bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of two-step chemical mechanisms and determination of thermokinetic parameters using frequency responses to small temperature oscillations
Authors: Closa F. , Gosse C. , Jullien L. , Lemarchand A.
Published: June 2013

Increased focus on kinetic signatures in biology, coupled with the lack of simple tools for chemical dynamics characterization, lead us to develop an efficient method for mechanism identification. A small thermal modulation is used to reveal chemical dynamics, which makes the technique compatible with in cellulo imaging. Then, the detection of concentration oscillations in an appropriate frequency range followed by a judicious analytical treatment of the data is sufficient to determine the number of chemical characteristic times, the reaction mechanism, and the full set of associated rate constants and enthalpies of reaction. To illustrate the scope of the method, dimeric protein folding is chosen as a biologically relevant example of nonlinear mechanism with one or two characteristic times.
Multiple-pressure-tapped core holder combined with X-ray computed tomography scanning for gas–water permeability measurements of methane-hydrate-bearing sediments
Authors: Konno Yoshihiro , Jin Yusuke , Uchiumi Takashi , Nagao Jiro
Published: June 2013

We present a novel setup for measuring the effective gas–water permeability of methane-hydrate-bearing sediments. We developed a core holder with multiple pressure taps for measuring the pressure gradient of the gas and water phases. The gas–water flooding process was simultaneously detected using an X-ray computed tomography scanner. We successfully measured the effective gas–water permeability of an artificial sandy core with methane hydrate during the gas–water flooding test.
Electrocardiogram classification using delay differential equations
Authors: Lainscsek Claudia , Sejnowski Terrence J.
Published: June 2013

Time series analysis with nonlinear delay differential equations (DDEs) reveals nonlinear as well as spectral properties of the underlying dynamical system. Here, global DDE models were used to analyze 5 min data segments of electrocardiographic (ECG) recordings in order to capture distinguishing features for different heart conditions such as normal heart beat, congestive heart failure, and atrial fibrillation. The number of terms and delays in the model as well as the order of nonlinearity of the model have to be selected that are the most discriminative. The DDE model form that best separates the three classes of data was chosen by exhaustive search up to third order polynomials. Such an approach can provide deep insight into the nature of the data since linear terms of a DDE correspond to the main time-scales in the signal and the nonlinear terms in the DDE are related to nonlinear couplings between the harmonic signal parts. The DDEs were able to detect atrial fibrillation with an accuracy of 72%, congestive heart failure with an accuracy of 88%, and normal heart beat with an accuracy of 97% from 5 min of ECG, a much shorter time interval than required to achieve comparable performance with other methods.
Biomolecule recognition using piezoresistive nanomechanical force probes
Authors: Tosolini Giordano , Scarponi Filippo , Cannistraro Salvatore , Bausells Joan
Published: June 2013

Highly sensitive sensors are one of the enabling technologies for the biomarker detection in early stage diagnosis of pathologies. We have developed a self-sensing nanomechanical force probe able for detecting the unbinding of single couples of biomolecular partners in nearly physiological conditions. The embedding of a piezoresistive transducer into a nanomechanical cantilever enabled high force measurement capability with sub 10-pN resolution. Here, we present the design, microfabrication, optimization, and complete characterization of the sensor. The exceptional electromechanical performance obtained allowed us to detect biorecognition specific events underlying the biotin-avidin complex formation, by integrating the sensor in a commercial atomic force microscope.
Two-dimensional photonic crystal slab with embedded silicon nanocrystals: Efficient photoluminescence extraction
Authors: Ondič Lukáš , Varga Marian , Hruška Karel , Kromka Alexander , Herynková Kateřina , Hönerlage Bernd , Pelant Ivan
Published: June 2013

A two-dimensional photonic crystal (PhC) slab was fabricated from a luminescent planar waveguide, formed by a (800 nm thick) layer of silicon nanocrystals (SiNCs) embedded in a polished silica plate. Dimensions of the PhC were designed so that light emitted by SiNCs under excitation with an external UV source can, during its propagation in the layer, interact with the periodicity and be Bragg-diffracted into air. This approach leads to up to 8-fold vertical extraction enhancement of SiNCs luminescence from the PhC slab compared to the bare planar layer. Results of the experiment are supported by the computer simulation.
Structural and optical properties of Ag-doped copper oxide thin films on polyethylene napthalate substrate prepared by low temperature microwave annealing
Authors: Das Sayantan , Alford T. L.
Published: June 2013

