, Basem Ameen; Nabil, Emad; Badr, Amr

2018-01-01

T-cell epitope structure identification is a significant challenging immunoinformatic problem within epitope-based vaccine design. Epitopes or antigenic peptides are a set of amino acids that bind with the Major Histocompatibility Complex (MHC) molecules. The aim of this process is presented by Antigen Presenting Cells to be inspected by T-cells. MHC-molecule-binding epitopes are responsible for triggering the immune response to antigens. The epitope's three-dimensional (3D) molecular structure (i.e., tertiary structure) reflects its proper function. Therefore, the identification of MHC class-II epitopes structure is a significant step towards epitope-based vaccine design and understanding of the immune system. In this paper, we propose a new technique using a Genetic Algorithm for Predicting the Epitope Structure (GAPES), to predict the structure of MHC class-II epitopes based on their sequence. The proposed Elitist-based genetic algorithm for predicting the epitope's tertiary structure is based on Ab-Initio Empirical Conformational Energy Program for Peptides (ECEPP) Force Field Model. The developed secondary structure prediction technique relies on Ramachandran Plot. We used two alignment algorithms: the ROSS alignment and TM-Score alignment. We applied four different alignment approaches to calculate the similarity scores of the dataset under test. We utilized the support vector machine (SVM) classifier as an evaluation of the prediction performance. The prediction accuracy and the Area Under Receiver Operating Characteristic (ROC) Curve (AUC) were calculated as measures of performance. The calculations are performed on twelve similarity-reduced datasets of the Immune Epitope Data Base (IEDB) and a large dataset of peptide-binding affinities to HLA-DRB1*0101. The results showed that GAPES was reliable and very accurate. We achieved an average prediction accuracy of 93.50% and an average AUC of 0.974 in the IEDB dataset. Also, we achieved an accuracy of 95.125% and an AUC of 0.987 on the HLA-DRB1*0101 allele of the Wang benchmark dataset. The results indicate that the proposed prediction technique "GAPES" is a promising technique that will help researchers and scientists to predict the protein structure and it will assist them in the intelligent design of new epitope-based vaccines. Copyright © 2017 Elsevier B.V. All rights reserved.

EDDIE Seismology: Introductory spectral analysis for undergraduates

NASA Astrophysics Data System (ADS)

Soule, D. C.; Gougis, R.; O'Reilly, C.

2016-12-01

We present a spectral seismology lesson in which students use spectral analysis to describe the frequency of seismic arrivals based on a conceptual presentation of waveforms and filters. The goal is for students to surpass basic waveform terminology and relate a time domain signals to their conjugates in the frequency domain. Although seismology instruction commonly engages students in analysis of authentic seismological data, this is less true for lower-level undergraduate seismology instruction due to coding barriers to many seismological analysis tasks. To address this, our module uses Seismic Canvas (Kroeger, 2015; https://seiscode.iris.washington.edu/projects/seismiccanvas), a graphically interactive application for accessing, viewing and analyzing waveform data, which we use to plot earthquake data in the time domain. Once students are familiarized with the general components of the waveform (i.e. frequency, wavelength, amplitude and period), they use Seismic Canvas to transform the data into the frequency domain. Bypassing the mathematics of Fourier Series allows focus on conceptual understanding by plotting and manipulating seismic data in both time and frequency domains. Pre/post-tests showed significant improvements in students' use of seismograms and spectrograms to estimate the frequency content of the primary wave, which demonstrated students' understanding of frequency and how data on the spectrogram and seismogram are related. Students were also able to identify the time and frequency of the largest amplitude arrival, indicating understanding of amplitude and use of a spectrogram as an analysis tool. Students were also asked to compare plots of raw data and the same data filtered with a high-pass filter, and identify the filter used to create the second plot. Students demonstrated an improved understanding of how frequency content can be removed from a signal in the spectral domain.

Micromechanics Analysis Code Post-Processing (MACPOST) User Guide. 1.0

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.; Comiskey, Michele D.; Bednarcyk, Brett A.

1999-01-01

As advanced composite materials have gained wider usage. the need for analytical models and computer codes to predict the thermomechanical deformation response of these materials has increased significantly. Recently, a micromechanics technique called the generalized method of cells (GMC) has been developed, which has the capability to fulfill this -oal. Tc provide a framework for GMC, the Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) has been developed. As MAC/GMC has been updated, significant improvements have been made to the post-processing capabilities of the code. Through the MACPOST program, which operates directly within the MSC/PATRAN graphical pre- and post-processing package, a direct link between the analysis capabilities of MAC/GMC and the post-processing capabilities of MSC/PATRAN has been established. MACPOST has simplified the production, printing. and exportation of results for unit cells analyzed by MAC/GMC. MACPOST allows different micro-level quantities to be plotted quickly and easily in contour plots. In addition, meaningful data for X-Y plots can be examined. MACPOST thus serves as an important analysis and visualization tool for the macro- and micro-level data generated by MAC/GMC. This report serves as the user's manual for the MACPOST program.

Analyzing Multiple-Choice Questions by Model Analysis and Item Response Curves

NASA Astrophysics Data System (ADS)

Wattanakasiwich, P.; Ananta, S.

2010-07-01

In physics education research, the main goal is to improve physics teaching so that most students understand physics conceptually and be able to apply concepts in solving problems. Therefore many multiple-choice instruments were developed to probe students' conceptual understanding in various topics. Two techniques including model analysis and item response curves were used to analyze students' responses from Force and Motion Conceptual Evaluation (FMCE). For this study FMCE data from more than 1000 students at Chiang Mai University were collected over the past three years. With model analysis, we can obtain students' alternative knowledge and the probabilities for students to use such knowledge in a range of equivalent contexts. The model analysis consists of two algorithms—concentration factor and model estimation. This paper only presents results from using the model estimation algorithm to obtain a model plot. The plot helps to identify a class model state whether it is in the misconception region or not. Item response curve (IRC) derived from item response theory is a plot between percentages of students selecting a particular choice versus their total score. Pros and cons of both techniques are compared and discussed.

ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface.

PubMed

Fähnrich, Anke; Krebbel, Moritz; Decker, Normann; Leucker, Martin; Lange, Felix D; Kalies, Kathrin; Möller, Steffen

2017-03-11

Next generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to elucidate immune functions in health and disease. Over the last few years, several algorithms and tools have been developed to support respective analyses of raw sequencing data of the immune repertoire. These tools focus on distinct aspects of the data processing and require a strong bioinformatics background. To facilitate the analysis of T and B cell repertoires by less experienced users, software is needed that combines the most common tools for repertoire analysis. We introduce a graphical user interface (GUI) providing a complete analysis pipeline for processing raw NGS data for human and animal TCR and BCR clonotype determination and advanced differential repertoire studies. It provides two applications. ClonoCalc prepares the raw data for downstream analyses. It combines a demultiplexer for barcode splitting and employs MiXCR for paired-end read merging and the extraction of human and animal TCR/BCR sequences. ClonoPlot wraps the R package tcR and further contributes self-developed plots for the descriptive comparative investigation of immune repertoires. This workflow reduces the amount of programming required to perform the respective analyses and supports both communication and training between scientists and technicians, and across scientific disciplines. The Open Source development in Java and R is modular and invites advanced users to extend its functionality. Software and documentation are freely available at https://bitbucket.org/ClonoSuite/clonocalc-plot .

PERFILS: a program for the quantitative treatment of footprinting data.

PubMed

Salas, X; Portugal, J

1993-10-01

PERFILS, a computer program written in Borland TurboPascal, performs quantitative analysis of footprinting experiments using any IBM PC or compatible microcomputer. The program uses the height of the bands obtained from densitometric scanning of footprinting autoradiographs to calculate a differential cleavage plot. Such a plot displays, on a logarithmic scale, the difference of susceptibility of a DNA fragment to DNase I, or any other cleaving agent, in the presence of any ligand versus the sequence. PERFILS calculates the fractional cleavage values for control and ligand, giving a table of values for each internucleotidic bond and rendering the differential cleavage plot in only a few seconds.

Allan Deviation Plot as a Tool for Quartz-Enhanced Photoacoustic Sensors Noise Analysis.

PubMed

Giglio, Marilena; Patimisco, Pietro; Sampaolo, Angelo; Scamarcio, Gaetano; Tittel, Frank K; Spagnolo, Vincenzo

2016-04-01

We report here on the use of the Allan deviation plot to analyze the long-term stability of a quartz-enhanced photoacoustic (QEPAS) gas sensor. The Allan plot provides information about the optimum averaging time for the QEPAS signal and allows the prediction of its ultimate detection limit. The Allan deviation can also be used to determine the main sources of noise coming from the individual components of the sensor. Quartz tuning fork thermal noise dominates for integration times up to 275 s, whereas at longer averaging times, the main contribution to the sensor noise originates from laser power instabilities.

Isocratic and gradient impedance plot analysis and comparison of some recently introduced large size core-shell and fully porous particles.

PubMed

Vanderheyden, Yoachim; Cabooter, Deirdre; Desmet, Gert; Broeckhoven, Ken

2013-10-18

The intrinsic kinetic performance of three recently commercialized large size (≥4μm) core-shell particles packed in columns with different lengths has been measured and compared with that of standard fully porous particles of similar and smaller size (5 and 3.5μm, respectively). The kinetic performance is compared in both absolute (plot of t0 versus the plate count N or the peak capacity np for isocratic and gradient elution, respectively) and dimensionless units. The latter is realized by switching to so-called impedance plots, a format which has been previously introduced (as a plot of t0/N(2) or E0 versus Nopt/N) and has in the present study been extended from isocratic to gradient elution (where the impedance plot corresponds to a plot of t0/np(4) versus np,opt(2)/np(2)). Both the isocratic and gradient impedance plot yielded a very similar picture: the clustered impedance plot curves divide into two distinct groups, one for the core-shell particles (lowest values, i.e. best performance) and one for the fully porous particles (highest values), confirming the clear intrinsic kinetic advantage of core-shell particles. If used around their optimal flow rate, the core-shell particles displayed a minimal separation impedance that is about 40% lower than the fully porous particles. Even larger gains in separation speed can be achieved in the C-term regime. Copyright © 2013 Elsevier B.V. All rights reserved.

Prescribed burning in a Eucalyptus woodland suppresses fruiting of hypogeous fungi, an important food source for mammals.

PubMed

Trappe, James M; Nicholls, A O; Claridge, Andrew W; Cork, Steven J

2006-11-01

Fruit bodies of hypogeous fungi are an important food source for many small mammals and are consumed by larger mammals as well. A controversial hypothesis that prescribed burning increases fruiting of certain hypogeous fungi based on observations in Tasmania was tested in the Australian Capital Territory to determine if it applied in a quite different habitat. Ten pairs of plots, burnt and nonburnt, were established at each of two sites prescribe-burnt in May 1999. When sampled in early July, after autumn rains had initiated the fungal fruiting season, species richness and numbers of fruit bodies on the burnt plots were extremely low: most plots produced none at all. Both species richness and fruit body numbers were simultaneously high on nonburnt plots. One of the sites was resampled a year after the initial sampling. At that time species richness and fruit body abundance were still significantly less on burnt plots than on nonburnt, but a strong trend towards fungal recovery on the burnt plots was evident. This was particularly so when numbers of fruit bodies of one species, the hypogeous agaric Dermocybe globuliformis, were removed from the analysis. This species strongly dominated the nonburnt plots but was absent from burnt plots in both years. The trend towards recovery of fruit body abundance in the burnt plots one year after the burn was much more pronounced with exclusion of the Dermocybe data. The Tasmanian-based hypothesis was based mostly on the fruiting of two fire-adapted species in the Mesophelliaceae. Neither species occurred on our plots. Accordingly, the results and conclusions of the Tasmanian study cannot be extrapolated to other habitats without extensive additional study. Implications for management of habitat for fungi and the animals that rely on the fungi as a food source are discussed.

