bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential variant calling in mutants from diverse genetic backgrounds: A case study in the nematodePristionchus pacificus
Authors: Rödelsperger Christian , Moreno Eduardo
Published: May 2017

Genome sequencing of mutants is one of the most widely used techniques to identify genes that control traits of interest including human diseases. Traditionally, variants are called against reference genomes and various filtering techniques are applied to reduce the number of candidate mutations. However, if the genetic background of the mutant is different from the reference genome, the number of background variants may exceed the number of true mutations by several orders of magnitude resulting in candidate lists that cannot be effectively reduced.

We introduce the problem of differential variant calling in mutants from diverse genetic backgrounds. In the example of a mutant strain of the nematodePristionchus pacificus, where the genetic background is not identical to the reference genome (≈1% genome-wide divergence), we show that simple intersection filtering does not effectively reduce the list of candidate mutations due to the combined effect of high number of background mutations, missing coverage in the wildtype sample, and problematic regions in the genome assembly. Although restriction to sites with coverage in mutant and wildtype sample greatly reduced the number of candidate sites, we further improved this candidate set by implementing a customized variant calling procedure. This takes the mutant sample and the control sample of same genetic background as input and calls variants exhibiting strong discriminative signals across the two samples. Intersecting the candidate mutations with an interval identfied from mapping by RAD-seq revealed a likely splice-site mutation in theP. pacificusdpy-1 gene, which has been previously shown to cause the associated morphological phenotype.

Our study shows that combined analysis of mutant and wildtype samples drastically increases the potential to find true mutations. We hope that these results may be helpful for other model systems, where the identification of candidate mutants is complicated by assembly errors, lab-derived mutations, or different genetic backgrounds.
A mechanism for prime-realignment during influenza A virus replication
Authors: Oymans Judith , te Velthuis Aartjan J.W.
Published: May 2017

The influenza A virus genome consists of eight segments of single-stranded RNA. These segments are replicated and transcribed by a viral RNA-dependent RNA polymerase (RdRp) that is made up of the influenza virus proteins PB1, PB2 and PA. To copy the viral RNA (vRNA) genome segments and the complementary RNA (cRNA) segments, the replicative intermediate of viral replication, the RdRp must use two promoters and two differentde novoinitiation mechanisms. On the vRNA promoter, the RdRp initiates on the 3’ terminus, while on the cRNA promoter the RdRp initiates internally and subsequently realigns the nascent vRNA product to ensure that the template is copied in full. In particular the latter process, which is also used by other RNA viruses, is not understood. Here we provide mechanistic insight into prime-realignment during influenza virus replication and show that it is controlled by the priming loop and a helix-loop-helix motif of the PB1 subunit of the RdRp. Overall, these observations advance our understanding of how the influenza A virus initiates viral replication and amplifies the genome correctly.

Importance

Influenza A viruses cause severe disease in humans and are considered a major threat to our economy and health. The viruses replicate and transcribe their genome using an enzyme called the RNA polymerases. To ensure that the genome is amplified faithfully and abundant viral mRNAs are made for viral protein synthesis, the RNA polymerase must work correctly. In this report, we provide insight into the mechanism that the RNA polymerase employs to ensure that the viral genome is copied correctly.
A 340/380 nm light emitting diode illuminator for Fura-2 AM ratiometric Ca2+ imaging of live cells with better than 5 nM precision
Authors: Tinning Peter W. , Franssen Aimee J. P.M. , Hridi Shehla U. , Bushell Trevor J. , McConnell Gail
Published: May 2017

We report the first demonstration of a fast wavelength-switchable 340/380 nm light emitting diode (LED) illuminator for Fura-2 ratiometric Ca2+ imaging of live cells. The LEDs closely match the excitation peaks of bound and free Fura-2 and enables the precise detection of cytosolic Ca2+ concentrations, which is only limited by the Ca2+ response of Fura-2. Using this illuminator, we have shown that Fura-2 acetoxymethyl ester (AM) concentrations as low as 250 nM can be used to detect induced Ca2+ events in tsA-201 cells and while utilizing the 150 μs switching speeds available, it was possible to image spontaneous Ca2+ transients in hippocampal neurons at a rate of 24.39 Hz that were blunted or absent at typical 0.5 Hz acquisition rates. Overall, the sensitivity and acquisition speeds available using this LED illuminator significantly improves the temporal resolution that can be obtained in comparison to current systems and supports optical imaging of fast Ca2+ events using Fura-2.
Aberrant Cortical Activity In Multiple GCaMP6-Expressing Transgenic Mouse Lines
Authors: Steinmetz Nicholas A. , Buetfering Christina , Lecoq Jerome , Lee Christian R. , Peters Andrew J. , Jacobs Elina A. K. , Coen Philip , Ollerenshaw Douglas R. , Valley Matthew T. , de Vries Saskia E. J. , Garrett Marina , Zhuang Jun , Groblewski Peter A. , Manavi Sahar , Miles Jesse , White Casey , Lee Eric , Griffin Fiona , Larkin Joshua D , Roll Kate , Cross Sissy , Nguyen Thuyanh V. , Larsen Rachael , Pendergraft Julie , Daigle Tanya , Tasic Bosiljka , Thompson Carol L. , Waters Jack , Olsen Shawn , Margolis David J. , Zeng Hongkui , Hausser Michael , Carandini Matteo , Harris Kenneth D.
Published: May 2017