Silver doped cupric oxide thin films are prepared on polyethylene naphthalate (flexible polymer) substrates. Thin films Ag-doped CuO are deposited on the substrate by co-sputtering followed by microwave assisted oxidation of the metal films. The low temperature tolerance of the polymer substrates led to the search for innovative low temperature processing techniques. Cupric oxide is a p-type semiconductor with an indirect band gap and is used as selective absorption layer solar cells. X-ray diffraction identifies the CuO phases. Rutherford backscattering spectrometry measurements confirm the stoichiometry of each copper oxide formed. The surface morphology is determined by atomic force microscopy. The microstructural properties such as crystallite size and the microstrain for (−111) and (111) planes are calculated and discussed. Incorporation of Ag led to the lowering of band gap in CuO. Consequently, it is determined that Ag addition has a strong effect on the structural, morphological, surface, and optical properties of CuO grown on flexible substrates by microwave annealing. Tauc's plot is used to determine the optical band gap of CuO and Ag doped CuO films. The values of the indirect and direct band gap for CuO are found to be 2.02 eV and 3.19 eV, respectively.
Highly selective biomechanical separation of cancer cells from leukocytes using microfluidic ratchets and hydrodynamic concentrator
Authors: Lin Bill K. , McFaul Sarah M. , Jin Chao , Black Peter C. , Ma Hongshen
Published: June 2013

The separation of cells based on their biomechanical properties, such as size and deformability, is important in applications such as the identification of circulating tumor cells, where morphological differences can be used to distinguish target cancer cells from contaminant leukocytes. Existing filtration-based separation processes are limited in their selectivity and their ability to extract the separated cells because of clogging in the filter microstructures. We present a cell separation device consisting of a hydrodynamic concentrator and a microfluidic ratchet mechanism operating in tandem. The hydrodynamic concentrator removes the majority of the fluid and a fraction of leukocytes based on size, while the microfluidic ratchet mechanism separates cancer cells from leukocytes based on a combination of size and deformability. The irreversible ratcheting process enables highly selective separation and robust extraction of separated cells. Using cancer cells spiked into leukocyte suspensions, the complete system demonstrated a yield of 97%, while enriching the concentration of target cancer cells 3000 fold relative to the concentration of leukocytes.
Tuning the optical bandgap of TiO2-TiN composite films as photocatalyst in the visible light
Authors: Xie Zheng , Liu Xiangxuan , Zhan Peng , Wang Weipeng , Zhang Zhengjun
Published: June 2013

TiO2-TiN composite catalysts were prepared by oxidizing the TiN films in air at 350 °C. By adjusting the oxidation time to control the oxidation stage of TiN films, the optical band gap of the TiO2-TiN composites can be varied in a wide range from 1.68 eV to 3.23 eV. These composite films all showed red shift in photo-response towards the visible region, and depending on the optical band gap, some composite films exhibited good catalytic activity in the visible light region. This study provides a simple but effective method to prepare film photocatalyst working in visible light.
Financial Institutions, Information, and Investing-At-A-Distance
Authors: Clark Gordon L , Monk Ashby H B
Published: June 2013

Seminal papers on the firm emphasise the benefits of in-sourcing over out-sourcing services from the market. This provides a rationale for the growth of firms, especially in circumstances of market risk and uncertainty concerning the price and quantity of available services. This model is less successful when considering what firms do and where they do it, given their assets and the complementarities between related activities. In this paper we develop a model of financial institutions that is sensitive to the production and consumption of information (internal and external). Links are made between what the institution does and where it does it in relation to the information systems that enable financial institutions to reach beyond what they are able to achieve within their own organisations. This model is particularly relevant to pension funds, insurance companies, endowments, and sovereign wealth funds, many of which face hard-to-realise expectations concerning their investment performance. Making good on these expectations depends on the degree to which they are able to mobilise information at the margin of markets. In the penultimate section of the paper we consider the virtues or otherwise of three particular models of investing-at-a-distance. In conclusion, lessons are drawn for the theory and practice of financial intermediation in the context of increasingly distant investment opportunities.
Air Transportation and Regional Growth: Which Way Does the Causality Run?
Authors: Mukkala Kirsi , Tervo Hannu
Published: June 2013

While there is typically a strong correlation between air traffic and economic growth, the direction of causation between the two is not clear. To address the existence of causality in this paper we consider the nature of this relationship in different types of regions. The empirical analysis is based on European-level annual data from eighty-six regions and thirteen countries on air traffic and regional economic performance in the period 1991 to 2010. Granger noncausality analysis in a panel framework, which allows possible heterogeneity between regions, was used. The results suggest that the causality processes are homogenous from regional growth to air traffic. There is causality from air traffic to regional growth in peripheral regions, but this causality is less evident in core regions. Thus, air transportation plays a crucial role in boosting development in remote regions. There might, therefore, be a case for subsidizing local airports in these regions.
Community Resilience in Resource-Dependent Communities: A Comparative Case Study
Authors: Matarrita-Cascante David , Trejos Bernardo
Published: June 2013