Using Discursis to enhance the qualitative analysis of hospital pharmacist-patient interactions

PubMed Central

Barras, Michael A.; Angus, Daniel J.

2018-01-01

Introduction Pharmacist-patient communication during medication counselling has been successfully investigated using Communication Accommodation Theory (CAT). Communication researchers in other healthcare professions have utilised Discursis software as an adjunct to their manual qualitative analysis processes. Discursis provides a visual, chronological representation of communication exchanges and identifies patterns of interactant engagement. Aim The aim of this study was to describe how Discursis software was used to enhance previously conducted qualitative analysis of pharmacist-patient interactions (by visualising pharmacist-patient speech patterns, episodes of engagement, and identifying CAT strategies employed by pharmacists within these episodes). Methods Visual plots from 48 transcribed audio recordings of pharmacist-patient exchanges were generated by Discursis. Representative plots were selected to show moderate-high and low- level speaker engagement. Details of engagement were investigated for pharmacist application of CAT strategies (approximation, interpretability, discourse management, emotional expression, and interpersonal control). Results Discursis plots allowed for identification of distinct patterns occurring within pharmacist-patient exchanges. Moderate-high pharmacist-patient engagement was characterised by multiple off-diagonal squares while alternating single coloured squares depicted low engagement. Engagement episodes were associated with multiple CAT strategies such as discourse management (open-ended questions). Patterns reflecting pharmacist or patient speaker dominance were dependant on clinical setting. Discussion and conclusions Discursis analysis of pharmacist-patient interactions, a novel application of the technology in health communication, was found to be an effective visualisation tool to pin-point episodes for CAT analysis. Discursis has numerous practical and theoretical applications for future health communication research and training. Researchers can use the software to support qualitative analysis where large data sets can be quickly reviewed to identify key areas for concentrated analysis. Because Discursis plots are easily generated from audio recorded transcripts, they are conducive as teaching tools for both students and practitioners to assess and develop their communication skills. PMID:29787568

Meta-analyses and Forest plots using a microsoft excel spreadsheet: step-by-step guide focusing on descriptive data analysis.

PubMed

Neyeloff, Jeruza L; Fuchs, Sandra C; Moreira, Leila B

2012-01-20

Meta-analyses are necessary to synthesize data obtained from primary research, and in many situations reviews of observational studies are the only available alternative. General purpose statistical packages can meta-analyze data, but usually require external macros or coding. Commercial specialist software is available, but may be expensive and focused in a particular type of primary data. Most available softwares have limitations in dealing with descriptive data, and the graphical display of summary statistics such as incidence and prevalence is unsatisfactory. Analyses can be conducted using Microsoft Excel, but there was no previous guide available. We constructed a step-by-step guide to perform a meta-analysis in a Microsoft Excel spreadsheet, using either fixed-effect or random-effects models. We have also developed a second spreadsheet capable of producing customized forest plots. It is possible to conduct a meta-analysis using only Microsoft Excel. More important, to our knowledge this is the first description of a method for producing a statistically adequate but graphically appealing forest plot summarizing descriptive data, using widely available software.

Meta-analyses and Forest plots using a microsoft excel spreadsheet: step-by-step guide focusing on descriptive data analysis

PubMed Central

2012-01-01

Background Meta-analyses are necessary to synthesize data obtained from primary research, and in many situations reviews of observational studies are the only available alternative. General purpose statistical packages can meta-analyze data, but usually require external macros or coding. Commercial specialist software is available, but may be expensive and focused in a particular type of primary data. Most available softwares have limitations in dealing with descriptive data, and the graphical display of summary statistics such as incidence and prevalence is unsatisfactory. Analyses can be conducted using Microsoft Excel, but there was no previous guide available. Findings We constructed a step-by-step guide to perform a meta-analysis in a Microsoft Excel spreadsheet, using either fixed-effect or random-effects models. We have also developed a second spreadsheet capable of producing customized forest plots. Conclusions It is possible to conduct a meta-analysis using only Microsoft Excel. More important, to our knowledge this is the first description of a method for producing a statistically adequate but graphically appealing forest plot summarizing descriptive data, using widely available software. PMID:22264277

Characterization of the efficiency of microbore liquid chromatography columns by van Deemter and kinetic plot analysis.

PubMed

Hetzel, Terence; Loeker, Denise; Teutenberg, Thorsten; Schmidt, Torsten C

2016-10-01

The efficiency of miniaturized liquid chromatography columns with inner diameters between 200 and 300 μm has been investigated using a dedicated micro-liquid chromatography system. Fully porous, core-shell and monolithic commercially available stationary phases were compared applying van Deemter and kinetic plot analysis. The sub-2 μm fully porous as well as the 2.7 μm core-shell particle packed columns showed superior efficiency and similar values for the minimum reduced plate heights (2.56-2.69) before correction for extra-column contribution compared to normal-bore columns. Moreover, the influence of extra-column contribution was investigated to demonstrate the difference between apparent and intrinsic efficiency by replacing the column by a zero dead volume union to determine the band spreading caused by the system. It was demonstrated that 72% of the intrinsic efficiency could be reached. The results of the kinetic plot analysis indicate the superior performance of the sub-2 μm fully porous particle packed column for ultra-fast liquid chromatography. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Short-Term Response of Soil Spiders to Cover-Crop Removal in an Organic Olive Orchard in a Mediterranean Setting

PubMed Central

Cárdenas, Manuel; Castro, Juan; Campos, Mercedes

2012-01-01

This study shows that disturbance caused by cover-crop removal (CCR) in an organic olive orchard affects ground-spider populations. The effect of CCR on various organic olive-orchard plots was assessed by monitoring the abundance and diversity of ground-dwelling spiders. Covered plots in the organic olive orchard were compared with uncovered plots where the covers had been removed mechanically. CCR positively affected the most abundant spider species Zodarion styliferum (Simon) (Araneae: Zodariidae) as well as other species of running spiders belonging to the families Gnaphosidae and Lycosidae. Over time, the two types of plots did not significantly differ in diversity or dominance. Similarly, no differences were detected between the study plots in terms of the distribution of individuals when a cluster-similarity analysis was performed. This lack of difference in diversity might be due to the spatial scale used in the study or climatology. Because of their general effects, CCR profoundly changed the abundance of spiders in the olive orchard, but with no clear impact on spider diversity. PMID:22938154

Comparison Tools for Assessing the Microgravity Environment of Space Missions, Carriers and Conditions

NASA Technical Reports Server (NTRS)

DeLombard, Richard; Hrovat, Kenneth; Moskowitz, Milton; McPherson, Kevin M.

1998-01-01

The microgravity environment of the NASA Shuttles and Russia's Mir space station have been measured by specially designed accelerometer systems. The need for comparisons between different missions, vehicles, conditions, etc. has been addressed by the two new processes described in this paper. The Principal Component Spectral Analysis (PCSA) and Quasi-steady Three-dimensional Histogram QTH techniques provide the means to describe the microgravity acceleration environment of a long time span of data on a single plot. As described in this paper, the PCSA and QTH techniques allow both the range and the median of the microgravity environment to be represented graphically on a single page. A variety of operating conditions may be made evident by using PCSA or QTH plots. The PCSA plot can help to distinguish between equipment operating full time or part time, as well as show the variability of the magnitude and/or frequency of an acceleration source. A QTH plot summarizes the magnitude and orientation of the low-frequency acceleration vector. This type of plot can show the microgravity effects of attitude, altitude, venting, etc.

Rapid Classification of Landsat TM Imagery for Phase 1 Stratification Using the Automated NDVI Threshold Supervised Classification (ANTSC) Methodology

Treesearch

William H. Cooke; Dennis M. Jacobs

2005-01-01

FIA annual inventories require rapid updating of pixel-based Phase 1 estimates. Scientists at the Southern Research Station are developing an automated methodology that uses a Normalized Difference Vegetation Index (NDVI) for identifying and eliminating problem FIA plots from the analysis. Problem plots are those that have questionable land use/land cover information....

Understanding Chemical Equilibrium: The Role of Gas Phases and Mixing Contributions in the Minimum of Free Energy Plots

ERIC Educational Resources Information Center

Tomba, J. Pablo

2017-01-01

The use of free energy plots to understand the concept of thermodynamic equilibrium has been shown to be of great pedagogical value in materials science. Although chemical equilibrium is also amenable to this kind of analysis, it is not part of the agenda of materials science textbooks. Something similar is found in chemistry branches, where free…

A density management diagram for longleaf pine stands with application to red-cockaded woodpecker habitat

Treesearch

John D. Shaw; James N. Long

2007-01-01

We developed a density management diagram (DMD) for longleaf pine (Pinus palustris P. Mill.) using data from Forest Inventory and Analysis plots. Selection criteria were for purity, defined as longleaf pine basal area (BA) that is 90% or more of plot BA, and even-agedness, as defined by a ratio between two calculations of stand density index. The...

Preliminary Evaluation of Methods for Classifying Forest Site Productivity Based on Species Composition in Western North Carolina

Treesearch

W. Henry McNab; F. Thomas Lloyd; David L. Loftis

2002-01-01

The species indicator approach to forest site classification was evaluated for 210 relatively undisturbed plots established by the USDA Forest Service Forest Inventory and Analysis uni (FIA) in western North Carolina. Plots were classified by low, medium, and high levels of productivity based on 10-year individual tree basal area increment data standardized for initial...

North Carolina, 2010 forest inventory and analysis factsheet

Treesearch

Mark J. Brown; Barry D. New

2012-01-01

North Carolina’s first annualized forest survey was completed in 2007 and results were published in e-Science Update SRS–029. There were 5,800 ground based samples distributed across the State. At that time, field measurements were collected on 20 percent (a panel) of these plots annually until all plots were completed. This factsheet is an annualized update of panel...

Strategies for Preserving Owner Privacy in the National Information Management System of the USDA Forest Service's Forest Inventory and Analysis Unit

Treesearch

Andrew Lister; Charles Scott; Susan King; Michael Hoppus; Brett Butler; Douglas Griffith

2005-01-01

The Food Security Act of 1985 prohibits the disclosure of any information collected by the USDA Forest Service's FIA program that would link individual landowners to inventory plot information. To address this, we developed a technique based on a "swapping" procedure in which plots with similar characteristics are exchanged, and on a ...

A GIS-based tool for estimating tree canopy cover on fixed-radius plots using high-resolution aerial imagery

Treesearch

Sara A. Goeking; Greg C. Liknes; Erik Lindblom; John Chase; Dennis M. Jacobs; Robert. Benton

2012-01-01

Recent changes to the Forest Inventory and Analysis (FIA) Program's definition of forest land precipitated the development of a geographic information system (GIS)-based tool for efficiently estimating tree canopy cover for all FIA plots. The FIA definition of forest land has shifted from a density-related criterion based on stocking to a 10 percent tree canopy...

Evaluating the Limits of Network Topology Inference Via Virtualized Network Emulation

DTIC Science & Technology

2015-06-01

76 xi Figure 5.33 Hop-plot of five best reduction methods. KDD most closely matches the Internet plot...respectively, located around the world. These monitors provide locations from which to perform network measurement experiments, primarily using the ping ...International Symposium on Modeling, Analysis and Simulation of Computer Telecommunication Systems. IEEE, 2001, pp. 346–353. 90 [21] C. Jin , Q. Chen, and S

Thinning strategies to increase the regional availability of oak timber in the Mid-Appalachian Region

Treesearch

John R. Brooks; Jingxin Wang; Chris. LeDoux

2011-01-01

Plot data from 6,727 fully stocked oak-hickory stands were selected from Forest Inventory and Analysis data from five ecoregions common to West Virginia, Pennsylvania, Maryland, Virginia, Kentucky, and Ohio. Each plot was thinned from below using an existing thinning algorithm, where 30, 50, and 70 percent of the existing basal area was removed. These thinning...

