bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sulfur management and miticide use in winegrapes grown in California
Authors: Zhang Minghua , Campos Jennifer , Zhan Yu , Grieneisen Michael L. 
Published: February 2012

AbstractProper sulfur management in winegrapes may potentially reduce both insecticide/miticide use and the human/social problems associated with sulfur's impacts on air quality and odors, particularly in wine tourism regions. Data from California's unique Pesticide Use Report (PUR) database, which records agricultural pesticide applications on all crops throughout the state, are used to determine if either winegrape grower's choice of sulfur formulation (dust only, wettable only, or a combination) or overall sulfur use rates (pounds per acre planted) correlate with annual miticide and insecticide use in Fresno and Madera (hotter–drier) and Napa and Sonoma counties (cooler–damper). Annual sulfur use has declined by 36–55% in these counties from 1993 to 2009. In 2000, the greatest number of growers in each county were combination users; wettable users were higher in Napa (38%) and Sonoma (34%) than in Fresno (24%) and Madera (10%); and dust-only users varied little (15–19%) across the four counties. Data for 2005 and 2009 showed similar trends. The use of high-toxicity insecticides in Fresno was 387% higher than in Napa–Sonoma in 2000, but was 25 and 8% lower in 2005 and 2009, respectively. In Fresno, wettable sulfur users used less high-toxicity insecticides; while in Fresno and Madera dust users used less lower-risk insecticides than combination or wettable sulfur users. No significant differences in insecticide use were evident between the three sulfur use categories in Napa–Sonoma (P = 0.97). On average, dust users in Fresno–Madera used more high-toxicity miticides than combination or wettable sulfur users in 2000. That trend decreased in the data for 2005 and 2009. Average miticide use in Fresno–Madera was higher than in Napa–Sonoma by 1349% in 2000, 1103% in 2005 and 146% in 2009. Higher sulfur use intensities among individual growers in Fresno–Madera were positively correlated with greater use of high-toxicity miticides in 2000 and 2005, but not 2009. The comparable results for Napa–Sonoma were less clear. Since PUR data represent statewide information on pesticide use decisions in real-world farming scenarios, it can complement data from field and laboratory studies. Expanding these analyses to compare pesticide use by individual growers across years, or to correlate pesticide usage with any published mite field surveys may shed more light on the enigmatic relationship between sulfur fungicide use and mite outbreaks in winegrapes.
Evaporation-induced cavitation in nanofluidic channels
Authors: Duan Chuanhua , Karnik Rohit , Lu Ming-Chang , Majumdar Arun 
Published: February 2012

Cavitation, known as the formation of vapor bubbles when liquids are under tension, is of great interest both in condensed matter science as well as in diverse applications such as botany, hydraulic engineering, and medicine. Although widely studied in bulk and microscale-confined liquids, cavitation in the nanoscale is generally believed to be energetically unfavorable and has never been experimentally demonstrated. Here we report evaporation-induced cavitation in water-filled hydrophilic nanochannels under enormous negative pressures up to -7 MPa. As opposed to receding menisci observed in microchannel evaporation, the menisci in nanochannels are pinned at the entrance while vapor bubbles form and expand inside. Evaporation in the channels is found to be aided by advective liquid transport, which leads to an evaporation rate that is an order of magnitude higher than that governed by Fickian vapor diffusion in macro- and microscale evaporation. The vapor bubbles also exhibit unusual motion as well as translational stability and symmetry, which occur because of a balance between two competing mass fluxes driven by thermocapillarity and evaporation. Our studies expand our understanding of cavitation and provide new insights for phase-change phenomena at the nanoscale.
A high-affinity, dimeric inhibitor of PSD-95 bivalently interacts with PDZ1-2 and protects against ischemic brain damage
Authors: Bach Anders , Clausen Bettina H. , Møller Magda , Vestergaard Bente , Chi Celestine N. , Round Adam , Sørensen Pernille L. , Nissen Klaus B. , Kastrup Jette S. , Gajhede Michael , Jemth Per , Kristensen Anders S. , Lundström Patrik , Lambertsen Kate L. , Strømgaard Kristian 
Published: February 2012