Transgenic mouse lines are invaluable tools for neuroscience but as with any technique, care must be taken to ensure that the tool itself does not unduly affect the system under study. Here we report aberrant electrical activity, similar to interictal spikes, and accompanying fluorescence events in some genotypes of transgenic mice expressing GCaMP6 genetically-encoded calcium sensors. These epileptiform events have been observed particularly, but not exclusively, in mice with Emx1-Cre and Ai93 transgenes, across multiple laboratories. The events occur at >0.1 Hz, are very large in amplitude (>1.0 mV local field potentials, >10% df/f widefield imaging signals), and typically cover large regions of cortex. Many properties of neuronal responses and behavior seem normal despite these events, though rare subjects exhibit overt generalized seizures. The underlying mechanisms of this phenomenon remain unclear, but we speculate about possible causes on the basis of diverse observations. We encourage researchers to be aware of these activity patterns while interpreting neuronal recordings from affected mouse lines and when considering which lines to study.
A theory that predicts behaviors of disordered cytoskeletal networks
Authors: Belmonte Julio , Leptin Maria , François Nédélec
Published: May 2017

Morphogenesis in animal tissues is largely driven by tensions of actomyosin networks, generated by an active contractile process that can be reconstitutedin vitro. Although the network components and their properties are known, the requirements for contractility are still poorly understood. Here, we describe a theory that predicts whether an isotropic network will contract, expand, or conserve its dimensions. This analytical theory correctly predicts the behavior of simulated networks consisting of filaments with varying combinations of connectors, and reveals conditions under which networks of rigid filaments are either contractile or expansile. Our results suggest that pulsatility is an intrinsic behavior of contractile networks if the filaments are not stable but turn over. The theory offers a unifying framework to think about mechanisms of contractions or expansion. It provides a foundation for the study of a broad range of processes involving cytoskeletal networks, and a basis for designing synthetic networks.
Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char
Authors: Moore Jean-Sébastien , Harris Les N. , Luyer Jérémy Le , Sutherland Ben J. G. , Rougemont Quentin , Tallman Ross F. , Fisk Aaron T. , Bernatchez Louis
Published: May 2017

Migration is a ubiquitous life history trait with profound evolutionary and ecological consequences. Recent developments in telemetry and genomics, when combined, can bring significant insights on the migratory ecology of non-model organisms in the wild. Here, we used this integrative approach to document dispersal, gene flow and potential for local adaptation in anadromous Arctic Char from six rivers in the Canadian Arctic. Acoustic telemetry data from 124 tracked individuals indicated asymmetric dispersal, with a large proportion of fish (72%) tagged in three different rivers migrating up the same short river in the fall. Population genomics data from 6,136 SNP markers revealed weak, albeit significant, population differentiation (average pairwiseFST= 0.011) and asymmetric dispersal was also revealed by population assignments. Approximate Bayesian Computation simulations suggested the presence of asymmetric gene flow, although in the opposite direction to that observed from the telemetry data, suggesting that dispersal does not necessarily lead to gene flow. These observations suggested that Arctic Char home to their natal river to spawn, but may overwinter in rivers with the shortest migratory route to minimize the costs of migration in non-breeding years. Genome scans and genetic-environment associations identified 90 outlier markers putatively under selection, 23 of which were in or near a gene. Of these, at least four were involved in muscle and cardiac function, consistent with the hypothesis that migratory harshness could drive local adaptation. Our study illustrates the power of integrating genomics and telemetry to study migrations in non-model organisms in logistically challenging environments such as the Arctic.
Predicting Protein Producibility in Filamentous Fungi
Authors: Dykstra Karmen L , Rousu Juho , Arvas Mikko
Published: May 2017

In this paper we study the problem of predicting the producibility of recombinant proteins in filamentous fungi, especially T. reesei, using machine learning methods. We train supervised and semi-supervised support vector machines with protein sequences, represented by their amino acid composition as well as protein family and domain information. Our results indicate, somewhat surprisingly, that quite modest amount of proteins with experimental data are required to build a state-of-the-art classifier and that additional unlabeled sequences in semi-supervised models do not bring increased predictive performance. Our experiments in cross-species prediction show that models trained for the filamentous fungus A. niger protein dataset can be generalized to predict protein producibility in T. reesei, and vice versa, without sacrificing too much accuracy, regardless of their approximately 500 millions years of divergence. However, predictors trained on E. coli and S. cerevisiae datasets gave variable performance when applied to the filamentous fungi datasets, indicating that while protein producibility prediction can be generalized accross related species, fully generic prediction tools applicable to any protein production host may not be realistic to achieve.
MetaMeta: Integrating metagenome analysis tools to improve taxonomic profiling
Authors: Piro Vitor C , Matschkowski Marcel , Renard Bernhard Y
Published: May 2017

Background

Many metagenome analysis tools are presently available to classify sequences and profile environmental samples. In particular, taxonomic profiling and binning methods are commonly used for such tasks. Tools available among these two categories make use of several techniques, e.g. read mapping, k-mer alignment, and composition analysis. Variations on the construction of the corresponding reference sequence databases are also common. In addition, different tools provide good results in different datasets and configurations. All this variation creates a complicated scenario to researchers to decide which methods to use. Installation, configuration and execution can also be difficult especially when dealing with multiple datasets and tools.

