bluuebunny/crossref_metadata_2025_split huggingface dataset:
PUmPER: phylogenies updated perpetually
Authors: Izquierdo-Carrasco Fernando , Cazes John , Smith Stephen A. , Stamatakis Alexandros 
Published: January 2014

AbstractSummary: New sequence data useful for phylogenetic and evolutionary analyses continues to be added to public databases. The construction of multiple sequence alignments and inference of huge phylogenies comprising large taxonomic groups are expensive tasks, both in terms of man hours and computational resources. Therefore, maintaining comprehensive phylogenies, based on representative and up-to-date molecular sequences, is challenging. PUmPER is a framework that can perpetually construct multi-gene alignments (with PHLAWD) and phylogenetic trees (with ExaML or RAxML-Light) for a given NCBI taxonomic group. When sufficient numbers of new gene sequences for the selected taxonomic group have accumulated in GenBank, PUmPER automatically extends the alignment and infers extended phylogenetic trees by using previously inferred smaller trees as starting topologies. Using our framework, large phylogenetic trees can be perpetually updated without human intervention. Importantly, resulting phylogenies are not statistically significantly worse than trees inferred from scratch.Availability and implementation: PUmPER can run in stand-alone mode on a single server, or offload the computationally expensive phylogenetic searches to a parallel computing cluster. Source code, documentation, and tutorials are available at https://github.com/fizquierdo/perpetually-updated-trees.Contact: Fernando.Izquierdo@h-its.orgSupplementary information: Supplementary Material is available at Bioinformatics online.
Opportunism and Honest Incompetence—Seeking Explanations for Noncompliance in Public Procurement
Authors: Kauppi Katri , van Raaij Erik M. 
Published: January 2014

AbstractThis article utilizes agency theory to explain maverick buying in governmental agencies, that is, noncompliance to centrally negotiated frame agreements. Traditional agency theory assumes the agent to be an opportunistic self-interest seeker. A complementary view of agency problems portrays man as an honest, yet not fully competent, actor; both agents and principals may be burdened by “honest incompetence.” We apply both perspectives on principal-agent relationships to study maverick buying in government procurement and link agency problems to three governance mechanisms: monitoring, training, and guidance. We find that guidance and training help to reduce governmental employees’ noncompliance, but output monitoring does not. Our findings further indicate that maverick buying is related to goal incongruence and two different types of information asymmetry: Agency problems may arise not only because the agent has information the principal is not aware of but also because the principal may have information the agent is not aware of. Future research in public management using agency theory to study instances of hidden action could benefit from applying a similar dual lens to behaviors previously examined as purely opportunistic.
Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2
Authors: Millán-Ariño Lluís , Islam Abul B. M. M. K. , Izquierdo-Bouldstridge Andrea , Mayor Regina , Terme Jean-Michel , Luque Neus , Sancho Mónica , López-Bigas Núria , Jordan Albert 
Published: January 2014

Abstract
Seven linker histone H1 variants are present in human somatic cells with distinct prevalence across cell types. Despite being key structural components of chromatin, it is not known whether the different variants have specific roles in the regulation of nuclear processes or are differentially distributed throughout the genome. Using variant-specific antibodies to H1 and hemagglutinin (HA)-tagged recombinant H1 variants expressed in breast cancer cells, we have investigated the distribution of six H1 variants in promoters and genome-wide. H1 is depleted at promoters depending on its transcriptional status and differs between variants. Notably, H1.2 is less abundant than other variants at the transcription start sites of inactive genes, and promoters enriched in H1.2 are different from those enriched in other variants and tend to be repressed. Additionally, H1.2 is enriched at chromosomal domains characterized by low guanine–cytosine (GC) content and is associated with lamina-associated domains. Meanwhile, other variants are associated with higher GC content, CpG islands and gene-rich domains. For instance, H1.0 and H1X are enriched at gene-rich chromosomes, whereas H1.2 is depleted. In short, histone H1 is not uniformly distributed along the genome and there are differences between variants, H1.2 being the one showing the most specific pattern and strongest correlation with low gene expression.
Multiplexing clonality: combining RGB marking and genetic barcoding
Authors: Cornils Kerstin , Thielecke Lars , Hüser Svenja , Forgber Michael , Thomaschewski Michael , Kleist Nadja , Hussein Kais , Riecken Kristoffer , Volz Tassilo , Gerdes Sebastian , Glauche Ingmar , Dahl Andreas , Dandri Maura , Roeder Ingo , Fehse Boris 
Published: January 2014