Application of the new Cross Recurrence Plots to multivariate data

NASA Astrophysics Data System (ADS)

Thiel, M.; Romano, C.; Kurths, J.

2003-04-01

We extend and then apply the method of the new Cross Recurrence Plots (XRPs) to multivariate data. After introducing the new method we carry out an analysis of spatiotemporal ecological data. We compute not only the Rényi entropies and cross entropies by XRP, that allow to draw conclusions about the coupling of the systems, but also find a prediction horizon for intermediate time scales.

FRANOPP: Framework for analysis and optimization problems user's guide

NASA Technical Reports Server (NTRS)

Riley, K. M.

1981-01-01

Framework for analysis and optimization problems (FRANOPP) is a software aid for the study and solution of design (optimization) problems which provides the driving program and plotting capability for a user generated programming system. In addition to FRANOPP, the programming system also contains the optimization code CONMIN, and two user supplied codes, one for analysis and one for output. With FRANOPP the user is provided with five options for studying a design problem. Three of the options utilize the plot capability and present an indepth study of the design problem. The study can be focused on a history of the optimization process or on the interaction of variables within the design problem.

Pyrolysis-mass spectrometry/pattern recognition on a well-characterized suite of humic samples

USGS Publications Warehouse

MacCarthy, P.; DeLuca, S.J.; Voorhees, K.J.; Malcolm, R.L.; Thurman, E.M.

1985-01-01

A suite of well-characterized humic and fulvic acids of freshwater, soil and plant origin was subjected to pyrolysis-mass spectrometry and the resulting data were analyzed by pattern recognition and factor analysis. A factor analysis plot of the data shows that the humic acids and fulvic acids can be segregated into two distinct classes. Carbohydrate and phenolic components are more pronounced in the pyrolysis products of the fulvic acids, and saturated and unsaturated hydrocarbons contribute more to the humic acid pyrolysis products. A second factor analysis plot shows a separation which appears to be based primarily on whether the samples are of aquatic or soil origin. ?? 1985.

Data reduction and analysis of HELIOS plasma wave data

NASA Technical Reports Server (NTRS)

Anderson, Roger R.

1988-01-01

Reduction of data acquired from the HELIOS Solar Wind Plasma Wave Experiments on HELIOS 1 and 2 was continued. Production of 24 hour survey plots of the HELIOS 1 plasma wave data were continued and microfilm copies were submitted to the National Space Science Data Center. Much of the effort involved the shock memory from both HELIOS 1 and 2. This data had to be deconvoluted and time ordered before it could be displayed and plotted in an organized form. The UNIVAX 418-III computer was replaced by a DEC VAX 11/780 computer. In order to continue the reduction and analysis of the data set, all data reduction and analysis computer programs had to be rewritten.

On load paths and load bearing topology from finite element analysis

NASA Astrophysics Data System (ADS)

Kelly, D.; Reidsema, C.; Lee, M.

2010-06-01

Load paths can be mapped from vector plots of 'pointing stress vectors'. They define a path along which a component of load remains constant as it traverses the solution domain. In this paper the theory for the paths is first defined. Properties of the plots that enable a designer to interpret the structural behavior from the contours are then identified. Because stress is a second order tensor defined on an orthogonal set of axes, the vector plots define separate paths for load transfer in each direction of the set of axes. An algorithm is therefore presented that combines the vectors to define a topology to carry the loads. The algorithm is shown to straighten the paths reducing bending moments and removing stress concentration. Application to a bolted joint, a racing car body and a yacht hull demonstrate the usefulness of the plots.

Use of recurrence plot and recurrence quantification analysis in Taiwan unemployment rate time series

NASA Astrophysics Data System (ADS)

Chen, Wei-Shing

2011-04-01

The aim of the article is to answer the question if the Taiwan unemployment rate dynamics is generated by a non-linear deterministic dynamic process. This paper applies a recurrence plot and recurrence quantification approach based on the analysis of non-stationary hidden transition patterns of the unemployment rate of Taiwan. The case study uses the time series data of the Taiwan’s unemployment rate during the period from 1978/01 to 2010/06. The results show that recurrence techniques are able to identify various phases in the evolution of unemployment transition in Taiwan.

Locating the source of projectile fluid droplets

NASA Astrophysics Data System (ADS)

Varney, Christopher R.; Gittes, Fred

2011-08-01

The ill-posed projectile problem of finding the source height from spattered droplets of viscous fluid is a longstanding obstacle to accident reconstruction and crime-scene analysis. It is widely known how to infer the impact angle of droplets on a surface from the elongation of their impact profiles. However, the lack of velocity information makes finding the height of the origin from the impact position and angle of individual drops not possible. From aggregate statistics of the spatter and basic equations of projectile motion, we introduce a reciprocal correlation plot that is effective when the polar launch angle is concentrated in a narrow range. The vertical coordinate depends on the orientation of the spattered surface and equals the tangent of the impact angle for a level surface. When the horizontal plot coordinate is twice the reciprocal of the impact distance, we can infer the source height as the slope of the data points in the reciprocal correlation plot. If the distribution of launch angles is not narrow, failure of the method is evident in the lack of linear correlation. We perform a number of experimental trials, as well as numerical calculations and show that the height estimate is relatively insensitive to aerodynamic drag. Besides its possible relevance for crime investigation, reciprocal-plot analysis of spatter may find application to volcanism and other topics and is most immediately applicable for undergraduate science and engineering students in the context of crime-scene analysis.

On the Kendrick Mass Defect Plots of Multiply Charged Polymer Ions: Splits, Misalignments, and How to Correct Them

NASA Astrophysics Data System (ADS)

Fouquet, Thierry N. J.; Cody, Robert B.; Ozeki, Yuka; Kitagawa, Shinya; Ohtani, Hajime; Sato, Hiroaki

2018-05-01

The Kendrick mass defect (KMD) analysis of multiply charged polymeric distributions has recently revealed a surprising isotopic split in their KMD plots—namely a 1/z difference between KMDs of isotopes of an oligomer at charge state z. Relying on the KMD analysis of actual and simulated distributions of poly(ethylene oxide) (PEO), the isotopic split is mathematically accounted for and found to go with an isotopic misalignment in certain cases. It is demonstrated that the divisibility (resp. indivisibility) of the nominal mass of the repeating unit (R) by z is the condition for homolog ions to line up horizontally (resp. misaligned obliquely) in a KMD plot. Computing KMDs using a fractional base unit R/z eventually corrects the misalignments for the associated charge state while using the least common multiple of all the charge states as the divisor realigns all the points at once. The isotopic split itself can be removed by using either a new charge-dependent KMD plot compatible with any fractional base unit or the remainders of KM (RKM) recently developed for low-resolution data all found to be linked in a unified theory. These original applications of the fractional base units and the RKM plots are of importance theoretically to satisfy the basics of a mass defect analysis and practically for a correct data handling of single stage and tandem mass spectra of multiply charged homo- and copolymers.

Perimeter Governed Minority Carrier Lifetimes in 4H-SiC p(+)-n Diodes Measured by Reverse Recovery Switching Transient Analysis

NASA Technical Reports Server (NTRS)

Neudeck, Philip G.

1998-01-01

Minority carrier lifetimes in epitaxial 4H-SiC p(+)-n junction diodes were measured via an analysis of reverse recovery switching characteristics. Behavior of reverse recovery storage time (t(s)) as a function of initial ON-state forward current (I(F)) and OFF-state reverse current (I(R)) followed well-documented trends which have been observed for decades in silicon p-n rectifiers. Average minority carrier (hole) lifetimes (tau(p)) calculated from plots of t(s) vs I(R)/I(F) strongly decreased with decreasing device area. Bulk and perimeter components of average hole lifetimes were separated by plotting 1/tau(p) as a function of device perimeter-to- area ratio (P/A). This plot reveals that perimeter recombination is dominant in these devices, whose areas are all less than 1 sq mm. The bulk minority carrier (hole) lifetime extracted from the 1/tau(p) vs P/A plot is approximately 0.7 micro-s, well above the 60 ns to 300 ns average iit'eptimes obtained when perimeter recombination effects are ignored in the analysis. Given the fact that there has been little previous investigation of bipolar diode and transistor performance as a function of perimeter-to-area ratio, this work raises the possibility that perimeter recombination may be partly responsible for poor effective minority carrier lifetimes and limited performance obtained in many previous SiC bipolar junction devices.

Perimeter Governed Minority Carrier Lifetimes in 4H-SiC p+n Diodes Measured by Reverse Recovery Switching Transient Analysis

NASA Technical Reports Server (NTRS)

Neudeck, Philip G.

1998-01-01

Minority carrier lifetimes in epitaxial 4H-SiC p-n junction diodes were measured via an analysis of reverse recovery switching characteristics. Behavior of reverse recovery storage time (t(sub s)) as a function of initial ON-state forward current (I(sub f)) and OFF-state reverse current (I(sub R)) followed well-documented trends which have been observed for decades in silicon p-n rectifiers. Average minority carrier (hole) lifetimes (tau(sub p)) calculated from plots of t(sub s) vs I(sub R)/I(sub F) strongly decreased with decreasing device area. Bulk and perimeter components of average hole lifetimes were separated by plotting tau(sub p) as a function of device perimeter-to-area ratio (P/A). This plot reveals that perimeter recombination is dominant in these devices, whose areas are all less than 1 square mm. The bulk minority carrier (hole) lifetime extracted from the 1/Tau(sub p) vs P/A plot is approximately 0.7 microns, well above the 60 ns to 300 ns average lifetimes obtained when perimeter recombination effects are ignored in the analysis. Given the fact that there has been little previous investigation of bipolar diode and transistor performance as a function of perimeter-to-area ratio, this work raises the possibility that perimeter recombination may be partly responsible for poor effective minority carrier lifetimes and limited performance obtained in many previous SiC bipolar junction devices.

Effect of pasture size on behavioural synchronization and spacing in German Blackface ewes (Ovis aries).

PubMed

Hauschildt, Verena; Gerken, Martina

2016-03-01

This study aims to assess plot size related changes in spacing and behavioural synchronization in a herd of 14 German Blackface ewes kept on three different pasture sizes: S (126m(2)), M (1100m(2)), and L (11,200m(2)). In direct field observations, behaviour and nearest neighbour distance were recorded individually. Additionally, interindividual and nearest neighbour distances were derived from aerial photographs of the herd taken on plot sizes S and M. Nearest neighbour distances <1m accounted for more than 60% of observations, and were more frequent on plot size L than on plot sizes S (Z=3.3; p<0.01) and M (Z=3.2; p<0.01). Average interindividual distances were significantly smaller on S (4.89±2.62m) than on M plots (5.99±3.06m; t=7.3; p<0.01). Synchronization tended to increase with plot size (K(S)=0.42; K(M)=0.52; K(L)=0.66), but was not accompanied by a concomitant increase in dispersion. Aerial photography proved a valuable tool in the analysis of spacing behaviour as intraindividual repeatability of the derived distances was highly significant (Kendall's W between 0.32 and 0.58; p<0.01). The sheep kept small distances on all plot sizes, thus the high degree of behavioural synchronization might be mainly attributed to the motivation for close proximity to any conspecific. Copyright © 2015 Elsevier B.V. All rights reserved.

Reducing sojourn points from recurrence plots to improve transition detection: Application to fetal heart rate transitions.

