bluuebunny/crossref_metadata_2025_split huggingface dataset:
What drives financial performance–resource efficiency or resource slack?
Authors: Modi Sachin B. , Mishra Saurabh 
Published: January 2011

AbstractExtant research in operations management has revealed divergent insights into the value potential of resource efficiency. While one view relates efficiency with good operations management and asserts that slack resources are a form of waste that should be minimized, the other view suggests that limited resource slack can impose heavy costs on firms by making them brittle. In this research, the authors build on these views to investigate the relationship of inventory, production, and marketing resource efficiency of firms with three metrics of financial performance (i.e., Stock‐Returns, Tobin's Q, and Returns‐on‐Assets). The authors evaluate the theoretical framework using secondary information on all U.S. based publicly‐owned manufacturing firms across the 16‐year time period of 1991–2006. Analysis utilizing a mixed‐model approach reveals that a focus on resource efficiency is positively associated with firm financial performance. However, findings also support the arguments favoring slack, indicating that the financial gains from resource efficiency exhibit diminishing returns.
Solitary intradural extramedullary metastasis of renal cell carcinoma to the conus medullaris
Authors: Lin Tzu‐Kang , Chen Shu‐Mei , Jung Shih‐Ming 
Published: January 2011

AbstractWe report the case of a 68‐year‐old man with a 6‐year history of renal cell carcinoma (RCC), who presented with severe low backache and paraparesis for a month before admission. In addition, he experienced urinary retention for 2 weeks. A spinal magnetic resonance imaging scan revealed the presence of an intradural extramedullary solitary mass at the conus medullaris. We performed a laminectomy and completely excised the tumor. The histopathological findings were suggestive of spinal metastasis of RCC. After the operation, the patient did not complain of backache and urinary retention, and paraparesis improved significantly. Spinal metastases of RCC are usually extradurally located. Intradural metastases of RCC are rare. Thus far, only six cases of RCC metastasizing to the cauda equina have been reported; however, RCC metastasis to the conus medullaris has not yet been reported. Conus medullaris lesions may cause symmetrical motor and sensory deficits accompanied by early autonomic system impairment. Surgery is the treatment of choice in cases of resectable RCC metastases, especially in cases of solitary metastasis.
An 1800-yr record of decadal-scale hydroclimatic variability in the upper Arkansas River basin from bristlecone pine
Authors: Woodhouse Connie A. , Pederson Gregory T. , Gray Stephen T. 
Published: January 2011

AbstractBristlecone pine trees are exceptionally long-lived, and with the incorporation of remnant material have been used to construct multi-millennial length ring–width chronologies. These chronologies can provide valuable information about past temperature and moisture variability. In this study, we outline a method to build a moisture-sensitive bristlecone chronology and assess the robustness and consistency of this sensitivity over the past 1200 yr using new reconstructions of Arkansas River flow (AD 1275–2002 and 1577–2002) and the summer Palmer Drought Sensitivity Index. The chronology, a composite built from parts of three collections in the central Rocky Mountains, is a proxy for decadal-scale moisture variability for the past 18 centuries. Since the sample size is small in some portions of the time series, the chronology should be considered preliminary; the timing and duration of drought events are likely the most robust characteristics. This chronology suggests that the region experienced increased aridity during the medieval period, as did much of western North America, but that the timing and duration of drought episodes within this period were somewhat different from those in other western locations, such as the upper Colorado River basin.
Monsoon variability and chemical weathering during the late Pleistocene in the Goriganga basin, higher central Himalaya, India
Authors: Beukema Steven P. , Krishnamurthy R.V. , Juyal N. , Basavaiah N. , Singhvi A.K. 
Published: January 2011

AbstractStable isotope analysis along with radiocarbon and luminescence dating of late Pleistocene lacustrine deposits at Burfu in the higher central Himalaya are used to interpret hydrologic changes in the lake basin. From 15.5 ka to ~ 14.5 ka the Burfu lake was largely fed by melting glaciers. A warming event at 14.5 ka suggests an enhanced monsoon and increased carbonate weathering. From ~ 13.5 ka to ~ 12.5 ka the isotopic data suggest large-amplitude climate variability. Following this, the isotope data suggest a short-lived, abrupt cooling event, comprising a ~ 300-yr intense cool period followed by a ~ 500-yr interval of moderate climate. A shift in isotope values at ~ 11.3 ka may signify a strengthening monsoon in this region. The inferred climatic excursions appear to be correlative, at least qualitatively, with global climatic events, and perhaps the Burfu lake sequence provides regional evidence of globally recorded excursions. This study also suggests a potential use of radiocarbon ages in specific environments as a paleoenvironmental proxy.
Integrating molecular and morphological approaches for characterizing parasite cryptic species: implications for parasitology
Authors: NADLER STEVEN A. , DE LEÓN GERARDO PÉREZ-PONCE 
Published: February 2011