A limited number of studies have been conducted to better understand community resilience in the context of changing resource-dependent communities. This study is intended to start bridging this gap by empirically examining three key factors associated with community resilience: local ownership of resources, residents' organizational capacities, and local institutional capacity to respond to change. Our objective is to deepen the understanding of such factors by uncovering the processes behind them in the context of two changing resource-dependent communities in Costa Rica. Findings suggest that community resilience is highly dependent on equity of resource distribution and access to financial resources, the quality of relationships between residents who live in the community as well as with newcomers, and the ability of local institutions to adapt in order to operate efficiently in the light of change.
A Multilevel Spatial Interaction Modelling Framework for Estimating Interregional Migration in Europe
Authors: Dennett Adam , Wilson Alan
Published: June 2013

This paper presents a new spatial interaction modelling framework for estimating subnational, international migration flows within Europe. We introduce a several-stage model which incorporates constraints at two geographical levels and produces estimates for a full matrices of interregional flows which adhere to known flows between countries in the EU system between 2002 and 2007. It is shown that internal migration data can be usefully employed to help distribute flows subnationally both through in-migration and out-migration distributions and through calibrated distance-decay parameters. Validation of the model outputs is achieved, in part, through comparison with national insurance number registration data from the UK.
Displaying Optic Flow to Simulate Locomotion: Comparing Heading and Steering
Authors: Kountouriotis Georgios K. , Wilkie Richard M.
Published: June 2013

Optic flow can be used by humans to determine their direction of heading as well as controlling steering. Dot-flow displays have been widely used to investigate these abilities but it is unclear whether photorealistic textures would provide better information for controlling high-speed steering. Here, we examine the accuracy of heading judgements from dot-flow displays of different densities and luminance and then compare to a scene containing a textured ground. We then examine steering behaviour using these same displays to determine whether accurate heading conditions necessarily equate to successful steering. Our findings suggest that the bright dense dot-flow displays led to equivalent performance as the ground texture when judging heading, and this was also true when steering. The intermediate dot-flow conditions (with fewer and faded dots) revealed that some conditions that led to accurate heading judgements were insufficient for accurate steering. It seems, therefore, that heading perception should not be considered synonymous with successful steering control, and displays that support one ability will not necessarily support the other.
Discovery of a glycerol 3-phosphate phosphatase reveals glycerophospholipid polar head recycling in
Mycobacterium tuberculosis
Authors: Larrouy-Maumus Gérald , Biswas Tapan , Hunt Debbie M. , Kelly Geoff , Tsodikov Oleg V. , de Carvalho Luiz Pedro Sório
Published: June 2013

Functional assignment of enzymes encoded by the
Mycobacterium tuberculosis
genome is largely incomplete despite recent advances in genomics and bioinformatics. Here, we applied an activity-based metabolomic profiling method to assign function to a unique phosphatase, Rv1692. In contrast to its annotation as a nucleotide phosphatase, metabolomic profiling and kinetic characterization indicate that Rv1692 is a
D,L-
glycerol 3-phosphate phosphatase. Crystal structures of Rv1692 reveal a unique architecture, a fusion of a predicted haloacid dehalogenase fold with a previously unidentified GCN5-related
N
-acetyltransferase region. Although not directly involved in acetyl transfer, or regulation of enzymatic activity in vitro, this GCN5-related N-acetyltransferase region is critical for the solubility of the phosphatase. Structural and biochemical analysis shows that the active site features are adapted for recognition of small polyol phosphates, and not nucleotide substrates. Functional assignment and metabolomic studies of
M. tuberculosis
lacking
rv1692
demonstrate that Rv1692 is the final enzyme involved in glycerophospholipid recycling/catabolism, a pathway not previously described in
M. tuberculosis
.
Fate of the replisome following arrest by UV-induced DNA damage in
Escherichia coli
Authors: Jeiranian H. Arthur , Schalow Brandy J. , Courcelle Charmain T. , Courcelle Justin
Published: June 2013

Accurate replication in the presence of DNA damage is essential to genome stability and viability in all cells. In
Escherichia coli
, DNA replication forks blocked by UV-induced damage undergo a partial resection and RecF-catalyzed regression before synthesis resumes. These processing events generate distinct structural intermediates on the DNA that can be visualized in vivo using 2D agarose gels. However, the fate and behavior of the stalled replisome remains a central uncharacterized question. Here, we use thermosensitive mutants to show that the replisome’s polymerases uncouple and transiently dissociate from the DNA in vivo. Inactivation of α, β, or τ subunits within the replisome is sufficient to signal and induce the RecF-mediated processing events observed following UV damage. By contrast, the helicase–primase complex (DnaB and DnaG) remains critically associated with the fork, leading to a loss of fork integrity, degradation, and aberrant intermediates when disrupted. The results reveal a dynamic replisome, capable of partial disassembly to allow access to the obstruction, while retaining subunits that maintain fork licensing and direct reassembly to the appropriate location after processing has occurred.
Do Beaver Dams Impede the Movement of Trout?
Authors: Lokteff Ryan L. , Roper Brett B. , Wheaton Joseph M.
Published: June 2013

