bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Java API for working with PubChem datasets
Authors: Southern Mark R. , Griffin Patrick R. 
Published: January 2011

Abstract
Summary: PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP.
These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose–response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development.
Availability: http://code.google.com/p/pubchemdb
Contact: southern@scripps.edu
MIRACH: efficient model checker for quantitative biological pathway models
Authors: Koh Chuan Hock , Nagasaki Masao , Saito Ayumu , Li Chen , Wong Limsoon , Miyano Satoru 
Published: January 2011

Abstract
Summary: Model checking is playing an increasingly important role in systems biology as larger and more complex biological pathways are being modeled. In this article we report the release of an efficient model checker MIRACH 1.0, which supports any model written in popular formats such as CSML and SBML. MIRACH is integrated with a Petri-net-based simulation engine, enabling efficient online (on-the-fly) checking. In our experiment, by using Levchenko et al. model, we reveal that timesaving gains by using MIRACH easily surpass 400% compared with its offline-based counterpart.
Availability and implementation: MIRACH 1.0 was developed using Java and thus executable on any platform installed with JDK 6.0 (not JRE 6.0) or later. MIRACH 1.0, along with its source codes, documentation and examples are available at http://sourceforge.net/projects/mirach/ under the LGPLv3 license.
Contact: masao@ims.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
A greedy, graph-based algorithm for the alignment of multiple homologous gene lists
Authors: Fostier Jan , Proost Sebastian , Dhoedt Bart , Saeys Yvan , Demeester Piet , Van de Peer Yves , Vandepoele Klaas 
Published: January 2011

Abstract
Motivation: Many comparative genomics studies rely on the correct identification of homologous genomic regions using accurate alignment tools. In such case, the alphabet of the input sequences consists of complete genes, rather than nucleotides or amino acids. As optimal multiple sequence alignment is computationally impractical, a progressive alignment strategy is often employed. However, such an approach is susceptible to the propagation of alignment errors in early pairwise alignment steps, especially when dealing with strongly diverged genomic regions. In this article, we present a novel accurate and efficient greedy, graph-based algorithm for the alignment of multiple homologous genomic segments, represented as ordered gene lists.
Results: Based on provable properties of the graph structure, several heuristics are developed to resolve local alignment conflicts that occur due to gene duplication and/or rearrangement events on the different genomic segments. The performance of the algorithm is assessed by comparing the alignment results of homologous genomic segments in Arabidopsis thaliana to those obtained by using both a progressive alignment method and an earlier graph-based implementation. Especially for datasets that contain strongly diverged segments, the proposed method achieves a substantially higher alignment accuracy, and proves to be sufficiently fast for large datasets including a few dozens of eukaryotic genomes.
Availability: http://bioinformatics.psb.ugent.be/software. The algorithm is implemented as a part of the i-ADHoRe 3.0 package.
Contact: yves.vandepeer@psb.vib-ugent.be
Supplementary information: Supplementary data are available at Bioinformatics online.
Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation
Authors: Cao Yang , Song Lin , Miao Zhichao , Hu Yun , Tian Liqing , Jiang Taijiao 
Published: January 2011

AbstractMotivation: Side-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the conformation space using discrete rigid rotamers for speed and efficiency. However, in the tightly packed environments of protein interiors, these methods will inherently lead to atomic clashes and hinder the prediction accuracy.Results: We present a side-chain modeling method (CIS-RR), which couples a novel clash-detection guided iterative search (CIS) algorithm with continuous torsion space optimization of rotamers (RR). Benchmark testing shows that compared with the existing popular side-chain modeling methods, CIS-RR removes atomic clashes much more effectively and achieves comparable or even better prediction accuracy while having comparable computational cost. We believe that CIS-RR could be a useful method for accurate side-chain modeling.Availability: CIS-RR is available to non-commercial users at our website: http://jianglab.ibp.ac.cn/lims/cisrr/cisrr.html.Contact: taijiao@moon.ibp.ac.cnSupplementary information: Supplementary data are available at Bioinformatics online.
A novel hybrid gene prediction method employing protein multiple sequence alignments
Authors: Keller Oliver , Kollmar Martin , Stanke Mario , Waack Stephan 
Published: January 2011