SUMMARYHerein we review theoretical and methodological considerations important for finding and delimiting cryptic species of parasites (species that are difficult to recognize using traditional systematic methods). Applications of molecular data in empirical investigations of cryptic species are discussed from an historical perspective, and we evaluate advantages and disadvantages of approaches that have been used to date. Developments concerning the theory and practice of species delimitation are emphasized because theory is critical to interpretation of data. The advantages and disadvantages of different molecular methodologies, including the number and kind of loci, are discussed relative to tree-based approaches for detecting and delimiting cryptic species. We conclude by discussing some implications that cryptic species have for research programmes in parasitology, emphasizing that careful attention to the theory and operational practices involved in finding, delimiting, and describing new species (including cryptic species) is essential, not only for fully characterizing parasite biodiversity and broader aspects of comparative biology such as systematics, evolution, ecology and biogeography, but to applied research efforts that strive to improve development and understanding of epidemiology, diagnostics, control and potential eradication of parasitic diseases.
Environmental mastery and depression in older adults in residential care
Authors: KNIGHT TESS , DAVISON TANYA ELLEN , MCCABE MARITA PATRICIA , MELLOR DAVID 
Published: February 2011

ABSTRACTThis study investigated the association between environmental mastery and depression in a sample of 96 older adults (aged 64–98 years) in residential care. The participants completed a scale that assessed depression along with measures for risk factors for depression such as functional capacity, self-evaluated physical health, bereavement experiences and environmental mastery. The results showed that 49 per cent of the variance in participants' scores in depression could be attributed to their self-reported level of environmental mastery. Given the complexity of depression and the likelihood of reduced environmental mastery among older adults in residential care, the construct was further assessed as a mediating variable between the risk factors and depression. With environmental mastery taken as such, the explained variance in depression increased to 56 per cent. It was concluded that environmental mastery may be one of the more important factors affecting the mental health of older adults living in residential care and that strategies for increasing the residents' environmental mastery are important to their psychological wellbeing. The discussion notes that among the questions needing further investigation are whether older adults who experience high environmental mastery make the transition from community living to residential nursing home care more successfully than others, and whether perceived mastery diminishes over time or occurs at the point of transition from community independent living to dependent supported living.
Magnetosome-like ferrimagnetic iron oxide nanocubes for highly sensitive MRI of single cells and transplanted pancreatic islets
Authors: Lee Nohyun , Kim Hyoungsu , Choi Seung Hong , Park Mihyun , Kim Dokyoon , Kim Hyo-Cheol , Choi Yoonseok , Lin Shunmei , Kim Byung Hyo , Jung Hye Seung , Kim Hyeonjin , Park Kyong Soo , Moon Woo Kyung , Hyeon Taeghwan 
Published: February 2011

For ultrasensitive magnetic resonance imaging (MRI), magnetic nanoparticles with extremely high r2 relaxivity are strongly desired. Magnetosome-like nanoparticles were prepared by coating polyethylene glycol-phospholipid (PEG-phospholipid) onto ferrimagnetic iron oxide nanocubes (FIONs). FIONs exhibited a very high relaxivity (r2) of 324 mM
-1
s
-1
, allowing efficient labeling of various kinds of cells. The magnetic resonance (MR) imaging of single cells labeled with FIONs is demonstrated not only in vitro but also in vivo. Pancreatic islet grafts and their rejection could be imaged using FIONs on a 1.5 T clinical MRI scanner. The strong contrast effect of FIONs enabled MR imaging of transplanted islets in small rodents as well as in large animals. Therefore, we expect that MR imaging of pancreatic islet grafts using FIONs has the potentials for clinical applications. Furthermore, FIONs will enable highly sensitive noninvasive assessment after cell transplantation.
Changes in electronic states and magnetic free energy in La1−zCez(FexSi1−x)13 magnetic refrigerants
Authors: Fujita A , Fujieda S , Fukamichi K 
Published: January 2011

The influence of partial substitution of Ce on the electronic structure and magnetic free energy has been investigated for La1−z
Ce
z
(Fe
x
Si1−x
)13. From the Mössbauer spectroscopy of La0.7Ce0.3(Fe0.88Si0.12)13, the distribution of the electric field gradient is found to be scarcely changed, therefore, the volume reduction by partial substitution is regarded as isotropic. The change of the isomer shift to positive sign after the partial substitution is closely correlated with the 5d and/or 4f electrons of Ce.
The change in magnetic free energy has been examined for La0.7Ce0.3(Fe0.86Si0.14)13 having a large magnetic entropy change ΔS
m and a small hysteretic behaviour. From the results analysed by the Landau expansion theory, the large ΔS
m and the small hysteresis of this compound are attributed to the magnitude and thermal variation of the fourth-order Landau coefficient in magnetic free energy. Consequently, the combination of partial substitution and control of Fe concentration is useful for highly efficient magnetic refrigerants.
Mechanism of the tonal emission from ac high voltage overhead transmission lines
Authors: Straumann Ueli 
Published: January 2011