Dams created by North American beavers Castor canadensis (hereafter, “beavers”) have numerous effects on stream habitat use by trout. Many of these changes to the stream are seen as positive, and many stream restoration projects seek either to reintroduce beavers or to mimic the habitat that they create. The extent to which beaver dams act as movement barriers to salmonids and whether successful dam passage differs among species are topics of frequent speculation and warrant further research. We investigated beaver dam passage by three trout species in two northern Utah streams. We captured 1,375 trout above and below 21 beaver dams and fitted them with PIT tags to establish whether fish passed the dams and to identify downstream and upstream passage; 187 individual trout were observed to make 481 passes of the 21 beaver dams. Native Bonneville Cutthroat Trout Oncorhynchus clarkii utah passed dams more frequently than nonnative Brown Trout Salmo trutta and nonnative Brook Trout Salvelinus fontinalis. We determined that spawn timing affected seasonal changes in dam passage for each species. Physical characteristics of dams, such as height and upstream location, affected the passage of each species. Movement behaviors of each trout species were also evaluated to help explain the observed patterns of dam passage. Our results suggest that beaver dams are not acting as movement barriers for Bonneville Cutthroat Trout or Brook Trout but may be impeding the movements of invasive Brown Trout.
Utility of an Adenosine Triphosphate Bioluminescence Assay to Evaluate Disinfection of Clostridium difficile Isolation Rooms
Authors: Deshpande Abhishek , Sitzlar Brett , Fertelli Dennis , Kundrapu Sirisha , Sunkesula Venkata C. K. , Ray Amy J. , Donskey Curtis J.
Published: June 2013

Effective disinfection of hospital rooms after discharge of patients with Clostridium difficile infection (CDI) is necessary to prevent transmission. Unfortunately, several studies have demonstrated that it is not uncommon for environmental cultures to remain positive for C. difficile after cleaning and disinfection of rooms in which a patient with CDI has been hospitalized (CDI rooms) by environmental services personnel. Cultures for C. difficile could potentially be useful to monitor disinfection of CDI rooms, but they are neither widely available nor efficient. There is a need for easy-to use and rapid methods to assess the effectiveness of CDI room disinfection. Adenosine triphosphate (ATP) bioluminescence assays provide a rapid assessment of cleaning effectiveness, because detection of ATP on surfaces indicates the presence of residual organic material (eg, bacteria, human secretions or excretions, and food). Detection of ATP is commonly used in the food and beverage industry and is increasingly being used in health care facilities to assess the adequacy of cleaning procedures. It is not known whether measurement of ATP on surfaces is useful to evaluate disinfection of CDI rooms. Here, we tested the hypothesis that low ATP readings on cleaned surfaces in CDI rooms would be predictive of negative cultures for C. difficile.
Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations
Authors: Chowdhury Salim Akhter , Shackney Stanley E. , Heselmeyer-Haddad Kerstin , Ried Thomas , Schäffer Alejandro A. , Schwartz Russell
Published: June 2013

Motivation: Development and progression of solid tumors can be attributed to a process of mutations, which typically includes changes in the number of copies of genes or genomic regions. Although comparisons of cells within single tumors show extensive heterogeneity, recurring features of their evolutionary process may be discerned by comparing multiple regions or cells of a tumor. A useful source of data for studying likely progression of individual tumors is fluorescence in situ hybridization (FISH), which allows one to count copy numbers of several genes in hundreds of single cells. Novel algorithms for interpreting such data phylogenetically are needed, however, to reconstruct likely evolutionary trajectories from states of single cells and facilitate analysis of tumor evolution.

Results: In this article, we develop phylogenetic methods to infer likely models of tumor progression using FISH copy number data and apply them to a study of FISH data from two cancer types. Statistical analyses of topological characteristics of the tree-based model provide insights into likely tumor progression pathways consistent with the prior literature. Furthermore, tree statistics from the resulting phylogenies can be used as features for prediction methods. This results in improved accuracy, relative to unstructured gene copy number data, at predicting tumor state and future metastasis.

Availability: Source code for software that does FISH tree building (FISHtrees) and the data on cervical and breast cancer examined here are available at ftp://ftp.ncbi.nlm.nih.gov/pub/FISHtrees.

Contact:  sachowdh@andrew.cmu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Protein threading using context-specific alignment potential
Authors: Ma Jianzhu , Wang Sheng , Zhao Feng , Xu Jinbo
Published: June 2013

Motivation: Template-based modeling, including homology modeling and protein threading, is the most reliable method for protein 3D structure prediction. However, alignment errors and template selection are still the main bottleneck for current template-base modeling methods, especially when proteins under consideration are distantly related.

