Unconstrained Analysis Research Articles

REDESCRIPTION AND PHYLOGENETIC POSITION OF CAYPULLISAURUS (ICHTHYOSAURIA: OPHTHALMOSAURIDAE)

Abstract The ophthalmosaurid Caypullisaurus from the Late Jurassic–Early Cretaceous of the Neuquen Basin, Argentina, is redescribed based on new information from recent discoveries. Cladistic analysis of Caypullisaurus, based on previous ichthyopterygian data sets and using NONA, yielded two most parsimonious trees. Two clades are recognized within the Ophthalmosauridae. Caypullisaurus is found to be nested with Brachypterygius and Platypterygius. Simultaneous, unconstrained analysis, using unambiguous character optimization, is suggested as the best way to analyze data sets with large amounts of missing data.

Cosmological Constraints from the Red‐Sequence Cluster Survey

[abridged] We present a first cosmological analysis of a refined cluster catalog from the Red-Sequence Cluster Survey (RCS). The input cluster sample is derived from 72.07 square degrees of imaging data [...] The catalog contains 956 clusters over 0.35<z<0.95, limited by cluster richness and richness error. The calibration of the survey images has been extensively cross-checked against publicly available Sloan Digital Sky Survey imaging [...] We analyze the cluster sample via a general self-calibration technique including scatter in the mass-richness relation [...]. We fit simultaneously for Omega_M and sigma_8, and four parameters describing the calibration of cluster richness to mass, its evolution with redshift, and scatter in the richness-mass relation. The principal goal of this general analysis is to establish the consistency (or lack thereof) between the fitted parameters (both cosmological and cluster mass observables) and available results on both from independent measures. From an unconstrained analysis, Omega_M and sigma_8 are 0.31+0.11-0.10 and 0.67+0.18-0.13 respectively. An analysis including Gaussian priors on the slope and zeropoint of the mass-richness relation gives very similar results: 0.30+0.12-0.11 and 0.70+0.27-0.15. Both analyses are in good agreement with the current literature. The parameters describing the mass-richness relation in the unconstrained fit are also eminently reasonable and agree with existing follow-up data on both the RCS-1 and other cluster samples. Our results directly demonstrate that future surveys (optical and otherwise), with much larger samples of clusters, can give constraints competitive with other probes of cosmology.

A Fast Global Fitting Algorithm for Fluorescence Lifetime Imaging Microscopy Based on Image Segmentation

Global fitting algorithms have been shown to improve effectively the accuracy and precision of the analysis of fluorescence lifetime imaging microscopy data. Global analysis performs better than unconstrained data fitting when prior information exists, such as the spatial invariance of the lifetimes of individual fluorescent species. The highly coupled nature of global analysis often results in a significantly slower convergence of the data fitting algorithm as compared with unconstrained analysis. Convergence speed can be greatly accelerated by providing appropriate initial guesses. Realizing that the image morphology often correlates with fluorophore distribution, a global fitting algorithm has been developed to assign initial guesses throughout an image based on a segmentation analysis. This algorithm was tested on both simulated data sets and time-domain lifetime measurements. We have successfully measured fluorophore distribution in fibroblasts stained with Hoechst and calcein. This method further allows second harmonic generation from collagen and elastin autofluorescence to be differentiated in fluorescence lifetime imaging microscopy images of ex vivo human skin. On our experimental measurement, this algorithm increased convergence speed by over two orders of magnitude and achieved significantly better fits.

Beta-Pseudopeptide foldamers. The homo-oligomers of (4R)-(2-oxo-1,3-oxazolidin-4-yl)-acetic acid (D-Oxac).

A total synthesis in solution and a conformational analysis of the homo-oligomers of (4R)-(2-oxo-1,3-oxazolidin-4-yl)-acetic acid (D-Oxac) to the tetramer level are described. As the D-Oxac building block contains both an oxazolidin-2-one and a beta-amino acid group, it may represent a new type of conformationally constrained tool for the construction of beta-pseudopeptide foldamers. A conformational investigation using NMR and an extensive, unconstrained analysis with a Monte Carlo search to the octamer level, both in water and in chloroform, showed that these homo-oligomers tend to fold in a regular helical structure in a competitive solvent, such as water. Since aqueous solutions are of major relevance for biological systems, these molecules are good candidates for application to these environments.

