bluuebunny/crossref_metadata_2025_split huggingface dataset:
BNFinder: exact and efficient method for learning Bayesian networks
Authors: Wilczyński Bartek , Dojer Norbert 
Published: October 2008

Abstract
Motivation: Bayesian methods are widely used in many different areas of research. Recently, it has become a very popular tool for biological network reconstruction, due to its ability to handle noisy data. Even though there are many software packages allowing for Bayesian network reconstruction, only few of them are freely available to researchers. Moreover, they usually require at least basic programming abilities, which restricts their potential user base. Our goal was to provide software which would be freely available, efficient and usable to non-programmers.
Results: We present a BNFinder software, which allows for Bayesian network reconstruction from experimental data. It supports dynamic Bayesian networks and, if the variables are partially ordered, also static Bayesian networks. The main advantage of BNFinder is the use exact algorithm, which is at the same time very efficient (polynomial with respect to the number of observations).
Availability: The software, supplementary information and manual is available at http://bioputer.mimuw.edu.pl/software/bnf/. Besides the availability of the standalone application and the source code, we have developed a web interface to BNFinder application running on our servers. A web tutorial on different options of BNFinder is also available.
Contact: dojer@mimuw.edu.pl
Smarter clustering methods for SNP genotype calling
Authors: Lin Yan , Tseng George C. , Cheong Soo Yeon , Bean Lora J. H. , Sherman Stephanie L. , Feingold Eleanor 
Published: October 2008

Abstract
Motivation: Most genotyping technologies for single nucleotide polymorphism (SNP) markers use standard clustering methods to ‘call’ the SNP genotypes. These methods are not always optimal in distinguishing the genotype clusters of a SNP because they do not take advantage of specific features of the genotype calling problem. In particular, when family data are available, pedigree information is ignored. Furthermore, prior information about the distribution of the measurements for each cluster can be used to choose an appropriate model-based clustering method and can significantly improve the genotype calls. One special genotyping problem that has never been discussed in the literature is that of genotyping of trisomic individuals, such as individuals with Down syndrome. Calling trisomic genotypes is a more complicated problem, and the addition of external information becomes very important.
Results: In this article, we discuss the impact of incorporating external information into clustering algorithms to call the genotypes for both disomic and trisomic data. We also propose two new methods to call genotypes using family data. One is a modification of the K-means method and uses the pedigree information by updating all members of a family together. The other is a likelihood-based method that combines the Gaussian or beta-mixture model with pedigree information. We compare the performance of these two methods and some other existing methods using simulation studies. We also compare the performance of these methods on a real dataset generated by the Illumina platform (www.illumina.com).
Availability: The R code for the family-based genotype calling methods (SNPCaller) is available to be downloaded from the following website: http://watson.hgen.pitt.edu/register.
Contact: liny@upmc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The Genus Antirrhinum (Snapdragon): A Flowering Plant Model for Evolution and Development
Authors: Hudson Andrew , Critchley Joanna , Erasmus Yvette 
Published: October 2008

INTRODUCTIONThe Antirrhinum species group comprises approximately 20 morphologically diverse members that are able to form fertile hybrids. It includes the cultivated snapdragon Antirrhinum majus, which has been used as a model for biochemical and developmental genetics for more than 75 yr. The research infrastructure for A. majus, together with the interfertility of the species group, allows Antirrhinum to be used to examine the genetic basis for plant diversity.
Planarians: A Versatile and Powerful Model System for Molecular Studies of Regeneration, Adult Stem Cell Regulation, Aging, and Behavior
Authors: Oviedo Néstor J. , Nicolas Cindy L. , Adams Dany S. , Levin Michael 
Published: October 2008

INTRODUCTIONIn recent years, planarians have been increasingly recognized as an emerging model organism amenable to molecular genetic techniques aimed at understanding complex biological tasks commonly observed among metazoans. Growing evidence suggests that this model organism is uniquely poised to inform us about the mechanisms of tissue regeneration, stem cell regulation, tissue turnover, pharmacological action of diverse drugs, cancer, and aging. This article provides an overview of the planarian model system with special attention to the species Schmidtea mediterranea. Additionally, information is provided about the most popular use of this organism, together with modern genomic resources and technical approaches.
Cultivating Antirrhinum
Authors: Hudson Andrew , Critchley Joanna , Erasmus Yvette 
Published: October 2008