Inhibition of the ternary protein complex of the synaptic scaffolding protein postsynaptic density protein-95 (PSD-95), neuronal nitric oxide synthase (nNOS), and the
N
-methyl-
d
-aspartate (NMDA) receptor is a potential strategy for treating ischemic brain damage, but high-affinity inhibitors are lacking. Here we report the design and synthesis of a novel dimeric inhibitor, Tat-
N
PEG4(IETDV)
2
(Tat-
N
-dimer), which binds the tandem PDZ1-2 domain of PSD-95 with an unprecedented high affinity of 4.6 nM, and displays extensive protease-resistance as evaluated in vitro by stability-measurements in human blood plasma. X-ray crystallography, NMR, and small-angle X-ray scattering (SAXS) deduced a true bivalent interaction between dimeric inhibitor and PDZ1-2, and also provided a dynamic model of the conformational changes of PDZ1-2 induced by the dimeric inhibitor. A single intravenous injection of Tat-
N
-dimer (3 nmol/g) to mice subjected to focal cerebral ischemia reduces infarct volume with 40% and restores motor functions. Thus, Tat-
N
-dimer is a highly efficacious neuroprotective agent with therapeutic potential in stroke.
RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing
Authors: Krupp Markus , Marquardt Jens U. , Sahin Ugur , Galle Peter R. , Castle John , Teufel Andreas 
Published: February 2012

Abstract
Motivation: Next-generation sequencing technology enables an entirely new perspective for clinical research and will speed up personalized medicine. In contrast to microarray-based approaches, RNA-Seq analysis provides a much more comprehensive and unbiased view of gene expression. Although the perspective is clear and the long-term success of this new technology obvious, bioinformatics resources making these data easily available especially to the biomedical research community are still evolving.
Results: We have generated RNA-Seq Atlas, a web-based repository of RNA-Seq gene expression profiles and query tools. The website offers open and easy access to RNA-Seq gene expression profiles and tools to both compare tissues and find genes with specific expression patterns. To enlarge the scope of the RNA-Seq Atlas, the data were linked to common functional and genetic databases, in particular offering information on the respective gene, signaling pathway analysis and evaluation of biological functions by means of gene ontologies. Additionally, data were linked to several microarray gene profiles, including BioGPS normal tissue profiles and NCI60 cancer cell line expression data. Our data search interface allows an integrative detailed comparison between our RNA-Seq data and the microarray information. This is the first database providing data mining tools and open access to large scale RNA-Seq expression profiles. Its applications will be versatile, as it will be beneficial in identifying tissue specific genes and expression profiles, comparison of gene expression profiles among diverse tissues, but also systems biology approaches linking tissue function to gene expression changes.
Availability and implementation: http://medicalgenomics.org/rna_seq_atlas
Contact: kruppm@uni-mainz.de; teufel@uni-mainz.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Signal analysis for genome-wide maps of histone modifications measured by ChIP-seq
Authors: Beck Dominik , Brandl Miriam B. , Boelen Lies , Unnikrishnan Ashwin , Pimanda John E. , Wong Jason W. H. 
Published: February 2012

