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Showing papers by "Australian National University published in 1998"


Journal ArticleDOI
TL;DR: This issue's collection of essays should help familiarize readers with this interesting new racehorse in the Machine Learning stable, and give a practical guide and a new technique for implementing the algorithm efficiently.
Abstract: My first exposure to Support Vector Machines came this spring when heard Sue Dumais present impressive results on text categorization using this analysis technique. This issue's collection of essays should help familiarize our readers with this interesting new racehorse in the Machine Learning stable. Bernhard Scholkopf, in an introductory overview, points out that a particular advantage of SVMs over other learning algorithms is that it can be analyzed theoretically using concepts from computational learning theory, and at the same time can achieve good performance when applied to real problems. Examples of these real-world applications are provided by Sue Dumais, who describes the aforementioned text-categorization problem, yielding the best results to date on the Reuters collection, and Edgar Osuna, who presents strong results on application to face detection. Our fourth author, John Platt, gives us a practical guide and a new technique for implementing the algorithm efficiently.

4,319 citations


Journal ArticleDOI
TL;DR: A test based on two conserved CHD (chromo‐helicase‐DNA‐binding) genes that are located on the avian sex chromosomes of all birds, with the possible exception of the ratites (ostriches, etc.; Struthioniformes).
Abstract: Birds are difficult to sex. Nestlings rarely show sex-linked morphology and we estimate that adult females appear identical to males in over 50% of the world's bird species. This problem can hinder both evolutionary studies and human-assisted breeding of birds. DNA-based sex identification provides a solution. We describe a test based on two conserved CHD (chromo-helicase-DNA-binding) genes that are located on the avian sex chromosomes of all birds, with the possible exception of the ratites (ostriches, etc.; Struthioniformes). The CHD-W gene is located on the W chromosome; therefore it is unique to females. The other gene, CHD-Z, is found on the Z chromosome and therefore occurs in both sexes (female, ZW; male, ZZ). The test employs PCR with a single set of primers. It amplifies homologous sections of both genes and incorporates introns whose lengths usually differ. When examined on a gel there is a single CHD-Z band in males but females have a second, distinctive CHD-W band.

2,688 citations


Journal Article
TL;DR: In this paper, a test based on two conserved CHD (chromo-helicase-DNA-binding) genes that are located on the avian sex chromosomes of all birds, with the possible exception of the ratites (ostriches, etc.).

2,554 citations


Journal ArticleDOI
TL;DR: It is shown that techniques used in the analysis of Vapnik's support vector classifiers and of neural networks with small weights can be applied to voting methods to relate the margin distribution to the test error.
Abstract: One of the surprising recurring phenomena observed in experiments with boosting is that the test error of the generated classifier usually does not increase as its size becomes very large, and often is observed to decrease even after the training error reaches zero. In this paper, we show that this phenomenon is related to the distribution of margins of the training examples with respect to the generated voting classification rule, where the margin of an example is simply the difference between the number of correct votes and the maximum number of votes received by any incorrect label. We show that techniques used in the analysis of Vapnik's support vector classifiers and of neural networks with small weights can be applied to voting methods to relate the margin distribution to the test error. We also show theoretically and experimentally that boosting is especially effective at increasing the margins of the training examples. Finally, we compare our explanation to those based on the bias-variance decomposition.

2,257 citations


Journal ArticleDOI
15 Oct 1998-Nature
TL;DR: In this paper, the authors reported the discovery of transient optical emission in the error box of the gamma-ray burst GRB980425, the light curve of which was very different from that of previous optical afterglows associated with Gamma-ray bursts.
Abstract: The discovery of afterglows associated with gamma-ray bursts at X-ray, optical and radio wavelengths and the measurement of the redshifts of some of these events has established that gamma-ray bursts lie at extreme distances, making them the most powerful photon-emitters known in the Universe. Here we report the discovery of transient optical emission in the error box of the gamma-ray burst GRB980425, the light curve of which was very different from that of previous optical afterglows associated with gamma-ray bursts. The optical transient is located in a spiral arm of the galaxy ESO 184-GS2, which has a redshift velocity of only 2,550 km/ s. Its optical spectrum and location indicate that it is a very luminous supernova, which has been identified as SN1998bw. If this supernova and GRB980425 are indeed associated, the energy radiated in gamma-rays is at least four orders of magnitude less than in other gamma-ray bursts, although its appearance was otherwise unremarkable: this indicates that very different mechanisms can give rise to gamma-ray bursts. But independent of this association, the supernova is itself unusual, exhibiting an unusual light curve at radio wavelengths that requires that the gas emitting the radio photons be expanding relativistically.