PubMed

Zaylaa, Amira; Charara, Jamal; Girault, Jean-Marc

2015-08-01

The analysis of biomedical signals demonstrating complexity through recurrence plots is challenging. Quantification of recurrences is often biased by sojourn points that hide dynamic transitions. To overcome this problem, time series have previously been embedded at high dimensions. However, no one has quantified the elimination of sojourn points and rate of detection, nor the enhancement of transition detection has been investigated. This paper reports our on-going efforts to improve the detection of dynamic transitions from logistic maps and fetal hearts by reducing sojourn points. Three signal-based recurrence plots were developed, i.e. embedded with specific settings, derivative-based and m-time pattern. Determinism, cross-determinism and percentage of reduced sojourn points were computed to detect transitions. For logistic maps, an increase of 50% and 34.3% in sensitivity of detection over alternatives was achieved by m-time pattern and embedded recurrence plots with specific settings, respectively, and with a 100% specificity. For fetal heart rates, embedded recurrence plots with specific settings provided the best performance, followed by derivative-based recurrence plot, then unembedded recurrence plot using the determinism parameter. The relative errors between healthy and distressed fetuses were 153%, 95% and 91%. More than 50% of sojourn points were eliminated, allowing better detection of heart transitions triggered by gaseous exchange factors. This could be significant in improving the diagnosis of fetal state. Copyright © 2014 Elsevier Ltd. All rights reserved.

A joint probability approach for coincidental flood frequency analysis at ungauged basin confluences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Cheng

2016-03-12

A reliable and accurate flood frequency analysis at the confluence of streams is of importance. Given that long-term peak flow observations are often unavailable at tributary confluences, at a practical level, this paper presents a joint probability approach (JPA) to address the coincidental flood frequency analysis at the ungauged confluence of two streams based on the flow rate data from the upstream tributaries. One case study is performed for comparison against several traditional approaches, including the position-plotting formula, the univariate flood frequency analysis, and the National Flood Frequency Program developed by US Geological Survey. It shows that the results generatedmore » by the JPA approach agree well with the floods estimated by the plotting position and univariate flood frequency analysis based on the observation data.« less

Vegetation and floristics of a lowland tropical rainforest in northeast Australia

PubMed Central

Apgaua, Deborah M. G.; Campbell, Mason J; Cox, Casey J; Crayn, Darren M; Ishida, Françoise Y; Laidlaw, Melinda J; Liddell, Michael J; Seager, Michael; Laurance, Susan G. W.

2016-01-01

Abstract Background Full floristic data, tree demography, and biomass estimates incorporating non-tree lifeforms are seldom collected and reported for forest plots in the tropics. Established research stations serve as important repositories of such biodiversity and ecological data. With a canopy crane setup within a tropical lowland rainforest estate, the 42-ha Daintree Rainforest Observatory (DRO) in Cape Tribulation, northern Australia is a research facility of international significance. We obtained an estimate of the vascular plant species richness for the site, by surveying all vascular plant species from various mature-phase, remnant and open vegetation patches within the site. We also integrate and report the demography and basal areas of trees ≥ 10 cm diameter at breast height (dbh) in a new 1-ha core plot, an extension to the pre-existing forest 1-ha plot under the canopy crane. In addition, we report for the canopy crane plot new demography and basal areas for smaller-size shrubs and treelets subsampled from nine 20 m2 quadrats, and liana basal area and abundance from the whole plot. The DRO site has an estimated total vascular plant species richness of 441 species, of which 172 species (39%) are endemic to Australia, and 4 species are endemics to the Daintree region. The 2 x 1-ha plots contains a total of 262 vascular plant species of which 116 (1531 individuals) are tree species ≥ 10 cm dbh. We estimate a stem basal area of 34.9 m2 ha-1, of which small stems (tree saplings and shrubs <10cm dbh) and lianas collectively contribute c.4.2%. Comparing the stem density-diversity patterns of the DRO forest with other tropical rainforests globally, our meta-analysis shows that DRO forests has a comparatively high stem density and moderate species diversity, due to the influence of cyclones. These data will provide an important foundation for ecological and conservation studies in lowland tropical forest. New information We present a floristic checklist, a lifeform breakdown, and demography data from two 1-ha rainforest plots from a lowland tropical rainforest study site. We also present a meta-analysis of stem densities and species diversity from comparable-sized plots across the tropics. PMID:27099552

Comparison of type 2 diabetes mellitus incidence in different phases of hepatitis B virus infection: A meta-analysis.

PubMed

Shen, Yi; Zhang, Sheng; Wang, Xulin; Wang, Yuanyuan; Zhang, Jian; Qin, Gang; Li, Wenchao; Ding, Kun; Zhang, Lei; Liang, Feng

2017-10-01

Because whether hepatitis B virus infection increases the risk of type 2 diabetes mellitus has been a controversial topic, pair-wise and network meta-analyses of published literature were carried out to accurately evaluate the association between different phases of hepatitis B virus infection and the risk of type 2 diabetes mellitus. A comprehensive literature retrieval was conducted from the PubMed, Embase, Cochrane Library and Chinese Database to identify epidemiological studies on the association between hepatitis B virus infection and the risk of type 2 diabetes mellitus that were published from 1999 to 2015. A pair-wise meta-analysis of direct evidence was performed to estimate the pooled odds ratios and 95% confidence intervals. A network meta-analysis was conducted, including the construction of a network plot, inconsistency plot, predictive interval plot, comparison-adjusted funnel plot and rank diagram, to graphically link the direct and indirect comparisons between different hepatitis B virus infective phases. Eighteen publications (n=113 639) describing 32 studies were included in this meta-analysis. In the pair-wise meta-analysis, the pooled odds ratio for type 2 diabetes mellitus in chronic hepatitis B cirrhosis patients was 1.76 (95% confidence interval: 1.44-2.14) when compared with non-cirrhotic chronic hepatitis B patients. In the network meta-analysis, six comparisons of four hepatitis B virus infectious states indicated the following descending order for the risk of type 2 diabetes mellitus: hepatitis B cirrhosis patients, non-cirrhotic chronic hepatitis B patients, hepatitis B virus carriers and non-hepatitis B virus controls. This study suggests that hepatitis B virus infection is not an independent risk factor for type 2 diabetes mellitus, but the development of cirrhosis may increase the incidence of type 2 diabetes mellitus cirrhosis. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

[Primary Study on Predicting the Termination of Paroxysmal Atrial Fibrillation Based on a Novel RdR RR Intervals Scatter Plot].

PubMed

Lu, Hongwei; Zhang, Chenxi; Sun, Ying; Hao, Zhidong; Wang, Chunfang; Tian, Jiajia

2015-08-01

Predicting the termination of paroxysmal atrial fibrillation (AF) may provide a signal to decide whether there is a need to intervene the AF timely. We proposed a novel RdR RR intervals scatter plot in our study. The abscissa of the RdR scatter plot was set to RR intervals and the ordinate was set as the difference between successive RR intervals. The RdR scatter plot includes information of RR intervals and difference between successive RR intervals, which captures more heart rate variability (HRV) information. By RdR scatter plot analysis of one minute RR intervals for 50 segments with non-terminating AF and immediately terminating AF, it was found that the points in RdR scatter plot of non-terminating AF were more decentralized than the ones of immediately terminating AF. By dividing the RdR scatter plot into uniform grids and counting the number of non-empty grids, non-terminating AF and immediately terminating AF segments were differentiated. By utilizing 49 RR intervals, for 20 segments of learning set, 17 segments were correctly detected, and for 30 segments of test set, 20 segments were detected. While utilizing 66 RR intervals, for 18 segments of learning set, 16 segments were correctly detected, and for 28 segments of test set, 20 segments were detected. The results demonstrated that during the last one minute before the termination of paroxysmal AF, the variance of the RR intervals and the difference of the neighboring two RR intervals became smaller. The termination of paroxysmal AF could be successfully predicted by utilizing the RdR scatter plot, while the predicting accuracy should be further improved.

Sensitivity of temporal heart rate variability in Poincaré plot to changes in parasympathetic nervous system activity.

PubMed

Karmakar, Chandan K; Khandoker, Ahsan H; Voss, Andreas; Palaniswami, Marimuthu

2011-03-03

A novel descriptor (Complex Correlation Measure (CCM)) for measuring the variability in the temporal structure of Poincaré plot has been developed to characterize or distinguish between Poincaré plots with similar shapes. This study was designed to assess the changes in temporal structure of the Poincaré plot using CCM during atropine infusion, 70° head-up tilt and scopolamine administration in healthy human subjects. CCM quantifies the point-to-point variation of the signal rather than gross description of the Poincaré plot. The physiological relevance of CCM was demonstrated by comparing the changes in CCM values with autonomic perturbation during all phases of the experiment. The sensitivities of short term variability (SD1), long term variability (SD2) and variability in temporal structure (CCM) were analyzed by changing the temporal structure by shuffling the sequences of points of the Poincaré plot. Surrogate analysis was used to show CCM as a measure of changes in temporal structure rather than random noise and sensitivity of CCM with changes in parasympathetic activity. CCM was found to be most sensitive to changes in temporal structure of the Poincaré plot as compared to SD1 and SD2. The values of all descriptors decreased with decrease in parasympathetic activity during atropine infusion and 70° head-up tilt phase. In contrast, values of all descriptors increased with increase in parasympathetic activity during scopolamine administration. The concordant reduction and enhancement in CCM values with parasympathetic activity indicates that the temporal variability of Poincaré plot is modulated by the parasympathetic activity which correlates with changes in CCM values. CCM is more sensitive than SD1 and SD2 to changes of parasympathetic activity.

Remeasured FIA plots reveal tree-level diameter growth and tree mortality impacts of nitrogen deposition on California’s forests

Treesearch

Mark E. Fenn; Jeremy S. Fried; Haiganoush K. Preisler; Andrzej Bytnerowicz; Susan Schilling; Sarah Jovan; Olaf Kuegler

2015-01-01

The air in California’s forests spans a broad range of purity, from virtually no locally generated pollutants to highly elevated levels of pollutants in forests downwind of urban and agricultural source areas. Ten-year remeasurement data from Forest Inventory and Analysis (FIA) plots in California were used in combination with modelled atmospheric nitrogen (N)...

A spatial econometric analysis of land-use change with land cover trends data: an application to the Pacific Northwest

Treesearch

David J. Lewis; Ralph J. Alig

2014-01-01

This paper develops a plot-level spatial econometric land-use model and estimates it with U.S. Geological Survey Land Cover Trends (LCT) geographic information system panel data for the western halves of the states of Oregon and Washington. The discrete-choice framework we use models plot-scale choices of the three dominant land uses in this region: forest, agriculture...

Numerical characteristics of recurrence plots as applied to the evaluation of mechanical damage in materials

NASA Astrophysics Data System (ADS)

Hilarov, V. L.

2017-09-01

The response of a material with a random uniform distribution of pores to a sound impulse was studied. The behavior of the numerical characteristics of the recurrence plots (RP) of the normal displacement vector component depending on the degree of damage was investigated. It was shown that the recurrence quantification analysis (RQA) parameters could be very informative for sonic fault detection.

Analysis of down wood volme and percent ground cover for the Missouri Ozark forest ecosystem project

Treesearch

Laura A. Herbeck

2000-01-01

Volume and percent ground cover of down wood were estimated on the MOFEP sites from two separate sampling inventories, line transects and fixed-area plots. Line transects were used to sample down wood in the 1990-91 and 1994-95 inventories and fixed-area plots were used in an additional inventory in 1995. Line transect inventories estimated a range in ground cover...

