bluuebunny/crossref_metadata_2025_split huggingface dataset:
A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge
Authors: Tian Ze , Hwang TaeHyun , Kuang Rui 
Published: August 2009

Abstract
Motivation: Incorporating biological prior knowledge into predictive models is a challenging data integration problem in analyzing high-dimensional genomic data. We introduce a hypergraph-based semi-supervised learning algorithm called HyperPrior to classify gene expression and array-based comparative genomic hybridization (arrayCGH) data using biological knowledge as constraints on graph-based learning. HyperPrior is a robust two-step iterative method that alternatively finds the optimal labeling of the samples and the optimal weighting of the features, guided by constraints encoding prior knowledge. The prior knowledge for analyzing gene expression data is that cancer-related genes tend to interact with each other in a protein–protein interaction network. Similarly, the prior knowledge for analyzing arrayCGH data is that probes that are spatially nearby in their layout along the chromosomes tend to be involved in the same amplification or deletion event. Based on the prior knowledge, HyperPrior imposes a consistent weighting of the correlated genomic features in graph-based learning.
Results: We applied HyperPrior to test two arrayCGH datasets and two gene expression datasets for both cancer classification and biomarker identification. On all the datasets, HyperPrior achieved competitive classification performance, compared with SVMs and the other baselines utilizing the same prior knowledge. HyperPrior also identified several discriminative regions on chromosomes and discriminative subnetworks in the PPI, both of which contain cancer-related genomic elements. Our results suggest that HyperPrior is promising in utilizing biological prior knowledge to achieve better classification performance and more biologically interpretable findings in gene expression and arrayCGH data.
Availability: http://compbio.cs.umn.edu/HyperPrior
Contact: kuang@cs.umn.edu
Supplementary information: Supplementary data are available at bioinformatics online.
metahdep: meta-analysis of hierarchically dependent gene expression studies
Authors: Stevens John R. , Nicholas Gabriel 
Published: August 2009

Abstract
Summary: The metahdep package contains tools for combining the results of multiple gene expression studies. Unlike previous microarray meta-analysis packages, metahdep accounts for both sampling and hierarchical dependence among studies, as well as fundamental covariate differences between studies.
Availability: http://bioconductor.org/packages/release/Software.html
Contact: john.r.stevens@usu.edu
Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks
Authors: Tian Feng , Shah Parantu K. , Liu Xiangjun , Negre Nicolas , Chen Jia , Karpenko Oleksiy , White Kevin P. , Grossman Robert L. 
Published: August 2009

Abstract
Motivation: The highly coordinated expression of thousands of genes in an organism is regulated by the concerted action of transcription factors, chromatin proteins and epigenetic mechanisms. High-throughput experimental data for genome wide in vivo protein–DNA interactions and epigenetic marks are becoming available from large projects, such as the model organism ENCyclopedia Of DNA Elements (modENCODE) and from individual labs. Dissemination and visualization of these datasets in an explorable form is an important challenge.
Results: To support research on Drosophila melanogaster transcription regulation and make the genome wide in vivo protein–DNA interactions data available to the scientific community as a whole, we have developed a system called Flynet. Currently, Flynet contains 101 datasets for 38 transcription factors and chromatin regulator proteins in different experimental conditions. These factors exhibit different types of binding profiles ranging from sharp localized peaks to broad binding regions. The protein–DNA interaction data in Flynet was obtained from the analysis of chromatin immunoprecipitation experiments on one color and two color genomic tiling arrays as well as chromatin immunoprecipitation followed by massively parallel sequencing. A web-based interface, integrated with an AJAX based genome browser, has been built for queries and presenting analysis results. Flynet also makes available the cis-regulatory modules reported in literature, known and de novo identified sequence motifs across the genome, and other resources to study gene regulation.
Contact: grossman@uic.edu
Availability: Flynet is available at https://www.cistrack.org/flynet/.
Supplementary information: Supplementary data are available at Bioinformatics online.
Efficacy and safety of nebivolol in elderly heart failure patients with impaired renal function: insights from the SENIORS trial
Authors: Cohen‐Solal Alain , Kotecha Dipak , van Veldhuisen Dirk J , Babalis Daphne , Böhm Michael , Coats Andrew J. , Roughton Michael , Poole‐Wilson Philip , Tavazzi Luigi , Flather Marcus ,   on behalf of the SENIORS Investigators
Published: August 2009

