bluuebunny/crossref_metadata_2025_split huggingface dataset:
Image Quality, Overall Evaluability, and Effective Radiation Dose of Coronary Computed Tomography Angiography With Prospective Electrocardiographic Triggering Plus Intracycle Motion Correction Algorithm in Patients With a Heart Rate Over 65 Beats Per Minute
Authors: Pontone Gianluca , Muscogiuri Giuseppe , Baggiano Andrea , Andreini Daniele , Guaricci Andrea I. , Guglielmo Marco , Fazzari Fabio , Mushtaq Saima , Conte Edoardo , Annoni Andrea , Formenti Alberto , Mancini Elisabetta , Verdecchia Massimo , Fusini Laura , Bonfanti Lorenzo , Consiglio Elisa , Rabbat Mark G. , Bartorelli Antonio L. , Pepi Mauro 
Published: January 2018

Purpose:
Recently, a new intracycle motion correction algorithm (MCA) was introduced to reduce motion artifacts from heart rate (HR) in coronary computed tomography angiography (cCTA). The aim of the study was to evaluate the image quality, overall evaluability, and effective radiation dose (ED) of cCTA with prospective electrocardiographic (ECG) triggering plus MCA as compared with standard protocol with retrospective ECG triggering in patients with HR≥65 bpm.

Materials and Methods:
One hundred consecutive patients (67±10 y) scheduled for cCTA with 65<HR<80 bpm were retrospectively analyzed. The patients were assigned to 2 groups undergoing prospective (group 1) or retrospective (group 2) triggered cCTA. The study protocol was approved by the Institutional Ethics Committee and a written informed consent was obtained from all patients. Image noise, signal to noise ratio, contrast to noise ratio, Likert image quality score (score 1, nondiagnostic; score 2, adequate; score 3, good; score 4, excellent), overall image evaluability, and ED were measured and compared between the 2 groups. Both vessel-based and patient-based analyses were evaluated. Student test or Wilcoxon test were used to evaluate differences of continuous variables, whereas the χ2 test was used to study differences with regard to categorical data. A P-value <0.05 was considered statistically significant.

Results:
cCTA was successfully performed in all patients. In a segment-based model, group 1 compared with group 2 showed a lower rate of overall artifacts (67% vs. 83%; P<0.001) and motion artifacts (49% vs. 66%; P<0.001), resulting in a better Likert image quality score (2.83±1.03 vs. 2.37±1.02; P<0.01) and overall evaluability (85% vs. 75%; P<0.01). Group 1 showed a lower ED as compared with group 2 (3.1±1.9 vs. 11.9±3.3 mSv; P<0.01).

Conclusion:
MCA and cCTA with prospective ECG-triggering acquisition in patients with high HR improves image quality and overall evaluability compared with cCTA with standard retrospective ECG triggering.
Why are there associations between telomere length and behaviour?
Authors: Bateson Melissa , Nettle Daniel 
Published: January 2018

Individual differences in telomere length are associated with individual differences in behaviour in humans and birds. Within the human epidemiological literature this association is assumed to result from specific behaviour patterns causing changes in telomere dynamics. We argue that selective adoption—the hypothesis that individuals with short telomeres are more likely to adopt specific behaviours—is an alternative worthy of consideration. Selective adoption could occur either because telomere length directly affects behaviour or because behaviour and telomere length are both affected by a third variable, such as exposure to early-life adversity. We present differential predictions of the causation and selective adoption hypotheses and describe how these could be tested with longitudinal data on telomere length. Crucially, if behaviour is causal then it should be associated with differential rates of telomere attrition. Using smoking behaviour as an example, we show that the evidence that smoking accelerates the rate of telomere attrition within individuals is currently weak. We conclude that the selective adoption hypothesis for the association between behaviour and telomere length is both mechanistically plausible and, if anything, more compatible with existing empirical evidence than the hypothesis that behaviour is causal.
This article is part of the theme issue ‘Understanding diversity in telomere dynamics’.
The paternal age at conception effect on offspring telomere length: mechanistic, comparative and adaptive perspectives
Authors: Eisenberg Dan T. A. , Kuzawa Christopher W. 
Published: January 2018