INTRODUCTIONIn this protocol, we describe methods for cultivating Antirrhinum (snapdragon) species. These plants are easily grown, provided that they have sufficient light and are not overwatered. In good conditions, most species will flower and produce seeds within 3-4 mo. Strongly growing plants should suffer from few pests or diseases, but we also prescribe methods for dealing with microbes and insects that commonly damage Antirrhinum.
Isolation of Pristionchus Nematodes from Beetles
Authors: Rae Robbie , Schlager Benjamin , Sommer Ralf J. 
Published: October 2008

INTRODUCTIONIn this procedure, nematodes disembark from a beetle carcass and feed on Escherichia coli OP50. The nematodes are then monitored for a few days and identified using simple morphological characteristics. This method is rapid, easy, and biased for Pristionchus species.
Detection of Cell Proliferation in Spider Embryos Using BrdU Labeling
Authors: Prpic Nikola-Michael , Schoppmeier Michael , Damen Wim G.M. 
Published: October 2008

INTRODUCTIONThe spider Cupiennius salei, commonly known as the American wandering spider, is particularly useful for embryological studies because of the availability of tools to study and manipulate its embryonic development. Cupiennius is used to study axis formation, segmentation, appendage development, neurogenesis, and silk production. These studies contribute to our understanding of the evolution of these processes, but they also help us to understand the origin and diversification of evolutionary novelties. Comparisons between spiders and insects can show the degree of conservation and divergence of developmental mechanisms during arthropod evolution. Any embryological feature conserved between spiders and insects is likely to represent an ancestral feature for arthropods. Comparative molecular embryological work in insects and spiders should eventually allow us to define a molecular archetype for the phylum Arthropoda. This will be a necessary cornerstone for comparing the different metazoan phyla, including chordates. This protocol describes the detection of proliferating cells in whole-mount Cupiennius embryos. When labeled nucleotides are introduced into mitotically dividing cells, these cells incorporate the labels into the newly synthesized DNA. Thus, only cells that have synthesized DNA after the addition of the label will be detected. This protocol uses 5-bromo-2′-deoxy-uridine (BrdU) as a label that is subsequently detected by immunocytochemistry. BrdU labeling is a relatively easy way to detect cells that have recently synthesized DNA. The main advantage of this technique is that the label accumulates over time and, by varying the incubation time before fixation, an increasingly cumulative picture of cell proliferation activity can be obtained.
Dissecting Spider Embryos for Light Microscopy: Figure 1.
Authors: Prpic Nikola-Michael , Schoppmeier Michael , Damen Wim G.M. 
Published: October 2008

INTRODUCTIONThe spider Cupiennius salei, commonly known as the American wandering spider, is a particularly useful laboratory model for embryological studies because of the availability of tools to study and manipulate its embryonic development. Cupiennius is used to study axis formation, segmentation, appendage development, neurogenesis, and silk production. These studies contribute to our understanding of the evolution of these processes, but they also help us to understand the origin and diversification of evolutionary novelties. Comparisons between spiders and insects can show the degree of conservation and divergence of developmental mechanisms during arthropod evolution. Any embryological feature conserved between spiders and insects is likely to represent an ancestral feature for arthropods. Comparative molecular embryological work in insects and spiders should eventually allow us to define a molecular archetype for the phylum Arthropoda. This in itself will be a necessary cornerstone for comparing the different metazoan phyla, including chordates. Spider embryos can be studied as whole mounts under the dissection microscope. Alternatively, the embryos can be dissected and observed under the compound microscope. Preparing and dissecting spider embryos for compound microscopy is difficult due to the high amount of yolk, which makes the embryos very fragile. The following protocol describes how to make the necessary tools, then use them to obtain good preparations. Not all embryonic stages can be dissected and prepared; very young stages can only be examined as whole mounts.
Harvesting Monodelphis Embryos
Authors: Keyte Anna L. , Smith Kathleen K. 
Published: October 2008