AimTo determine the safety and efficacy of nebivolol in elderly heart failure (HF) patients with renal dysfunction.Methods and resultsSENIORS recruited patients aged 70 years or older with symptomatic HF, irrespective of ejection fraction, and randomized them to nebivolol or placebo. Patients (n = 2112) were divided by tertile of estimated glomerular filtration rate (eGFR). Mean age of patients was 76.1 years, 35% of patients had an ejection fraction of >35%, and 37% were women resulting in a unique cohort, far more representative of clinical practice than previous trials. eGFR was strongly associated with outcomes and nebivolol was similarly efficacious across eGFR tertiles. The primary outcome rate (all‐cause mortality or cardiovascular hospital admission) and adjusted hazard ratio for nebivolol use in those with low eGFR was 40% and 0.84 (95% CI 0.67–1.07), 31% and 0.79 (0.60–1.04) in the middle tertile, and 29% and 0.86 (0.65–1.14) in the highest eGFR tertile. There was no interaction noted between renal function and the treatment effect (P = 0.442). Nebivolol use in patients with moderate renal impairment (eGFR <60) was not associated with major safety concerns, apart from higher rates of drug‐discontinuation due to bradycardia.ConclusionNebivolol is safe and has a similar effect in elderly HF patients with mild or moderate renal impairment.
Outbreak of Powdery Mildew Caused by Erysiphe cruciferarum on Spider Flower (Cleome hassleriana) in Italy
Authors: Garibaldi A. , Bertetti D. , Gullino M. L. 
Published: August 2009

Spider flower (Cleome hassleriana L. [synonym = C. spinosa]) is used as a tall border in parks and gardens worldwide. During July 2008, severe outbreaks of a powdery mildew were observed in a public park in Torino (northern Italy). Leaves were covered with dense, white hyphae and conidia, especially on the adaxial surface. Hyphae were also present on petioles and fruits, but not on petals and stems. As the disease progressed, infected leaves turned chlorotic, curled, and wilted. Conidia were hyaline, cylindrical, single, and measured 31.1 to 48.2 × 12.9 to 17.6 μm (average 37.1 × 15.6 μm). Germ tubes terminating in a moderately lobed appressorium were produced terminally. The cylindrical foot cells of the erect condiophores were 19.2 to 27.8 × 6.5 to 8.6 μm (average 23.3 × 7.7 μm). Fibrosin bodies were absent. Chasmothecia were observed mostly on the lower surfaces of leaves. At maturity, they were dark amber and spherical with a diameter of 92.9 to 151.0 μm (average 121.4 μm). Each chasmothecium contained six stalked asci (average size 63.7 × 35.9 μm). Each ascus contained four ellipsoid ascospores that measured 17.3 to 26.4 × 10.9 to 15.6 μm (average 23.3 × 12.8 μm). The internal transcribed spacer (ITS) region of rDNA was amplified using primers ITS4/ITS6 and sequenced (1). The 602-bp sequence was deposited in GenBank under the Accession No. GQ149478 and was 99% similar to that of Erysiphe cruciferarum (Accession No. EU140958). As proof of pathogenicity, diseased leaves of C. hassleriana were pressed against leaves of three healthy 4-month-old potted plants of the same species for 10 min. Three noninoculated plants served as controls. Inoculated and noninoculated plants were maintained in a greenhouse at 22 to 25°C in isolation. After 11 days, typical powdery mildew colonies developed on inoculated plants. Noninoculated plants did not develop symptoms. The pathogenicity test was repeated once. Powdery mildew on C. hassleriana caused by E. cruciferarum was reported in Italy (2) but the pathogen was not characterized. Herbarium specimens are deposited at AGROINNOVA Collection, University of Torino, Italy. References: (1) S. F. Altschul et al. Nucleic Acids Res. 25:3389, 1997. (2) U. Braun. The Powdery Mildews (Erysiphales) of Europe. Gustav Fischer Verlag, Jena, Germany, 1995.
First Report of Downy Mildew on Field-Grown Sweet Basil Caused by a Peronospora sp. in San Diego County, California
Authors: Blomquist C. L. , Rooney-Latham S. , Nolan P. A. 
Published: August 2009