1,823 citations


Journal ArticleDOI
TL;DR: Results in this paper show that if a large neural network is used for a pattern classification problem and the learning algorithm finds a network with small weights that has small squared error on the training patterns, then the generalization performance depends on the size of the weights rather than the number of weights.
Abstract: Sample complexity results from computational learning theory, when applied to neural network learning for pattern classification problems, suggest that for good generalization performance the number of training examples should grow at least linearly with the number of adjustable parameters in the network. Results in this paper show that if a large neural network is used for a pattern classification problem and the learning algorithm finds a network with small weights that has small squared error on the training patterns, then the generalization performance depends on the size of the weights rather than the number of weights. For example, consider a two-layer feedforward network of sigmoid units, in which the sum of the magnitudes of the weights associated with each unit is bounded by A and the input dimension is n. We show that the misclassification probability is no more than a certain error estimate (that is related to squared error on the training set) plus A/sup 3/ /spl radic/((log n)/m) (ignoring log A and log m factors), where m is the number of training patterns. This may explain the generalization performance of neural networks, particularly when the number of training examples is considerably smaller than the number of weights. It also supports heuristics (such as weight decay and early stopping) that attempt to keep the weights small during training. The proof techniques appear to be useful for the analysis of other pattern classifiers: when the input domain is a totally bounded metric space, we use the same approach to give upper bounds on misclassification probability for classifiers with decision boundaries that are far from the training examples.

1,234 citations


Journal ArticleDOI
01 Dec 1998-Lithos
TL;DR: In this paper, strong peraluminous (SP) granites have formed as a result of post-collisional processes in various orogens, with the pelite-derived SP granites tending to have lower CaO/Na2O ratios than their psammite derived counterparts.

1,092 citations


Journal ArticleDOI
TL;DR: A detailed overview of the physics and applications of optical dark solitons can be found in this article, where the authors discuss the instability-induced dynamics of dark-solitons in the models of generalized (i.e., non-Kerr) optical nonlinearities.

1,076 citations


Journal ArticleDOI
TL;DR: Combining phylogeographic data from mitochondrial DNA of Nearctic and Palearctic freshwater and anadromous fishes with historical events to assess the influence of historical events on evolutionary patterns and processes in regional fish faunas demonstrates that comparative phylOgeography can be used to evaluate not only phylo geographic patterns but also evolutionary processes.
Abstract: Combining phylogeographic data from mitochondrial DNA (mtDNA) of Nearctic and Palearctic freshwater and anadromous fishes, we used a comparative approach to assess the influence of historical events on evolutionary patterns and processes in regional fish faunas. Specifically, we (i) determined whether regional faunas differentially affected by Pleistocene glaciations show predictable differences in phylogeographic patterns; (ii) evaluated how processes of divergence and speciation have been influenced by such differential responses; and (iii) assessed the general contribution of phylogeographic studies to conservation issues. Comparisons among case studies revealed fundamental differences in phylogeographic patterns among regional faunas. Tree topologies were typically deeper for species from nonglaciated regions compared to northern species, whereas species with partially glaciated ranges were intermediate in their characteristics. Phylogeographic patterns were strikingly similar among southern species, whereas species in glaciated areas showed reduced concordance. The extent and locations of secondary contact among mtDNA lineages varied greatly among northern species, resulting in reduced intraspecific concordance of genetic markers for some northern species. Regression analysis of phylogeographic data for 42 species revealed significant latitudinal shifts in intraspecific genetic diversity. Both relative nucleotide diversity and estimates of evolutionary effective population size showed significant breakpoints matching the median latitude for the southern limit of the Pleistocene glaciations. Similarly, analysis of clade depth of phylogenetically distinct lineages vs. area occupied showed that evolutionary dispersal rates of species from glaciated and nonglaciated regions differed by two orders of magnitude. A negative relationship was also found between sequence divergence among sister species as a function of their median distributional latitude, indicating that recent bursts of speciation events have occurred in deglaciated habitats. Phylogeographic evidence for parallel evolution of sympatric northern species pairs in postglacial times suggested that differentiation of cospecific morphotypes may be driven by ecological release. Altogether, these results demonstrate that comparative phylogeography can be used to evaluate not only phylogeographic patterns but also evolutionary processes. As well as having significant implications for conservation programs, this approach enables new avenues of research for examining the regional, historical, and ecological factors involved in shaping intraspecific genetic diversity.