Results: We present a novel context-specific alignment potential for protein threading, including alignment and template selection. Our alignment potential measures the log-odds ratio of one alignment being generated from two related proteins to being generated from two unrelated proteins, by integrating both local and global context-specific information. The local alignment potential quantifies how well one sequence residue can be aligned to one template residue based on context-specific information of the residues. The global alignment potential quantifies how well two sequence residues can be placed into two template positions at a given distance, again based on context-specific information. By accounting for correlation among a variety of protein features and making use of context-specific information, our alignment potential is much more sensitive than the widely used context-independent or profile-based scoring function. Experimental results confirm that our method generates significantly better alignments and threading results than the best profile-based methods on several large benchmarks. Our method works particularly well for distantly related proteins or proteins with sparse sequence profiles because of the effective integration of context-specific, structure and global information.

Availability: http://raptorx.uchicago.edu/download/.

Contact: jinboxu@gmail.com
Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM
Authors: Sedgewick Andrew J. , Benz Stephen C. , Rabizadeh Shahrooz , Soon-Shiong Patrick , Vaske Charles J.
Published: June 2013

High-dimensional ‘-omics’ profiling provides a detailed molecular view of individual cancers; however, understanding the mechanisms by which tumors evade cellular defenses requires deep knowledge of the underlying cellular pathways within each cancer sample. We extended the PARADIGM algorithm (Vaske et al., 2010, Bioinformatics, 26, i237–i245), a pathway analysis method for combining multiple ‘-omics’ data types, to learn the strength and direction of 9139 gene and protein interactions curated from the literature. Using genomic and mRNA expression data from 1936 samples in The Cancer Genome Atlas (TCGA) cohort, we learned interactions that provided support for and relative strength of 7138 (78%) of the curated links. Gene set enrichment found that genes involved in the strongest interactions were significantly enriched for transcriptional regulation, apoptosis, cell cycle regulation and response to tumor cells. Within the TCGA breast cancer cohort, we assessed different interaction strengths between breast cancer subtypes, and found interactions associated with the MYC pathway and the ER alpha network to be among the most differential between basal and luminal A subtypes. PARADIGM with the Naive Bayesian assumption produced gene activity predictions that, when clustered, found groups of patients with better separation in survival than both the original version of PARADIGM and a version without the assumption. We found that this Naive Bayes assumption was valid for the vast majority of co-regulators, indicating that most co-regulators act independently on their shared target.

Availability:  http://paradigm.five3genomics.com

Contact:  charlie@five3genomics.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
First Report of Squash vein yellowing virus Affecting Watermelon and Bitter Gourd in Puerto Rico
Authors: Acevedo V. , Rodrigues J. C. V. , de Jensen C. E. , Webster C. G. , Adkins S. , Wessel-Beaver L.
Published: June 2013

In 2005, symptoms of watermelon vine decline (WVD) were observed on a 200-acre watermelon farm in Santa Isabel, on the south central coast of Puerto Rico. WVD symptoms included leaf curling, mosaics, and internode necrosis. In early growth stages of WVD, reduced vigor and plant stunting occurred. At flowering, symptoms progressed to necrosis and wilting of vines. A 2006 to 2007 survey demonstrated that fungal pathogens were not associated with the presence of WVD symptoms (3,4). By 2006, other watermelon fields were also affected. Field trials in 2007 and 2008 with insect-proof cages and insecticides suggested a role of whiteflies (Bemisia tabaci) in the transmission of a virus (3,4). Here, we report that watermelon and pumpkin plants were successfully infected in Puerto Rico by mechanical inoculation and through B. tabaci transmission assays, similarly to transmissions previously conducted in Florida with Squash vein yellowing virus (SqVYV) (1). In addition, plants of Cucurbita moschata exhibited vein clearing symptoms typical of SqVYV after mechanical inoculation with extracts from watermelon plants with WVD symptoms. In 2011, eight watermelon samples from plants exhibiting WVD syndrome were collected in Guánica, Santa Isabel, Juana Díaz, and Mayagüez, and two Momordica charantia samples were collected from Mayagüez. RNA was extracted from all 10 original samples, as well as from plants that were used in mechanical and vector transmission assays, using RNeasy Plant Mini Kit (Qiagen, Valencia, California), and all samples were found positive for SqVYV by reverse transcription-PCR, using previously described primers and methods (1,2). In all cases, a single ~1-kb PCR fragment was revealed, and PCR fragments from four samples were selected for direct sequencing. All sequences showed high levels (>99%) of nucleotide identity with SqVYV sequences from Florida (JF897989, JF897985, and JF897984). Sequences of the SqVYV CP gene from Puerto Rico were deposited in GenBank under accession numbers KC713961 to KC713964. To our knowledge, this is the first report of SqVYV in Puerto Rico associated with WVD syndrome in cucurbits, and thus has implications for management of viral diseases of watermelon in the Caribbean. This is also the first detection of SqVYV outside of the continental United States in both watermelon and a wild species, M. charantia (bitter gourd).