Results

We propose MetaMeta: a pipeline to execute and integrate results from metagenome analysis tools. MetaMeta provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample. MetaMeta includes a database generation, pre-processing, execution, and integration steps, allowing easy execution and parallelization. The integration relies on the co-occurrence of organisms from different methods as the main feature to improve community profiling while accounting for differences in their databases.

Conclusions

In a controlled case with simulated and real data we show that the integrated profiles of MetaMeta overcome the best single profile. Using the same input data, it provides more sensitive and reliable results with the presence of each organism being supported by several methods. MetaMeta uses Snakemake and has six pre-configured tools, all available at BioConda channel for easy installation (conda install-c bioconda metameta). The MetaMeta pipeline is open-source and can be downloaded at:https://github.com/pirovc/metameta
Comparative genomics sheds light on niche differentiation and the evolutionary history of comammoxNitrospira
Authors: Palomo Alejandro , Pedersen Anders G , Jane Fowler S , Dechesne Arnaud , Sicheritz-Pontén Thomas , Smets Barth F
Published: May 2017

The description of comammoxNitrospiraspp., performing complete ammonium-to-nitrate oxidation, and their co-occurrence with canonical betaproteobacterial ammonium oxidizing bacteria (β-AOB) in the environment, call into question the metabolic potential of comammoxNitrospiraand the evolutionary history of their ammonium oxidation pathway. We report four new comammoxNitrospiragenomes, constituting two novel species, and the first comparative genomic analysis on comammoxNitrospira.

ComammoxNitrospirahas lost the potential to use external nitrite as energy and nitrogen source: compared to strictly nitrite oxidizingNitrospira; they lack genes for assimilative nitrite reduction and reverse electron transport from nitrite. By contrast, compared to otherNitrospira, their ammonium oxidizer physiology is exemplified by genes for ammonium and urea transporters and copper homeostasis and the lack of cyanate hydratase genes. Two comammox clades are different in their ammonium uptake systems. Contrary to β-AOB, comammoxNitrospiragenomes have single copies of the two central ammonium oxidation pathway genes, lack genes involved in nitric oxide reduction, and encode genes that would allow efficient growth at low oxygen concentrations. Hence, comammoxNitrospiraseems attuned to oligotrophy and hypoxia compared to β-AOB.

β-AOBs are the clear origin of the ammonium oxidation pathway in comammoxNitrospira: reconciliation analysis indicates two separate earlyamoAgene transfer events from β-AOB to an ancestor of comammoxNitrospira, followed by clade specific losses. ForhaoA, one early transfer from β-AOB to comammoxNitrospirais predicted – followed by intra-clade transfers. We postulate that the absence of comammox genes in mostNitrospiragenomes is the result of subsequent loss.

Significance

The recent discovery of comammox bacteria - members of theNitrospiragenus able to fully oxidize ammonia to nitrate - upset the long-held conviction that nitrification is a two-step process. It also opened key questions on the ecological and evolutionary relations of these bacteria with other nitrifying prokaryotes. Here, we report the first comparative genomic analysis of comammoxNitrospiraand related nitrifiers. Ammonium oxidation genes in comammoxNitrospirahad a surprisingly complex evolution, originating from ancient transfer from the phylogenetically distantly related ammonia-oxidizing betaproteobacteria, followed by within-lineage transfers and losses. The resulting comammox genomes are uniquely adapted to ammonia oxidation in nutrient-limited and low-oxygen environments and appear to have lost the genetic potential to grow by nitrite oxidation alone.
DisruptingPitx1regulatory topology results in overtly normal limb development
Authors: Sarro Richard , Emera Deena , Uebbing Severin , Dutrow Emily V. , Weatherbee Scott D. , Nottoli Timothy , Noonan James P.
Published: May 2017

Gene expression patterns during development are orchestrated in part by thousands of distant-acting transcriptional enhancers. However, identifying enhancers that are essential for expression of their target genes has proven challenging. Genetic perturbation of individual enhancers in some cases results in profound molecular and developmental phenotypes, but in mild or no phenotypes in others. Topological maps of long-range regulatory interactions may provide the means to identify enhancers critical for developmental gene expression. Here, we leveraged chromatin topology to characterize and disrupt the major promoter-enhancer interaction forPitx1, which is essential for hindlimb development. We found thatPitx1primarily interacts with a single distal enhancer in the hindlimb. Using genome editing, we deleted this enhancer in the mouse. Although loss of the enhancer completely disrupts the predominant topological interaction in thePitx1locus,Pitx1expression in the hindlimb is only reduced by ~14%, with no apparent changes in spatial distribution or evidence of regulatory compensation.Pitx1enhancer null mice did not exhibit any of the characteristic morphological defects of thePitx1−/−mutant. Our results indicate thatPitx1expression is robust to the loss of its primary enhancer interaction, suggesting disruptions of regulatory topology at essential developmental genes may have mild phenotypic effects.
Role ofChymotrypsin-like Elastase 1in Lung Physiology and in α1-Antitrypsin Deficiency
Authors: Joshi Rashika , Heinz Andrea , Fan Qiang , Guo Shuling , Monia Brett , Schmelzer Christian E.H. , Weiss Anthony S. , Batie Matthew , Parameswaran Harikrishnan , Varisco Brian M.
Published: May 2017