849 citations


Journal ArticleDOI
30 Jan 1998-Science
TL;DR: Chemical and ultrastructural analyses together with map-based cloning indicate that the RSW1 locus of Arabidopsis encodes the catalytic subunit of cellulose synthase, which complements the rsw1 mutant whose temperature-sensitive allele is changed in one amino acid.
Abstract: Cellulose, an abundant, crystalline polysaccharide, is central to plant morphogenesis and to many industries. Chemical and ultrastructural analyses together with map-based cloning indicate that the RSW1 locus of Arabidopsis encodes the catalytic subunit of cellulose synthase. The cloned gene complements the rsw1 mutant whose temperature-sensitive allele is changed in one amino acid. The mutant allele causes a specific reduction in cellulose synthesis, accumulation of noncrystalline beta-1,4-glucan, disassembly of cellulose synthase, and widespread morphological abnormalities. Microfibril crystallization may require proper assembly of the RSW1 gene product into synthase complexes whereas glucan biosynthesis per se does not.

799 citations


Journal ArticleDOI
TL;DR: In this paper, the eustatic component of relative sea-level change provides a measure of the amount of ice transferred between the continents and oceans during glacial cycles, which has been quantified for the period since the last glacial maximum by correcting observed sea level change for the glacio-hydro-isostatic contributions using realistic ice distribution and earth models.

Journal ArticleDOI
TL;DR: In this paper, an ArF excimer laser coupled to a quadrupole inductively coupled plasma mass spectrometry (ICP-MS) was used for the measurement of a range of elements during excavation of a deepening ablation pit in a synthetic glass.

Journal ArticleDOI
TL;DR: A provisional primate classification based on DNA evidence and the time scale provided by fossils and the model of local molecular clocks has all named taxa represent clades and assigns the same taxonomic rank to those clades of roughly equivalent age.

Journal ArticleDOI
TL;DR: The use of electrophysiological and molecular biology techniques has shed light on reactive oxygen species (ROS)-induced impairment of surface and internal membranes that control cellular signaling as mentioned in this paper.
Abstract: The use of electrophysiological and molecular biology techniques has shed light on reactive oxygen species (ROS)-induced impairment of surface and internal membranes that control cellular signaling...

Journal ArticleDOI
01 Jun 1998-Botany
TL;DR: This review examines the potential diversity of both Rubisco and chloroplast-based CCMs across algal divisions, including both green and nongreen algae, and seeks to highlight recent advances in the understanding of the area and future areas for research.
Abstract: Algae have adopted two primary strategies to maximize the performance of Rubisco in photosynthetic CO2 fixation. This has included either the development of a CO2-concentrating mechanism (CCM), bas...