AbstractMotivation: As improved DNA sequencing techniques have increased enormously the speed of producing new eukaryotic genome assemblies, the further development of automated gene prediction methods continues to be essential.While the classification of proteins into families is a task heavily relying on correct gene predictions, it can at the same time provide a source of additional information for the prediction, complementary to those presently used.Results: We extended the gene prediction software AUGUSTUS by a method that employs block profiles generated from multiple sequence alignments as a protein signature to improve the accuracy of the prediction. Equipped with profiles modelling human dynein heavy chain (DHC) proteins and other families, AUGUSTUS was run on the genomic sequences known to contain members of these families. Compared with AUGUSTUS' ab initio version, the rate of genes predicted with high accuracy showed a dramatic increase.Availability: The AUGUSTUS project web page is located at http://augustus.gobics.de, with the executable program as well as the source code available for download.Contact: keller@cs.uni-goettingen.de; mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online.
The CCPN Metabolomics Project: a fast protocol for metabolite identification by 2D-NMR
Authors: Chignola Francesca , Mari Silvia , Stevens Tim J. , Fogh Rasmus H. , Mannella Valeria , Boucher Wayne , Musco Giovanna 
Published: January 2011

Abstract
Summary: We present here the freely available Metabolomics Project resource specifically designed to work under the CcpNmr Analysis program produced by CCPN (Collaborative Computing Project for NMR) (Vranken et al., 2005, The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins, 59, 687–696). The project consists of a database of assigned 1D and 2D spectra of many common metabolites. The project aims to help the user to analyze and assign 1D and 2D NMR spectra of unknown metabolite mixtures. Spectra of unknown mixtures can be easily superimposed and compared with the database spectra, thus facilitating their assignment and identification.
Availability: The CCPN Metabolomics Project, together with an annotated example dataset, is freely available via: http://www.ccpn.ac.uk/metabolomics/.
Contact: mari.silvia@hsr.it (experiments & protocol); tjs23@cam.ac.uk (software).
Supplementary Information: Supplementary data are available at Bioinformatics online.
Spatial structure of commercial marine fisheries in Northwest Mexico
Authors: Erisman Brad E. , Paredes Gustavo A. , Plomozo-Lugo Tomas , Cota-Nieto Juan J. , Hastings Philip A. , Aburto-Oropeza Octavio 
Published: January 2011

AbstractErisman, B. E., Paredes, G. A., Plomozo-Lugo, T., Cota-Nieto, J. J., Hastings, P. A., and Aburto-Oropeza, O. 2011. Spatial structure of commercial marine fisheries in Northwest Mexico. – ICES Journal of Marine Science, 68: . The spatial structure of commercial marine fisheries in Northwest (NW) Mexico was investigated using official landings data from 39 local fisheries offices in the region. Multivariate analyses revealed a clear spatial pattern in fishing activities, in which there was a positive linear relationship between the species composition of fisheries offices and both latitude and longitude. Fisheries offices formed eight distinct clusters organized by similarities in geographic location, species-group composition, and coastal habitat type. Five of the eight clusters comprised offices from the same geographic region and coastal ecosystem, and the other three clusters contained the largest industrial fishing ports in NW Mexico. The results of this study suggest that NW Mexico would benefit from an ecosystem-based management framework that focuses on the direct, spatial connection that exists between coastal habitats, harvested species groups, and fishing activities within each region. Subdivision into five separate regions is proposed, with management attention paid specially to the few industrialized ports whose fishing capacities and geographic ranges of fishing far exceed the other areas.
Low allozyme heterozygosity in North Pacific and Bering Sea populations of red king crab (Paralithodes camtschaticus): adaptive specialization, population bottleneck, or metapopulation structure?
Authors: Grant W. Stewart , Merkouris Susan E. , Kruse Gordon H. , Seeb Lisa W. 
Published: January 2011

AbstractGrant, W. S., Merkouris, S. E., Kruse, G. H., and Seeb, L. W. 2011. Low allozyme heterozygosity in North Pacific and Bering Sea populations of red king crab (Paralithodes camtschaticus): adaptive specialization, population bottleneck, or metapopulation structure? – ICES Journal of Marine Science, 68: . Populations of red king crab in the North Pacific and Bering Sea have declined in response to ocean-climate shifts and to harvesting. An understanding of how populations are geographically structured is important to the management of these depressed resources. Here, the Mendelian variability at 38 enzyme-encoding loci was surveyed in 27 samples (n = 2427) from 18 general locations. Sample heterozygosities were low, averaging HE = 0.015 among samples. Weak genetic structure was detected among three groups of populations, the Bering Sea, central Gulf of Alaska, and Southeast Alaska, but without significant isolation by distance among populations. A sample from Adak Island in the western Aleutians was genetically different from the remaining samples. The lack of differentiation among populations within regions may, in part, be due to post-glacial expansions and a lack of migration-drift equilibrium and to limited statistical power imposed by low levels of polymorphism. Departures from neutrality may reflect the effects of both selective and historical factors. The low allozyme diversity in red king crab may, in part, be attributable to adaptive specialization, background selection, ice-age population bottlenecks, or metapopulation dynamics in a climatically unstable North Pacific.
HIV-1 Modulates the tRNA Pool to Improve Translation Efficiency
Authors: van Weringh Anna , Ragonnet-Cronin Manon , Pranckeviciene Erinija , Pavon-Eternod Mariana , Kleiman Lawrence , Xia Xuhua 
Published: January 2011