α1-antitrypsin related lung disease (AAT-RLD) is the fourth leading indication for lung transplantation and is characterized by protease-mediated progressive emphysema that manifests in the 4thor 5thdecade of life.Chymotrypsin-like elastase 1(Cela1) is a digestive enzyme that binds to elastin in a stretch-dependent manner and is covalently neutralized by AAT. We hypothesized a role forCela1in AAT-RLD.Cela1-/-mice where phenotypically similar to wild type but had higher lung elastance and lacked stretch-inducible elastase activity. Wild-type mice administered anti-AAT oligo had reduced amounts of lung Cela1-AAT fusion protein in lung homogenate and spontaneously developed emphysema after 6 weeks.Cela1-/-mice administered anti-AAT oligo were completely protected from these emphysematous changes. Cela1 recombinant protein did not require propeptide cleavage for elastolysis, and its elastolytic profile was similar to that of other pancreatic elastases. Phylogenetic analysis of vertebrateCelapromoter and protein sequences showed that placental mammalCela1was distinct from otherCela’s, and that the placental mammal theCela1gene was invariantly conserved despite variable loss of otherCelagenes in non-carnivores. These data demonstrate that the pancreatic enzymeCela1has been evolutionarily co-opted for a role in reducing lung elastance in the placental mammal lineage and that its stretch-regulated expression and elastolytic activity is responsible for emphysema in the absence of its anti-protease: AAT.
Systematic effects of mRNA secondary structure on gene expression and molecular function in budding yeast
Authors: Wang Xia , Li Pidong , Gutenkunst Ryan N.
Published: May 2017

Dynamic control of gene expression is crucial for cellular adaptation to environmental challenges. mRNA secondary structure is known to be associated with mRNA and protein abundance, but little is known about how mRNA secondary structure affects gene expression dynamics. We report a genome-wide computational analysis of mRNA secondary structure, codon usage, and gene expression in budding yeast. We show that mRNA secondary structure combined with codon optimality regulates gene expression in multiple ways, from transcription to mRNA stability to translation. Moreover, we find that the effect of mRNA secondary structure on mRNA abundance is primarily mediated by transcription, not mRNA stability. Notably, genes with low mRNA secondary structure were substantially enriched for functions relevant to stress response, acting in the mitochondrion, endoplasmic reticulum, and ribosome. On the other hand, genes with high mRNA secondary structure were enriched for functions relevant to cellular maintenance, including macromolecular metabolism and biosynthesis. Our results suggest that mRNA secondary structure affects gene expression through coordination of multiple stages in protein biogenesis, with important consequences for stress response. The coupling of transcription to mRNA stability to translation makes concerted changes in mRNA and protein abundance possible and may amplify the effect of regulation to make quick responses to environmental variations.
A thermostable Cas9 with increased lifetime in human plasma
Authors: Harrington Lucas B. , Paez-Espino David , Chen Janice S. , Ma Enbo , Staahl Brett T. , Kyrpides Nikos C. , Doudna Jennifer
Published: May 2017

CRISPR-Cas9 is a powerful technology that has enabled genome editing in a wide range of species. However, the currently developed Cas9 homologs all originate from mesophilic bacteria, making them susceptible to proteolytic degradation and unsuitable for applications requiring function at elevated temperatures. Here, we show that the Cas9 protein from the thermophilic bacteriumGeobacillus stearothermophilus(GeoCas9) catalyzes RNA-guided DNA cleavage over a wide temperature range and has an enhanced protein lifetime in human plasma. GeoCas9 is active at temperatures up to 70°C, compared to 45°C forStreptococcus pyogenesCas9 (SpyCas9), which greatly expands the temperature range for CRISPR-Cas9 applications. By comparing features of two closely relatedGeobacillushomologs, we created a variant of GeoCas9 that doubles the DNA target sequences that can be recognized by this system. We also found that GeoCas9 is an effective tool for editing mammalian genomes when delivered as a ribonucleoprotein (RNP) complex. Together with an increased lifetime in human plasma, the thermostable GeoCas9 provides the foundation for improved RNP deliveryin vivoand expands the temperature range of CRISPR-Cas9.
Evaluation of ddRADseq for reduced representation metagenome sequencing
Authors: Liu Michael , Worden Paul , Monahan Leigh G. , DeMaere Matthew Z. , Burke Catherine M. , Djordjevic Steven P. , Charles Ian G. , Darling Aaron E.
Published: May 2017

Background

‘Who is doing what’ is the ultimate open question in microbiome study. Shotgun metagenomics is often applied to gain knowledge of functional roles for bacteria in microbial communities, where the data can be used to predict protein encoding genes and enzymatic pathways present in the community, sometimes leading to testable hypotheses for microbial function. We describe a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling. This technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection.