Book
15 Jul 1998
TL;DR: The core of the book is Pienemann's Processability Theory which spells out which second language forms are processable at which developmental stage and is based on recent research into language processing and is formalised within Lexical-Functional Grammar.
Abstract: This book marks a new development in the field of second language acquisition research It explores the way in which language processing mechanisms shape the course of language development Language Processing and Second Language Development thus adds one major psychological component to the search for a theory of second language acquisition The core of the book is Pienemann’s Processability Theory which spells out which second language forms are processable at which developmental stage The theory is based on recent research into language processing and is formalised within Lexical-Functional Grammar The predictions of the theory are applied to the second language development of English, German, Japanese and Swedish The theory is also tested in on-line experiments In addition, Processability Theory has major implications for interlanguage variation (including task variation) and age-related differences in language acquisition All of these issues are explored from a processing perspective with theoretical and empirical rigor

Journal ArticleDOI
TL;DR: A result is presented that allows one to trade off errors on the training sample against improved generalization performance, and a more general result in terms of "luckiness" functions, which provides a quite general way for exploiting serendipitous simplicity in observed data to obtain better prediction accuracy from small training sets.
Abstract: The paper introduces some generalizations of Vapnik's (1982) method of structural risk minimization (SRM). As well as making explicit some of the details on SRM, it provides a result that allows one to trade off errors on the training sample against improved generalization performance. It then considers the more general case when the hierarchy of classes is chosen in response to the data. A result is presented on the generalization performance of classifiers with a "large margin". This theoretically explains the impressive generalization performance of the maximal margin hyperplane algorithm of Vapnik and co-workers (which is the basis for their support vector machines). The paper concludes with a more general result in terms of "luckiness" functions, which provides a quite general way for exploiting serendipitous simplicity in observed data to obtain better prediction accuracy from small training sets. Four examples are given of such functions, including the Vapnik-Chervonenkis (1971) dimension measured on the sample.

Journal ArticleDOI
TL;DR: In this paper, an inverse solution for the sea-level data are sought that include both ice- and earth-model parameters as unknowns, and both global (northwestern Europe as a whole) and regional (subsets of the data) solutions have been made for earth model parameters and ice height scaling parameters.
Abstract: Northwestern Europe remains a key region for testing models of glacial isostasy because of the good geological record of crustal response to the glacial unloading since the time of the Last Glacial Maximum. Models for this rebound and associated sea-level change require a detailed knowledge of the ice-sheet geometry, including the ice thickness through time. Existing ice-sheet reconstructions are strongly model-dependent, and inversions of sea-level data for the mantle response may be a function of the model assumptions. Thus inverse solutions for the sea-level data are sought that include both ice- and earth-model parameters as unknowns. Sea-level data from Fennoscandia, the North Sea, the British Isles and the Atlantic and English Channel coasts have been evaluated and incorporated into the solutions. The starting ice sheet for Fennoscandia is based on a reconstruction of a model by Denton & Hughes (1981) that is characterized by quasi-parabolic cross-sections and symmetry about the load centre. Both global (northwestern Europe as a whole) and regional (subsets of the data) solutions have been made for earth-model parameters and ice-height scaling parameters. The key results are as follows. (1) The response of the upper mantle to the changing ice and water loads is spatially relatively homogenous across Scandinavia, the North Sea and the British Isles. (2) This response can be adequately modelled by an effective elastic lithosphere of thickness 65–85 km and by an effective upper-mantle viscosity (from the base of the lithosphere to the 670 km depth seismic discontinuity) of about 3–4×1020 Pa s. The effective lower-mantle viscosity is at least an order of magnitude greater. (3) The ice thickness over Scandinavia at the time of maximum glaciation was only about 2000 m, much less than the 3400 m assumed in the Denton & Hughes model. (4) The ice profiles are asymmetric about the centre of the ice sheet with those over the western part being consistent with quasi-parabolic functions whereas the ice heights over the eastern and southern regions increase much more slowly with distance inwards from the ice margin.