Abstract
Motivation: Chromatin structure, including post-translational modifications of histones, regulates gene expression, alternative splicing and cell identity. ChIP-seq is an increasingly used assay to study chromatin function. However, tools for downstream bioinformatics analysis are limited and are only based on the evaluation of signal intensities. We reasoned that new methods taking into account other signal characteristics such as peak shape, location and frequencies might reveal new insights into chromatin function, particularly in situation where differences in read intensities are subtle.
Results: We introduced an analysis pipeline, based on linear predictive coding (LPC), which allows the capture and comparison of ChIP-seq histone profiles. First, we show that the modeled signal profiles distinguish differentially expressed genes with comparable accuracy to signal intensities. The method was robust against parameter variations and performed well up to a signal-to-noise ratio of 0.55. Additionally, we show that LPC profiles of activating and repressive histone marks cluster into distinct groups and can be used to predict their function.
Availability and implementation: http://www.cancerresearch.unsw.edu.au/crcweb.nsf/page/LPCHP A Matlab implementation along with usage instructions and an example input file are available from: http://www.cancerresearch.unsw.edu.au/crcweb.nsf/page/LPCHP
Contact: d.beck@student.unsw.edu.au; jpimanda@unsw.edu.au; jason.wong@unsw.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Recycling of Methylthioadenosine Is Essential for Normal Vascular Development and Reproduction in Arabidopsis
Authors: Waduwara-Jayabahu Ishari , Oppermann Yasmin , Wirtz Markus , Hull Zachary T. , Schoor Sarah , Plotnikov Alexander N. , Hell Rüdiger , Sauter Margret , Moffatt Barbara A. 
Published: February 2012

Abstract5′-Methylthioadenosine (MTA) is the common by-product of polyamine (PA), nicotianamine (NA), and ethylene biosynthesis in Arabidopsis (Arabidopsis thaliana). The methylthiol moiety of MTA is salvaged by 5′-methylthioadenosine nucleosidase (MTN) in a reaction producing methylthioribose (MTR) and adenine. The MTN double mutant, mtn1-1mtn2-1, retains approximately 14% of the MTN enzyme activity present in the wild type and displays a pleiotropic phenotype that includes altered vasculature and impaired fertility. These abnormal traits were associated with increased MTA levels, altered PA profiles, and reduced NA content. Exogenous feeding of PAs partially recovered fertility, whereas NA supplementation improved fertility and also reversed interveinal chlorosis. The analysis of PA synthase crystal structures containing bound MTA suggests that the corresponding enzyme activities are sensitive to available MTA. Mutant plants that expressed either MTN or human methylthioadenosine phosphorylase (which metabolizes MTA without producing MTR) appeared wild type, proving that the abnormal traits of the mutant are due to MTA accumulation rather than reduced MTR. Based on our results, we propose that the key targets affected by increased MTA content are thermospermine synthase activity and spermidine-dependent posttranslational modification of eukaryotic initiation factor 5A.
ANAP: An Integrated Knowledge Base for Arabidopsis Protein Interaction Network Analysis
Authors: Wang Congmao , Marshall Alex , Zhang Dabing , Wilson Zoe A. 
Published: February 2012

Abstract
Protein interactions are fundamental to the molecular processes occurring within an organism and can be utilized in network biology to help organize, simplify, and understand biological complexity. Currently, there are more than 10 publicly available Arabidopsis (Arabidopsis thaliana) protein interaction databases. However, there are limitations with these databases, including different types of interaction evidence, a lack of defined standards for protein identifiers, differing levels of information, and, critically, a lack of integration between them. In this paper, we present an interactive bioinformatics Web tool, ANAP (Arabidopsis Network Analysis Pipeline), which serves to effectively integrate the different data sets and maximize access to available data. ANAP has been developed for Arabidopsis protein interaction integration and network-based study to facilitate functional protein network analysis. ANAP integrates 11 Arabidopsis protein interaction databases, comprising 201,699 unique protein interaction pairs, 15,208 identifiers (including 11,931 The Arabidopsis Information Resource Arabidopsis Genome Initiative codes), 89 interaction detection methods, 73 species that interact with Arabidopsis, and 6,161 references. ANAP can be used as a knowledge base for constructing protein interaction networks based on user input and supports both direct and indirect interaction analysis. It has an intuitive graphical interface allowing easy network visualization and provides extensive detailed evidence for each interaction. In addition, ANAP displays the gene and protein annotation in the generated interactive network with links to The Arabidopsis Information Resource, the AtGenExpress Visualization Tool, the Arabidopsis 1,001 Genomes GBrowse, the Protein Knowledgebase, the Kyoto Encyclopedia of Genes and Genomes, and the Ensembl Genome Browser to significantly aid functional network analysis. The tool is available open access at http://gmdd.shgmo.org/Computational-Biology/ANAP.
SR1, a Calmodulin-Binding Transcription Factor, Modulates Plant Defense and Ethylene-Induced Senescence by Directly Regulating NDR1 and EIN3
Authors: Nie Haozhen , Zhao Chunzhao , Wu Guangheng , Wu Yingying , Chen Yongfang , Tang Dingzhong 
Published: February 2012

