Semi‐automated workflows for acquiring specimen data from label images in herbarium collections

Computational workflow environments are an active area of computer science and informatics research; they promise to be effective for automating biological information processing for increasing research efficiency and impact. In this project, semi‐automated data processing workflows were developed to test the efficiency of computerizing information contained in herbarium plant specimen labels. Our test sample consisted of mexican and Central American plant specimens held in the University of michigan Herbarium (MICH). The initial data acquisition process consisted of two parts: (1) the capture of digital images of specimen labels and of full‐specimen herbarium sheets, and (2) creation of a minimal field database, or "pre‐catalog", of records that contain only information necessary to uniquely identify specimens. For entering "pre‐catalog" data, two methods were tested: key‐stroking the information (a) from the specimen labels directly, or (b) from digital images of specimen labels. In a second step, locality and latitude/longitude data fields were filled in if the values were present on the labels or images. If values were not available, geo‐coordinates were assigned based on further analysis of the descriptive locality information on the label. Time and effort for the various steps were measured and recorded. Our analysis demonstrates a clear efficiency benefit of articulating a biological specimen data acquisition workflow into discrete steps, which in turn could be individually optimized. First, we separated the step of capturing data from the specimen from most keystroke data entry tasks. We did this by capturing a digital image of the specimen for the first step, and also by limiting initial key‐stroking of data to create only a minimal "pre‐catalog" database for the latter tasks. By doing this, specimen handling logistics were streamlined to minimize staff time and cost. Second, by then obtaining most of the specimen data from the label images, the more intellectually challenging task of label data interpretation could be moved electronically out of the herbarium to the location of more highly trained specialists for greater efficiency and accuracy. This project used experts in the plants’ country of origin, mexico, to verify localities, geography, and to derive geo‐coordinates. Third, with careful choice of data fields for the "pre‐catalog" database, specimen image files linked to the minimal tracking records could be sorted by collector and date of collection to minimize key‐stroking of redundant data in a continuous series of labels, resulting in improved data entry efficiency and data quality.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146956/1/tax596014.pd

A Non-Equilibrium Defect-Unbinding Transition: Defect Trajectories and Loop Statistics

In a Ginzburg-Landau model for parametrically driven waves a transition between a state of ordered and one of disordered spatio-temporal defect chaos is found. To characterize the two different chaotic states and to get insight into the break-down of the order, the trajectories of the defects are tracked in detail. Since the defects are always created and annihilated in pairs the trajectories form loops in space time. The probability distribution functions for the size of the loops and the number of defects involved in them undergo a transition from exponential decay in the ordered regime to a power-law decay in the disordered regime. These power laws are also found in a simple lattice model of randomly created defect pairs that diffuse and annihilate upon collision.Comment: 4 pages 5 figure

Aging of poled ferroelectric ceramics due to relaxation of random depolarization fields by space-charge accumulation near grain boundaries

Migration of charged point defects triggered by the local random depolarization field is shown to plausibly explain aging of poled ferroelectric ceramics providing reasonable time and acceptor concentration dependences of the emerging internal bias field. The theory is based on the evaluation of the energy of the local depolarization field caused by mismatch of the polarizations of neighbor grains. The kinetics of charge migration assumes presence of mobile oxygen vacancies in the material due to the intentional or unintentional acceptor doping. Satisfactory agreement of the theory with experiment on the Fe-doped lead zirconate titanate is demonstrated.Comment: theory and experiment, 22 pages, 3 figure

Phase Diffusion in Localized Spatio-Temporal Amplitude Chaos

We present numerical simulations of coupled Ginzburg-Landau equations describing parametrically excited waves which reveal persistent dynamics due to the occurrence of phase slips in sequential pairs, with the second phase slip quickly following and negating the first. Of particular interest are solutions where these double phase slips occur irregularly in space and time within a spatially localized region. An effective phase diffusion equation utilizing the long term phase conservation of the solution explains the localization of this new form of amplitude chaos.Comment: 4 pages incl. 5 figures uucompresse