Foul weather conditions can lead to corona discharges on high voltage overhead transmission lines which are perceivable as an audible broadband crackling and hissing noise. In such situations this noise is often accompanied by a humming noise at twice the mains frequency (2f).
While the crackling and hissing noise component was widely investigated in the past, the 2f-component went largely uncommented. Only a scant amount of literature suggests mechanisms explaining the occurrence of this emission, but these suggestions are either vague or controversial.
In this paper a mechanism analogous to that of ion loudspeakers is presented, which describes the sound levels of audible 2f-emissions from high voltage model lines quantitatively in a satisfactory manner. While the broadband component of corona noise emissions has its immediate origin in the discharges themselves, the 2f-emissions arise from the drift of ions left behind by the discharges. Due to collisions with gas molecules, these ions cause in the sum a rise of heat in and a force applying on the neutral gas, thus producing the 2f-emissions. Depending on the situation, both can give rise to contributions of similar magnitude.
Modular analysis of the probabilistic genetic interaction network
Authors: Hou Lin , Wang Lin , Qian Minping , Li Dong , Tang Chao , Zhu Yunping , Deng Minghua , Li Fangting 
Published: January 2011

Abstract
Motivation: Epistatic Miniarray Profiles (EMAP) has enabled the mapping of large-scale genetic interaction networks; however, the quantitative information gained from EMAP cannot be fully exploited since the data are usually interpreted as a discrete network based on an arbitrary hard threshold. To address such limitations, we adopted a mixture modeling procedure to construct a probabilistic genetic interaction network and then implemented a Bayesian approach to identify densely interacting modules in the probabilistic network.
Results: Mixture modeling has been demonstrated as an effective soft-threshold technique of EMAP measures. The Bayesian approach was applied to an EMAP dataset studying the early secretory pathway in Saccharomyces cerevisiae. Twenty-seven modules were identified, and 14 of those were enriched by gold standard functional gene sets. We also conducted a detailed comparison with state-of-the-art algorithms, hierarchical cluster and Markov clustering. The experimental results show that the Bayesian approach outperforms others in efficiently recovering biologically significant modules.
Contact: dengmh@pku.edu.cn; fangtingli@pku.edu.cn; zhuyp@hupo.org.cn
Supplementary Information: Supplementary data are available at Bioinformatics online.
Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format
Authors: Edmonson Michael N. , Zhang Jinghui , Yan Chunhua , Finney Richard P. , Meerzaman Daoud M. , Buetow Kenneth H. 
Published: January 2011

Abstract
Summary: Bambino is a variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. The variant detector takes advantage of SAM-specific annotations, and produces detailed output suitable for genotyping and identification of somatic mutations. The assembly viewer can display reads in the context of either a user-provided or automatically generated reference sequence, retrieve genome annotation features from a UCSC genome annotation database, display histograms of non-reference allele frequencies, and predict protein-coding changes caused by SNPs.
Availability: Bambino is written in platform-independent Java and available from https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html, along with documentation and example data. Bambino may be launched online via Java Web Start or downloaded and run locally.
Contact: edmonson@nih.gov.
Conveyor: a workflow engine for bioinformatic analyses
Authors: Linke Burkhard , Giegerich Robert , Goesmann Alexander 
Published: January 2011

Abstract
Motivation: The rapidly increasing amounts of data available from new high-throughput methods have made data processing without automated pipelines infeasible. As was pointed out in several publications, integration of data and analytic resources into workflow systems provides a solution to this problem, simplifying the task of data analysis. Various applications for defining and running workflows in the field of bioinformatics have been proposed and published, e.g. Galaxy, Mobyle, Taverna, Pegasus or Kepler. One of the main aims of such workflow systems is to enable scientists to focus on analysing their datasets instead of taking care for data management, job management or monitoring the execution of computational tasks. The currently available workflow systems achieve this goal, but fundamentally differ in their way of executing workflows.
Results: We have developed the Conveyor software library, a multitiered generic workflow engine for composition, execution and monitoring of complex workflows. It features an open, extensible system architecture and concurrent program execution to exploit resources available on modern multicore CPU hardware. It offers the ability to build complex workflows with branches, loops and other control structures. Two example use cases illustrate the application of the versatile Conveyor engine to common bioinformatics problems.
Availability: The Conveyor application including client and server are available at http://conveyor.cebitec.uni-bielefeld.de.
Contact: conveyor@CeBiTec.Uni-Bielefeld.DE; blinke@ceBiTec.Uni-Bielefeld.De.
Supplementary information: Supplementary data are available at Bioinformatics online.
PiNGO: a Cytoscape plugin to find candidate genes in biological networks
Authors: Smoot Michael , Ono Keiichiro , Ideker Trey , Maere Steven 
Published: January 2011