Effects of Market Prices and Silvicultural Practices on Lumber Value of Standing Trees In Uneven-Ages Plots

Treesearch

David W. Patterson

1998-01-01

Uneven-aged management plots were established using three variables (site index, basal area, and maximum diameter). This study looked at the significance of the variables on the lumber volume per acre, lumber value per thousand board feet (Mbf), and stand value per acre as well as the influence on these analysis by market prices (May 1997, May 1998, and October 1998)....

Basidiomycete fungal communities in Australian sclerophyll forest soil are altered by repeated prescribed burning.

PubMed

Anderson, Ian C; Bastias, Brigitte A; Genney, David R; Parkin, Pamela I; Cairney, John W G

2007-04-01

Soil basidiomycetes play key roles in forest nutrient and carbon cycling processes, yet the diversity and structure of below ground basidiomycete communities remain poorly understood. Prescribed burning is a commonly used forest management practice and there is evidence that single fire events can have an impact on soil fungal communities but little is known about the effects of repeated prescribed burning. We have used internal transcribed spacer (ITS) terminal restriction fragment length polymorphism (T-RFLP) analysis to investigate the impacts of repeated prescribed burning every two or four years over a period of 30 years on soil basidiomycete communities in an Australian wet sclerophyll forest. Detrended correspondence analysis of ITS T-RFLP profiles separated basidiomycete communities in unburned control plots from those in burned plots, with those burned every two years being the most different from controls. Burning had no effect on basidiomycete species richness, thus these differences appear to be due to changes in community structure. Basidiomycete communities in the unburned control plots were vertically stratified in the upper 20 cm of soil, but no evidence was found for stratification in the burned plots, suggesting that repeated prescribed burning results in more uniform basidiomycete communities. Overall, the results demonstrate that repeated prescribed burning alters soil basidiomycete communities, with the effect being greater with more frequent burning.

Dispersive analysis of ω→3 π and ϕ→3 π decays

NASA Astrophysics Data System (ADS)

Niecknig, Franz; Kubis, Bastian; Schneider, Sebastian P.

2012-05-01

We study the three-pion decays of the lightest isoscalar vector mesons, ω and ϕ, in a dispersive framework that allows for a consistent description of final-state interactions between all three pions. Our results are solely dependent on the phenomenological input for the pion-pion P-wave scattering phase shift. We predict the Dalitz plot distributions for both decays and compare our findings to recent measurements of the ϕ→3 π Dalitz plot by the KLOE and CMD-2 collaborations. Dalitz plot parameters for future precision measurements of ω→3 π are predicted. We also calculate the ππ P-wave inelasticity contribution from ωπ intermediate states.

Consistent Dalitz plot analysis of Cabibbo-favored D+ → K bar ππ+ decays

NASA Astrophysics Data System (ADS)

Niecknig, Franz; Kubis, Bastian

2018-05-01

We resume the study of the Cabibbo-favored charmed-meson decays D+ → K bar ππ+ in a dispersive framework that satisfies unitarity, analyticity, and crossing symmetry by construction. The formalism explicitly describes the strong final-state interactions between all three decay products and relies on pion-pion and pion-kaon phase shift input. For the first time, we show that the D+ →KSπ0π+ Dalitz plot obtained by the BESIII collaboration as well as the D+ →K-π+π+ Dalitz plot data by CLEO and FOCUS can be described consistently, exploiting the isospin relation between the two coupled decay channels that provides better constraints on the subtraction constants.

Species of Philometra (Nematoda, Philometridae) from fishes off the Mediterranean coast of Africa, with a description of Philometra rara n. sp. from Hyporthodus haifensis and a molecular analysis of Philometra saltatrix from Pomatomus saltatrix.

PubMed

Moravec, František; Chaabane, Amira; Neifar, Lassad; Gey, Delphine; Justine, Jean-Lou

2017-01-01

Two gonad-infecting species of Philometra Costa, 1845 (Nematoda, Philometridae) were recorded for the first time from marine perciform fishes off Tunisia and Libya: Philometra rara n. sp. from the rare, deep-water Haifa grouper Hyporthodus haifensis (Serranidae) off Libya and Philometra saltatrix Ramachandran, 1973 from the bluefish Pomatomus saltatrix (Pomatomidae) off Tunisia. Identification of both fish species was confirmed by molecular barcoding. Light and scanning electron microscope studies of Ph. rara n. sp. showed that it is characterized by the length of spicules (216-219 μm) and the gubernaculum (90-93 μm), the gubernaculum/spicules length ratio (1:2.32-2.43), and mainly by the shape and structure of the distal end of the gubernaculum (shovel-shaped with a wide median smooth field in dorsal view), appearing as having a dorsal protuberance in lateral view, and by the structure of the male caudal mound (dorsally interrupted); large subgravid females (70-137 mm long) are characterized by the presence of four oval submedian cephalic elevations, each of them bearing a pair of cephalic papillae of the outer circle. The finding of Ph. saltatrix off Tunisia confirms that this species is widespread throughout the Mediterranean region. A molecular analysis of our Ph. saltatrix specimens and other available philometrid cytochrome c oxidase 1 (COI) sequences showed that most species have robust clades. Sequences of Ph. saltatrix from Tunisia diverge from Ph. saltatrix from Brazil and the USA, suggesting that speciation is currently occurring between populations from both sides of the Atlantic Ocean. © F. Moravec et al., published by EDP Sciences, 2017.

Species of Philometra (Nematoda, Philometridae) from fishes off the Mediterranean coast of Africa, with a description of Philometra rara n. sp. from Hyporthodus haifensis and a molecular analysis of Philometra saltatrix from Pomatomus saltatrix

PubMed Central

2017-01-01

Two gonad-infecting species of Philometra Costa, 1845 (Nematoda, Philometridae) were recorded for the first time from marine perciform fishes off Tunisia and Libya: Philometra rara n. sp. from the rare, deep-water Haifa grouper Hyporthodus haifensis (Serranidae) off Libya and Philometra saltatrix Ramachandran, 1973 from the bluefish Pomatomus saltatrix (Pomatomidae) off Tunisia. Identification of both fish species was confirmed by molecular barcoding. Light and scanning electron microscope studies of Ph. rara n. sp. showed that it is characterized by the length of spicules (216–219 μm) and the gubernaculum (90–93 μm), the gubernaculum/spicules length ratio (1:2.32–2.43), and mainly by the shape and structure of the distal end of the gubernaculum (shovel-shaped with a wide median smooth field in dorsal view), appearing as having a dorsal protuberance in lateral view, and by the structure of the male caudal mound (dorsally interrupted); large subgravid females (70–137 mm long) are characterized by the presence of four oval submedian cephalic elevations, each of them bearing a pair of cephalic papillae of the outer circle. The finding of Ph. saltatrix off Tunisia confirms that this species is widespread throughout the Mediterranean region. A molecular analysis of our Ph. saltatrix specimens and other available philometrid cytochrome c oxidase 1 (COI) sequences showed that most species have robust clades. Sequences of Ph. saltatrix from Tunisia diverge from Ph. saltatrix from Brazil and the USA, suggesting that speciation is currently occurring between populations from both sides of the Atlantic Ocean. PMID:28287390

Landscape context and scale differentially impact coffee leaf rust, coffee berry borer, and coffee root-knot nematodes.

PubMed

Avelino, Jacques; Romero-Gurdián, Alí; Cruz-Cuellar, Héctor F; Declerck, Fabrice A J

2012-03-01

Crop pest and disease incidences at plot scale vary as a result of landscape effects. Two main effects can be distinguished. First, landscape context provides habitats of variable quality for pests, pathogens, and beneficial and vector organisms. Second, the movements of these organisms are dependent on the connectivity status of the landscape. Most of the studies focus on indirect effects of landscape context on pest abundance through their predators and parasitoids, and only a few on direct effects on pests and pathogens. Here we studied three coffee pests and pathogens, with limited or no pressure from host-specific natural enemies, and with widely varying life histories, to test their relationships with landscape context: a fungus, Hemileia vastatrix, causal agent of coffee leaf rust; an insect, the coffee berry borer, Hypothenemus hampei (Coleoptera: Curculionidae); and root-knot nematodes, Meloidogyne spp. Their incidence was assessed in 29 coffee plots from Turrialba, Costa Rica. In addition, we characterized the landscape context around these coffee plots in 12 nested circular sectors ranging from 50 to 1500 m in radius. We then performed correlation analysis between proportions of different land uses at different scales and coffee pest and disease incidences. We obtained significant positive correlations, peaking at the 150 m radius, between coffee berry borer abundance and proportion of coffee in the landscape. We also found significant positive correlations between coffee leaf rust incidence and proportion of pasture, peaking at the 200 m radius. Even after accounting for plot level predictors of coffee leaf rust and coffee berry borer through covariance analysis, the significance of landscape structure was maintained. We hypothesized that connected coffee plots favored coffee berry borer movements and improved its survival. We also hypothesized that wind turbulence, produced by low-wind-resistance land uses such as pasture, favored removal of coffee leaf rust spore clusters from host surfaces, resulting in increased epidemics. In contrast, root-knot nematode population density was not correlated to landscape context, possibly because nematodes are almost immobile in the soil. We propose fragmenting coffee plots with forest corridors to control coffee berry borer movements between coffee plots without favoring coffee leaf rust dispersal.

Isotopic Characterisation of Methane Emissions: use of Keeling-plot Methods to Identify Source Signatures in Boreal Wetlands and Other Settings

NASA Astrophysics Data System (ADS)

Fisher, R. E.; Lowry, D.; France, J.; Lanoiselle, M.; Zazzeri, G.; Nisbet, E. G.

2012-12-01

Different methane sources have different δ13CCH4 and δDCH4 signatures, which potentially provides a powerful constraint on models of methane emission budgets. However source signatures remain poorly known and need to be studied in more detail if isotopic measurements of ambient air are to be used to constrain regional and global emissions. The Keeling plot method (plotting δ13CCH4 or δDCH4 against 1/CH4 concentration in samples of ambient air in the close vicinity of known sources) directly assesses the source signature of the methane that is actually emitted to the air. This contrasts with chamber studies, measuring air within a chamber, where local micro-meteorological and microbiological processes are occurring. Keeling plot methods have been applied to a wide variety of settings in this study. The selection of appropriate background measurements for Keeling plot analysis is also considered. The method has been used on a local scale to identify the source signature of summer emissions from subarctic wetlands in Fennoscandia. Samples are collected from low height (0.3-3m) over the wetlands during 24-hour periods, to collect daily emissions maxima (warm late afternoons), inversion maxima (at the coldest time of the 24hr daylight: usually earliest morning), and ambient minima when mixing occurs (often mid afternoon). Some results are comparable to parallel chamber studies, but in other cases there are small but significant shifts between CH4 in chamber air and CH4 that is dispersing in the above-ground air. On a regional to continental scale the isotopic signature of bulk sources of emissions can be identified using Keeling plots. The methodology is very applicable for use in urban and urban-rural settings. For example, the winter SE monsoon sweeps from inland central Asia over China to Hong Kong. Application of back trajectory analysis and Keeling plot methods implied coal emissions may be a significant Chinese source of methane in January, although in other months biological sources dominate. Similarly, in London the method has been used to test the London methane emission inventory.

SWMPrats.net: A Web-Based Resource for Exploring SWMP ...