Journal ArticleDOI
TL;DR: In this paper, the conditions for plate tectonics are studied by considering brittle behavior, using Byerlee's law to limit the maximum stress in the lithosphere, in a mantle convection model with temperature-dependent viscosity.
Abstract: SUMMARY Plates are an integral part of the convection system in the fluid mantle, but plate boundaries are the product of brittle faulting and plate motions are strongly influenced by the existence of such faults. The conditions for plate tectonics are studied by considering brittle behaviour, using Byerlee’s law to limit the maximum stress in the lithosphere, in a mantle convection model with temperature-dependent viscosity. When the yield stress is high, convection is confined below a thick, stagnant lithosphere. At low yield stress, brittle deformation mobilizes the lithosphere which becomes a part of the overall circulation; surface deformation occurs in localized regions close to upwellings and downwellings in the system. At intermediate levels of the yield stress, there is a cycling between these two states: thick lithosphere episodically mobilizes and collapses into the interior before reforming. The mobile-lid regime resembles convection of a fluid with temperature-dependent viscosity and the boundary-layer scalings are found to be analogous. This regime has a well defined Nusselt number‐Rayleigh number relationship which is in good agreement with scaling theory. The surface velocity is nearly independent of the yield stress, indicating that the ‘plate’ motion is resisted by viscous stresses in the mantle. Analysis suggests that mobilization of the Earth’s lithosphere can occur if the friction coeYcient in the lithosphere is less than 0.03‐0.13—lower than laboratory values but consistent with seismic field studies. On Venus, the friction coeYcient may be high as a result of the dry conditions, and brittle mobilization of the lithosphere would then be episodic and catastrophic.

Journal ArticleDOI
TL;DR: In this paper, the authors examine whether progress has been made on both understanding the EKC phenomenon and on addressing the various criticisms raised against some of the empirical studies and their interpretation in the policy literature.
Abstract: The environmental Kuznets curve (EKC) hypothesis proposes that there is an inverted U-shape relation between environmental degradation and income per capita. This has been taken to imply that economic growth will eventually redress the environmental impacts of the early stages of economic development. The literature on this issue has developed rapidly over the last few years. This paper examines whether progress has been made on both understanding the EKC phenomenon and on addressing the various criticisms raised against some of the empirical studies and their interpretation in the policy literature. Though basic EKC studies continue to be carried out, recent work has focused on the effect of a variety of conditioning variables on the environmental impact-GDP relationship. Some attempts have also been made to examine the history of the relationship in individual countries. The econometric techniques used have improved. However, empirical decompositions of the EKC into proximate or underlying causes are either limited in scope or non-systematic, and explicit testing of the various theoretical models has not yet been attempted.

Journal ArticleDOI
TL;DR: Differences between species in organic leaf nitrogen content per se were no longer important and higher PNUEmax of the high SLA species was due to a higher fraction of N in␣photosynthetic compounds and a higher Rubisco specific activity (for high-light grown plants).
Abstract: Factors that contribute to interspecific varia- tion in photosynthetic nitrogen-use eAciency (PNUE, the ratio of CO2 assimilation rate to leaf organic nitro- gen content) were investigated, comparing ten dicoty- ledonous species that diAer inherently in specific leaf area (SLA, leaf area:leaf dry mass). Plants were grown hydroponically in controlled environment cabinets at two irradiances (200 and 1000 lmol m -2 s -1 ). CO2 and irradiance response curves of photosynthesis were mea- sured followed by analysis of the chlorophyll, Rubisco, nitrate and total nitrogen contents of the leaves. At both irradiances, SLA ranged more than twofold across spe- cies. High-SLA species had higher in situ rates of pho- tosynthesis per unit leaf mass, but similar rates on an area basis. The organic N content per unit leaf area was lower for the high-SLA species and consequently PNUE at ambient light conditions (PNUEamb) was higher in those plants. DiAerences were somewhat smaller, but still present, when PNUE was determined at saturating irradiances (PNUEmax). An assessment was made of the relative importance of the various factors that underlay interspecific variation in PNUE. For plants grown under low irradiance, PNUEamb of high-SLA species was higher primarily due to their lower N content per unit leaf area. Low-SLA species clearly had an overinvest- ment in photosynthetic N under these conditions. In addition, high SLA-species allocated a larger fraction of organic nitrogen to thylakoids and Rubisco, which fur- ther increased PNUEamb. High-SLA species grown un- der high irradiance showed higher PNUEamb mainly due to a higher Rubisco specific activity. Other factors that contributed were again their lower contents of Norg per unit leaf area and a higher fraction of photosynthetic N in electron transport and Rubisco. For PNUEmax, dif- ferences between species in organic leaf nitrogen content per se were no longer important and higher PNUEmax of the high SLA species was due to a higher fraction of N in photosynthetic compounds (for low-light plants) and a higher Rubisco specific activity (for high-light grown plants).