Results

We assessed the performance of the metagenomic ddRADseq approach by applying the method to human stool samples and generating sequence data. We evaluate the extent to which ddRADseq data provides an unbiased reduced representation for microbiome profiling.

Conclusion

Although ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.
Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes
Authors: Gazzara Matthew R. , Mallory Michael J. , Roytenberg Renat , Lindberg John P. , Jha Anupama , Lynch Kristen W. , Barash Yoseph
Published: May 2017

Over 95% of human multi-exon genes undergo alternative splicing, a process important in normal development and often dysregulated in disease. We sought to analyze the global splicing regulatory network of CELF2 in human T cells, a well-studied splicing regulator critical to T cell development and function. By integrating high-throughput sequencing data for binding and splicing quantification with sequence features and probabilistic splicing code models, we find evidence of splicing antagonism between CELF2 and the RBFOX family of splicing factors. We validate this functional antagonism through knockdown and overexpression experiments in human cells and find CELF2 represses RBFOX2 mRNA and protein levels. Because both families of proteins have been implicated in the development and maintenance of neuronal, muscle, and heart tissues, we analyzed publicly available data in these systems. Our analysis suggests global, antagonistic coregulation of splicing by the CELF and RBFOX proteins in mouse muscle and heart in several physiologically relevant targets, including proteins involved in calcium signaling and members of the MEF2 family of transcription factors. Importantly, a number of these coregulated events are aberrantly spliced in mouse models and human patients with diseases that affect these tissues, including heart failure, diabetes, or myotonic dystrophy. Finally, analysis of exons regulated by ancient CELF family homologs in chicken, Drosophila, and Caenorhabditis elegans suggests this antagonism is conserved throughout evolution.
Alternative difference analysis scheme combining R-space EXAFS fit with global optimization XANES fit for X-ray transient absorption spectroscopy
Authors: Zhan Fei , Tao Ye , Zhao Haifeng
Published: May 2017

Time-resolved X-ray absorption spectroscopy (TR-XAS), based on the laser-pump/X-ray-probe method, is powerful in capturing the change of the geometrical and electronic structure of the absorbing atom upon excitation. TR-XAS data analysis is generally performed on the laser-on minus laser-off difference spectrum. Here, a new analysis scheme is presented for the TR-XAS difference fitting in both the extended X-ray absorption fine-structure (EXAFS) and the X-ray absorption near-edge structure (XANES) regions. R-space EXAFS difference fitting could quickly provide the main quantitative structure change of the first shell. The XANES fitting part introduces a global non-derivative optimization algorithm and optimizes the local structure change in a flexible way where both the core XAS calculation package and the search method in the fitting shell are changeable. The scheme was applied to the TR-XAS difference analysis of Fe(phen)3 spin crossover complex and yielded reliable distance change and excitation population.
Potential of propagation-based synchrotron X-ray phase-contrast computed tomography for cardiac tissue engineering
Authors: Izadifar Mohammad , Babyn Paul , Chapman Dean , Kelly Michael E. , Chen Xiongbiao
Published: May 2017

Hydrogel-based cardiac tissue engineering offers great promise for myocardial infarction repair. The ability to visualize engineered systems in vivo in animal models is desired to monitor the performance of cardiac constructs. However, due to the low density and weak X-ray attenuation of hydrogels, conventional radiography and micro-computed tomography are unable to visualize the hydrogel cardiac constructs upon their implantation, thus limiting their use in animal systems. This paper presents a study on the optimization of synchrotron X-ray propagation-based phase-contrast imaging computed tomography (PCI-CT) for three-dimensional (3D) visualization and assessment of the hydrogel cardiac patches. First, alginate hydrogel was 3D-printed into cardiac patches, with the pores filled by fibrin. The hydrogel patches were then surgically implanted on rat hearts. A week after surgery, the hearts including patches were excised and embedded in a soft-tissue-mimicking gel for imaging by using PCI-CT at an X-ray energy of 25 keV. During imaging, the sample-to-detector distances, CT-scan time and the region of interest (ROI) were varied and examined for their effects on both imaging quality and radiation dose. The results showed that phase-retrieved PCI-CT images provided edge-enhancement fringes at a sample-to-detector distance of 147 cm that enabled visualization of anatomical and microstructural features of the myocardium and the implanted patch in the tissue-mimicking gel. For visualization of these features, PCI-CT offered a significantly higher performance than the dual absorption-phase and clinical magnetic resonance (3 T) imaging techniques. Furthermore, by reducing the total CT-scan time and ROI, PCI-CT was examined for lowering the effective dose, meanwhile without much loss of imaging quality. In effect, the higher soft tissue contrast and low-dose potential of PCI-CT has been used along with an acceptable overall animal dose to achieve the high spatial resolution needed for cardiac implant visualization. As a result, PCI-CT at the identified imaging parameters offers great potential for 3D assessment of microstructural features of hydrogel cardiac patches.
Preclinical radiotherapy at the Australian Synchrotron's Imaging and Medical Beamline: instrumentation, dosimetry and a small-animal feasibility study
Authors: Livingstone Jayde , Adam Jean-François , Crosbie Jeffrey C. , Hall Chris J. , Lye Jessica E. , McKinlay Jonathan , Pelliccia Daniele , Pouzoulet Frédéric , Prezado Yolanda , Stevenson Andrew W. , Häusermann Daniel
Published: May 2017