Abstract
Plant defense responses are tightly controlled by many positive and negative regulators to cope with attacks from various pathogens. Arabidopsis (Arabidopsis thaliana) ENHANCED DISEASE RESISTANCE2 (EDR2) is a negative regulator of powdery mildew resistance, and edr2 mutants display enhanced resistance to powdery mildew (Golovinomyces cichoracearum). To identify components acting in the EDR2 pathway, we screened for edr2 suppressors and identified a gain-of-function mutation in SIGNAL RESPONSIVE1 (SR1), which encodes a calmodulin-binding transcription activator. The sr1-4D gain-of-function mutation suppresses all edr2-associated phenotypes, including powdery mildew resistance, mildew-induced cell death, and ethylene-induced senescence. The sr1-4D single mutant is more susceptible to a Pseudomonas syringae pv tomato DC3000 virulent strain and to avirulent strains carrying avrRpt2 or avrRPS4 than the wild type. We show that SR1 directly binds to the promoter region of NON-RACE-SPECIFIC DISEASE RESISTANCE1 (NDR1), a key component in RESISTANCE TO PSEUDOMONAS SYRINGAE2-mediated plant immunity. Also, the ndr1 mutation suppresses the sr1-1 null allele, which shows enhanced resistance to both P. syringae pv tomato DC3000 avrRpt2 and G. cichoracearum. In addition, we show that SR1 regulates ethylene-induced senescence by directly binding to the ETHYLENE INSENSITIVE3 (EIN3) promoter region in vivo. Enhanced ethylene-induced senescence in sr1-1 is suppressed by ein3. Our data indicate that SR1 plays an important role in plant immunity and ethylene signaling by directly regulating NDR1 and EIN3.
Nucleotide and RNA Metabolism Prime Translational Initiation in the Earliest Events of Mitochondrial Biogenesis during Arabidopsis Germination
Authors: Law Simon R. , Narsai Reena , Taylor Nicolas L. , Delannoy Etienne , Carrie Chris , Giraud Estelle , Millar A. Harvey , Small Ian , Whelan James 
Published: February 2012

Abstract
Mitochondria play a crucial role in germination and early seedling growth in Arabidopsis (Arabidopsis thaliana). Morphological observations of mitochondria revealed that mitochondrial numbers, typical size, and oval morphology were evident after 12 h of imbibition in continuous light (following 48 h of stratification). The transition from a dormant to an active metabolic state was punctuated by an early molecular switch, characterized by a transient burst in the expression of genes encoding mitochondrial proteins. Factors involved in mitochondrial transcription and RNA processing were overrepresented among these early-expressed genes. This was closely followed by an increase in the transcript abundance of genes encoding proteins involved in mitochondrial DNA replication and translation. This burst in the expression of factors implicated in mitochondrial RNA and DNA metabolism was accompanied by an increase in transcripts encoding components required for nucleotide biosynthesis in the cytosol and increases in transcript abundance of specific members of the mitochondrial carrier protein family that have previously been associated with nucleotide transport into mitochondria. Only after these genes peaked in expression and largely declined were typical mitochondrial numbers and morphology observed. Subsequently, there was an increase in transcript abundance for various bioenergetic and metabolic functions of mitochondria. The coordination of nucleus- and organelle-encoded gene expression was also examined by quantitative reverse transcription-polymerase chain reaction, specifically for components of the mitochondrial electron transport chain and the chloroplastic photosynthetic machinery. Analysis of protein abundance using western-blot analysis and mass spectrometry revealed that for many proteins, patterns of protein and transcript abundance changes displayed significant positive correlations. A model for mitochondrial biogenesis during germination is proposed, in which an early increase in the abundance of transcripts encoding biogenesis functions (RNA metabolism and import components) precedes a later cascade of gene expression encoding the bioenergetic and metabolic functions of mitochondria.
Aspects regarding the application of the quality principles in the university library
Authors: Albu Cristina , Cristian Adriana , Pistol Nicoleta 
Published: February 2012