Sweet basil (Ocimum basilicum) is a culinary herb grown in fields and greenhouses in California. In August of 2008, samples were submitted to the San Diego County Plant Diagnostic Laboratory with a grayish brown, downy growth that covered areas of the abaxial side of the leaf. Early symptoms included leaf chlorosis followed by the appearance of scattered grayish brown conidia and conidiophores in the chlorotic areas. Conidiophore emergence progressed to a grayish brown, velvety growth with some of the chlorotic areas becoming necrotic. Similarly affected plants were submitted to the laboratory from another field 32 km (20 miles) away in the same county. Both fields were drip irrigated and located in inland valleys. Approximately 50 to 60% of the plants were symptomatic. Conidiophores, on the abaxial side of the leaves that were characteristic of Peronospora, branched dichotomously three to five times and measured 390 to 1,100 × 2.5 to 7.0 μm (675.6 × 4.9 μm average). Light brown, globose to ellipsoidal conidia measured 20 to 34 × 18 to 26 μm (26 × 22 μm average). To confirm pathogenicity, three basil plants in 10.2-cm (4-inch) pots were sprayed with a suspension of 4.5 × 105 conidia/ml and incubated in a dew chamber at 20°C for 48 h in the dark. Three noninoculated plants were sprayed with water. Plants were then placed in a growth chamber at 18°C with a 16-h photoperiod. Relative humidity was maintained near 95% by placing the plants over a tray of water and covering each group with a plastic tent. Signs of grayish brown, downy growth were seen approximately 14 days after inoculation. Pathogenicity experiments were repeated once. No symptoms developed on plants sprayed with water. Sequence of the intergenic spacer regions and 5.8S gene was obtained from a sample collected in one field, through amplification with primers DC6 and ITS4 and sequencing with primers ITS6 and ITS4 (2). The sequence (Accession No. FJ436024) from the field sample was identical to GenBank Accession No. AY884605 that represented a Peronospora sp. from basil in Switzerland. On the basis of morphological and sequence information, the Peronospora sp. from San Diego County is most likely the same Peronospora sp. that was identified from sweet basil in Switzerland, Italy (1), and South Africa (4), as well as coleus in New York and Louisiana (3). The basil Peronospora sp. has been shown to be present in seed (1). Since both growers purchased their seed from the same supplier, seeds could have been a possible inoculum source. To our knowledge, this is the first report of a downy mildew on sweet basil in California. References: (1) L. Belbahri et al. Mycol. Res. 109:1276, 2005. (2) D. E. L. Cooke et al. Fungal Genet. Biol. 30:17, 2000. (3) M. L. Daughtrey et al. Plant Dis. 90:1111, 2006. (4) A. McLeod et al. Plant Dis. 90:1115, 2006.
Obesity and Erectile Dysfunction: Is Androgen Deficiency the Common Link?
Authors: Feeley Robert J. , Traish Abdulmaged M. 
Published: August 2009

Obesity is associated with increased risk of erectile dysfunction (ED); however, the underlying causes of ED in obese individuals remain poorly defined. The aim of this review is to discuss the evidence available on the relationship between obesity and ED. A search of published studies in PubMed from 1970 through 2009 was conducted, and relevant articles were evaluated and discussed.Visceral obesity is a public health threat, and is associated with increased risk of diabetes, vascular disease, endothelial dysfunction, and ED. Plasma testosterone levels are reduced in obesity, further contributing to an increased risk of vascular pathology in obesity. The recognition of the relationship between obesity, reduced testosterone levels, and ED has paved the way for new approaches to manage and treat obese, hypogonadal patients with ED. Obesity profoundly and adversely impacts overall health and, in particular, vascular health, by increasing proinflammatory factors, altering endothelial function and the androgen endocrine milieu, thus increasing the risk of ED.
BRASSINOSTEROID UPREGULATED1, Encoding a Helix-Loop-Helix Protein, Is a Novel Gene Involved in Brassinosteroid Signaling and Controls Bending of the Lamina Joint in Rice
Authors: Tanaka Atsunori , Nakagawa Hitoshi , Tomita Chikako , Shimatani Zenpei , Ohtake Miki , Nomura Takahito , Jiang Chang-Jie , Dubouzet Joseph G. , Kikuchi Shoshi , Sekimoto Hitoshi , Yokota Takao , Asami Tadao , Kamakura Takashi , Mori Masaki 
Published: August 2009