EPA Pesticide Factsheets

SWMPrats.net is a web-based resource that provides accessible approaches to using SWMP data. The website includes a user forum with instructional ‘Plots of the Month’; links to workshop content; and a description of the SWMPr data analysis package for R. Interactive “widgets” allow users to skip the boring parts of data analysis and get right to the fun: visualization and exploration! There are three widgets, each performing a different analysis: system-wide overviews, detailed temporal summaries of a single variable at a single site, and inter-comparisons between sites or variables through time. Users can visually explore system-wide trends in data using the Trends Map widget. For a more detailed analysis, users can create monthly and annual graphs of single variables and locations in the Summary Plot widget. Lastly, users can compare two variables or NERRS locations through time using the Aggregation widget. For all widgets, users can adjust the time period of interest. Plots and tables can also be downloaded for use in outreach, education, or further analysis. The tools and forums are meant to build a community of practice to move SWMP data analysis forward. All widgets will be demonstrated live at the poster session. This abstract is for a poster presentation at the 2016 annual meeting for the National Estuarine Research Reserve System, Nov. 13-18. We will describe our online web resources for the analysis and interpretation of monitoring da

Distributive On-line Processing, Visualization and Analysis System for Gridded Remote Sensing Data

NASA Technical Reports Server (NTRS)

Leptoukh, G.; Berrick, S.; Liu, Z.; Pham, L.; Rui, H.; Shen, S.; Teng, W.; Zhu, T.

2004-01-01

The ability to use data stored in the current Earth Observing System (EOS) archives for studying regional or global phenomena is highly dependent on having a detailed understanding of the data's internal structure and physical implementation. Gaining this understanding and applying it to data reduction is a time- consuming task that must be undertaken before the core investigation can begin. This is an especially difficult challenge when science objectives require users to deal with large multi-sensor data sets that are usually of different formats, structures, and resolutions, for example, when preparing data for input into modeling systems. The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) has taken a major step towards meeting this challenge by developing an infrastructure with a Web interface that allows users to perform interactive analysis online without downloading any data, the GES-DISC Interactive Online Visualization and Analysis Infrastructure or "Giovanni." Giovanni provides interactive, online, analysis tools for data users to facilitate their research. There have been several instances of this interface created to serve TRMM users, Aerosol scientists, Ocean Color and Agriculture applications users. The first generation of these tools support gridded data only. The user selects geophysical parameters, area of interest, time period; and the system generates an output on screen in a matter of seconds. The currently available output options are: Area plot averaged or accumulated over any available data period for any rectangular area; Time plot time series averaged over any rectangular area; Time plots image view of any longitude-time and latitude-time cross sections; ASCII output for all plot types; Image animation for area plot. In the future, we will add correlation plots, GIS-compatible outputs, etc. This allow user to focus on data content (i.e. science parameters) and eliminate the need for expensive learning, development and processing tasks that are redundantly incurred by an archive's user community. The current implementation utilizes the GrADS-DODS Server (GDS), a stable, secure data server that provides subsetting and analysis services across the Internet for any GrADS-readable dataset. The subsetting capability allows users to retrieve a specified temporal and/or spatial subdomain from a large dataset, eliminating the need to download everything simply to access a small relevant portion of a dataset. The analysis capability allows users to retrieve the results of an operation applied to one or more datasets on the server. In our case, we use this approach to read pre-processed binary files and/or to read and extract the needed parts from HDF or HDF-EOS files. These subsets then serve as inputs into GrADS processing and analysis scripts. It can be used in a wide variety of Earth science applications: climate and weather events study and monitoring; modeling. It can be easily configured for new applications.

Insights into gait disorders: walking variability using phase plot analysis, Parkinson's disease.

PubMed

Esser, Patrick; Dawes, Helen; Collett, Johnny; Howells, Ken

2013-09-01

Gait variability may have greater utility than spatio-temporal parameters and can, be an indication for risk of falling in people with Parkinson's disease (PD). Current methods rely on prolonged data collection in order to obtain large datasets which may be demanding to obtain. We set out to explore a phase plot variability analysis to differentiate typically developed adults (TDAs) from PD obtained from two 10 m walks. Fourteen people with PD and good mobility (Rivermead Mobility Index≥8) and ten aged matched TDA were recruited and walked over 10-m at self-selected walking speed. An inertial measurement unit was placed over the projected centre of mass (CoM) sampling at 100 Hz. Vertical CoM excursion was derived to determine modelled spatiotemporal data after which the phase plot analysis was applied producing a cloud of datapoints. SDA described the spread and SDB the width of the cloud with β the angular vector of the data points. The ratio (∀) was defined as SDA: SDB. Cadence (p=.342) and stride length (p=.615) did not show a significance between TDA and PD. A difference was found for walking speed (p=.041). Furthermore a significant difference was found for β (p=.010), SDA (p=.004) other than SDB (p=.385) or ratio ∀ (p=.830). Two sequential 10-m walks showed no difference in PD for cadence (p=.193), stride length (p=.683), walking speed (p=.684) and β (p=.194), SDA (p=.051), SDB (p=.145) or ∀ (p=.226). The proposed phase plot analysis, performed on CoM motion could be used to reliably differentiate PD from TDA over a 10-m walk. Copyright © 2013 Elsevier B.V. All rights reserved.

The effect of habitat modification on plant-pollinator network

NASA Astrophysics Data System (ADS)

Aminatun, Tien; Putra, Nugroho Susetya

2017-08-01

The research aimed to determine; (1) the mutualism interaction pattern of plant-pollinator on several habitat modifications; and (2) the habitat modification which showed the most stable pattern of interaction. The study was conducted in one planting season with 20 plots which each plot had 2x2 m2 width and 2 m spacing among plots, and each plot was planted with the same variety of tomato plants, i.e. "intan". Nitrogen manipulation treatment was conducted with four kinds of fertilizers, i.e. NPK (code PU), compost (code PKM), vermicompost (code PC), and manure (code PK). Each treatment had 5 plot replications. We observed the growth of tomato plants, weed and arthropod populationstwo weekly while pollinator visitation twice a week during tomato plant flowering with counting population and visitation frequence of each pollinator on each sample of tomato plants. The nectar of tomato plant flower of each treatment was tested in laboratory to see its reducing sugar and sucrose. Oganic matter and nitrogen of the soil samples of each treatment were tested in laboratory in the beginning and the end of this research. We analized the plant-pollinator network with bipartite program in R-statistics, and the abiotic and other biotic factors with descriptive analysis. The results of the research were; (1) the mutualism interaction pattern of plant-pollinator network of four treatments were varied, and (2) The pattern of plant-pollinator network of NPK fertilizer treatment showed the more stable interaction based on analysis of interaction evenness, Shannon diversity, frequency and longevity of pollinator visitation.

Multi-Reader ROC studies with Split-Plot Designs: A Comparison of Statistical Methods

PubMed Central

Obuchowski, Nancy A.; Gallas, Brandon D.; Hillis, Stephen L.

2012-01-01

Rationale and Objectives Multi-reader imaging trials often use a factorial design, where study patients undergo testing with all imaging modalities and readers interpret the results of all tests for all patients. A drawback of the design is the large number of interpretations required of each reader. Split-plot designs have been proposed as an alternative, in which one or a subset of readers interprets all images of a sample of patients, while other readers interpret the images of other samples of patients. In this paper we compare three methods of analysis for the split-plot design. Materials and Methods Three statistical methods are presented: Obuchowski-Rockette method modified for the split-plot design, a newly proposed marginal-mean ANOVA approach, and an extension of the three-sample U-statistic method. A simulation study using the Roe-Metz model was performed to compare the type I error rate, power and confidence interval coverage of the three test statistics. Results The type I error rates for all three methods are close to the nominal level but tend to be slightly conservative. The statistical power is nearly identical for the three methods. The coverage of 95% CIs fall close to the nominal coverage for small and large sample sizes. Conclusions The split-plot MRMC study design can be statistically efficient compared with the factorial design, reducing the number of interpretations required per reader. Three methods of analysis, shown to have nominal type I error rate, similar power, and nominal CI coverage, are available for this study design. PMID:23122570

Poincaré plot analysis of autocorrelation function of RR intervals in patients with acute myocardial infarction.

PubMed

Chuang, Shin-Shin; Wu, Kung-Tai; Lin, Chen-Yang; Lee, Steven; Chen, Gau-Yang; Kuo, Cheng-Deng

2014-08-01

The Poincaré plot of RR intervals (RRI) is obtained by plotting RRIn+1 against RRIn. The Pearson correlation coefficient (ρRRI), slope (SRRI), Y-intercept (YRRI), standard deviation of instantaneous beat-to-beat RRI variability (SD1RR), and standard deviation of continuous long-term RRI variability (SD2RR) can be defined to characterize the plot. Similarly, the Poincaré plot of autocorrelation function (ACF) of RRI can be obtained by plotting ACFk+1 against ACFk. The corresponding Pearson correlation coefficient (ρACF), slope (SACF), Y-intercept (YACF), SD1ACF, and SD2ACF can be defined similarly to characterize the plot. By comparing the indices of Poincaré plots of RRI and ACF between patients with acute myocardial infarction (AMI) and patients with patent coronary artery (PCA), we found that the ρACF and SACF were significantly larger, whereas the RMSSDACF/SDACF and SD1ACF/SD2ACF were significantly smaller in AMI patients. The ρACF and SACF correlated significantly and negatively with normalized high-frequency power (nHFP), and significantly and positively with normalized very low-frequency power (nVLFP) of heart rate variability in both groups of patients. On the contrary, the RMSSDACF/SDACF and SD1ACF/SD2ACF correlated significantly and positively with nHFP, and significantly and negatively with nVLFP and low-/high-frequency power ratio (LHR) in both groups of patients. We concluded that the ρACF, SACF, RMSSDACF/SDACF, and SD1ACF/SD2ACF, among many other indices of ACF Poincaré plot, can be used to differentiate between patients with AMI and patients with PCA, and that the increase in ρACF and SACF and the decrease in RMSSDACF/SDACF and SD1ACF/SD2ACF suggest an increased sympathetic and decreased vagal modulations in both groups of patients.

Biodiversity Measurement Using Indices Based on Hyperspectral Reflectance on the Coast of Lagos

NASA Astrophysics Data System (ADS)

Omodanisi, E. O.; Salami, A. T.

2013-12-01

Hyperspectral measurements provide explicit measurements which can be used in the analysis of biodiversity change. This study was carried out in the coastal area of Lagos State, Nigeria. The objective of this study was to determine if gasoline seepage affects vegetation species distribution and reflectance; with the view to analyzing the vegetation condition. To evaluate the potential of different reflectance spectroscopy of species, the ASD Handheld2 Spectrometer was used. Three identified impacted plots of 30m by 30m were selected randomly and a control plot established in relatively undisturbed vegetated areas away from but perpendicular to the source of seepage. Each identified plot and the control consisted of five transects and measurement were taken at every 2m with about four reflectance measurement per sample point, to average out differences in reflectance as a result of different leaf angles. The radiance output of the spectrometer was converted into reflectance using the reflectance of a white reference over a standardized white spectralon panel. Indices such as Normalized Differential Vegetation Index, RedEdge Normalized Difference Vegetation Index, Soil Adjusted Vegetation Index, Ratio Vegetation Index and Volgelmann RedEdge Index 1 were calculated to accurately estimate the chlorophyll content in the vegetation within optimal band wavelength. Shannon-Weiner's index, Spearman's rank correlation and Analysis of Variance were used to analyze the data. Cocos nucifera was observed to be the most dominant species with a relative abundance of 47.27% while Ananas comosus recorded the lowest relative abundance of 21.8%. In the control plot, Cocos nucifera had the highest relative abundance of 42.3% and Mangifera indica with the least relative abundance of 16.7%. The relationship between the indices and chlorophyll content of the vegetation were significantly higher at (p>0.01) for all the indices in all the plots; however, RedEdgeNDVI and VOG1 indices had the highest occurring frequency among the entire plots. Thus they were used to distinguish relatively healthy from relatively unhealthy vegetation and it was statistically higher at F-ratio 4.825 (p<0.01) and 3.194 (p<0.01) respectively. It was concluded that gasoline affected the condition of vegetation.Table 2: Spearman's rank correlation analysis for relating indices with chlorophyll content for the field data at p>0.01, rho - correlation coefficient. (Source: Author: 2012) Field Spectral Indices Measurement The measurement above is the averaged value for the entire transect in each plot.(Source: Author, 2012)

NMR Spectroscopy Identifies Metabolites Translocated from Powdery Mildew Resistant Rootstocks to Susceptible Watermelon Scions.