Therapeutic applications of synchrotron X-rays such as microbeam (MRT) and minibeam (MBRT) radiation therapy promise significant advantages over conventional clinical techniques for some diseases if successfully transferred to clinical practice. Preclinical studies show clear evidence that a number of normal tissues in animal models display a tolerance to much higher doses from MRT compared with conventional radiotherapy. However, a wide spread in the parameters studied makes it difficult to make any conclusions about the associated tumour control or normal tissue complication probabilities. To facilitate more systematic and reproducible preclinical synchrotron radiotherapy studies, a dedicated preclinical station including small-animal irradiation stage was designed and installed at the Imaging and Medical Beamline (IMBL) at the Australian Synchrotron. The stage was characterized in terms of the accuracy and reliability of the vertical scanning speed, as this is the key variable in dose delivery. The measured speed was found to be within 1% of the nominal speed for the range of speeds measured by an interferometer. Furthermore, dose measurements confirm the expected relationship between speed and dose and show that the measured dose is independent of the scan direction. Important dosimetric parameters such as peak dose, valley dose, the collimator output factor and peak-to-valley dose ratio are presented for 5 mm × 5 mm, 10 mm × 10 mm and 20 mm × 20 mm field sizes. Finally, a feasibility study on three glioma-bearing rats was performed. MRT and MBRT doses were prescribed to achieve an average dose of 65 Gy in the target, and magnetic resonance imaging follow-up was performed at various time points after irradiation to follow the tumour volume. Although it is impossible to draw conclusions on the different treatments with such a small number of animals, the feasibility of end-to-end preclinical synchrotron radiotherapy studies using the IMBL preclinical stage is demonstrated.
How to requisitely holistically consider internal gaps of business ethic
Authors: Nedelko Zlatko , Mulej Matjaz , Potocan Vojko
Published: May 2017

Purpose

The aim of this paper is to report about a requisitely holistic examination of the business ethics, focused on internal gaps between company’s and employees’ ethics. Contribution considers reasons for emergence of business ethics’ internal gaps and their appearance forms.

Design/methodology/approach

The authors specify and test model drawing upon modified versions of the ethics and management theory. In all, 1,125 responses were analyzed from an on-going survey conducted biannually among employees in Slovenian companies in the past decade.

Findings

Results reveal that company’s real business ethics remained steady over the decade, while employees’ real business ethics have significantly improved. Significant differences exist between employees’ and company’s real business ethics and shape internal business ethics’ incompatibilities. Finally, results reveal a significant influence of employees’ real business ethics on company’s real business ethics.

Research limitations/implications

Research is limited to postulated hypotheses, qualitative consideration of internal gaps of business ethics and quantitative analysis of business ethics’ development in the considered Slovenian companies in the past 10 years.

Practical implications

The authors rethought the habit of separated consideration of managerial business ethics and employees’ ethics as well as the presumption about congruence between company’s and employees’ business ethics. The requisitely holistic understanding and consideration of internal gaps of business ethics is suggested.

Originality/value

Available literature does not provide a similar model for a requisitely holistic consideration of internal gaps of business ethics. The study confirms the proposed model of business ethics gaps.
Research on integrated product service system driven by customer value based on ontology technology
Authors: Zhu Haihua , Li Jing , Gao James , Lu Weihua
Published: May 2017

Purpose

With the customers’ increasing expectation on the product value, manufacturing enterprises around the world have made significant efforts to provide high value-added services in addition to their traditional product development and manufacturing business. For this reason, it is of great importance to research product service system. The purpose of this paper is to research on the key problem of integrated product service system (IPSS) design.

Design/methodology/approach

A value-oriented IPSS is developed, which is set up based on “requirements-functions-processes-structures” mapping model to give full consideration to customer value and service functions. An extended product-service blueprint, which stems from the service blueprint, is developed to describe product behaviors, service deliver processes, stakeholders’ activities and supporting activities. An ontology-based design support system is proposed to improve design efficiency and help designers making better-informed decisions. A computer-aided prototype system has been developed, and an initial attempt has been made to demonstrate the role of IPSS in the aerospace industry.

Findings

Many traditional design methods cannot effectively address the objects and processes integration problem of products and services. Moreover, both product and service should be considered in IPSS design, and both of them extremely depend on designers’ own experience and knowledge. Thus, a broader range of knowledge is required to understand product-service system (PSS) design.

