bluuebunny/crossref_metadata_2025_split huggingface dataset:
Winter Pond Fertilization Can Increase Phytoplankton Density in Aquaculture Ponds
Authors: Mischke Charles C 
Published: January 2014

Abstract
Effective winter fertilization would be beneficial under certain production systems in the southeastern USA. Maintaining a phytoplankton bloom during the winter has the potential to shade macrophytes, discourage filamentous algae, and provide natural foraging opportunities for fish during warmer days; this would be advantageous. An additional benefit of a winter bloom would be to produce turbidity, thereby possibly reducing bird predation. The objective of this study was to determine if winter fertilization could increase phytoplankton to greater biomass than in nonfertilized control ponds. Six ponds served as controls and six ponds received an initial dose of nitrogen at 20 kg/ha and phosphorus at 2 kg/ha in mid-November. Over the following five weeks, treatment ponds received one-half the initial dose once per week, and then continued to receive the half dose once per month in January, February, and March. Fertilization led to increases in total ammonia nitrogen, nitrite, and nitrate. The water temperature ranged from a low of 5°C to a high of 16.8°C (mean of 10.2°C) over the entire study. Even though water temperatures were low and light intensity is less in winter, fertilization caused a significant increase in chlorophyll a over the study. The increase in total algal biomass was not due to an increase in any specific algal group, but rather a general biomass increase in most algal groups. Cryptophyta tended to be the most common phytoplankton division throughout the study. Although this fertilization protocol increased algal biomass, there were no differences in zooplankton abundance between fertilized and nonfertilized ponds. In contrast to the currently held belief that winter fertilization is ineffective, this study shows that winter fertilization can increase algal blooms. Therefore, future studies should determine if blooms created from winter fertilization can increase growth of planktivorous fish, shade macrophytes, discourage filamentous algae, or produce turbidity which could reduce bird predation.
BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads
Authors: Heo Yun , Wu Xiao-Long , Chen Deming , Ma Jian , Hwu Wen-Mei 
Published: January 2014

AbstractMotivation: Rapid advances in next-generation sequencing (NGS) technology have led to exponential increase in the amount of genomic information. However, NGS reads contain far more errors than data from traditional sequencing methods, and downstream genomic analysis results can be improved by correcting the errors. Unfortunately, all the previous error correction methods required a large amount of memory, making it unsuitable to process reads from large genomes with commodity computers.Results: We present a novel algorithm that produces accurate correction results with much less memory compared with previous solutions. The algorithm, named BLoom-filter-based Error correction Solution for high-throughput Sequencing reads (BLESS), uses a single minimum-sized Bloom filter, and is also able to tolerate a higher false-positive rate, thus allowing us to correct errors with a 40× memory usage reduction on average compared with previous methods. Meanwhile, BLESS can extend reads like DNA assemblers to correct errors at the end of reads. Evaluations using real and simulated reads showed that BLESS could generate more accurate results than existing solutions. After errors were corrected using BLESS, 69% of initially unaligned reads could be aligned correctly. Additionally, de novo assembly results became 50% longer with 66% fewer assembly errors.Availability and implementation: Freely available at http://sourceforge.net/p/bless-ecContact: dchen@illinois.eduSupplementary information: Supplementary data are available at Bioinformatics online.
InterProScan 5: genome-scale protein function classification
Authors: Jones Philip , Binns David , Chang Hsin-Yu , Fraser Matthew , Li Weizhong , McAnulla Craig , McWilliam Hamish , Maslen John , Mitchell Alex , Nuka Gift , Pesseat Sebastien , Quinn Antony F. , Sangrador-Vegas Amaia , Scheremetjew Maxim , Yong Siew-Yit , Lopez Rodrigo , Hunter Sarah 
Published: January 2014

Abstract
Motivation: Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. Developments include improvements and additions to the outputs of the software and the complete reimplementation of the software framework, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis. InterProScan is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at Google Code.
Availability and implementation: InterProScan is distributed via FTP at ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/ and the source code is available from http://code.google.com/p/interproscan/.
Contact: http://www.ebi.ac.uk/support or interhelp@ebi.ac.uk or mitchell@ebi.ac.uk
jmodeltest.org: selection of nucleotide substitution models on the cloud
Authors: Santorum Jose Manuel , Darriba Diego , Taboada Guillermo L. , Posada David 
Published: January 2014

