bluuebunny/crossref_metadata_2025_split huggingface dataset:
A segmental maximum a posteriori approach to genome-wide copy number profiling
Authors: Andersson Robin , Bruder Carl E. G. , Piotrowski Arkadiusz , Menzel Uwe , Nord Helena , Sandgren Johanna , Hvidsten Torgeir R. , Diaz de Ståhl Teresita , Dumanski Jan P. , Komorowski Jan 
Published: January 2008

Abstract
Motivation: Copy number profiling methods aim at assigning DNA copy numbers to chromosomal regions using measurements from microarray-based comparative genomic hybridizations. Among the proposed methods to this end, Hidden Markov Model (HMM)-based approaches seem promising since DNA copy number transitions are naturally captured in the model. Current discrete-index HMM-based approaches do not, however, take into account heterogeneous information regarding the genomic overlap between clones. Moreover, the majority of existing methods are restricted to chromosome-wise analysis.
Results: We introduce a novel Segmental Maximum A Posteriori approach, SMAP, for DNA copy number profiling. Our method is based on discrete-index Hidden Markov Modeling and incorporates genomic distance and overlap between clones. We exploit a priori information through user-controllable parameterization that enables the identification of copy number deviations of various lengths and amplitudes. The model parameters may be inferred at a genome-wide scale to avoid overfitting of model parameters often resulting from chromosome-wise model inference. We report superior performances of SMAP on synthetic data when compared with two recent methods. When applied on our new experimental data, SMAP readily recognizes already known genetic aberrations including both large-scale regions with aberrant DNA copy number and changes affecting only single features on the array. We highlight the differences between the prediction of SMAP and the compared methods and show that SMAP accurately determines copy number changes and benefits from overlap consideration.
Availability: SMAP is available from Bioconductor and within the Linnaeus Centre for Bioinformatics Data Warehouse.
Contact: Jan.Komorowski@lcb.uu.se
Supplementary information: Supplementary data are available at http://www.lcb.uu.se/papers/r_andersson/SMAP/
HCGene: a software tool to support the hierarchical classification of genes
Authors: Valentini Giorgio , Cesa-Bianchi Nicolò 
Published: January 2008

Abstract
Summary: The R package HCGene (Hierarchical Classification of Genes) implements methods to process and analyze the Gene Ontology and the FunCat taxonomy in order to support the functional classification of genes. HCGene allows the extraction of subgraphs and subtrees related to specific biological problems, the labeling of genes and gene products with multiple and hierarchical functional classes, and the association of different types of bio-molecular data to genes for learning to predict their functions.
Availability: http://homes.dsi.unimi.it/~valenti/SW/hcgene/download/hcgene_1.0.tar.gz
Contact: valentini@dsi.unimi.it
Supplementary information: Supplementary data are available at http://homes.dsi.unimi.it/~valenti/SW/hcgene
Estimation and assessment of raw copy numbers at the single locus level
Authors: Bengtsson H. , Irizarry R. , Carvalho B. , Speed T. P. 
Published: January 2008

Abstract
Motivation: Although copy-number aberrations are known to contribute to the diversity of the human DNA and cause various diseases, many aberrations and their phenotypes are still to be explored. The recent development of single-nucleotide polymorphism (SNP) arrays provides researchers with tools for calling genotypes and identifying chromosomal aberrations at an order-of-magnitude greater resolution than possible a few years ago. The fundamental problem in array-based copy-number (CN) analysis is to obtain CN estimates at a single-locus resolution with high accuracy and precision such that downstream segmentation methods are more likely to succeed.
Results: We propose a preprocessing method for estimating raw CNs from Affymetrix SNP arrays. Its core utilizes a multichip probe-level model analogous to that for high-density oligonucleotide expression arrays. We extend this model by adding an adjustment for sequence-specific allelic imbalances such as cross-hybridization between allele A and allele B probes. We focus on total CN estimates, which allows us to further constrain the probe-level model to increase the signal-to-noise ratio of CN estimates. Further improvement is obtained by controlling for PCR effects. Each part of the model is fitted robustly. The performance is assessed by quantifying how well raw CNs alone differentiate between one and two copies on Chromosome X (ChrX) at a single-locus resolution (27kb) up to a 200kb resolution. The evaluation is done with publicly available HapMap data.
Availability: The proposed method is available as part of an open-source R package named aroma.affymetrix. Because it is a bounded-memory algorithm, any number of arrays can be analyzed.
Contact: hb@stat.berkeley.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Using repeated measurements to validate hierarchical gene clusters
Authors: Bréhélin Laurent , Gascuel Olivier , Martin Olivier 
Published: January 2008