References: (1) S. Adkins et al. Phytopathology 97:145, 2007. (2) S. Adkins et al. Plant Dis. 92:1119, 2008. (3) C. Estévez de Jensen et al. Phytopathology 98:S52, 2008. (4) L. Polanco-Florián. El marchitamiento súbito de la sandía [Citrullus lanatus (Thumb.) Matsum & Nakai]. M.S. thesis, University of Puerto Rico, Mayagüez, PR, 2009.
Genetic Diversity and Potential Vectors and Reservoirs of Cucurbit aphid-borne yellows virus in Southeastern Spain
Authors: Kassem Mona A. , Juarez Miguel , Gómez Pedro , Mengual Carmen M. , Sempere Raquel N. , Plaza María , Elena Santiago F. , Moreno Aranzazu , Fereres Alberto , Aranda Miguel A.
Published: June 2013

The genetic variability of a Cucurbit aphid-borne yellows virus (CABYV) (genus Polerovirus, family Luteoviridae) population was evaluated by determining the nucleotide sequences of two genomic regions of CABYV isolates collected in open-field melon and squash crops during three consecutive years in Murcia (southeastern Spain). A phylogenetic analysis showed the existence of two major clades. The sequences did not cluster according to host, year, or locality of collection, and nucleotide similarities among isolates were 97 to 100 and 94 to 97% within and between clades, respectively. The ratio of nonsynonymous to synonymous nucleotide substitutions reflected that all open reading frames have been under purifying selection. Estimates of the population's genetic diversity were of the same magnitude as those previously reported for other plant virus populations sampled at larger spatial and temporal scales, suggesting either the presence of CABYV in the surveyed area long before it was first described, multiple introductions, or a particularly rapid diversification. We also determined the full-length sequences of three isolates, identifying the occurrence and location of recombination events along the CABYV genome. Furthermore, our field surveys indicated that Aphis gossypii was the major vector species of CABYV and the most abundant aphid species colonizing melon fields in the Murcia (Spain) region. Our surveys also suggested the importance of the weed species Ecballium elaterium as an alternative host and potential virus reservoir.
A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation
Authors: Aitken Stuart , Alexander Ross D. , Beggs Jean D.
Published: June 2013

The complexity of many RNA processing pathways is such that a conventional systems modelling approach is inadequate to represent all the molecular species involved. We demonstrate that rule-based modelling permits a detailed model of a complex RNA signalling pathway to be defined. Phosphorylation of the RNA polymerase II (RNAPII) C-terminal domain (CTD; a flexible tail-like extension of the largest subunit) couples pre-messenger RNA capping, splicing and 3′ end maturation to transcriptional elongation and termination, and plays a central role in integrating these processes. The phosphorylation states of the serine residues of many heptapeptide repeats of the CTD alter along the coding region of genes as a function of distance from the promoter. From a mechanistic perspective, both the changes in phosphorylation and the location at which they take place on the genes are a function of the time spent by RNAPII in elongation as this interval provides the opportunity for the kinases and phosphatases to interact with the CTD. On this basis, we synthesize the available data to create a kinetic model of the action of the known kinases and phosphatases to resolve the phosphorylation pathways and their kinetics.
Cranial sutures work collectively to distribute strain throughout the reptile skull
Authors: Curtis Neil , Jones M. E. H. , Evans S. E. , O'Higgins P. , Fagan M. J.
Published: June 2013

The skull is composed of many bones that come together at sutures. These sutures are important sites of growth, and as growth ceases some become fused while others remain patent. Their mechanical behaviour and how they interact with changing form and loadings to ensure balanced craniofacial development is still poorly understood. Early suture fusion often leads to disfiguring syndromes, thus is it imperative that we understand the function of sutures more clearly. By applying advanced engineering modelling techniques, we reveal for the first time that patent sutures generate a more widely distributed, high level of strain throughout the reptile skull. Without patent sutures, large regions of the skull are only subjected to infrequent low-level strains that could weaken the bone and result in abnormal development. Sutures are therefore not only sites of bone growth, but could also be essential for the modulation of strains necessary for normal growth and development in reptiles.
Bringing tropical forest biodiversity conservation into financial accounting calculation
Authors: Cuckston Thomas
Published: June 2013

Purpose

This paper seeks to examine how the biodiversity comprising a tropical forest ecosystem is being protected as a result of having its conservation brought into financial accounting calculations by constructing a greenhouse gas emissions offset product to sell on the voluntary over‐the‐counter carbon markets.

Design/methodology/approach

The research examines a single embedded case study of a biodiversity conservation project in Kenya. The resulting discussion builds upon the existing accounting and organisation studies literature regarding the construction of markets.

Findings

Whilst the case examined does successfully bring tropical forest biodiversity conservation into the financial accounting calculations of the sellers and buyers of the offset product, via processes of objectification and singularisation, there are considerable accounting obstacles to constructing a calculative mechanism capable of achieving this on a global scale to facilitate financing of the conservation of all the world's remaining tropical forest biodiversity.