Searching for larval support for majoid families (Crustacea: Brachyura) with particular reference to Inachoididae Dana, 1851

Summary We re-evaluated the larval support for families within majoids using the Wilcoxon signed-rank test with emphasis on Inachoididae. To accomplish our objectives, we added 10 new taxa, two of which are traditionally assigned to the family of special interest, to a previous larval database for majoids, and re-appraised the larval characters used in earlier studies. Phylogenetic analysis was performed with PAUP* using the heuristic search with 50 replicates or the branch-and-bound algorithm when possible. Multi-state transformation series were considered unordered; initially characters were equally weighted followed by successive weighting, and trees were rooted at the Oregoniidae node. Ten different topological constraints were enforced for families to evaluate tree length under the assumption of monophyly for each taxonomic entity. Our results showed that the tree length of most constrained topologies was not considerably greater than that of unconstrained analysis in which most families nested as paraphyletic taxa. This may indicate that the present larval database does not provide strong support for paraphyly of the taxa in question. For Inachoididae, although the Wilcoxon signed-rank test rejected a significant difference between unconstrained and constrained cladograms, we were unable to provide a single synapomorphy for this clade. Except for the conflicting position of Leurocyclus and Stenorhynchus, the two clades correspond to the traditional taxonomic arrangement. Among inachoidids, the clade (Anasimus (Paradasygyius (Collodes +Pyromaia))) is supported, whereas for inachids, the clade (Inachus (Macropodia +Achaeus)) is one of the most supported clades within majids. As often stated, only additional characters will provide a better test for the monophyly of Inachoididae and other families within Majoidea.

Analysis of the Motion of a Flexible Beam Fixed on a Moving Cart and Carrying a Concentrated Mass

In this paper, the equations of motion of a Bernoulli-Euler cantilever beam fixed on a moving cart and carrying a lumped mass concentrated at an arbitrary position along the beam is derived. The motion of the beam-mass-cart system is analyzed through unconstrained modal analysis, and a unified characteristic equation for calculating the natural frequencies of the system is obtained. The changes of natural frequencies and the corresponding mode shapes with respect to the changes in mass ratios of the system and to the concentrated position of the lumped mass are investigated with the frequency equation, which can be generally applied to this kind of systems. The exact and assumed-mode solutions including the dynamics of the base cart are obtained, and the open-loop responses of the system by arbitrarily designed forcing function are given by numerical simulations. The results match well with physical phenomena even at the extreme cases where the concentrated mass is attached to the bottom and to the top of the beam.

The Phylogeny of the Myrmecophagidae (Mammalia, Xenarthra, Vermilingua) and the Relationship of Eurotamandua to the Vermilingua

A cladistic investigation of the phylogenetic relationships among the three extant anteater genera and the three undoubted extinct myrmecophagid genera is performed based upon osteological characteristics of the skull and postcranial skeleton. One hundred seven discrete morphological characters are analyzed using the computer program PAUP. Characters are polarized via comparison to the successive xenarthran outgroups Tardigrada (represented by the living sloth Bradypus) and Cingulata (represented by the recent armadillos Dasypus and Euphractus). The analysis results in a single most-parsimonious tree (TL = 190, CI = 0.699, RI = 0.713). The tree corroborates the monophyly of the subfamilies Cyclopinae and Myrmecophaginae, the former including the extant Cyclopes and the Pliocene genus Palaeomyrmidon. Within the Myrmecophaginae the Miocene genus Protamandua is the sister taxon to a clade including the remaining three genera. The recent Tamandua is in turn the sister taxon to the extant Myrmecophaga plus the Pliocene genus Neotamandua. Contrary to the suggestions of recent authors, weak support is provided for the taxonomic distinctiveness of the latter genus from the recent Myrmecophaga. The monophyly of the Myrmecophagidae is supported by 15 unequivocal synapomorphies. The monophyly of the Cyclopinae and Myrmecophaginae is supported by 3 and 13 unambiguous synapomorphies, respectively. The enigmatic Eocene genus Eurotamandua, from the Messel fauna of Germany, is coded for the 107 morphological characters above and included in two subsequent PAUP analyses. The palaeanodont Metacheiromys is also added to these two analyses as a nonxenarthran outgroup to test for the possibility that Eurotamandua lies outside the Xenarthra. In the first analysis, Eurotamandua is constrained a priori to membership in the Vermilingua. The single most-parsimonious tree (TL = 224, CI = 0.618) that results places Eurotamandua as the sister group to the remaining anteater genera, contra Storch and Habersetzer's (1991) assignment of Eurotamandua to the vermilinguan subfamily Myrmecophaginae. Eurotamandua shares six unequivocal synapomorphies with other anteaters, including the absence of teeth and the presence of a lateral tuberosity on the fifth metatarsal. The remaining vermilinguans are united by 11 unequivocal synapomorphies, plus an additional 10 ambiguous synapomorphies. In the second analysis, the position of Eurotamandua is unconstrained. The resulting single most-parsimonious tree (TL = 219, CI = 0.632) places Eurotamandua outside Vermilingua as the sister group to the Pilosa (Vermilingua plus Bradypus). The monophyly of this node is supported by four unambiguous synapomorphies in the unconstrained analysis. Further manipulation of this second analysis shows that placement of Eurotamandua as the sister group to the Xenarthra or to the Palaeanodonta adds three steps to the shortest tree but is more parsimonious than its placement as a sister group to the Vermilingua is the previous analysis. The addition of pangolins to the analysis does little to alter the major phylogenetic conclusions of the study. The allocation of Eurotamandua to the Xenarthra, but as a sister group to the Pilosa, is a novel arrangement which leaves open the biogeographic question of how a xenarthran reached Western Europe during the Eocene.