Abstract
Summary: PiNGO is a tool to screen biological networks for candidate genes, i.e. genes predicted to be involved in a biological process of interest. The user can narrow the search to genes with particular known functions or exclude genes belonging to particular functional classes. PiNGO provides support for a wide range of organisms and Gene Ontology classification schemes, and it can easily be customized for other organisms and functional classifications. PiNGO is implemented as a plugin for Cytoscape, a popular network visualization platform.
Availability: PiNGO is distributed as an open-source Java package under the GNU General Public License (http://www.gnu.org/), and can be downloaded via the Cytoscape plugin manager. A detailed user guide and tutorial are available on the PiNGO website (http://www.psb.ugent.be/esb/PiNGO.
Contact: steven.maere@psb.vib-ugent.be
SHRiMP2: Sensitive yet Practical Short Read Mapping
Authors: David Matei , Dzamba Misko , Lister Dan , Ilie Lucian , Brudno Michael 
Published: January 2011

Abstract
Summary: We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to achieve high accuracy at a very reasonable speed. SHRiMP2 supports both letter space and color space (AB/SOLiD) reads, enables for direct alignment of paired reads and uses parallel computation to fully utilize multi-core architectures.
Availability: SHRiMP2 executables and source code are freely available at: http://compbio.cs.toronto.edu/shrimp/.
Contact: shrimp@cs.toronto.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Modeling and comparing the organization of circular genomes
Authors: Shieh Grace S. , Zheng Shurong , Johnson Richard A. , Chang Yi-Feng , Shimizu Kunio , Wang Chia-Chang , Tang Sen-Lin 
Published: January 2011

Abstract
Motivation: Most prokaryotic genomes are circular with a single chromosome (called circular genomes), which consist of bacteria and archaea. Orthologous genes (abbreviated as orthologs) are genes directly evolved from an ancestor gene, and can be traced through different species in evolution. Shared orthologs between bacterial genomes have been used to measure their genome evolution. Here, organization of circular genomes is analyzed via distributions of shared orthologs between genomes. However, these distributions are often asymmetric and bimodal; to date, there is no joint distribution to model such data. This motivated us to develop a family of bivariate distributions with generalized von Mises marginals (BGVM) and its statistical inference.
Results: A new measure based on circular grade correlation and the fraction of shared orthologs is proposed for association between circular genomes, and a visualization tool developed to depict genome structure similarity. The proposed procedures are applied to eight pairs of prokaryotes separated from domain down to species, and 13 mycoplasma bacteria that are mammalian pathogens belonging to the same genus. We close with remarks on further applications to many features of genomic organization, e.g. shared transcription factor binding sites, between any pair of circular genomes. Thus, the proposed procedures may be applied to identifying conserved chromosome backbones, among others, for genome construction in synthetic biology.
Availability: All codes of the BGVM procedures and 1000+ prokaryotic genomes are available at http://www.stat.sinica.edu.tw/∼gshieh/bgvm.htm.
Contact: gshieh@stat.sinica.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
A Ruby API to query the Ensembl database for genomic features
Authors: Strozzi Francesco , Aerts Jan 
Published: January 2011

Abstract
Summary: The Ensembl database makes genomic features available via its Genome Browser. It is also possible to access the underlying data through a Perl API for advanced querying. We have developed a full-featured Ruby API to the Ensembl databases, providing the same functionality as the Perl interface with additional features. A single Ruby API is used to access different releases of the Ensembl databases and is also able to query multi-species databases.
Availability and Implementation: Most functionality of the API is provided using the ActiveRecord pattern. The library depends on introspection to make it release independent. The API is available through the Rubygem system and can be installed with the command gem install ruby-ensembl-api.
Contact: jan.aerts@esat.kuleuven.be
How to do (or not to do) … Assessing the impact of a policy change with routine longitudinal data
Authors: Lagarde Mylene 
Published: January 2011

AbstractA lack of good quality evidence on the effect of alternative social policies in low- and middle-income countries has been recently underlined and the value of randomized trials increasingly advocated. However, it is also acknowledged that randomization is not always feasible or politically acceptable. Analyses using longitudinal data series before and after an intervention can also deliver robust results and such data are often reasonably easy to access.Using the example of evaluating the impact on utilization of a change in health financing policy, this article explains how studies in the literature have often failed to address the possible biases that can arise in a simple analysis of routine longitudinal data. It then describes two possible statistical approaches to estimate impact in a more reliable manner and illustrates in detail the more simple method. Advantages and limitations of this quasi-experimental approach to evaluating the impact of health policies are discussed.