Abstract
Brassinosteroids (BRs) are involved in many developmental processes and regulate many subsets of downstream genes throughout the plant kingdom. However, little is known about the BR signal transduction and response network in monocots. To identify novel BR-related genes in rice (Oryza sativa), we monitored the transcriptomic response of the brassinosteroid deficient1 (brd1) mutant, with a defective BR biosynthetic gene, to brassinolide treatment. Here, we describe a novel BR-induced rice gene BRASSINOSTEROID UPREGULATED1 (BU1), encoding a helix-loop-helix protein. Rice plants overexpressing BU1 (BU1:OX) showed enhanced bending of the lamina joint, increased grain size, and resistance to brassinazole, an inhibitor of BR biosynthesis. In contrast to BU1:OX, RNAi plants designed to repress both BU1 and its homologs displayed erect leaves. In addition, compared to the wild type, the induction of BU1 by exogenous brassinolide did not require de novo protein synthesis and it was weaker in a BR receptor mutant OsbriI (Oryza sativa brassinosteroid insensitive1, d61) and a rice G protein alpha subunit (RGA1) mutant d1. These results indicate that BU1 protein is a positive regulator of BR response: it controls bending of the lamina joint in rice and it is a novel primary response gene that participates in two BR signaling pathways through OsBRI1 and RGA1. Furthermore, expression analyses showed that BU1 is expressed in several organs including lamina joint, phloem, and epithelial cells in embryos. These results indicate that BU1 may participate in some other unknown processes modulated by BR in rice.
The ArabidopsisGRF-INTERACTING FACTORGene Family Performs an Overlapping Function in Determining Organ Size as Well as Multiple Developmental Properties
Authors: Lee Byung Ha , Ko Jae-Heung , Lee Sangman , Lee Yi , Pak Jae-Hong , Kim Jeong Hoe 
Published: August 2009

AbstractPreviously, the GRF-INTERACTING FACTOR1 (GIF1)/ANGUSTIFOLIA3 (AN3) transcription coactivator gene, a member of a small gene family comprising three genes, was characterized as a positive regulator of cell proliferation in lateral organs, such as leaves and flowers, of Arabidopsis (Arabidopsis thaliana). As yet, it remains unclear how GIF1/AN3 affects the cell proliferation process. In this study, we demonstrate that the other members of the GIF gene family, GIF2 and GIF3, are also required for cell proliferation and lateral organ growth, as gif1, gif2, and gif3 mutations cause a synergistic reduction in cell numbers, leading to small lateral organs. Furthermore, GIF1, GIF2, and GIF3 overexpression complemented a cell proliferation defect of the gif1 mutant and significantly increased lateral organ growth of wild-type plants as well, indicating that members of the GIF gene family are functionally redundant. Kinematic analysis on leaf growth revealed that the gif triple mutant as well as other strong gif mutants developed leaf primordia with fewer cells, which was due to the low rate of cell proliferation, eventually resulting in earlier exit from the proliferative phase of organ growth. The low proliferative activity of primordial leaves was accompanied by decreased expression of cell cycle-regulating genes, indicating that GIF genes may act upstream of cell cycle regulators. Analysis of gif double and triple mutants clarified a previously undescribed role of the GIF gene family: gif mutants had small vegetative shoot apical meristems, which was correlated with the development of small leaf primordia. gif triple mutants also displayed defective structures of floral organs. Taken together, our results suggest that the GIF gene family plays important roles in the control of cell proliferation via cell cycle regulation and in other developmental properties that are associated with shoot apical meristem function.
CHOTTO1, a Putative Double APETALA2 Repeat Transcription Factor, Is Involved in Abscisic Acid-Mediated Repression of Gibberellin Biosynthesis during Seed Germination in Arabidopsis
Authors: Yano Ryoichi , Kanno Yuri , Jikumaru Yusuke , Nakabayashi Kazumi , Kamiya Yuji , Nambara Eiji 
Published: August 2009