Abstract
Motivation: Hierarchical clustering is a common approach to study protein and gene expression data. This unsupervised technique is used to find clusters of genes or proteins which are expressed in a coordinated manner across a set of conditions. Because of both the biological and technical variability, experimental repetitions are generally performed. In this work, we propose an approach to evaluate the stability of clusters derived from hierarchical clustering by taking repeated measurements into account.
Results: The method is based on the bootstrap technique that is used to obtain pseudo-hierarchies of genes from resampled datasets. Based on a fast dynamic programming algorithm, we compare the original hierarchy to the pseudo-hierarchies and assess the stability of the original gene clusters. Then a shuffling procedure can be used to assess the significance of the cluster stabilities. Our approach is illustrated on simulated data and on two microarray datasets. Compared to the standard hierarchical clustering methodology, it allows to point out the dubious and stable clusters, and thus avoids misleading interpretations.
Availability: The programs were developed in C and R languages.
Contact: brehelin@lirmm.fr
Supplementary information: Supplementary Material and source code are available at address http://www.lirmm.fr/~brehelin/Stability/
DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein–protein interactions
Authors: Bernauer Julie , Bahadur Ranjit Prasad , Rodier Francis , Janin Joël , Poupon Anne 
Published: January 2008

Abstract
Motivation: Knowledge of the oligomeric state of a protein is often essential for understanding its function and mechanism. Within a protein crystal, each protein monomer is in contact with many others, forming many small interfaces and a few larger ones that are biologically significant if the protein is a homodimer in solution, but not if the protein is monomeric. Telling such ‘crystal dimers’ from real ones remains a difficult task.
Results: It has already been demonstrated that the interfaces of native and non-native protein–protein complexes can be distinguished using a combination of parameters computed with a method on the Voronoi tessellation. We show in this article that the same parameters highlight significant differences between the interfaces of biological and crystal dimers. Using these parameters as descriptors in machine learning methods leads to accurate classification of specific and non-specific protein–protein interfaces.
Availability: Software is available at http://fifi.ibbmc.u-psud.fr/DiMoVo
Contact: anne@rezo.net
GENESIS: genome evolution scenarios
Authors: Gog Simon , Bader Martin , Ohlebusch Enno 
Published: January 2008

Abstract
Summary: We implemented a software tool called GENESIS for three different genome rearrangement problems: Sorting a unichromosomal genome by weighted reversals and transpositions (SwRT), sorting a multichromosomal genome by reversals, translocations, fusions and fissions (SRTl), and sorting a multichromosomal genome by weighted reversals, translocations, fusions, fissions and transpositions (SwRTTl).
Availability: Source code can be obtained by the authors, or use the web interface http://www.uni-ulm.de/in/theo/research/genesis.html
Contact: simon.gog@uni-ulm.de
TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism
Authors: Moore J. D. , Allaby R. G. 
Published: January 2008

Abstract
Summary: TreeMos is a novel high-throughput graphical analysis application that allows the user to search for phylogenetic mosaicism among one or more DNA or protein sequence multiple alignments and additional unaligned sequences. TreeMos uses a sliding window and local alignment algorithm to identify the nearest neighbour of each sequence segment, and visualizes instances of sequence segments whose nearest neighbour is anomalous to that identified using the global alignment. Data sets can include whole genome sequences allowing phylogenomic analyses in which mosaicism may be attributed to recombination between any two points in the genome. TreeMos can be run from the command line, or within a web browser allowing the relationships between taxa to be explored by drill-through.
Availability: http://www2.warwick.ac.uk/fac/sci/whri/research/archaeobotany
Contact: jonathan.moore@warwick.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Light Induces Peroxisome Proliferation in Arabidopsis Seedlings through the Photoreceptor Phytochrome A, the Transcription Factor HY5 HOMOLOG, and the Peroxisomal Protein PEROXIN11b
Authors: Desai Mintu , Hu Jianping 
Published: January 2008