INTRODUCTIONMonodelphis domestica, the gray, short-tailed, or laboratory opossum, is the most commonly used laboratory marsupial. In addition to the factors that make it a convenient laboratory animal (small size, ease of care, nonseasonal breeding), it is the first marsupial whose genome has been sequenced. Monodelphis has proven useful as a model organism for studies on spinal cord regeneration, ultraviolet (UV)-induced melanoma, and genetic influences on cholesterol, as well as comparative studies of the immune system. In addition, Monodelphis has been used to understand the basic functions of the olfactory system and the role of various olfactory chemicals in social and reproductive behavior. Recently, Monodelphis has been used to understand fundamental aspects of marsupial development, anatomy, evolution, and evolutionary consequences of the derived marsupial mode of development and reproduction. Monodelphis embryos are easily harvested, as described in this protocol. Depending on the specific use for the embryo, there may be slight differences in euthanasia procedure, fixation, and embryo treatment. Most commonly, specimens will be used for anatomical or molecular (e.g., in situ hybridization) techniques, in which case they will be fixed in standard fixatives appropriate for the particular protocol.
Whole-Mount In Situ Hybridization in Monodelphis Embryos
Authors: Keyte Anna L. , Smith Kathleen K. 
Published: October 2008

INTRODUCTIONMonodelphis domestica, the gray, short-tailed, or laboratory opossum, is the most commonly used laboratory marsupial. In addition to the factors that make it a convenient laboratory animal (small size, ease of care, nonseasonal breeding), it is the first marsupial whose genome has been sequenced. Monodelphis has proven useful as a model organism for studies on spinal cord regeneration, ultraviolet (UV)-induced melanoma, and genetic influences on cholesterol, as well as comparative studies of the immune system. In addition, Monodelphis has been used to understand the basic functions of the olfactory system and the role of various olfactory chemicals in social and reproductive behavior. Recently, Monodelphis has been used to understand fundamental aspects of marsupial development, anatomy, evolution, and evolutionary consequences of the derived marsupial mode of development and reproduction. This protocol details whole-mount in situ hybridization of Monodelphis embryos, but it is broadly applicable to any marsupial. Special conditions have been included throughout the protocol for various stages of marsupial embryos. Nevertheless, whole, preterm embryonic stages (~stage 33 to birth) have proven to be difficult to work with because formation of the cuticle prevents probe and antibody penetration.
Release of the Repressive Activity of Rice DELLA Protein SLR1 by Gibberellin Does Not Require SLR1 Degradation in the gid2 Mutant
Authors: Ueguchi-Tanaka Miyako , Hirano Ko , Hasegawa Yasuko , Kitano Hidemi , Matsuoka Makoto 
Published: October 2008

Abstract
The rice (Oryza sativa) DELLA protein SLR1 acts as a repressor of gibberellin (GA) signaling. GA perception by GID1 causes SLR1 protein degradation involving the F-box protein GID2; this triggers GA-associated responses such as shoot elongation and seed germination. In GA-insensitive and GA biosynthesis mutants, SLENDER RICE1 (SLR1) accumulates to high levels, and the severity of dwarfism is usually correlated with the level of SLR1 accumulation. An exception is the GA-insensitive F-box mutant gid2, which shows milder dwarfism than mutants such as gid1 and cps even though it accumulates higher levels of SLR1. The level of SLR1 protein in gid2 was decreased by loss of GID1 function or treatment with a GA biosynthesis inhibitor, and dwarfism was enhanced. Conversely, overproduction of GID1 or treatment with GA3 increased the SLR1 level in gid2 and reduced dwarfism. These results indicate that derepression of SLR1 repressive activity can be accomplished by GA and GID1 alone and does not require F-box (GID2) function. Evidence for GA signaling without GID2 was also provided by the expression behavior of GA-regulated genes such as GA-20oxidase1, GID1, and SLR1 in the gid2 mutant. Based on these observations, we propose a model for the release of GA suppression that does not require DELLA protein degradation.
Distribution and Evolution of Circular Miniproteins in Flowering Plants
Authors: Gruber Christian W. , Elliott Alysha G. , Ireland David C. , Delprete Piero G. , Dessein Steven , Göransson Ulf , Trabi Manuela , Wang Conan K. , Kinghorn Andrew B. , Robbrecht Elmar , Craik David J. 
Published: October 2008