Abstract
RGB marking and DNA barcoding are two cutting-edge technologies in the field of clonal cell marking. To combine the virtues of both approaches, we equipped LeGO vectors encoding red, green or blue fluorescent proteins with complex DNA barcodes carrying color-specific signatures. For these vectors, we generated highly complex plasmid libraries that were used for the production of barcoded lentiviral vector particles. In proof-of-principle experiments, we used barcoded vectors for RGB marking of cell lines and primary murine hepatocytes. We applied single-cell polymerase chain reaction to decipher barcode signatures of individual RGB-marked cells expressing defined color hues. This enabled us to prove clonal identity of cells with one and the same RGB color. Also, we made use of barcoded vectors to investigate clonal development of leukemia induced by ectopic oncogene expression in murine hematopoietic cells. In conclusion, by combining RGB marking and DNA barcoding, we have established a novel technique for the unambiguous genetic marking of individual cells in the context of normal regeneration as well as malignant outgrowth. Moreover, the introduction of color-specific signatures in barcodes will facilitate studies on the impact of different variables (e.g. vector type, transgenes, culture conditions) in the context of competitive repopulation studies.
Structural basis of sodium–potassium exchange of a human telomeric DNA quadruplex without topological conversion
Authors: Wang Zi-Fu , Li Ming-Hao , Hsu Shang-Te Danny , Chang Ta-Chau 
Published: January 2014

Abstract
Understanding the mechanism of Na+/K+-dependent spectral conversion of human telomeric G-quadruplex (G4) sequences has been limited not only because of the structural polymorphism but also the lack of sufficient structural information at different stages along the conversion process for one given oligonucleotide. In this work, we have determined the topology of the Na+ form of Tel23 G4, which is the same hybrid form as the K+ form of Tel23 G4 despite the distinct spectral patterns in their respective nuclear magnetic resonance (NMR) and circular dichroism spectra. The spectral difference, particularly the well-resolved imino proton NMR signals, allows us to monitor the structural conversion from Na+ form to K+ form during Na+/K+ exchange. Time-resolved NMR experiments of hydrogen–deuterium exchange and hybridization clearly exclude involvement of the global unfolding for the fast Na+/K+ spectral conversion. In addition, the K+ titration monitored by NMR reveals that the Na+/K+ exchange in Tel23 G4 is a two-step process. The addition of K+ significantly stabilizes the unfolding kinetics of Tel23 G4. These results offer a possible explanation of rapid spectral conversion of Na+/K+ exchange and insight into the mechanism of Na+/K+ structural conversion in human telomeric G4s.
Vascular Access in Resuscitation
Authors: Anson Jonathan A. 
Published: January 2014

Abstract
Intraosseous vascular access is a time-tested procedure which has been incorporated into the 2010 American Heart Association Guidelines for Cardiopulmonary Resuscitation. Intravenous access is often difficult to achieve in shock patients, and central line placement can be time consuming. Intraosseous vascular access, however, can be achieved quickly with minimal disruption of chest compressions. Newer insertion devices are easy to use, making the intraosseous route an attractive alternative for venous access during a resuscitation event. It is critical that anesthesiologists, who are often at the forefront of patient resuscitation, understand how to properly use this potentially life-saving procedure.
Local spillovers and durable adoption: evidence from durable consumptions in rural China
Authors: Rong Zhao , Feng Yao 
Published: January 2014

Purpose
– The effects of social learning and network externalities in the diffusion of a new product imply that there should be local spillovers from existing owners to new adopters in a closely related community. Using the data from a unique household survey in rural China, this paper aims to examine the importance of local spillovers in the diffusion of two major durable goods, washing machine and refrigerator.

Design/methodology/approach
– Based on a 1999 rural household survey of durable goods consumption conducted by the National Bureau of Statistics (NBS) of China, the authors examine the likelihood of rural households adopting a washing machine and a refrigerator during 1998-1999, respectively.

Findings
– The estimation results indicate that a household is more likely to buy its first durable good in villages where a large share of households already own one. Further evidence suggests that these patterns are unlikely to be explained by unobserved local characteristics. When examined in more detail, the extent of local spillovers appears to be positively related to the household education level.

Originality/value
– First, the study reveals the importance of local spillovers in the diffusion of these two durables. Specifically, 64 percent of washing machine adoptions during 1998-1999 are due to these spillovers. For refrigerator adoptions, the proportion is 55 percent. Second, to the authors' best knowledge, the authors are among the first to test and provide evidence on the interaction between education level and local spillovers based on the learning hypothesis.
An economy-wide analysis of impacts on Taiwan of reducing tariff escalation on agriculture-related products in WTO Doha Round negotiations
Authors: Lee Huey-Lin , Chang Ching-Cheng , Weng Yungho , Hsu Sheng-Ming , Hsu Shih-Hsun , Chen Yi-Chieh 
Published: January 2014