PubMed

Mahmud, Iqbal; Kousik, Chandrasekar; Hassell, Richard; Chowdhury, Kamal; Boroujerdi, Arezue F

2015-09-16

Powdery mildew (PM) disease causes significant loss in watermelon. Due to the unavailability of a commercial watermelon variety that is resistant to PM, grafting susceptible cultivars on wild resistant rootstocks is being explored as a short-term management strategy to combat this disease. Nuclear magnetic resonance-based metabolic profiles of susceptible and resistant rootstocks of watermelon and their corresponding susceptible scions (Mickey Lee) were compared to screen for potential metabolites related to PM resistance using multivariate principal component analysis. Significant score plot differences between the susceptible and resistant groups were revealed through Mahalanobis distance analysis. Significantly different spectral buckets and their corresponding metabolites (including choline, fumarate, 5-hydroxyindole-3-acetate, and melatonin) have been identified quantitatively using multivariate loading plots and verified by volcano plot analyses. The data suggest that these metabolites were translocated from the powdery mildew resistant rootstocks to their corresponding powdery mildew susceptible scions and can be related to PM disease resistance.

On the relationship between matched filter theory as applied to gust loads and phased design loads analysis

NASA Technical Reports Server (NTRS)

Zeiler, Thomas A.; Pototzky, Anthony S.

1989-01-01

A theoretical basis and example calculations are given that demonstrate the relationship between the Matched Filter Theory approach to the calculation of time-correlated gust loads and Phased Design Load Analysis in common use in the aerospace industry. The relationship depends upon the duality between Matched Filter Theory and Random Process Theory and upon the fact that Random Process Theory is used in Phased Design Loads Analysis in determining an equiprobable loads design ellipse. Extensive background information describing the relevant points of Phased Design Loads Analysis, calculating time-correlated gust loads with Matched Filter Theory, and the duality between Matched Filter Theory and Random Process Theory is given. It is then shown that the time histories of two time-correlated gust load responses, determined using the Matched Filter Theory approach, can be plotted as parametric functions of time and that the resulting plot, when superposed upon the design ellipse corresponding to the two loads, is tangent to the ellipse. The question is raised of whether or not it is possible for a parametric load plot to extend outside the associated design ellipse. If it is possible, then the use of the equiprobable loads design ellipse will not be a conservative design practice in some circumstances.

Advanced Poincaré plot analysis differentiates between hypertensive pregnancy disorders.

PubMed

Seeck, A; Baumert, M; Fischer, C; Khandoker, A; Faber, R; Voss, A

2011-10-01

Hypertensive pregnancy disorders affect 6% to 8% of all pregnancies and can result in severe complications for the mother and the foetus of which pre-eclampsia (PE) has the worst perinatal outcome. Several studies suggested that the autonomic nervous system plays an important role in the process of developing hypertensive pregnancy disorders, especially PE. The aim of this retrospective study was to investigate whether women with PE could be differentiated from women with various other hypertensive pregnancy disorders, by employing an enhanced Poincaré plot analysis (PPA), the segmented Poincaré plot analysis (SPPA), to their beat-to-beat interval and blood pressure signals. Sixty-nine pregnant women with hypertensive disorders (29 PE, 40 with chronic or gestational hypertension) were included. The SPPA as well as the traditional PPA found significant differences between PE and other hypertensive disorders of diastolic blood pressure (p < 0.001 versus p < 0.001) but only the SPPA method revealed significant differences (p < 0.001) also of the systolic blood pressure. Further on, linear discrimination analysis demonstrated that indices derived from SPPA are more suitable for differentiation between chronic and gestational hypertension and PE than those from traditional PPA (area under the ROC curve 0.85 versus 0.69). Therefore this procedure could contribute to the differential diagnosis of hypertensive pregnancy disorders.

UV Resonance Raman Elucidation of the Terminal and Internal Peptide Bond Conformations of Crystalline and Solution Oligoglycines.

PubMed

Bykov, Sergei V; Asher, Sanford A

2010-11-30

Spectroscopic investigations of macromolecules generally attempt to interpret the measured spectra in terms of the summed contributions of the different molecular fragments. This is the basis of the local mode approximation in vibrational spectroscopy. In the case of resonance Raman spectroscopy independent contributions of molecular fragments require both a local mode-like behavior and the uncoupled electronic transitions. Here we show that the deep UV resonance Raman spectra of aqueous solution phase oligoglycines show independent peptide bond molecular fragment contributions indicating that peptide bonds electronic transitions and vibrational modes are uncoupled. We utilize this result to separately determine the conformational distributions of the internal and penultimate peptide bonds of oligoglycines. Our data indicate that in aqueous solution the oligoglycine terminal residues populate conformations similar to those found in crystals (3(1)-helices and β-strands), but with a broader distribution, while the internal peptide bond conformations are centered around the 3(1)-helix Ramachandran angles.

α/β coiled coils

PubMed Central

Hartmann, Marcus D; Mendler, Claudia T; Bassler, Jens; Karamichali, Ioanna; Ridderbusch, Oswin; Lupas, Andrei N; Hernandez Alvarez, Birte

2016-01-01

Coiled coils are the best-understood protein fold, as their backbone structure can uniquely be described by parametric equations. This level of understanding has allowed their manipulation in unprecedented detail. They do not seem a likely source of surprises, yet we describe here the unexpected formation of a new type of fiber by the simple insertion of two or six residues into the underlying heptad repeat of a parallel, trimeric coiled coil. These insertions strain the supercoil to the breaking point, causing the local formation of short β-strands, which move the path of the chain by 120° around the trimer axis. The result is an α/β coiled coil, which retains only one backbone hydrogen bond per repeat unit from the parent coiled coil. Our results show that a substantially novel backbone structure is possible within the allowed regions of the Ramachandran space with only minor mutations to a known fold. DOI: http://dx.doi.org/10.7554/eLife.11861.001 PMID:26771248

A Plastic Temporal Brain Code for Conscious State Generation

PubMed Central

Dresp-Langley, Birgitta; Durup, Jean

2009-01-01

Consciousness is known to be limited in processing capacity and often described in terms of a unique processing stream across a single dimension: time. In this paper, we discuss a purely temporal pattern code, functionally decoupled from spatial signals, for conscious state generation in the brain. Arguments in favour of such a code include Dehaene et al.'s long-distance reverberation postulate, Ramachandran's remapping hypothesis, evidence for a temporal coherence index and coincidence detectors, and Grossberg's Adaptive Resonance Theory. A time-bin resonance model is developed, where temporal signatures of conscious states are generated on the basis of signal reverberation across large distances in highly plastic neural circuits. The temporal signatures are delivered by neural activity patterns which, beyond a certain statistical threshold, activate, maintain, and terminate a conscious brain state like a bar code would activate, maintain, or inactivate the electronic locks of a safe. Such temporal resonance would reflect a higher level of neural processing, independent from sensorial or perceptual brain mechanisms. PMID:19644552

Dual Solutions for Nonlinear Flow Using Lie Group Analysis

PubMed Central

Awais, Muhammad; Hayat, Tasawar; Irum, Sania; Saleem, Salman

2015-01-01

`The aim of this analysis is to investigate the existence of the dual solutions for magnetohydrodynamic (MHD) flow of an upper-convected Maxwell (UCM) fluid over a porous shrinking wall. We have employed the Lie group analysis for the simplification of the nonlinear differential system and computed the absolute invariants explicitly. An efficient numerical technique namely the shooting method has been employed for the constructions of solutions. Dual solutions are computed for velocity profile of an upper-convected Maxwell (UCM) fluid flow. Plots reflecting the impact of dual solutions for the variations of Deborah number, Hartman number, wall mass transfer are presented and analyzed. Streamlines are also plotted for the wall mass transfer effects when suction and blowing situations are considered. PMID:26575996

Multiscale recurrence quantification analysis of order recurrence plots

NASA Astrophysics Data System (ADS)

Xu, Mengjia; Shang, Pengjian; Lin, Aijing

2017-03-01

In this paper, we propose a new method of multiscale recurrence quantification analysis (MSRQA) to analyze the structure of order recurrence plots. The MSRQA is based on order patterns over a range of time scales. Compared with conventional recurrence quantification analysis (RQA), the MSRQA can show richer and more recognizable information on the local characteristics of diverse systems which successfully describes their recurrence properties. Both synthetic series and stock market indexes exhibit their properties of recurrence at large time scales that quite differ from those at a single time scale. Some systems present more accurate recurrence patterns under large time scales. It demonstrates that the new approach is effective for distinguishing three similar stock market systems and showing some inherent differences.

Three-dimensional evidence network plot system: covariate imbalances and effects in network meta-analysis explored using a new software tool.

PubMed

Batson, Sarah; Score, Robert; Sutton, Alex J

2017-06-01

The aim of the study was to develop the three-dimensional (3D) evidence network plot system-a novel web-based interactive 3D tool to facilitate the visualization and exploration of covariate distributions and imbalances across evidence networks for network meta-analysis (NMA). We developed the 3D evidence network plot system within an AngularJS environment using a third party JavaScript library (Three.js) to create the 3D element of the application. Data used to enable the creation of the 3D element for a particular topic are inputted via a Microsoft Excel template spreadsheet that has been specifically formatted to hold these data. We display and discuss the findings of applying the tool to two NMA examples considering multiple covariates. These two examples have been previously identified as having potentially important covariate effects and allow us to document the various features of the tool while illustrating how it can be used. The 3D evidence network plot system provides an immediate, intuitive, and accessible way to assess the similarity and differences between the values of covariates for individual studies within and between each treatment contrast in an evidence network. In this way, differences between the studies, which may invalidate the usual assumptions of an NMA, can be identified for further scrutiny. Hence, the tool facilitates NMA feasibility/validity assessments and aids in the interpretation of NMA results. The 3D evidence network plot system is the first tool designed specifically to visualize covariate distributions and imbalances across evidence networks in 3D. This will be of primary interest to systematic review and meta-analysis researchers and, more generally, those assessing the validity and robustness of an NMA to inform reimbursement decisions. Copyright © 2017 Elsevier Inc. All rights reserved.

Opportunities for Integrated Ecological Analysis across Inland Australia with Standardised Data from Ausplots Rangelands.

PubMed

Guerin, Greg R; Sparrow, Ben; Tokmakoff, Andrew; Smyth, Anita; Leitch, Emrys; Baruch, Zdravko; Lowe, Andrew J

2017-01-01

Australian rangelands ecosystems cover 81% of the continent but are understudied and continental-scale research has been limited in part by a lack of precise data that are standardised between jurisdictions. We present a new dataset from AusPlots Rangelands that enables integrative rangelands analysis due to its geographic scope and standardised methodology. The method provides data on vegetation and soils, enabling comparison of a suite of metrics including fractional vegetation cover, basal area, and species richness, diversity, and composition. Cover estimates are robust and repeatable, allowing comparisons among environments and detection of modest change. The 442 field plots presented here span a rainfall gradient of 129-1437 mm Mean annual precipitation with varying seasonality. Vegetation measurements include vouchered vascular plant species, growth form, basal area, height, cover and substrate type from 1010 point intercepts as well as systematically recorded absences, which are useful for predictive modelling and validation of remote sensing applications. Leaf and soil samples are sampled for downstream chemical and genomic analysis. We overview the sampling of vegetation parameters and environments, applying the data to the question of how species abundance distributions (SADs) vary over climatic gradients, a key question for the influence of environmental change on ecosystem processes. We found linear relationships between SAD shape and rainfall within grassland and shrubland communities, indicating more uneven abundance in deserts and suggesting relative abundance may shift as a consequence of climate change, resulting in altered diversity and ecosystem function. The standardised data of AusPlots enables such analyses at large spatial scales, and the testing of predictions through time with longitudinal sampling. In future, the AusPlots field program will be directed towards improving coverage of space, under-represented environments, vegetation types and fauna and, increasingly, re-sampling of established plots. Providing up-to-date data access methods to enhance re-use is also a priority.