Abstract
Summary: The selection of models of nucleotide substitution is one of the major steps of modern phylogenetic analysis. Different tools exist to accomplish this task, among which jModelTest 2 (jMT2) is one of the most popular. Still, to deal with large DNA alignments with hundreds or thousands of loci, users of jMT2 need to have access to High Performance Computing clusters, including installation and configuration capabilities, conditions not always met. Here we present jmodeltest.org, a novel web server for the transparent execution of jMT2 across different platforms and for a wide range of users. Its main benefit is straightforward execution, avoiding any configuration/execution issues, and reducing significantly in most cases the time required to complete the analysis.
Availability and implementation: jmodeltest.org is accessible using modern browsers, such as Firefox, Chrome, Opera, Safari and IE from http://jmodeltest.org. User registration is not mandatory, but users wanting to have additional functionalities, like access to previous analyses, have the possibility of opening a user account.
Contact: info@jmodeltest.org
Purification, characterization and crystallization of the human 80S ribosome
Authors: Khatter Heena , Myasnikov Alexander G. , Mastio Leslie , Billas Isabelle M. L. , Birck Catherine , Stella Stefano , Klaholz Bruno P. 
Published: January 2014

Abstract
Ribosomes are key macromolecular protein synthesis machineries in the cell. Human ribosomes have so far not been studied to atomic resolution because of their particularly complex structure as compared with other eukaryotic or prokaryotic ribosomes, and they are difficult to prepare to high homogeneity, which is a key requisite for high-resolution structural work. We established a purification protocol for human 80S ribosomes isolated from HeLa cells that allows obtaining large quantities of homogenous samples as characterized by biophysical methods using analytical ultracentrifugation and multiangle laser light scattering. Samples prepared under different conditions were characterized by direct single particle imaging using cryo electron microscopy, which helped optimizing the preparation protocol. From a small data set, a 3D reconstruction at subnanometric resolution was obtained showing all prominent structural features of the human ribosome, and revealing a salt concentration dependence of the presence of the exit site tRNA, which we show is critical for obtaining crystals. With these well-characterized samples first human 80S ribosome crystals were obtained from several crystallization conditions in capillaries and sitting drops, which diffract to 26 Å resolution at cryo temperatures and for which the crystallographic parameters were determined, paving the way for future high-resolution work.
A ribozyme that triphosphorylates RNA 5′-hydroxyl groups
Authors: Moretti Janina E. , Müller Ulrich F. 
Published: January 2014

Abstract
The RNA world hypothesis describes a stage in the early evolution of life in which RNA served as genome and as the only genome-encoded catalyst. To test whether RNA world organisms could have used cyclic trimetaphosphate as an energy source, we developed an in vitro selection strategy for isolating ribozymes that catalyze the triphosphorylation of RNA 5′-hydroxyl groups with trimetaphosphate. Several active sequences were isolated, and one ribozyme was analyzed in more detail. The ribozyme was truncated to 96 nt, while retaining full activity. It was converted to a trans-format and reacted with rates of 0.16 min−1 under optimal conditions. The secondary structure appears to contain a four-helical junction motif. This study showed that ribozymes can use trimetaphosphate to triphosphorylate RNA 5′-hydroxyl groups and suggested that RNA world organisms could have used trimetaphosphate as their energy source.
Single nucleotide polymorphisms shed light on correlations between environmental vairalbe and adaptive genetic divergence in Chum salmon (Oncorhynchus keta)
Authors: Deng Xilin , Henry Philippe 
Published: January 2014

AbstractIdentifying the genetic and ecological basis of adaptation is of immense importance in evolutionary biology. In our study, we applied a panel of 58 biallelic single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonidOncorhynchus keta.Samples included 4164 individuals from 43 populations ranging from Coastal Western Alaska to southern British Colombia and northern Washington. Signatures of natural selection were detected by identifying seven outlier loci using two independent approaches: one based on outlier detection and another based on environmental correlations. Evidence of divergent selection at two candidate SNP loci,Oke_RFC2-168 and Oke_MARCKS-362, indicates significant environmental correlations, particularly with the number of frost-free days (NFFD). Important associations found between environmental variables and outlier loci indicate that those environmental variables could be the major driving forces of allele frequency divergence at the candidate loci. NFFD, in particular, may play an important adaptive role in shaping genetic variation inO. keta.Correlations between divergent selection and local environmental variables will help shed light on processes of natural selection and molecular adaptation to local environmental conditions.
An accelerated miRNA-based screen implicates Atf-3 in odorant receptor expression
Authors: Bhat Shreelatha , Shin Minjung , Bahk Suhyoung , Kim Young-Joon , Jones Walton D. 
Published: January 2014