AbstractPeroxisomes are single membrane-delimited subcellular organelles that carry out numerous vital metabolic reactions in nearly all eukaryotes. Peroxisomes alter their morphology, abundance, and enzymatic constituents in response to environmental cues, yet little is known about the underlying mechanisms. In this work, we investigated the regulatory role of light in peroxisome proliferation in Arabidopsis (Arabidopsis thaliana). We provide evidence that light induces proliferation of peroxisomes in Arabidopsis seedlings and that the peroxisomal protein PEX11b plays an important role in mediating this process. The far-red light receptor phytochrome A (phyA) and the bZIP transcription factor HY5 HOMOLOG (HYH) are both required for the up-regulation of PEX11b in the light. We further demonstrate that the phyA and hyh mutants exhibit reduced peroxisome abundance, a phenotype that can be rescued by overexpressing PEX11b in these plants. The HYH protein is able to bind to the promoter of PEX11b, suggesting that the PEX11b gene is a direct target of HYH. We conclude that HYH and PEX11b constitute a novel branch of the phyA-mediated light signaling cascade, which promotes peroxisome proliferation during seedling photomorphogenesis.
The MaizeViviparous8Locus, Encoding a Putative ALTERED MERISTEM PROGRAM1-Like Peptidase, Regulates Abscisic Acid Accumulation and Coordinates Embryo and Endosperm Development
Authors: Suzuki Masaharu , Latshaw Susan , Sato Yutaka , Settles A. Mark , Koch Karen E. , Hannah L. Curtis , Kojima Mikiko , Sakakibara Hitoshi , McCarty Donald R. 
Published: January 2008

AbstractWe describe a mutant of Zea mays isolated from a W22 inbred transposon population, widow's peak mutant1 (wpk1), with an altered pattern of anthocyanin synthesis and aleurone cell differentiation in endosperm. In addition, a failure of the developing mutant embryo to form leaf initials is associated with decreased expression of a subset of meristem regulatory genes that includes Abphyl1 and Td1. We show that the viviparous8 (vp8) mutant has a similar pleiotropic phenotype in the W22 inbred background in contrast to the viviparous embryo phenotype exhibited in the standard genetic background, and we confirmed that wpk1 is allelic to vp8. Further genetic analysis revealed that the standard vp8 stock contains an unlinked, partially dominant suppressor of the vp8 mutation that is not present in W22. Consistent with the early-onset viviparous phenotype of vp8, expression of several embryonic regulators, including LEC1/B3 domain transcription factors, was reduced in the mutant embryo. Moreover, reduced abscisic acid (ABA) content of vp8/wpk1 embryos was correlated with altered regulation of ABA biosynthesis, as well as ABA catabolic pathways. The ABA biosynthetic gene Vp14 was down-regulated in the nonsuppressed background, whereas the ZmABA8′oxA1a ABA 8′-hydroxylase gene was strongly up-regulated in both genetic backgrounds. Molecular analysis revealed that Vp8 encodes a putative peptidase closely related to Arabidopsis thaliana ALTERED MERISTEM PROGRAM1. Because the Vp8 regulates meristem development as well as seed maturation processes, including ABA accumulation, we propose that VP8 is required for synthesis of an unidentified signal that integrates meristem and embryo formation in seeds.
Direct Repression ofKNOXLoci by the ASYMMETRIC LEAVES1 Complex ofArabidopsis
Authors: Guo Mengjuan , Thomas Julie , Collins Galen , Timmermans Marja C.P. 
Published: January 2008