Originality/value

The paper contributes to the debate on accounting for biodiversity by examining market construction as a theoretical framework for turning the loss/conservation of biodiversity from an externality into an entity that is taken into account in organisations' calculations of profit and loss.
Biodiversity reporting in Denmark
Authors: van Liempd Dennis , Busch Jacob
Published: June 2013

Purpose

This paper aims to suggest that companies have ethical reasons to report about biodiversity issues and to investigate whether companies act on these reasons by examining the extent of biodiversity reporting in Denmark.

Design/methodology/approach

For the first purpose, desk research was conducted using consequentialist ethics, while for the second purpose, data were gathered from the 2009‐2011 annual reports, CSR‐type reports and homepages of 24 Danish large‐cap companies.

Findings

Philosophically, it is shown that biodiversity preservation and reporting is an ethical issue, even on the assumption that biodiversity does not possess intrinsic value. Empirically, it is shown that Danish companies score poorly overall, both quantitatively and qualitatively, with regards to reporting on biodiversity.

Research limitations/implications

Even though the importance of biodiversity can be justified on different assumptions, biodiversity reporting is under‐researched offering potential for future research on a globally important issue.

Practical implications

Justifying the preservation of biodiversity from an instrumental viewpoint might convince accounting audiences that are sceptical of normative ethical argumentation based on intrinsic value. The relative lack of biodiversity reporting in Denmark shows the need for the State and accounting standard setters to address this issue together with business and other stakeholders.

Originality/value

Few studies theorize on why there is a need for environmental reporting. Those that do are based on non‐instrumental considerations. This paper gives philosophical arguments for biodiversity reporting normally outside the scope of accounting. It emphasizes how even those who deny that biodiversity has intrinsic value are morally obliged to account for biodiversity. The argument also provides novel reasons for why thinking about discount rates should be governed by pure preference considerations. Empirically, this is only the second paper examining biodiversity reporting and the first about the Danish context.
Exploring hegemonic change in China: a case of accounting evolution
Authors: Xu Lina , Cortese Corinne , Zhang Eagle
Published: June 2013

Purpose

This paper aims to provide an understanding of how accounting systems have changed across four distinct periods of hegemonic leadership in China.

Design/methodology/approach

Using Gramsci's concept of hegemony, periods of leadership and accounting change throughout Chinese history are examined, including the Confucian tradition, the rise of the socialist system followed by the Cultural Revolution in the Maoist era, and the move towards the socialist‐market system in the Dengist era.

Findings

This paper shows how political leaders in these different time periods effectively achieved leadership by destroying an existing hegemony, creating a new ideology, and implanting this into people's daily lives in order to successfully mobilise their ideological systems. Consistent with changes in leadership, Chinese accounting systems are shown to have responded to hegemonic shifts across these periods.

Originality/value

This paper contributes to understandings of Gramsci's concept of hegemony, explanations of, and motivations for, accounting change, and provides an insight into the evolution of accounting systems throughout time in the context of China.
Investigating the drivers that influence the adoption of differentiated food products
Authors: Loizou Efstratios , Michailidis Anastasios , Chatzitheodoridis Fotios
Published: June 2013

Purpose

Over the last years, food safety, health, environmental and societal issues are a few among many other reasons that force people to adopt new differentiated food products. This interesting shift of the consumption pattern from conventional food products to new differentiated products that incorporate innovative features, consist the main reasoning of the present study. The purpose of this paper is to investigate the drivers that influence the adoption of those differentiated food products and shed new light on consumer's behavior, by modeling and understanding better their attitude.

Design/methodology/approach

A two‐step cluster analysis was employed to explore the different levels of differentiated products adoption and a categorical regression model was estimated to explain this variation. Data were collected through a survey addressing 500 consumers, carried out in 2009 in a typical Greek urban area.

Findings

From the three different food product categories (organic, functional and genetically modified) four consumers' profiles were identified which were found to differ in terms of several socioeconomic characteristics. The increased level of disposable income, along with exposure to innovative food products, may well explain such a differential food product adoption.

Research limitations/implications

Due to the small sample, the indefinable number of food products adopters (population) and to specific characteristics of the study area consumers, the results might face generalisability deficiencies.

Practical implications

From a practical point of view, to identify the reasons driving consumers to adopt or not new differentiated products with novelties is important generally for society, policy makers, food‐producing companies and related economic sectors.

Originality/value

The contribution of this research is in having examined, the adoption drivers of differentiated food product categories, for which there has been longstanding interest. The food product categories are examined comparatively as a group (organic, functional and genetically modified) and not individually.
Strategic management for product development
Authors: Aho Anne‐Maria , Uden Lorna
Published: June 2013

Purpose

The purpose of this paper is to shed light on understanding how value creation can be improved by developing dynamic capabilities in product development, in the case of a software engineering process.