AbstractDespite its poorly adapted codon usage, HIV-1 replicates and is expressed extremely well in human host cells. HIV-1 has recently been shown to package non-lysyl transfer RNAs (tRNAs) in addition to the tRNALys needed for priming reverse transcription and integration of the HIV-1 genome. By comparing the codon usage of HIV-1 genes with that of its human host, we found that tRNAs decoding codons that are highly used by HIV-1 but avoided by its host are overrepresented in HIV-1 virions. In particular, tRNAs decoding A-ending codons, required for the expression of HIV's A-rich genome, are highly enriched. Because the affinity of Gag-Pol for all tRNAs is nonspecific, HIV packaging is most likely passive and reflects the tRNA pool at the time of viral particle formation. Codon usage of HIV-1 early genes is similar to that of highly expressed host genes, but codon usage of HIV-1 late genes was better adapted to the selectively enriched tRNA pool, suggesting that alterations in the tRNA pool are induced late in viral infection. If HIV-1 genes are adapting to an altered tRNA pool, codon adaptation of HIV-1 may be better than previously thought.
The PP2A Regulatory Subunit Tap46, a Component of the TOR Signaling Pathway, Modulates Growth and Metabolism in Plants
Authors: Ahn Chang Sook , Han Jeong-A , Lee Ho-Seok , Lee Semi , Pai Hyun-Sook 
Published: January 2011

AbstractTap42/α4, a regulatory subunit of protein phosphatase 2A, is a downstream effector of the target of rapamycin (TOR) protein kinase, which regulates cell growth in coordination with nutrient and environmental conditions in yeast and mammals. In this study, we characterized the functions and phosphatase regulation of plant Tap46. Depletion of Tap46 resulted in growth arrest and acute plant death with morphological markers of programmed cell death. Tap46 interacted with PP2A and PP2A-like phosphatases PP4 and PP6. Tap46 silencing modulated cellular PP2A activities in a time-dependent fashion similar to TOR silencing. Immunoprecipitated full-length and deletion forms of Arabidopsis thaliana TOR phosphorylated recombinant Tap46 protein in vitro, supporting a functional link between Tap46 and TOR. Tap46 depletion reproduced the signature phenotypes of TOR inactivation, such as dramatic repression of global translation and activation of autophagy and nitrogen mobilization, indicating that Tap46 may act as a positive effector of TOR signaling in controlling those processes. Additionally, Tap46 silencing in tobacco (Nicotiana tabacum) BY-2 cells caused chromatin bridge formation at anaphase, indicating its role in sister chromatid segregation. These findings suggest that Tap46, in conjunction with associated phosphatases, plays an essential role in plant growth and development as a component of the TOR signaling pathway.
The Nucleus-Encodedtrans-Acting Factor MCA1 Plays a Critical Role in the Regulation of CytochromefSynthesis inChlamydomonasChloroplasts
Authors: Boulouis Alix , Raynaud Cécile , Bujaldon Sandrine , Aznar Aude , Wollman Francis-André , Choquet Yves 
Published: January 2011

AbstractOrganelle gene expression is characterized by nucleus-encoded trans-acting factors that control posttranscriptional steps in a gene-specific manner. As a typical example, in Chlamydomonas reinhardtii, expression of the chloroplast petA gene encoding cytochrome f, a major subunit of the cytochrome b 6 f complex, depends on MCA1 and TCA1, required for the accumulation and translation of the petA mRNA. Here, we show that these two proteins associate in high molecular mass complexes that also contain the petA mRNA. We demonstrate that MCA1 is degraded upon interaction with unassembled cytochrome f that transiently accumulates during the biogenesis of the cytochrome b 6 f complex. Strikingly, this interaction relies on the very same residues that form the repressor motif involved in the Control by Epistasy of cytochrome f Synthesis (CES), a negative feedback mechanism that downregulates cytochrome f synthesis when its assembly within the cytochrome b 6 f complex is compromised. Based on these new findings, we present a revised picture for the CES regulation of petA mRNA translation that involves proteolysis of the translation enhancer MCA1, triggered by its interaction with unassembled cytochrome f.
Google Generation II: web behaviour experiments with the BBC
Authors: Nicholas David , Rowlands Ian , Clark David , Williams Peter 
Published: January 2011