AbstractKNOTTED1-like homeobox (KNOX) genes promote stem cell activity and must be repressed to form determinate lateral organs. Stable KNOX gene silencing during organogenesis is known to involve the predicted DNA binding proteins ASYMMETRIC LEAVES1 (AS1) and AS2 as well as the chromatin-remodeling factor HIRA. However, the mechanism of silencing is unknown. Here, we show that AS1 and AS2 form a repressor complex that binds directly to the regulatory motifs CWGTTD and KMKTTGAHW present at two sites in the promoters of the KNOX genes BREVIPEDICELLUS (BP) and KNAT2. The two binding sites act nonredundantly, and interaction between AS1-AS2 complexes at these sites is required to repress BP. Promoter deletion analysis further indicates that enhancer elements required for BP expression in the leaf are located between the AS1-AS2 complex binding sites. We propose that AS1-AS2 complexes interact to create a loop in the KNOX promoter and, likely through recruitment of HIRA, form a repressive chromatin state that blocks enhancer activity during organogenesis. Our model for AS1-AS2–mediated KNOX gene silencing is conceptually similar to the action of an insulator. This regulatory mechanism may be conserved in simple leafed species of monocot and dicot lineages and constitutes a potential key determinant in the evolution of compound leaves.
Membrane Association of theArabidopsisARF Exchange Factor GNOM Involves Interaction of Conserved Domains
Authors: Anders Nadine , Nielsen Michael , Keicher Jutta , Stierhof York-Dieter , Furutani Masahiko , Tasaka Masao , Skriver Karen , Jürgens Gerd 
Published: January 2008

AbstractThe GNOM protein plays a fundamental role in Arabidopsis thaliana development by regulating endosome–to–plasma membrane trafficking required for polar localization of the auxin efflux carrier PIN1. GNOM is a family member of large ARF guanine nucleotide exchange factors (ARF-GEFs), which regulate vesicle formation by activating ARF GTPases on specific membranes in animals, plants, and fungi. However, apart from the catalytic exchange activity of the SEC7 domain, the functional significance of other conserved domains is virtually unknown. Here, we show that a distinct N-terminal domain of GNOM mediates dimerization and in addition interacts heterotypically with two other conserved domains in vivo. In contrast with N-terminal dimerization, the heterotypic interaction is essential for GNOM function, as mutations abolishing this interaction inactivate the GNOM protein and compromise its membrane association. Our results suggest a general model of large ARF-GEF function in which regulated changes in protein conformation control membrane association of the exchange factor and, thus, activation of ARFs.
Sad3andSad4Are Required for Saponin Biosynthesis and Root Development in Oat
Authors: Mylona Panagiota , Owatworakit Amorn , Papadopoulou Kalliopi , Jenner Helen , Qin Bo , Findlay Kim , Hill Lionel , Qi Xiaoquan , Bakht Saleha , Melton Rachel , Osbourn Anne 
Published: January 2008

AbstractAvenacins are antimicrobial triterpene glycosides that are produced by oat (Avena) roots. These compounds confer broad-spectrum resistance to soil pathogens. Avenacin A-1, the major avenacin produced by oats, is strongly UV fluorescent and accumulates in root epidermal cells. We previously defined nine loci required for avenacin synthesis, eight of which are clustered. Mutants affected at seven of these (including Saponin-deficient1 [Sad1], the gene for the first committed enzyme in the pathway) have normal root morphology but reduced root fluorescence. In this study, we focus on mutations at the other two loci, Sad3 (also within the gene cluster) and Sad4 (unlinked), which result in stunted root growth, membrane trafficking defects in the root epidermis, and root hair deficiency. While sad3 and sad4 mutants both accumulate the same intermediate, monodeglucosyl avenacin A-1, the effect on avenacin A-1 glucosylation in sad4 mutants is only partial. sad1/sad1 sad3/sad3 and sad1/sad1 sad4/sad4 double mutants have normal root morphology, implying that the accumulation of incompletely glucosylated avenacin A-1 disrupts membrane trafficking and causes degeneration of the epidermis, with consequential effects on root hair formation. Various lines of evidence indicate that these effects are dosage-dependent. The significance of these data for the evolution and maintenance of the avenacin gene cluster is discussed.
Effect of testing temperature on corrosion behaviour of different heat treated stainless steels in the active‐passive region
Authors: Slemnik Mojca 
Published: January 2008