AbstractCyclotides are disulfide-rich miniproteins with the unique structural features of a circular backbone and knotted arrangement of three conserved disulfide bonds. Cyclotides have been found only in two plant families: in every analyzed species of the violet family (Violaceae) and in few species of the coffee family (Rubiaceae). In this study, we analyzed &gt;200 Rubiaceae species and confirmed the presence of cyclotides in 22 species. Additionally, we analyzed &gt;140 species in related plant families to Rubiaceae and Violaceae and report the occurrence of cyclotides in the Apocynaceae. We further report new cyclotide sequences that provide insights into the mechanistic basis of cyclotide evolution. On the basis of the phylogeny of cyclotide-bearing plants and the analysis of cyclotide precursor gene sequences, we hypothesize that cyclotide evolution occurred independently in various plant families after the divergence of Asterids and Rosids (∼125 million years ago). This is strongly supported by recent findings on the in planta biosynthesis of cyclotides, which involves the serendipitous recruitment of ubiquitous proteolytic enzymes for cyclization. We further predict that the number of cyclotides within the Rubiaceae may exceed tens of thousands, potentially making cyclotides one of the largest protein families in the plant kingdom.
Distribution of Palaeozoic reworking in the Western Arunta Region and northwestern Amadeus Basin from40Ar/39Ar thermochronology: implications for the evolution of intracratonic basins
Authors: McLaren Sandra , Sandiford Mike , Dunlap W. James , Scrimgeour Ian , Close Dorothy , Edgoose Christine 
Published: October 2008

ABSTRACTThe Centralian Superbasin in central Australia is one of the most extensive intracratonic basins known from a stable continental setting, but the factors controlling its formation and subsequent structural dismemberment continue to be debated. Argon thermochronology of K‐feldspar, sensitive to a broad range of temperatures (∼150 to 350 °C), provides evidence for the former extent and thickness of the superbasin and points toward thickening of the superbasin succession over the now exhumed Arunta Region basement. These data suggest that before Palaeozoic tectonism, there was around 5–6 km of sediment present over what is now the northern margin of the Amadeus Basin, and, if the Centralian superbasin was continuous, between 6 and 8 km over the now exhumed basement.40Ar/39Ar data from neoformed fine‐grained muscovite suggests that Palaeozoic deformation and new mineral growth occurred during the earliest compressional phase of the Alice Springs Orogeny (ASO) (440–375 Ma) and was restricted to shear zones. Significantly, several shear zones active during the late Mesoproterozoic Teapot Orogeny were not reactivated at this time, suggesting that the presence of pre‐existing structures was not the only controlling factor in localizing Palaeozoic deformation. A range of Palaeozoic ages of 440–300 Ma from samples within and external to shear zones points to thermal disturbance from at least the early Silurian through until the late Carboniferous and suggests final cooling and exhumation of the terrane in this interval. The absence of evidence for active deformation and/or new mineral growth in the late stages of the ASO (350–300 Ma) is consistent with a change in orogenic dynamics from thick‐skinned regionally extensive deformation to a more restricted localized high‐geothermal gradient event.
Functional implications of temperature‐correlated colour polymorphism in an iridescent, scarabaeine dung beetle
Authors: DAVIS ADRIAN L.V. , BRINK D. JOHAN , SCHOLTZ CLARKE H. , PRINSLOO LINDA C. , DESCHODT CHRISTIAN M. 
Published: October 2008