Purpose– The purpose of this paper is to assess the degree of tariff escalation in Taiwan's agriculture-related commodities and the economy-wide impact of tariff harmonization.Design/methodology/approach– A computable general equilibrium model of the Taiwan economy is applied to simulate for the economy-wide impact of three alternative proposals that reduce tariff rates as well as the degree of tariff escalation in agriculture-related products.Findings– The paper shows that reduction in tariff wedge helps increase social welfare of Taiwan at the expense of some agricultural sectors. Based on the pair-wise comparisons of the three tariff reduction proposals, the scenario where the upstream products have the least reduction would have agricultural sectors fare better than in the other scenarios where more negative impact on output and employment would occur to agricultural sectors.Originality/value– The paper assesses quantitatively the economy-wide impact of reducing tariff wedges between unprocessed and processed products, which is rarely seen in the literature using a detailed computable general equilibrium model.
Do China's food safety standards affect agricultural trade? The case of dairy products
Authors: Sun Dingqiang , Huang Jikun , Yang Jun 
Published: January 2014

Purpose
– The purpose of this paper is to empirically examine how China's food safety standards affect agricultural trade in the case of dairy products.

Design/methodology/approach
– A gravity model is applied to quantitatively address the impacts of changing food safety standards in China in the case of its dairy imports. The paper considers the trade impacts of not only a specific hazard substance but also overall strictness of safety standards.

Findings
– The paper shows that changes in food safety standards of dairy products have no effect on China's dairy imports. The finding is not particularly surprising considering special characteristics of China's food safety standards. Given the fact that China's safety standards are relatively lower than that in its major exporters, the trade-impeding effect may not be substantial.

Research limitations/implications
– First, this study is unable to estimate the trade-enhancing and trade-impending effects separately. Second, the study does not account for a potential endogeneity issue associated with food safety standards.

Originality/value
– This paper contributes to the debate on how food safety standards affect trade by demonstrating that safety standards in developing countries like China can affect international trade differently from that in developed countries. Although results are specific to China's dairy imports, the explanations are applicable to food safety standards in other developing countries.
Relationship of OPAC users' satisfaction with their demographic characteristics, computer skills, user education, user assistance and user-friendly OPAC
Authors: Kumar Shiv 
Published: January 2014

Purpose
– The main aim of this paper is to identify whether user demographic characteristics, computer skills, user education, user assistance and user-friendly OPAC (online public access catalog) have an impact on their satisfaction in the context of users in an Indian university setting.

Design/methodology/approach
– The survey method was utilized and a questionnaire was designed to collect data. The study is based on a sample of the 384 questionnaires from the three universities located in the Union Territory of Chandigarh and Punjab State. To analyze the data collected, SPSS package (version 14.0) was used, and also to produce requisite cross-tabulations. Chi-square testing was performed to determine the association of user satisfaction with the variables covered in the study.

Findings
– The findings highlighted that overall there was a low degree of satisfaction among the users. With the exception of academic majors, in general, there were no significant differences between satisfaction and user demographic characteristics. Overall satisfaction was significantly higher for those who were possessed with adequate knowledge on OPAC, and had received staff assistance, as well as necessary education on OPAC. The study showed that satisfaction with ease of usage of OPAC was higher. It was also found that users were well-equipped with computers and had attained skills while frequently searching the web, however, it was also revealed that mere possession of computer skills was not sufficient for efficient use of OPAC, resulting in the attainment of a high level of satisfaction.

Originality/value
– The paper brings out the fact of how user demographic characteristics, computer skills, user education, user assistance, and user-friendly OPAC, influence user satisfaction in a university educational set up. The findings will be beneficial for increasing user satisfaction levels in order to retain existing OPAC users because OPAC will continue to be a necessary tool for accessing quality academic information available in both print and electronic format.
Exploring the value and innovative pricing strategy of digital archives
Authors: Wang Ping , Hu In-Lin , Chang Chen-Chi 
Published: January 2014

Purpose
– The research issues of digital preservation have apparently moved from how to set up the digital archives to on-going business models. The aim of this paper is to investigate the key factors for digital archives' success. This paper provides a business model for the sustainability of digital archives.

Design/methodology/approach
– Both pricing strategies and business models related to digital archives are very important. From the point of archive preservation, how to preserve digital archives permanently and make them accessible are the most important research issues. This paper, based on a review of the academic literature, adopts the innovative pricing approach to develop the business models and pricing strategy.

Findings
– The research defines the different needs at start-up versus the on-going operations for digital preservation. Considering digital archives as information goods, this study adopts the TRIZ method to establish a pricing strategy for digital preservation. It discusses the pricing strategy for digital preservation using an innovative method of creative problem-solving theory from the perspectives of the archives institutes, materials providers and consumers.