PurposeThis paper aims to focus on the effects of temperature of the immersion media on the corrosion behaviour of differently heat‐treated X20Cr13 stainless steel.Design/methodology/approachSpecimens, quenched on air, quenched in oil and quenched in oil and then tempered, were tested during exposure in 0.1 M H2SO4 at 30, 40 and 50°C. The results were interpreted on the base of potentiodynamic and impedance measurements.FindingsFrom the impedance spectra a reaction mechanism can be determined: after samples had reached and passed the active peak, expressed as the highest peak on the potentiodynamic curve, corrosion products at interfaces, which were adsorbed at metal surface, led to an increase in the charge transfer resistance. Elevated temperature of immersion media has had appreciable influence on the corrosion rate and adsorption of products, but at this temperature level did not affect the principle of corrosion reactions. Activation energies were calculated to exhibit temperature dependence of current density, which was the highest for the oil‐ and the lowest for the air‐quenched sample.Originality/valueThe paper provides further research on stainless steel, the corrosion behaviour of which can be controlled already by heat treatment.
Schiff bases of ethylenediamine/triethylenetetramine with benzaldehyde/cinnamic aldehyde/salicylaldehyde as corrosion inhibitors of zinc in sulphuric acid
Authors: Desai M.N. , Talati J.D. , Shah N.K. 
Published: January 2008

PurposeA survey of technical literature indicates that there is a shortage of excellent corrosion inhibitors for zinc in non‐oxidizing acids, particularly sulphuric acid. This paper aims to describe the behaviour of ethylenediamine‐N‐N′‐dibenzylidene, ethylenediamine‐N‐N′‐disalicylidene, ethylenediamine‐N‐N′‐dicinnamylidene, triethylenetetramine tribenzylidene and triethylenetetramine trisalicylidene as corrosion inhibitors for zinc in sulphuric acid solutions. The objective of this research work also is to have an insight into the action mechanism of these inhibitors.Design/methodology/approachThe effect of the various parameters affecting the action of the above‐mentioned corrosion inhibitors has been studied using weight‐loss data and polarisation measurements. Adsorption data also were utilized.FindingsThe inhibitors showed excellent corrosion inhibition (>99 per cent) at effective inhibitor concentrations. The two salicylidenes were better corrosion inhibitors than were corresponding benzylidenes. It appeared from this study that an efficient inhibitor is characterised by a relatively greater decrease in free energy of adsorption, lower entropy of adsorption and relatively lower heat of adsorption. Basically, these inhibitors were cathodic, as was revealed by polarisation data, and the inhibitors followed Langmuir adsorption isotherm behaviour. In general, the conjoint action of the inhibitor and the cathodic current was synergistic.Research limitations/implicationsPowerful Schiff bases still need to be synthesized so as to be effective at extremely low concentrations. The behaviour with other metals and alloys in diverse media also requires to be investigated.Originality/valueVery few inhibitors demonstrate such excellent corrosion inhibition of zinc in aggressive corrosive media. Such detailed investigations on corrosion inhibitors are unusual.
Scholarly monographs on rock music: a bibliographic essay
Authors: Berger Monica 
Published: January 2008

PurposeThe purpose of this article is to give an overview of scholarly monographs on rock music from 1980 to the present. It aims to provide an overview to the literature for practical purposes of collection development as well as giving the reader insight into key issues and trends related to a interdisciplinary topic that attracts scholars from many disciplines in the humanities and social sciences.Design/methodology/approachThis bibliographic essay, focusing on works related to American culture and of a general nature, includes an overview and historical background; a discussion of how music and ethnomusiciological scholars approach the topic; geographic approaches; literature on four key icons (Elvis, Dylan, Springsteen, and Madonna); American studies; subcultures and genres; other methodologies; and concludes by discussing notable recent works.FindingsThe scholarly literature on rock incorporates a wide variety of approaches and methodologies. Many music‐related scholars appropriate methodology from other disciplines and some non‐music‐related scholars use the formalistic analysis of music scholars. Authenticity is a major theme in the literature on rock.Originality/valueThis essay covers the widest range of monographs on the topic, providing insight into not only the key scholars but also the diversity of approaches to the topic. The historical approach to the literature gives the reader a sense of how the academic discourse on rock has evolved. This essay is of interest to librarians, scholars of rock music, and others concerned with how American scholarship in the humanities and the social sciences has grown since the advent of cultural studies.