PurposeThe purpose of this paper is to report on continuing research undertaken on the way the Google Generation behave on the internet and to compare this with an earlier highly publicised study by the paper's authors.Design/methodology/approachThis research use a televised practical experiment and a remote web global test incorporating search, working memory and multi‐tasking experiments.FindingsThe Google Generation appears to behave very differently from older generations. By their own admission they are less confident about their searching prowess and this is also demonstrated by the fact that they viewed fewer pages, visited fewer domains and undertook fewer searches. Also, tellingly, their search statements were much more the product of cut and paste. The Google Generation also have poorer working memories and are less competent at multi‐tasking, both of which may have implications for researching in an online environment.Originality/valueThe paper introduces of multi‐tasking and cognitive measurement in evaluating and describing information‐seeking behaviour; comparing the web behaviour of young and old; the first time this has been shown on public television.
EIAH data model
Authors: Khazraee Emad , Moaddeli Saeed , Sanjari Azadeh , Shakeri Shadi 
Published: January 2011

PurposeThe purpose of this paper is to provide a clear image of the information architecture used in the Encyclopedia of Iranian Architectural History (EIAH) and to show how it was crafted to meet the need for accessibility, expressiveness and interoperability.Design/methodology/approachIn order to assess the level of interoperability in the system, two essential concepts of the system are identified and traced in every level of the three‐layer information architecture. Federated repositories are studied for the level of accessibility that they can offer. Knowledge representation level, mediator level and the semantic portal are studied for expressiveness capabilities.FindingsEIAH information architecture is capable of establishing links among resources available in the information pools connected to the system by using EIAH metadata application profile (EMAP). Different modules in this architecture, which are localized for the Persian language, can work on similar environments for other languages, for example Arabic.Originality/valueEIAH is the first example of a digital encyclopedia for the history of Iranian architecture, which is basically different from other digital encyclopedias in the way that it offers information to users. EIAH is aimed at domain experts and provides them not with pre‐written and quality articles but with a wide range of resources and documents relative to what they are seeking.
Modelling the information‐seeking behaviour of children and young people
Authors: Shenton Andrew K. , Hay‐Gibson Naomi V. 
Published: January 2011

PurposeThe paper seeks to draw on Sice's systems model, itself based on Senge's “fixes that fail” archetype, and on data from two previous research projects conducted by one of the authors. The purpose of this paper is to synthesise a new model that portrays the information‐seeking behaviour of children and young people.Design/methodology/approachThe systems model provides the backbone of the new framework but additions, accommodations and revisions were made to ensure that the version featured here represents the phenomenon of information seeking by the young as appropriately as possible in terms of the data that were gathered.FindingsOne of the new model's most significant characteristics is its emphasis on problems and issues that prevent information seeking from proceeding smoothly. Information seeking is also shown to be an iterative process, with the individual often revisiting previous stages, frequently in response to difficulties.Research limitations/implicationsData were collected from pupils in just seven schools. The undertaking of research further a‐field would be invaluable, if the extent to which the model is applicable to other information‐seekers in different environments is to be ascertained.Practical implicationsThe model demonstrates the importance of the information professional's educative role, in terms of both delivering formal information literacy instruction and providing assistance at the point of need.Originality/valueAlthough the use of ideas and frameworks from other disciplines, with the aim of increasing understanding of phenomena within LIS, is a growing trend, this paper represents one of the first attempts to apply an existing model associated with systems thinking to information behaviour.
A study on the development of Korean academic libraries' duty model based on the job analysis
Authors: Kim Sin‐Young , Lee Jee‐Yeon 
Published: January 2011

PurposeThe purpose of this paper is to analyze the jobs and duties involved in Korean academic libraries and to provide a clear picture of relative issues. This research will assist universities with the HR management and institutional development that are essential for appropriate role division, organizational diagnosis and rational reform, and increasing the expertise of librarians.Design/methodology/approachAll of the various duties being executed in academic libraries were identified. Korean academic libraries were requested to assist with the survey. Questionnaires were collected surveying the level of awareness of all the duties involved in the academic libraries and survey responses analyzed to determine the importance, difficulty, and professionalism of 189 library duties.FindingsThrough this study, perceived levels of frequency, importance, and difficulty of duties related to academic libraries were surveyed and average values for each duty were compared and analyzed to formulate a duty model and action plan.Originality/valueThis paper presents a basic library duty model reflecting the rapidly changing information technologies and information types of Korean academic libraries based on the job analysis. Through this process, university libraries will be able to optimize human resources management and achieve efficiency in organizational management, as well as creating materials to support education/training and performance management, thus ultimately helping with the rationalization of their operation.