PurposeProviding a wealth of documents and appropriate information in support of the university curriculum and research syllabus represents the ultimate goal of all the efforts made by university libraries. The paper aims to study the quality of services as an indicator of quality improvement in the educational process.Design/methodology/approachThe users should be permanently consulted and their satisfaction should be a permanent concern. The periodical evaluation of the services offered by the academic library, by means of questionnaires is done in order to monitor the difficulties encountered by users. The analysis of the strong and weak points of the services provided leads to improvements in the quality of service.FindingsThe paper reveals that assessment criteria, within the excellence models, provide a basis for the organization to compare its own performances against the performances of other similar organizationsPractical implicationsPractical implications are a better use of the information resources.Originality/valueThe paper will help librarians to improve their library services by increasing quality and user satisfaction.
Focusing on the human resources in academic librarianship:an outlook from Serbia
Authors: Župan Vesna 
Published: February 2012

PurposeThis article aims to overcome the attitude that information is most important for social development. It also aims to stress the ways of human resources development in the academic librarianship of Serbia.Design/methodology/approachAn empirical method is implemented in this paper.FindingsThis article shows how librarians in Serbia follow world positive practice and adjust themselves in order to achieve higher levels of professional competence.Research limitations/implicationsThe bibliography of researchers is pointed out as an achievement in the Serbian academic environment which is very important for the development of collaboration between readers in a professional field and researchers.Practical implicationsHuman resources managers in academic libraries may rely on the experience of Serbian librarians and implement those solutions they would estimate the most useful for their academic practice.Social implicationsSome results of librarians' work are to be found in free access. These are the results of cataloguing and subject indexing through which librarians also contribute to global knowledge. Generally speaking librarians instruct users in the information society; therefore, the professional environment should create conditions for permanent improvement of human resources quality in academic libraries.Originality/valueThis article provides librarians with an alternative method to achieving stronger professional skills from information literacy tutorials and to produce reporting without the need for conventional learning management systems (LMS).
Bibliometric practices and activities at the University of Vienna
Authors: Gumpenberger Christian , Wieland Martin , Gorraiz Juan 
Published: February 2012

PurposeThe purpose of this paper is to describe bibliometrics as an emergent field for academic libraries. There is a constant need to adapt to the ongoing changes and new demands of today's information environment, and the increasing importance of bibliometrics certainly presents a great opportunity for librarians to broaden their horizon.Design/methodology/approachThe ideas outlined here are based on supporting information derived from literature and on practical experience gained at the Vienna University Library, Austria. A rationale is given why libraries should provide bibliometric services followed by a short overview of how the Bibliometrics Department in Vienna came into being. The focus of the paper is set on a detailed description of its practices and activities.FindingsBibliometrics is ideal for librarians to develop and provide innovative services for both academic and administrative university staff. In doing so they make sure to actively participate in the development of new strategies and in fostering innovation. Peer‐review is increasingly complemented by quantitative methods like bibliometrics, and librarians are predestined to fill this role and strengthen their on‐campus position. Furthermore bibliometrics is an emerging field in “Information Science”, thus librarians should make use of their experiences gained from bibliometric services provided or projects engaged in and disseminate their findings in the scientific community.Practical implicationsThe case study of the Bibliometrics Department in Vienna can be useful for other academic libraries who wish to become more engaged in this field or even plan to implement according services.Originality/valueThis is an original paper, which has been presented at the QQML 2011 in Athens. It provides useful information on how an academic library can adopt bibliometrics as a core role.