SummaryLarge scale genetic screening is tedious and time-consuming. To address this problem, we propose a novel two-tiered screening system comprising an initial “pooling” screen that identifies miRNAs whose tissue-specific over-expression causes a phenotype of interest followed by a more focused secondary screen that uses gene-specific RNAi. As miRNAs inhibit translation or direct the destruction of their target mRNAs, any phenotype observed with miRNA over-expression can be attributed to the loss-of-function of one or more target mRNAs. Since miRNA-target pairing is sequence-specific, a list of predicted targets for miRNAs identified in the initial screen serves as a list of candidates for the secondary RNAi-based screen. These predicted miRNA targets can be prioritized by expression pattern, and if multiple miRNAs produce the same phenotype, overlapping target predictions can be given higher priority in the follow-up screen.Since miRNAs are short, miRNA misexpression will likely uncover artifactual miRNA-target relation-ships. Thus, we are using miRNAs as a tool to accelerate genetic screening rather than focus on the biology of miRNAs themselves. This two-tiered system allows us to rapidly identify individual target genes involved in a phenomenon of interest, often in less than 200 crosses. Here we demonstrate the effectiveness of this method by identifying miRNAs that alterDrosophilaodorant receptor expression. With subsequent miRNA target prediction and follow-up RNAi screening we identify and validate a novel role for the transcription factor Atf3 in the expression of the socially relevant receptor Or47b.
Information gathering during enterprise system selection: insight from practice
Authors: Lech Przemysław 
Published: January 2014

PurposeThe purpose of this paper is to examine the information gathering methods used during enterprise system (ES) selection among Polish organizations and to have IT consulting experts evaluate these methods, which will result in identification of the preferred approach for the information‐gathering task during system selection.Design/methodology/approachThe research has a qualitative exploratory design with grounded theory being the main research method. A mixed quantitative‐qualitative approach to data collection was used: an e‐mail‐based survey was used as an introductory stage to gather data on information‐gathering methods. The results of the survey were evaluated by ES experts during unstructured interviews. The interviews were then transcribed and coded according to the grounded theory coding techniques.FindingsThe evaluation of selection approaches revealed that the approach to information gathering should depend on the level of configurability of the systems subject to selection. Two generic approaches were identified: requirements driven – for highly configurable systems, and system functionality driven – for the systems offering limited configurability. Interaction between the customer and the bidder was also identified as the main condition for preparing the unbiased offer by the bidders.Research limitations/implicationsRegarding the survey study, as the survey sample was small and the sample selection process was not random, the results should not be generalised to the whole population of Polish enterprises. It would be also beneficial to test the validity of the findings from the grounded theory study on the big population of ES bidders with the use of statistical methods.Practical implicationsFor highly configurable systems, a model that includes a business process analysis, detailed requirements' specification and dedicated system functionality presentation is the preferred approach. A workshop is preferred to obtaining a ready requirements list. For systems offering limited configurability, an approach centred on system presentation is more suitable. In this case the requirements should be gathered during the presentation on a “gap‐fit” basis.Originality/valueThere is a significant lack of research that explores the selection process, with the stress on organizational needs and system functionality information gathering and makes indications for improvement of this process from the consulting enterprise (bidder) point of view. The paper fills this gap by presenting the results of a survey among Polish enterprises regarding selection routines and the evaluation of these routines by expert ES professionals, resulting in the development of the preferred set of information‐gathering methods.
Reducing emotional exhaustion and increasing organizational support
Authors: Alexander Hamwi G. , Rutherford Brian N. , Boles James S. 
Published: January 2014

PurposeThe purpose of this study is to explore stressors that may influence salespersons' emotional exhaustion and their perception of organizational support.Design/methodology/approachStructural equation modeling is used to assess: the effects of role conflict and work‐family conflict on emotional exhaustion; role conflict and role ambiguity's effects on perceived organizational support; and whether perceived organization support is directly or indirectly linked to emotional exhaustion.FindingsFindings from the study suggest that work‐family conflict and role conflict both significantly affect emotional exhaustion. Work‐family conflict also was found to impact on the relationship between perceived organizational support and emotional exhaustion. Finally, role conflict and role ambiguity were found to have a negative impact on perceived organizational support.Originality/valueThis study provides a foundation for reducing salespersons' emotional exhaustion and provides a method of increasing a salesforce's perception of organizational support.
An exploration of key connections within sales‐marketing interface
Authors: Malshe Avinash 
Published: January 2014