Abstract1. In many Coleoptera, iridescent colouration is generated by exoskeleton ultra‐structure, within which multilayer interference reflects only certain wavelengths. Published work indicates that the colour polymorphism shown by some iridescent beetles is under genetic control. However, the present study suggests environmental involvement in the polymorphic southern African dung beetle,Gymnopleurus humanusMacleay.2. At 24 study sites across a 1000‐km latitudinal temperature gradient, population samples ofG. humanuswere dominated by blue individuals in the cooler south, by cupreous individuals in the warmer north, and by locally co‐occurring blue, green and cupreous individuals in intermediate situations.3. Using digital reflectance spectrophotometry, we measured wavelength intensity values across the visible spectrum (400–800 nm) and used the 70 measured specimens to estimate maximum reflectance from a further 3912 beetles. Differences in mean reflectance values between 24 populations were strongly correlated with average annual temperatures at study sites.4. Much stronger correlations between mean reflectance values and average temperatures of the cool dry season months suggest that the cross‐climatic patterns may be related to interaction between breeding seasonality and development under different cooler temperatures.5. Published evidence suggests that inherent physical properties of cholesteric liquid crystals and their responses to different thermal conditions could, potentially, generate the different exocuticle ultra‐structure responsible for different reflected colour wavelengths. Furthermore, colour polymorphism could be advantageous across a gradient from cooler to warmer climate as a result of the different thermal properties of different colours.6. Given the correlation with temperature, it is predicted that the prevailing reflected colour balance in southern populations would shift in response to global climatic change.
The effects of the invasive Argentine ant (Linepithema humile) and the native ant Prenolepis imparis on the structure of insect herbivore communities on willow trees (Salix lasiolepis)
Authors: NYGARD JULIE P. , SANDERS NATHAN J. , CONNOR EDWARD F. 
Published: October 2008

Abstract 1. We examined the relative effects of the invasive Argentine ant, Linepithema humile, and a common native ant, Prenolepis imparis, on the community of herbivorous insects occurring on willow trees, Salix lasiolepis in Northern California, U.S.A.2. Using paired control and treatment branches from which we excluded ants and other non‐volant predators, we found that effects of Argentine ants on the herbivore community were generally similar to those of P. imparis. Argentine ants and P. imparis suppressed the damage by skeletonising insects by 50%, but had little effect on most other external‐feeding or internal‐feeding guilds.3. The abundance of aphids was 100% greater in the presence of Argentine ants, but there was no effect on aphid numbers in the presence of P. imparis. Late season aphid numbers were substantially higher in the presence of Argentine ants, but not P. imparis.4. The effects of Argentine ants on skeletonising insects and aphids combined with the overwhelming abundance of Argentine ant workers, suggests that they may have substantial, but often overlooked, effects on the herbivore communities on other plant species in or near riparian habitats in which they invade.
Effects of competition, cannibalism and intra‐guild predation on larval development of the European coccinellid Adalia bipunctata and the invasive species Harmonia axyridis
Authors: WARE REMY , YGUEL BENJAMIN , MAJERUS MICHAEL 
Published: October 2008

Abstract 1. Resource competition and intra‐guild predation (IGP) are important determinants of the structure of aphidophagous guilds. The likelihood and outcome of IGP is influenced by the density of extra‐guild prey and the characteristics of the species involved.2. The nature of intra‐guild interactions between alien and indigenous coccinellids often determines the success of coccinellid invasions, as exemplified by Adalia bipunctata in Japan and Harmonia axyridis in North America and Europe.3. Harmonia axyridis has negatively impinged on indigenous species in its introduced range, and its recent arrival in Britain poses a threat for members of native aphidophagous guilds. IGP and inter‐specific competition between H. axyridis and British coccinellids are predicted to occur. However, the results of such interactions have been little studied.4. Here we investigate the effects of different diets, designed to mimic possible conditions in the wild, on the survival, development, and adult size of H. axyridis and A. bipunctata. Results demonstrate a skew in the consequences of IGP between the two species: the supplementation of a limited aphid diet with non‐conspecific eggs leads to a significant advantage for H. axyridis in respect of all parameters assessed, but gives no benefit to A. bipunctata.5. We conclude that IGP of A. bipunctata by H. axyridis will contribute to the spread and increase of H. axyridis in Britain.6. We further conclude that the skewed nature of IGP between A. bipunctata and H. axyridis at least in part explains the limited spread of A. bipunctata in Japan.