Numerical Zonation of Log Suites and Logfacies Recognition by Multivariate Clustering

Zonation of well logs and the correlation of zones between wells are routine fundamental tasks in subsurface geological analysis. Objective numerical multivariate clustering is an effective procedure to simultaneously comprehend a suite of well logs and partition it into geologically meaningful zones and for identifying zone-specific logfacies. Discrimination of zones and logfacies from log suites was established by a hierarchical clustering algorithm that defines clusters so that their within-cluster dispersion is minimal. Logfacies are defined by an unconstrained analysis of unzoned data, whereas the special requirements of the stratigraphic context of the zonation are observed by an adjacency constraint which prohibits merging individual depth levels or lower order clu ters if their members are not vertically contiguous. Two test cases, one involving a succession composed of several alternating lithologies and the other entailing a uniform carbonate sequence with only subtle changes, demonstrate the applicability and efficacy of the method. In both cases, the numerical zonation matched the manual lithostratigraphic division extremely well. The geological validity of the numerically defined zones was also borne out by density-neutron crossplots. The unconstrained analysis successfully identified logfacies which are zone-specific, indicating that logfacies can serve as important leads for the recognition of reverse faults in boreholes and for interwell correlations.

The effect of land classification and stratification on derivation of timber supply and allowable cut in harvest scheduling

The effects of boundary designations of timber management units on the allowable cuts were examined, and a new approach to derive marginal-cost curves for timber supply was developed. The maximum even-flow allowable cut from the whole forest as a unit was 1.33–2.13% larger than the sum of the five maximum even-flow allowable cuts from the five working circles. Maximum even-flow allowable cuts found with linear programming using stand aggregation were 1.31–2.10% larger than allowable cuts using area aggregation. Maximum per period cost constraints were found, on average, to increase predicted differences from unconstrained stand-based versus area-based analysis. Use of the maximum cost constraints led to the ability to develop curves for the marginal cost of allowable cut for both stand-based and area-based analyses. By incrementally examining increases in the allowable cuts generated on the independent management units at different cost constraints, a curve for the average marginal cost of allowable cut was derived. Careful use of this curve will allow woodland managers to select the least costly method of analysis for any particular desired allowable cut. As well, the selected curve can aid managers in determining the marginal cost of timber supply at any production level and to set upper limits on external wood purchase prices. While biological data were easier to derive for stand-based aggregation, area-based aggregation led to smaller linear programming models, which were thus cheaper to solve, and it was much easier to develop location-dependent economic data for these type models than for stand-based models.

There's No Percentage in It: Intersite Spatial Analysis of Bushman (San) Pottery Decorations

Grass-tempered bowls made by the forbears of historical Karoo Bushmen between ca. A.D. 1500 and 1800 were decorated with many different stamp-impressed motifs. Five of the seven observed motif groups appear to be distributed randomly across the 2,000 km2 study area in the upper Seacow River valley, South Africa. When their percentage frequencies per site cluster were mapped, however, localized concentrations appeared. The validity of the percentage concentrations is tested here by unconstrained cluster analysis, which is not subject to the closure effect. Also, several other tests, all avoiding the use of percentage frequency maps, are introduced as alternative ways to deal with unevenly distributed sites and scarce artifacts or traits unevenly distributed among the sites themselves. The results demonstrate that percentage-frequency mapping can produce occasionally spurious and misleading patterns. Because stratigraphic evidence is scarce and inconclusive, and direct dating of sherds has not yet been conducted, a test also is proposed for determining contemporaneity of motif groups.

CONISS: a FORTRAN 77 program for stratigraphically constrained cluster analysis by the method of incremental sum of squares

Stratigraphically constrained cluster analysis is a multivariate method for quantitative definition of stratigraphic zones. As opposed to ordinary, unconstrained cluster analysis, only stratigraphically adjacent clusters are considered for merging. The method of incremental sum of squares has been used widely for unconstrained analyses and has proved particularly satisfactory for pollen frequency data. CONISS is a FORTRAN 77 program for stratigraphically constrained cluster analysis by this method. Several data transformations lead to different implicit dissimilarity coefficients. As an option, the program also will perform an unconstrained analysis, which can be useful for comparison with the constrained analysis.

GENFOLD2: A set of models and algorithms for the general UnFOLDing analysis of preference/dominance data

A general set of multidimensional unfolding models and algorithms is presented to analyze preference or dominance data. This class of models termed GENFOLD2 (GENeral UnFOLDing Analysis-Version 2) allows one to perform internal or external analysis, constrained or unconstrained analysis, conditional or unconditional analysis, metric or nonmetric analysis, while providing the flexibility of specifying and/or testing a variety of different types of unfolding-type preference models mentioned in the literature including Caroll's (1972, 1980) simple, weighted, and general unfolding analysis. An alternating weighted least-squares algorithm is utilized and discussed in terms of preventing degenerate solutions in the estimation of the specified parameters. Finally, two applications of this new method are discussed concerning preference data for ten brands of pain relievers and twelve models of residential communication devices.