Research limitations/implications

This research provides a solid foundation for PSS C and promotes an effective means for PSS design.

Originality/value

A customer value-oriented IPSS is presented. Customer requirements are considered during the design phase of PSS as well as both product and service knowledge.
Research on social e-commerce reputation formation and state-introduced model
Authors: Wei Chuang , Yu Zhao-Ji , Chen Xiao-Nan
Published: May 2017

Purpose

This paper aims to solve the problem of information overload and reduce search costs. It proposes a social e-commerce online reputation formation model and community state-introduced model. A system dynamics trend simulation has been run to capture the relationship among the sellers, buyers, social e-commerce platforms and external environment to obtain an online reputation.

Design/methodology/approach

Empirical research relating to social e-commerce reputation has been used to confirm the influencing factors in social e-commerce, and a conceptual framework is developed for social e-commerce reputation formation. Thereafter, a trend simulation is generated to classify the relationship among the factors based on system dynamics. Also, the improved algorithm for community detection and a state-introduced model based on a Markov network are proposed to achieve better network partition for better online reputation management.

Findings

The empirical model captures the interaction effect of social e-commerce reputation and the state-introduced model to guide community public opinion and improve the efficiency of social e-commerce reputation formation. This helps minimize searching cost thereby improving social e-commerce reputation construction and management.

Research limitations/implications

There is no appropriate online reputation system to be constructed to test the relationship proposed in the study for a field experiment. Also, deeper investigation for the nodes’ attributes in social networks should be made in future research. Besides, researchers are advised to explore measurement for the reputation of a given seller by using social media data as from Twitter or micro blogs.

Originality/value

Investigations that study online reputation in the social e-commerce are limited. The empirical research figured out the factors which can influence the formation of online reputation in social e-commerce. An SD model was proposed to explain the factors interaction and trend simulation was run. Also, a state-introduced model was proposed to highlight the effect of nodes’ attributes on communities’ detection to give a deeper investigation for the online reputation management.
Game-theoretic analysis of Stackelberg oligopoly with arbitrary rank reflexive behavior of agents
Authors: Geraskin Mikhail
Published: May 2017

Purpose

This paper aims to consider the problem of determining the equilibriums on oligopoly market in case of Stackelberg leader (leaders) and reflexive behavior of market agents.

Design/methodology/approach

This paper includes economic and mathematical modeling, optimization methods and game theory.

Findings

This paper explains models of reflexive games on oligopoly market, taking into account the diversity of agents’ reasoning about strategies of environing and equilibrium mechanisms for coincidence or opposition of agents’ reflexive reasoning on the same rank of reflection.

Research limitations/implications

This paper considers the oligopoly market with linear function of demand and costs of agents, the rational behavior of agents and the reflexive reasoning on the same rank of reflection. The set of agents’ reasoning about the environing strategies is considered as a set of market states for which the problem of agent’s optimal action choosing solves with the complete awareness.

Practical implications

Identification of reflexive behavior of environing allows agents to increase their market shares and profit.

Social implications

Oligopoly markets play a leading role in the world oil trade and reflexive behavior affects the market equilibrium.

Originality/value

In the paper, the mechanisms of equilibrium in reflexive games on the linear duopoly market for arbitrary rank reflection are developed.
Comprehension of handwriting development: Pen‐grip kinetics in handwriting tasks and its relation to fine motor skills among school‐age children
Authors: Lin Yu‐Chen , Chao Yen‐Li , Wu Shyi‐Kuen , Lin Ho‐Hsio , Hsu Chieh‐Hsiang , Hsu Hsiao‐Man , Kuo Li‐Chieh
Published: May 2017

Background/aim

Numerous tools have been developed to evaluate handwriting performances by analysing written products. However, few studies have directly investigated kinetic performances of digits when holding a pen. This study thus attempts to investigate pen‐grip kinetics during writing tasks of school‐age children and explore the relationship between the kinetic factors and fine motor skills.

Methods

This study recruited 181 children aged from 5 to 12 years old and investigated the effects of age on handwriting kinetics and the relationship between these and fine motor skills. The forces applied from the digits and pen‐tip were measured during writing tasks via a force acquisition pen, and the children's fine motor performances were also evaluated.

Results

The results indicate that peak force and average force might not be direct indicators of handwriting performance for normally developing children at this age. Younger children showed larger force variation and lower adjustment frequency during writing, which might indicate they had poorer force control than the older children. Force control when handling a pen is significantly correlated with fine motor performance, especially in relation to the manual dexterity.