Average Stand Age from Forest Inventory Plots Does Not Describe Historical Fire Regimes in Ponderosa Pine and Mixed-Conifer Forests of Western North America.

PubMed

Stevens, Jens T; Safford, Hugh D; North, Malcolm P; Fried, Jeremy S; Gray, Andrew N; Brown, Peter M; Dolanc, Christopher R; Dobrowski, Solomon Z; Falk, Donald A; Farris, Calvin A; Franklin, Jerry F; Fulé, Peter Z; Hagmann, R Keala; Knapp, Eric E; Miller, Jay D; Smith, Douglas F; Swetnam, Thomas W; Taylor, Alan H

Quantifying historical fire regimes provides important information for managing contemporary forests. Historical fire frequency and severity can be estimated using several methods; each method has strengths and weaknesses and presents challenges for interpretation and verification. Recent efforts to quantify the timing of historical high-severity fire events in forests of western North America have assumed that the "stand age" variable from the US Forest Service Forest Inventory and Analysis (FIA) program reflects the timing of historical high-severity (i.e. stand-replacing) fire in ponderosa pine and mixed-conifer forests. To test this assumption, we re-analyze the dataset used in a previous analysis, and compare information from fire history records with information from co-located FIA plots. We demonstrate that 1) the FIA stand age variable does not reflect the large range of individual tree ages in the FIA plots: older trees comprised more than 10% of pre-stand age basal area in 58% of plots analyzed and more than 30% of pre-stand age basal area in 32% of plots, and 2) recruitment events are not necessarily related to high-severity fire occurrence. Because the FIA stand age variable is estimated from a sample of tree ages within the tree size class containing a plurality of canopy trees in the plot, it does not necessarily include the oldest trees, especially in uneven-aged stands. Thus, the FIA stand age variable does not indicate whether the trees in the predominant size class established in response to severe fire, or established during the absence of fire. FIA stand age was not designed to measure the time since a stand-replacing disturbance. Quantification of historical "mixed-severity" fire regimes must be explicit about the spatial scale of high-severity fire effects, which is not possible using FIA stand age data.

Average Stand Age from Forest Inventory Plots Does Not Describe Historical Fire Regimes in Ponderosa Pine and Mixed-Conifer Forests of Western North America

PubMed Central

Stevens, Jens T.; Safford, Hugh D.; North, Malcolm P.; Fried, Jeremy S.; Gray, Andrew N.; Brown, Peter M.; Dolanc, Christopher R.; Dobrowski, Solomon Z.; Falk, Donald A.; Farris, Calvin A.; Franklin, Jerry F.; Fulé, Peter Z.; Hagmann, R. Keala; Knapp, Eric E.; Miller, Jay D.; Smith, Douglas F.; Swetnam, Thomas W.; Taylor, Alan H.

2016-01-01

Quantifying historical fire regimes provides important information for managing contemporary forests. Historical fire frequency and severity can be estimated using several methods; each method has strengths and weaknesses and presents challenges for interpretation and verification. Recent efforts to quantify the timing of historical high-severity fire events in forests of western North America have assumed that the “stand age” variable from the US Forest Service Forest Inventory and Analysis (FIA) program reflects the timing of historical high-severity (i.e. stand-replacing) fire in ponderosa pine and mixed-conifer forests. To test this assumption, we re-analyze the dataset used in a previous analysis, and compare information from fire history records with information from co-located FIA plots. We demonstrate that 1) the FIA stand age variable does not reflect the large range of individual tree ages in the FIA plots: older trees comprised more than 10% of pre-stand age basal area in 58% of plots analyzed and more than 30% of pre-stand age basal area in 32% of plots, and 2) recruitment events are not necessarily related to high-severity fire occurrence. Because the FIA stand age variable is estimated from a sample of tree ages within the tree size class containing a plurality of canopy trees in the plot, it does not necessarily include the oldest trees, especially in uneven-aged stands. Thus, the FIA stand age variable does not indicate whether the trees in the predominant size class established in response to severe fire, or established during the absence of fire. FIA stand age was not designed to measure the time since a stand-replacing disturbance. Quantification of historical “mixed-severity” fire regimes must be explicit about the spatial scale of high-severity fire effects, which is not possible using FIA stand age data. PMID:27196621

Nearest Neighbor Interactions Affect the Conformational Distribution in the Unfolded State of Peptides

NASA Astrophysics Data System (ADS)

Toal, Siobhan; Schweitzer-Stenner, Reinhard; Rybka, Karin; Schwalbe, Hardol

2013-03-01

In order to enable structural predictions of intrinsically disordered proteins (IDPs) the intrinsic conformational propensities of amino acids must be complimented by information on nearest-neighbor interactions. To explore the influence of nearest-neighbors on conformational distributions, we preformed a joint vibrational (Infrared, Vibrational Circular Dichroism (VCD), polarized Raman) and 2D-NMR study of selected GxyG host-guest peptides: GDyG, GSyG, GxLG, GxVG, where x/y ={A,K,LV}. D and S (L and V) were chosen at the x (y) position due to their observance to drastically change the distribution of alanine in xAy tripeptide sequences in truncated coil libraries. The conformationally sensitive amide' profiles of the respective spectra were analyzed in terms of a statistical ensemble described as a superposition of 2D-Gaussian functions in Ramachandran space representing sub-ensembles of pPII-, β-strand-, helical-, and turn-like conformations. Our analysis and simulation of the amide I' band profiles exploits excitonic coupling between the local amide I' vibrational modes in the tetra-peptides. The resulting distributions reveal that D and S, which themselves have high propensities for turn-structures, strongly affect the conformational distribution of their downstream neighbor. Taken together, our results indicate that Dx and Sx motifs might act as conformational randomizers in proteins, attenuating intrinsic propensities of neighboring residues. Overall, our results show that nearest neighbor interactions contribute significantly to the Gibbs energy landscape of disordered peptides and proteins.

Recovery of heart rate variability after treadmill exercise analyzed by lagged Poincaré plot and spectral characteristics.

PubMed

Shi, Ping; Hu, Sijung; Yu, Hongliu

2018-02-01

The aim of this study was to analyze the recovery of heart rate variability (HRV) after treadmill exercise and to investigate the autonomic nervous system response after exercise. Frequency domain indices, i.e., LF(ms 2 ), HF(ms 2 ), LF(n.u.), HF(n.u.) and LF/HF, and lagged Poincaré plot width (SD1 m ) and length (SD2 m ) were introduced for comparison between the baseline period (Pre-E) before treadmill running and two periods after treadmill running (Post-E1 and Post-E2). The correlations between lagged Poincaré plot indices and frequency domain indices were applied to reveal the long-range correlation between linear and nonlinear indices during the recovery of HRV. The results suggested entirely attenuated autonomic nervous activity to the heart following the treadmill exercise. After the treadmill running, the sympathetic nerves achieved dominance and the parasympathetic activity was suppressed, which lasted for more than 4 min. The correlation coefficients between lagged Poincaré plot indices and spectral power indices could separate not only Pre-E and two sessions after the treadmill running, but also the two sessions in recovery periods, i.e., Post-E1 and Post-E2. Lagged Poincaré plot as an innovative nonlinear method showed a better performance over linear frequency domain analysis and conventional nonlinear Poincaré plot.

Exploring and accounting for publication bias in mental health: a brief overview of methods.

PubMed

Mavridis, Dimitris; Salanti, Georgia

2014-02-01

OBJECTIVE Publication bias undermines the integrity of published research. The aim of this paper is to present a synopsis of methods for exploring and accounting for publication bias. METHODS We discussed the main features of the following methods to assess publication bias: funnel plot analysis; trim-and-fill methods; regression techniques and selection models. We applied these methods to a well-known example of antidepressants trials that compared trials submitted to the Food and Drug Administration (FDA) for regulatory approval. RESULTS The funnel plot-related methods (visual inspection, trim-and-fill, regression models) revealed an association between effect size and SE. Contours of statistical significance showed that asymmetry in the funnel plot is probably due to publication bias. Selection model found a significant correlation between effect size and propensity for publication. CONCLUSIONS Researchers should always consider the possible impact of publication bias. Funnel plot-related methods should be seen as a means of examining for small-study effects and not be directly equated with publication bias. Possible causes for funnel plot asymmetry should be explored. Contours of statistical significance may help disentangle whether asymmetry in a funnel plot is caused by publication bias or not. Selection models, although underused, could be useful resource when publication bias and heterogeneity are suspected because they address directly the problem of publication bias and not that of small-study effects.

Effects of soil water table regime on tree community species richness and structure of alluvial forest fragments in Southeast Brazil.

PubMed

Silva, A C; Higuchi, P; van den Berg, E

2010-08-01

In order to determine the influence of soil water table fluctuation on tree species richness and structure of alluvial forest fragments, 24 plots were allocated in a point bar forest and 30 plots in five forest fragments located in a floodplain, in the municipality of São Sebastião da Bela Vista, Southeast Brazil, totalizing 54, 10 X 20 m, plots. The information recorded in each plot were the soil water table level, diameter at breast height (dbh), total height and botanical identity off all trees with dbh > 5 cm. The water table fluctuation was assessed through 1 m deep observation wells in each plot. Correlations analysis indicated that sites with shallower water table in the flooding plains had a low number of tree species and high tree density. Although the water table in the point bar remained below the wells during the study period, low tree species richness was observed. There are other events taking place within the point bar forest that assume a high ecological importance, such as the intensive water velocity during flooding and sedimentation processes.

A regional-scale survey and analysis of forest growth and mortality as affected by site and stand factors and acidic deposition

Treesearch

Robert T. Brooks

1994-01-01

Regression analyses were used to identify factors most closely related to species growth and mortality on continuous forest survey plots in Pennsylvania. In 1985, 200 plots with two prior measurements (in the 1960s and 1970s) were selected and measured for a third time to determine periodic forest growth and mortality rates. Growth and mortality were analyzed for...

Tree-level imputation techniques to estimate current plot-level attributes in the Pacific Northwest using paneled inventory data

Treesearch

Bianca Eskelson; Temesgen Hailemariam; Tara Barrett

2009-01-01

The Forest Inventory and Analysis program (FIA) of the US Forest Service conducts a nationwide annual inventory. One panel (20% or 10% of all plots in the eastern and western United States, respectively) is measured each year. The precision of the estimates for any given year from one panel is low, and the moving average (MA), which is considered to be the default...

Analysis of Sample Size, Counting Time, and Plot Size from an Avian Point Count Survey on Hoosier National Forest, Indiana

Treesearch

Frank R. Thompson; Monica J. Schwalbach

1995-01-01

We report results of a point count survey of breeding birds on Hoosier National Forest in Indiana. We determined sample size requirements to detect differences in means and the effects of count duration and plot size on individual detection rates. Sample size requirements ranged from 100 to >1000 points with Type I and II error rates of <0.1 and 0.2. Sample...