Effect of uniaxial stress on ferroelectric behavior of (Bi1/2Na1/2)TiO3-based lead-free piezoelectric ceramics

Prior studies have shown that a field-induced ferroelectricity in ceramics with general chemical formula (1-x-y) (Bi1/2 Na1/2) TiO3 -x BaTiO3 -y (K0.5 Na0.5) NbO3 and a very low remanent strain can produce very large piezoelectric strains. Here we show that both the longitudinal and transverse strains gradually change with applied electric fields even during the transition from the nonferroelectric to the ferroelectric state, in contrast to known Pb-containing antiferroelectrics. Hence, the volume change and, in turn, the phase transition can be affected using uniaxial compressive stresses, and the effect on ferroelectricity can thus be assessed. It is found that the 0.94 (Bi1/2 Na1/2) TiO3 -0.05 BaTiO3 -0.01 (K0.5 Na0.5) NbO3 ceramic (largely ferroelectric), with a rhombohedral R3c symmetry, displays large ferroelectric domains, significant ferroelastic deformation, and large remanent electrical polarizations even at a 250 MPa compressive stress. In comparison, the 0.91 (Bi1/2 Na1/2) TiO3 -0.07 BaTiO3 -0.02 (K0.5 Na0.5) NbO3 ceramic (largely nonferroelectric) possesses characteristics of a relaxor ferroelectric ceramic, including a pseudocubic structure, limited ferroelastic deformation, and low remanent polarization. The results are discussed with respect of the proposed antiferroelectric nature of the nonferroelectric state.open291

Modulation of Localized States in Electroconvection

We report on the effects of temporal modulation of the driving force on a particular class of localized states, known as worms, that have been observed in electroconvection in nematic liquid crystals. The worms consist of the superposition of traveling waves and have been observed to have unique, small widths, but to vary in length. The transition from the pure conduction state to worms occurs via a backward bifurcation. A possible explanation of the formation of the worms has been given in terms of coupled amplitude equations. Because the worms consist of the superposition of traveling waves, temporal modulation of the control parameter is a useful probe of the dynamics of the system. We observe that temporal modulation increases the average length of the worms and stabilizes worms below the transition point in the absence of modulation.Comment: 4 pages, 4 figure

Stratified spatiotemporal chaos in anisotropic reaction-diffusion systems

Numerical simulations of two dimensional pattern formation in an anisotropic bistable reaction-diffusion medium reveal a new dynamical state, stratified spatiotemporal chaos, characterized by strong correlations along one of the principal axes. Equations that describe the dependence of front motion on the angle illustrate the mechanism leading to stratified chaos

Phase chaos in the anisotropic complex Ginzburg-Landau Equation

Of the various interesting solutions found in the two-dimensional complex Ginzburg-Landau equation for anisotropic systems, the phase-chaotic states show particularly novel features. They exist in a broader parameter range than in the isotropic case, and often even broader than in one dimension. They typically represent the global attractor of the system. There exist two variants of phase chaos: a quasi-one dimensional and a two-dimensional solution. The transition to defect chaos is of intermittent type.Comment: 4 pages RevTeX, 5 figures, little changes in figures and references, typos removed, accepted as Rapid Commun. in Phys. Rev.

Post-agriculture versus post-hurricane succession in southeastern Nicaraguan rain forest

Wecompared five-year old forests developing after agriculture to those recoveringfrom Hurricane Joan (1988) and to the pre-hurricane forest, at two sites intropical rain forest in southeastern Nicaragua. We used non-parametric clusteranalysis to group transects by their species compositions, and compared theirspecies richness, estimated total species richness, dominance, density andbasalarea. Post-agriculture transects showed distinctive species compositions andlower diversity than post-hurricane transects, which were in turn more similarto the pre-hurricane forest. These results are similar to those found by otherresearchers in the Amazon and in Puerto Rico. Land use history was moreimportant than proximity in the landscape in determining the composition andstructure of post-disturbance forests in this region.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43884/1/11258_2004_Article_266487.pd