Journal ArticleDOI
TL;DR: An overview of the dynamics of one of the fundamental models of low-dimensional nonlinear physics, the Frenkel-Kontorova (FK) model, is presented in this article.

Journal ArticleDOI
13 Feb 1998-Science
TL;DR: The results suggest that the temperature increase enhanced the evaporative enrichment of 18O in seawater, and transport of part of the additional atmospheric water vapor to extratropical latitudes may have sustained the 18O/16O anomaly.
Abstract: Skeletal Sr/Ca and 18 O/ 16 O ratios in corals from the Great Barrier Reef, Australia, indicate that the tropical ocean surface ∼5350 years ago was 1°C warmer and enriched in 18 O by 0.5 per mil relative to modern seawater. The results suggest that the temperature increase enhanced the evaporative enrichment of 18 O in seawater. Transport of part of the additional atmospheric water vapor to extratropical latitudes may have sustained the 18 O/ 16 O anomaly. The reduced glacial-Holocene shift in seawater 18 O/ 16 O ratio produced by the mid-Holocene 18 O enrichment may help to reconcile the different temperature histories for the last deglaciation given by coral Sr/Ca thermometry and foraminiferal oxygen-isotope records.

Journal ArticleDOI
TL;DR: The Behavioural Inhibition System and Behavior Activation System (BIS/BAS) scales of Carver and White (1994) were used in an Australian community sample of 2725 individuals aged 18-79.

Journal ArticleDOI
TL;DR: A very general technique for generating families of combinatorial objects without isomorphs is described, which applies to almost any class of objects for which an inductive construction process exists.

Journal ArticleDOI
TL;DR: The hypothesis that LCOs and chitin oligosaccharides act by perturbing the auxin flow in the root during the earliest stages of nodule formation is supported, and it is shown that endogenous flavonoids could mediate this response.
Abstract: The expression of the auxin responsive reporter construct, GH3:gusA, was examined in transgenic white clover plants to assess changes in the auxin balance during the earliest stages of root nodule formation. Reporter gene expression was monitored at marked locations after the application of bacteria or signal molecules using two precise inoculation techniques: spot-inoculation and a novel method for ballistic microtargeting. Changes in GH3:gusA expression were monitored after the inoculation of Rhizobium leguminosarum biovar trifolii, non-host rhizobia, lipo-chitin oligosaccharides (LCOs), chitin oligosaccharides, a synthetic auxin transport inhibitor (naphthylphthalamic acid; NPA), auxin, the ENOD40-1 peptide or different flavonoids. The results show that clover-nodulating rhizobia induce a rapid, transient and local downregulation of GH3:gusA expression during nodule initiation followed by an upregulation of reporter gene expression at the site of nodule initiation. Microtargeting of auxin caused a local and acropetal upregulation of GH3:gusA expression, whereas NPA caused local and acropetal downregulation of expression. Both spot-inoculation and microtargeting of R. l. bv. trifolii LCOs or flavonoid aglycones induced similar changes to GH3:gusA expression as NPA. O-acetylated chitin oligosaccharides caused similar changes to GH3:gusA expression as R. l. bv. trifolii spot-inoculation, but only after delivery by microtargeting. Non-O-acetylated chitin oligosaccharides, flavonoid glucosides or the ENOD40-1 peptide failed to induce any detectable changes in GH3:gusA expression. GH3:gusA expression patterns during the later stages of nodule and lateral root development were similar. These results support the hypothesis that LCOs and chitin oligosaccharides act by perturbing the auxin flow in the root during the earliest stages of nodule formation, and that endogenous flavonoids could mediate this response.