AbstractThe phytohormones abscisic acid (ABA) and gibberellins (GAs) are the primary signals that regulate seed dormancy and germination. In this study, we investigated the role of a double APETALA2 repeat transcription factor, CHOTTO1 (CHO1), in seed dormancy, germination, and phytohormone metabolism of Arabidopsis (Arabidopsis thaliana). Wild-type seeds were dormant when freshly harvested seeds were sown, and these seeds were released from dormancy after a particular period of dry storage (after-ripening). The cho1 mutant seeds germinated easily even in a shorter period of storage than wild-type seeds. The cho1 mutants showed reduced responsiveness to ABA, whereas transgenic plants constitutively expressing CHO1 (p35S∷CHO1) showed an opposite phenotype. Notably, after-ripening reduced the ABA responsiveness of the wild type, cho1 mutants, and p35S∷CHO1 lines. Hormone profiling demonstrated that after-ripening treatment decreased the levels of ABA and salicylic acid and increased GA4, jasmonic acid, and isopentenyl adenine when wild-type seeds were imbibed. Expression analysis showed that the transcript levels of genes for ABA and GA metabolism were altered in the wild type by after-ripening. Hormone profiling and expression analyses indicate that cho1 seeds, with a short period of storage, resembled fully after-ripened wild-type seeds. Genetic analysis showed that the cho1 mutation partially restored delayed seed germination and reduced GA biosynthesis activity in the ABA-overaccumulating cyp707a2-1 mutant background but did not restore seed germination in the GA-deficient ga1-3 mutant background. These results indicate that CHO1 acts downstream of ABA to repress GA biosynthesis during seed germination.
An Extended AE-Rich N-Terminal Trunk in Secreted Pineapple Cystatin Enhances Inhibition of Fruit Bromelain and Is Posttranslationally Removed during Ripening
Authors: Neuteboom Leon W. , Matsumoto Kristie O. , Christopher David A. 
Published: August 2009

AbstractPhytocystatins are potent inhibitors of cysteine proteases and have been shown to participate in senescence, seed and organ biogenesis, and plant defense. However, phytocystatins are generally poor inhibitors of the cysteine protease, bromelain, of pineapple (Ananas comosus). Here, we demonstrated that pineapple cystatin, AcCYS1, inhibited (&gt;95%) stem and fruit bromelain. AcCYS1 is a unique cystatin in that it contains an extended N-terminal trunk (NTT) of 63 residues rich in alanine and glutamate. A signal peptide preceding the NTT is processed in vitro by microsomal membranes giving rise to a 27-kD species. AcCYS1 mRNA was present in roots and leaves but was most abundant in fruit. Using immunofluorescence and immunoelectron microscopy with an AcCYS1-specific antiserum, AcCYS1 was found in the apoplasm. Immunoblot analysis identified a 27-kD protein in fruit, roots, and leaves and a 15-kD species in mature ripe fruit. Ripe fruit extracts proteolytically removed the NTT of 27-kD AcCYS1 in vitro to produce the 15-kD species. Mass spectrometry analysis was used to map the primary cleavage site immediately after a conserved critical glycine-94. The AE-rich NTT was required to inhibit fruit and stem bromelain (&gt;95%), whereas its removal decreased inhibition to 20% (fruit) and 80% (stem) and increased the dissociation equilibrium constant by 1.8-fold as determined by surface plasmon resonance assays. We propose that proteolytic removal of the NTT results in the decrease of the inhibitory potency of AcCYS1 against fruit bromelain during fruit ripening to increase tissue proteolysis, softening, and degradation.
Partitioning the Apical Domain of theArabidopsisEmbryo Requires the BOBBER1 NudC Domain Protein
Authors: Jurkuta Rebecca Joy , Kaplinsky Nicholas J. , Spindel Jennifer E. , Barton M. Kathryn 
Published: August 2009

AbstractThe apical domain of the embryo is partitioned into distinct regions that will give rise to the cotyledons and the shoot apical meristem. In this article, we describe a novel screen to identify Arabidopsis thaliana embryo arrest mutants that are defective in this partitioning, and we describe the phenotype of one such mutant, bobber1. bobber1 mutants arrest at the globular stage of development, they express the meristem-specific SHOOTMERISTEMLESS gene throughout the top half of the embryo, and they fail to express the AINTEGUMENTA transcript normally found in cotyledons. Thus, BOBBER1 is required to limit the extent of the meristem domain and/or to promote the development of the cotyledon domains. Based on expression of early markers for apical development, bobber1 mutants differentiate protodermis and undergo normal early apical development. Consistent with a role for auxin in cotyledon development, BOBBER1 mutants fail to express localized maxima of the DR5:green fluorescent protein reporter. BOBBER1 encodes a protein with homology to the Aspergillus nidulans protein NUDC that has similarity to protein chaperones, indicating a possible role for BOBBER1 in synthesis or transport of proteins involved in patterning the Arabidopsis embryo.