Conclusions/significance of the study

A novel system is proposed for analysing school‐age children's force control while handwriting. We observed the development of force control in relation to pen grip among the children with different ages in this study. The findings suggested that manipulation skill may be crucial when children are establishing their handwriting capabilities.
The phenomenon of legislative advocacy among parents of children with disabilities
Authors: Burke Meghan M. , Sandman Linda , Perez Beatrize , O'Leary Meghann
Published: May 2017

Although parents of children with disabilities have forged systemic changes for individuals with disabilities, little is known about the phenomenon of legislative advocacy (LA) including methods and barriers. In this United States‐based study, 49 parents of individuals with disabilities participated in focus groups about LA reporting both positive and negative experiences with LA. One focus group was held in Spanish; notably, none of the Spanish‐speaking parents reported experiences with LA. When discussing methods of LA, parents reported a variety of strategies including: building relationships, educating legislators, collective advocacy, and encouraging fathers and other parents to meet with legislators. Parents also reported barriers to LA: lack of knowledge, disempowerment and feeling overwhelmed. Implications for research to better understand LA and policy are discussed.
The optimal allocation of decision and exit rights in organizations
Authors: Bester Helmut , Krähmer Daniel
Published: May 2017

We show that in a bilateral relation with conflicting preferences and transferable utility it is unambiguously optimal to assign the authority over project decisions to the privately informed rather than the uninformed party. This holds irrespective of the degree of conflict and the distribution of private information. Under the optimal contract, the uninformed party is protected by an exit option, which it will exert when the decision maker has not chosen the promised decision. Exit terminates the relation and diminishes the project surplus. We show that the first‐best efficient solution can be obtained by such a contract.
Relational contracting and endogenous formation of teamwork
Authors: Ishihara Akifumi
Published: May 2017

We study a relational contracting model with two agents where each agent faces multiple tasks: effort toward the agent's own project and helping effort toward another agent's project. We show that the optimal task structure is either specialization without help or teamwork with a substantial amount of help: teamwork with a small amount of help is never optimal. Specialization with high‐powered incentives can be implemented by relative performance evaluation. However, under teamwork, the evaluation scheme must be substantially different to overcome the multitasking problem. Consequently, a small amount of help is dominated by specialization with high powered incentives.
MicroRNA‐128 promotes apoptosis in lung cancer by directly targeting NIMA‐related kinase 2
Authors: Zhao Dejian , Han Wenzheng , Liu Xia , Cui Dawei , Chen Yu
Published: May 2017

Background

MicroRNA‐128 (miR‐128) serves as a regulator by inducing cancer cell apoptosis, differentiation, the epithelial‐to‐mesenchymal transition process, and tumor growth by mediating different targets. NIMA‐related kinase 2 (NEK2) is aberrantly expressed in lung cancer. The miR‐128/NEK2 pathway has been reported to predict prognosis in colorectal cancer; however, the determination of a relationship between miR‐128 and NEK2 in lung cancer has remained elusive. We explored the association between miR‐128 and NEK2 in lung cancer.

Methods

MiR‐128 and NEK2 expression were examined in 15 lung cancer tissues by real time‐PCR. Lung cancer SK‐MES‐1 cells were transfected with miR‐128 mimic, an inhibitor or a negative control. MiR‐128 and NEK2 expression levels were detected using quantitative real time‐PCR and Western blot. SK‐MES‐1 cell apoptosis was performed by flow cytometry.

Results

Compared to adjacent non‐tumor tissues, miR‐128 was downregulated and NEK2 was upregulated in 15 lung cancer tissues. Lung cancer SK‐MES‐1 cells transfected with miR‐128 mimic induced a higher apoptotic rate than those transfected with the negative control. Dual luciferase assay further confirmed that NEK2 was a direct target of miR‐128 in lung cancer, and transfection with miR‐128 mimic could decrease the NEK2 protein level while the miR‐128 inhibitor increased NEK2 expression. Finally, the apoptotic effect of lung cancer cells induced by miR‐128 mimic could be reversed by NEK2 overexpression.

Conclusions

NEK2 was regulated by miR‐128 in lung cancer and miR‐128 induced lung cancer cell apoptosis by mediating NEK2 expression.
Effects of Grapevine leafroll‐associated virus 3 on the physiology in asymptomatic plants of Vitis vinifera
Authors: Montero R. , El aou ouad H. , Pacifico D. , Marzachì C. , Castillo N. , García E. , Del Saz N.F. , Florez‐Sarasa I. , Flexas J. , Bota J.
Published: May 2017

Grapevine leafroll disease is one of the most important viral diseases of grapevine (Vitis vinifera) worldwide. Grapevine leafroll‐associated virus 3 (GLRaV‐3) is the most predominant virus species causing this disease. Therefore, it is important to identify GLRaV‐3 effects, especially in plants which do not systematically show visual symptoms. In this study, effects of GLRaV‐3 on grapevine physiology were evaluated in asymptomatic plants of Malvasía de Banyalbufar and Cabernet Sauvignon cvs. Absolute virus quantification was performed in order to determine the level of infection of the treatment. The net carbon dioxide (CO2) assimilation (AN) and electron transport rate (Jflux) were the main parameters affected by the virus. The AN reduction in infected plants was attributed to restrictions in CO2 diffusion caused by anatomical leaf changes and a reduction of Rubisco activity. Those effects were more evident in Malvasia de Banyalbufar plants. The reduction of AN leads to a decrease in the total oxygen uptake rate by the activity of the cytochrome oxidase pathway, producing slight differences in plant growth. Therefore, even though no symptoms were expressed in the plants, the effects of the virus compromised the plant vital processes, showing the importance of early detection of the virus in order to fight against the infection.