Journal ArticleDOI
TL;DR: It is emphasized that care must be taken in the calibration stage to prevent propagation of poor analytical work through NIRS, but, used properly, NirS offers ecologists enormous analytical power.
Abstract: Many ecological studies rely heavily on chemical analysis of plant and animal tissues. Often, there is limited time and money to perform all the required analyses and this can result in less than ideal sampling schemes and poor levels of replication. Near infrared reflectance spectroscopy (NIRS) can relieve these constraints because it can provide quick, non-destructive and quantitative analyses of an enormous range of organic constituents of plant and animal tissues. Near infrared spectra depend on the number and type of C\(\)H, N\(\)H and O\(\)H bonds in the material being analyzed. The spectral features are then combined with reliable compositional or functional analyses of the material in a predictive statistical model. This model is then used to predict the composition of new or unknown samples. NIRS can be used to analyze some specific elements (indirectly – e.g., N as protein) or well-defined compounds (e.g., starch) or more complex, poorly defined attributes of substances (e.g., fiber, animal food intake) have also been successfully modeled with NIRS technology. The accuracy and precision of the reference values for the calibration data set in part determines the quality of the predictions made by NIRS. However, NIRS analyses are often more precise than standard laboratory assays. The use of NIRS is not restricted to the simple determination of quantities of known compounds, but can also be used to discriminate between complex mixtures and to identify important compounds affecting attributes of interest. Near infrared reflectance spectroscopy is widely accepted for compositional and functional analyses in agriculture and manufacturing but its utility has not yet been recognized by the majority of ecologists conducting similar analyses. This paper aims to stimulate interest in NIRS and to illustrate some of the enormous variety of uses to which it can be put. We emphasize that care must be taken in the calibration stage to prevent propagation of poor analytical work through NIRS, but, used properly, NIRS offers ecologists enormous analytical power.

Journal ArticleDOI
R Peakall1, S Gilmore, W Keys, M Morgante, A Rafalski 
TL;DR: These findings and the emerging patterns in other plant studies suggest that in contrast to animals, successful cross-species amplification of SSRs in plants is largely restricted to congeners or closely related genera.
Abstract: We investigated the transferability of 31 soybean (Glycine max) simple sequence repeat (SSR) loci to wild congeners and to other legume genera. Up to 65% of the soybean primer pairs amplified SSRs within Glycine, but frequently, the SSRs were short and interrupted compared with those of soybeans. Nevertheless, 85% of the loci were polymorphic within G. clandestina. Cross-species amplification outside of the genus was much lower (3%-13%), with polymorphism restricted to one primer pair, AG81. AG81 amplified loci in Glycine, Kennedia, and Vigna (Phaseoleae), Vicia (Vicieae), Trifolium (Trifolieae), and Lupinus (Genisteae) within the Papilionoideae, and in Albizia within the Mimosoideae. The primer conservation at AG81 may be explained by its apparent proximity to the seryl-tRNA synthetase gene. Interspecific differences in allele size at AG81 loci reflected repeat length variation within the SSR region and indels in the flanking region. Alleles of identical size with different underlying sequences (size homoplasy) were observed. Our findings and the emerging patterns in other plant studies suggest that in contrast to animals, successful cross-species amplification of SSRs in plants is largely restricted to congeners or closely related genera. Because mutations in both the SSR region and the flanking region contribute to variation in allele size among species, knowledge of DNA sequence is essential before SSR loci can be meaningfully used to address applied and evolutionary questions.

Book ChapterDOI
TL;DR: Advances in experimental design and data analysis methods are making it possible to accurately define the assembly mechanisms and rate constants associated with macromolecular interactions.
Abstract: Surface plasmon resonance based biosensors are being used to define the kinetics of a wide variety of macromolecular interactions. As the popularity of this approach grows, experimental design and data analysis methods continue to evolve. These advances are making it possible to accurately define the assembly mechanisms and rate constants associated with macromolecular interactions.

Journal ArticleDOI
TL;DR: In this paper, the authors report new mass spectrometric U-series ages for eight Last Interglacial fossil reefs along the continental margin of Western Australia, which are selected in growth position from localities that are characterized by apparently low levels of diagenesis and relative tectonic stability.