PurposeThe paucity of empirical research on the sales‐marketing interface necessitates a detailed exploration of linkages that can forge stronger connection between these two functions. This paper aims to explicate the boundary conditions that may affect the role played by structure, language, and process linkages in forging sales‐marketing connections, and to identify additional linkages that may play an important role in this interface.Design/methodology/approachA total of 47 sales and marketing professionals across different organizations in diverse industries were interviewed.FindingsThe research finds that certain boundary conditions (e.g. organizational hierarchy, time horizon) may influence how structure, language, and process linkages may operate in this interface. It also extends linkage repertoire by identifying two critical linkages: social and philosophical. Its managerial contribution lies in stressing the importance of: vertical and horizontal communication bridges; marketing's flexibility; interpersonal relationships; and the philosophical bond between the two functions, in forging stronger connections.Originality/valueThis is one of the few qualitative empirical investigations of the sales‐marketing interface. It broadens one's understanding of sales‐marketing linkages, adds to linkage repertoire, and extends the interface literature.
Guanxi as a gateway in Chinese‐Western business relationships
Authors: Gao Hongzhi , Knight John G. , Ballantyne David 
Published: January 2014

PurposeThis article aims to identify critical aspects of Chinese‐Western intercultural guanxi relationships that have largely been ignored as a domain for study in international business and industrial marketing, and to suggest a way forward.Design/methodology/approachA theme analysis across a range of academic and business journal articles is undertaken to capture major themes involving China‐focused research that relates to international business and industrial marketing, and also to locate critical themes that may have been overlooked.FindingsIntercultural interaction at a personal level is both unavoidable and critical for successfully doing business with China. This study introduces the term guanxi gateway ties to highlight a special class of facilitating relationships that can emerge through interactions between guanxi insiders and guanxi outsiders. Insiders and outsiders can meet and work together in this middle‐cultural territory for the instrumental purpose of obtaining passage through the “gateway”.Research limitations/implicationsInevitably some journal articles of interest may have been missed in the review due to the chosen scanning boundary. Nevertheless the search method provides a sufficient base to reveal recurrent research themes, and also overlooked themes of potential significance.Practical implicationsGuanxi gateway ties assist companies and individual business actors to find a path through the cumbersome Chinese bureaucracy and hierarchical levels by activating personal relationships.Originality/valueThis study reveals a commonly overlooked perspective of guanxi, that is, as a facilitator of culture‐bridging ties. The conventional business perspective of guanxi can be viewed as evolving from a gated community into an intercultural facilitating mechanism.
How store brands build retailer brand image
Authors: Kremer Florence , Viot Catherine 
Published: January 2014

PurposeThe purpose of this research is to highlight the role store brands can play in retail branding. Does an image transfer take place between store brands and the retailer brand? To address this issue, the authors propose to identify and test the dimensions of image transfer from the store brand to the retailer brand.Design/methodology/approachA qualitative study of 138 consumers helped to complete the attributes of store brand image and retailer brand image identified in the literature. A total of 322 customers of three major French retailers responded to a questionnaire. The data collected were tested in a structural equation model.FindingsResults indicate that store brands have a positive impact on the retailer image. The price image of the store brand is positively related to the retailer price image. The values that customers associated with store brands improve the retailer brand image in terms of its values.Research limitations/implicationsStore brands are considered as a whole, without distinction between product categories. The paper focuses on standard store brands only, excluding “premium” store brands.Practical implicationsRetailers can find a rationale for investing in their store brand range in order to differentiate themselves from their competitors. Managers should ensure that their store brands' image is seen as congruent with their own retailer brand image. In particular, more attention should be paid to the values reflected by the store brands and the store brands' price image.Originality/valueThe results indicate that store brands not only benefit from the strength of the retailer brand, but they also contribute, in a reciprocal way, to the improvement of the retailer image.
Comparing user‐generated and librarian‐generated metadata on digital images
Authors: Petek Marija 
Published: January 2014

PurposeImages can be seen in a different way by different users. The purpose of this paper is to examine how users describe images and to ascertain whether differences exist between users and librarians in creating metadata on images.Design/methodology/approachThe paper compares metadata on digital images generated by users to metadata generated by librarians. A sample of images taken from Digital Library of Slovenia and Flickr is presented to students to assign tags. The tags are grouped into categories and classes of attributes and compared to keywords added by Slovene librarians and to tags created by Flickr visitors.FindingsThe number of assigned tags differs greatly among survey participants, librarians and Flickr users, the participants being the most productive. A majority of tags reflect perceptual attributes and tagging is mostly done for personal benefit. The matching rate for all images is 41.4 percent; matching is a little higher with the Flickr images.Practical implicationsSocial tagging can be used to develop control vocabularies reflecting users' language and to provide access to digital images.Originality/valueThe paper presents quantitative data on image attributes used by users in describing images.