Design/methodology/approach

The methodology involves a single‐case, longitudinal empirical study by progression of cycles of action research and data collection during a seven‐year period (1 January 2004‐31 November 2010), comprising 55 corporate projects.

Findings

This study will provide significant new information about value creation in multi‐disciplined product development. The study integrates value considerations into the principles and practices of software engineering, implements the aspect of dynamic capabilities in a software engineering process in order to create and sustain competitive advantage. As a result of the study, a model of value creation for software engineering process is created and guidelines are established.

Research limitations/implications

The contextual features were strongly present during the research process, which means that the model created needs to be tested in other settings by other researchers.

Practical implications

The results of the study provide management with guidelines for developing and maintaining the importance of value creation in the software engineering process.

Originality/value

The paper presents a new model of value creation for the software engineering process in product development, through which competitive advantage is created and sustained.
Damned if you do, damned if you don't: Texas A&M University Libraries' collection assessment for off‐site storage
Authors: Tabacaru Simona , Pickett Carmelita
Published: June 2013

Purpose

The purpose of this paper is to discuss the Texas A&M University (TAMU) Libraries’ policies that effectively reduced the size of onsite print collections, with minimal impact on the library user community. The paper also aims to examine some of the challenges encountered during the underlying collection assessment process.

Design/methodology/approach

Investment in electronic resources, digital preservation initiatives and local print repositories are reasonable solutions for academic libraries that need to responsibly relocate legacy print collections from their open stacks.

Findings

Balancing trust issues with local needs and embracing the opportunities offered by digital archives and local print repositories are key elements for successfully implementing collection management decisions.

Originality/value

This article examines local best practices for downsizing local print collections and recommends strategies applicable to any large academic library for addressing collection assessment challenges.
Managing emotions while managing crises
Authors: Guy Mary E. , Newman Meredith A. , Emel Ganapati N.
Published: June 2013

Purpose

Using the July 2012 massacre at a midnight showing of a Batman movie as a case study, the paper aims to demonstrate how emotional labor is required of responders and spokespersons and then enumerates the human resource functions that can enhance emotion work skills.

Design/methodology/approach

Using the massacre as a case in point, the authors demonstrate how emergency responders are called upon to manage their own emotions as well as those of victims and other constituencies. The authors then discuss human resource functions that can legitimize, enhance, and develop emotion work skills.

Findings

This case demonstrates multiple facets of emotional labor in emergency response. Special attention is paid to the case of public information spokespersons because they are the bridge between the event, the response, and the image of competency that is created in the eyes of the public. Recommendations are enumerated for how the human resource function can facilitate emotion work skills.

Practical implications

This paper provides practical guidance in how human resource practices can be used to hire, train, and retain first responders who are skilled in performing the emotive aspects of response work.

Originality/value

Despite the emotional intensity that accompanies crises, rarely so explicitly discussed is how emotional labor is a required aspect of the work. Also less known is what measures can be implemented to develop emotion work skills.
Teamwork, organizational learning, patient safety and job outcomes
Authors: Goh Swee C. , Chan Christopher , Kuziemsky Craig
Published: June 2013

Purpose

This article aims to encourage healthcare administrators to consider the learning organization concept and foster collaborative learning among teams in their attempt to improve patient safety.

Design/methodology/approach

Relevant healthcare, organizational behavior and human resource management literature was reviewed.

Findings

A patient safety culture, fostered by healthcare leaders, should include an organizational culture that encourages collaborative learning, replaces the blame culture, prioritizes patient safety and rewards individuals who identify serious mistakes.

Practical implications

As healthcare institution staffs are being asked to deliver more complex medical services with fewer resources, there is a need to understand how hospital staff can learn from other organizational settings, especially the non‐healthcare sectors.

Originality/value

The paper provides suggestions for improving patient safety which are drawn from the health and business management literature.
Service quality in healthcare institutions: establishing the gaps for policy action
Authors: Abuosi Aaron A. , Atinga Roger A.
Published: June 2013

Purpose

The authors seek to examine two key issues: to assess patients' hospital service quality perceptions and expectation using SERVQUAL; and to outline the distinct concepts used to assess patient perceptions.

Design/methodology/approach

Questionnaires were administered to 250 patients on admission and follow‐up visits. The 22 paired SERVQUAL expectation and perception items were adopted. Repeated t‐measures and factor analysis with Varimax rotation were used to analyse data.

Findings

Results showed that patient expectations were not being met during medical treatment. Perceived service quality was rated lower than expectations for all variables. The mean difference between perceptions and expectations was statistically significant. Contrary to the SERVQUAL five‐factor model, four service‐quality factors were identified in the study.

Practical implications

Findings have practical implications for hospital managers who should consider stepping up staffing levels backed by client‐centred training programmes to help clinicians deliver care to patients' expectations.

Originality/value

Limited studies are tailored towards patients' service‐quality perception and expectation in Ghanaian hospitals. The findings therefore provide valuable information for policy and practice.