Originality/value
– This study recommends the pricing strategies for the digital preservation programs and the government's price policy based on the TRIZ analysis method.
An intellectual structure of activity-based costing: a co-citation analysis
Authors: Kuo Hsiu-Kuei , Yang Chyan 
Published: January 2014

Purpose– The purpose of this paper is to show that by exploring the intellectual structure of activity-based costing (ABC) based on the citation database of Google Scholar, one can understand the evolution and core ideas of the ABC discipline.Design/methodology/approach– This study employs the document co-citation method to model the intellectual structure of ABC between 1988 and 2008. After an initial co-citation analysis of the condition-limited literature set to find the relationships between core articles, this study further implements multivariate statistical techniques to construct representations for the ABC intellectual structure.Findings– A total of four important subjects chronologically provide a panoramic view of the evolution of ABC. This study finds some dimensions of the results to be in accordance with prior research, but further achieves insights into the core ideas underpinning the ABC discipline. It demonstrates the validity of this study conducting a co-citation analysis based on the citation data of Google Scholar.Research limitations/implications– The classification, core articles, and evolution of the ABC literature published in the past two decades benefit academic researchers conducting future studies that build systematically on prior research.Practical implications– The intellectual structure of the ABC discipline explains and predicts the stages of ABC implementation's life cycle. For the accounting profession, this helps a consultant/practitioner in sub-fields of the ABC domain to quickly and easily enlarge the coverage and viewpoints or perspectives within his/her cluster of interest and to jointly consider the successful factors of implementing ABC in an organization.Originality/value– The empirical feasibility of using digitally archival information to model an intellectual structure of ABC is attained; and the intellectual structure and its various representations provide researchers, consultants, and practitioners with a macroscopic and dynamic view of the ABC discipline.
Towards dynamic and evolving digital libraries
Authors: Li Liew Chern 
Published: January 2014

Purpose– The overarching aim of this paper is to initiate a new conceptualisation of digital cultural heritage libraries' design and development that emphasises a holistic understanding of a digital cultural heritage as part of information ecology and of the activities taking place between and amongst the various elements of the ecology that are governed by social, cultural, political, economical, and technical affordances and constraints.Design/methodology/approach– A research framework is developed based on viewpoints, reviews of existing literature and concepts of information ecology and activity theory.Findings– The conceptual framework comprises of a set of dimensions: content; context; connectivity; consideration; collaboration; construction; confidence and continuity. These dimensions are indicative of the kinds of issues and questions that could be considered in transitioning a digital cultural heritage library into a system that is dynamic, and one which evolves within the stakeholders' socio-cultural contexts. The issues and questions highlighted and outlined under the dimensions may be used to help one to situate their digital cultural heritage in the space and environment it operates in, to discover which direction to take to transition the digital cultural heritage library and to safely navigate the journey for the transitioning. The dimensions may also signal the elements needing ongoing consideration as the digital cultural heritage library evolves on its journey within the ecologies concerned.Practical implications– These dimensions are indicative of the kinds of issues and questions that could be considered in transitioning a digital cultural heritage library into a system that is dynamic and one which evolves within the stakeholders' socio-cultural contexts. The issues and questions highlighted and outlined under the dimensions may be used to help one to situate their digital cultural heritage in the space and environment it operates in, to discover which direction to take to transition the digital cultural heritage library and to safely navigate the journey for the transitioning. The dimensions may also signal the elements needing ongoing consideration as the digital cultural heritage library evolves on its journey within the ecologies concerned.Originality/value– This research presents concepts from information ecology and activity theory that could be incorporated in digital library research, design and development.
Metadata quality in learning object repositories: a case study
Authors: Palavitsinis Nikolaos , Manouselis Nikos , Sanchez-Alonso Salvador 
Published: January 2014

Purpose
– This paper aims to address the issue of poor quality of metadata records describing educational content in Learning Object Repositories (LORs). Through this, it aims to improve the discoverability of learning objects in such LORs through a structured process that supports metadata creation.

Design/methodology/approach
– This paper presents a proposed metadata quality assessment certification process for LORs. The process was designed as a generic approach that may be customized to fit various application domains.

Findings
– Initial results from the application of the process in the context of a specific LOR report an improvement of the quality of about 11,000 metadata records. More specifically, metadata completeness for all metadata elements used in the repository under examination was significantly improved from 30 percent to 85 percent.

Research limitations/implications
– The main limitation of the findings is that they come from the application of the proposed process on a relatively small repository, which does not allow safe generalizations without further experimental study in bigger ones where resources and requirements scale up.

Practical implications
– This paper addresses implications for the development of a repository in the educational domain, identifying issues related to the metadata application profile, the support to domain experts and the mechanisms that may be put in place to support metadata creation.

Originality/value
– The value and also the originality of the approach presented lies within the fact the proposed approach quantifies issues related to metadata creation and management by studying actions and perceptions of stakeholders who are involved in the repository lifecycle.