Telomeres are repeating DNA found at the ends of chromosomes that, in the absence of restorative processes, shorten with cell replications and are implicated as a cause of senescence. It appears that sperm telomere length (TL) increases with age in humans, and as a result offspring of older fathers inherit longer telomeres. We review possible mechanisms underlying this paternal age at conception (PAC) effect on TL, including sperm telomere extension due to telomerase activity, age-dependent changes in the spermatogonial stem cell population (possibly driven by ‘selfish’ spermatogonia) and non-causal confounding. In contrast to the lengthening of TL with PAC, higher maternal age at conception appears to predict shorter offspring TL in humans. We review evidence for heterogeneity across species in the PAC effect on TL, which could relate to differences in statistical power, sperm production rates or testicular telomerase activity. Finally, we review the hypothesis that the PAC effect on TL may allow a gradual multi-generational adaptive calibration of maintenance effort, and reproductive lifespan, to local demographic conditions: descendants of males who reproduced at a later age are likely to find themselves in an environment where increased maintenance effort, allowing later reproduction, represents a fitness improving resource allocation.
This article is part of the theme issue ‘Understanding diversity in telomere dynamics’.
Evolution of telomere maintenance and tumour suppressor mechanisms across mammals
Authors: Tian Xiao , Doerig Katherine , Park Rosa , Can Ran Qin Alice , Hwang Chaewon , Neary Alexander , Gilbert Michael , Seluanov Andrei , Gorbunova Vera 
Published: January 2018

Mammalian species differ dramatically in telomere biology. Species larger than 5–10 kg repress somatic telomerase activity and have shorter telomeres, leading to replicative senescence. It has been proposed that evolution of replicative senescence in large-bodied species is an anti-tumour mechanism counteracting increased risk of cancer due to increased cell numbers. By contrast, small-bodied species express high telomerase activity and have longer telomeres. To counteract cancer risk due to longer lifespan, long-lived small-bodied species evolved additional telomere-independent tumour suppressor mechanisms. Here, we tested the connection between telomere biology and tumorigenesis by analysing the propensity of fibroblasts from 18 rodent species to form tumours. We found a negative correlation between species lifespan and anchorage-independent growth. Small-bodied species required inactivation of Rb and/or p53 and expression of oncogenic H-Ras to form tumours. Large-bodied species displayed a continuum of phenotypes requiring additional genetic ‘hits’ for malignant transformation. Based on these data we refine the model of the evolution of tumour suppressor mechanisms and telomeres. We propose that two different strategies evolved in small and large species because small-bodied species cannot tolerate small tumours that form prior to activation of the telomere barrier, and must instead use telomere-independent strategies that act earlier, at the hyperplasia stage.
This article is part of the theme issue ‘Understanding diversity in telomere dynamics’.
Stability of association betweenArabidopsis thalianaandPseudomonaspathogens over evolutionary time scales
Authors: Karasov Talia L. , Almario Juliana , Friedemann Claudia , Ding Wei , Giolai Michael , Heavens Darren , Kersten Sonja , Lundberg Derek S. , Neumann Manuela , Regalado Julian , Neher Richard A. , Kemen Eric , Weigel Detlef 
Published: January 2018

SummaryCrop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild plant pathogens, we carried out a multi-year multi-site survey ofPseudomonasin the natural hostArabidopsis thaliana.The most commonPseudomonaslineage corresponded to a pathogenic clade present in all sites. Sequencing of 1,524Pseudomonasgenomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically distinct pathogenic sublineages. These sublineages have expanded in parallel within the same populations and are differentiated both at the level of gene content and disease phenotype. Such coexistence of diverse sublineages indicates that in contrast to crop systems, no single strain has been able to overtake theseA. thalianapopulations in the recent past. Our results suggest that the selective pressures acting on a plant pathogen in wild hosts may be more complex than those in agricultural systems.
Loop Assembly: a simple and open system for recursive fabrication of DNA circuits
Authors: Pollak Bernardo , Cerda Ariel , Delmans Mihails , Álamos Simón , Moyano Tomás , West Anthony , Gutiérrez Rodrigo A. , Patron Nicola , Federici Fernán , Haseloff Jim 
Published: January 2018

AbstractHigh efficiency methods for DNA assembly are based on sequence overlap between fragments or Type IIS restriction endonuclease cleavage and ligation. These have enabled routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customisation, elaborate vector sets and serial manipulations for the different stages of assembly. We present Loop assembly, based on a recursive approach to DNA fabrication. Alternate use of two Type IIS restriction endonucleases and corresponding vector sets allows efficient and parallel assembly of large DNA circuits. Plasmids containing standard Level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly provides a simple generalised solution for DNA construction with standardised parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.
Reproducible, flexible and high-throughput data extraction from primary literature: The metaDigitise R package
Authors: Pick Joel L. , Nakagawa Shinichi , Noble Daniel W.A. 
Published: January 2018

AbstractResearch synthesis, such as comparative and meta-analyses, requires the extraction of effect sizes from primary literature, which are commonly calculated from descriptive statistics. However, the exact values of such statistics are commonly hidden in figures.Extracting descriptive statistics from figures can be a slow process that is not easily reproducible. Additionally, current software lacks an ability to incorporate important meta-data (e.g., sample sizes, treatment / variable names) about experiments and is not integrated with other software to streamline analysis pipelines.Here we present the R package metaDigitise which extracts descriptive statistics such as means, standard deviations and correlations from four plot types: 1) mean/error plots (e.g. bar graphs with standard errors), 2) box plots, 3) scatter plots and 4) histograms. metaDigitise is user-friendly and easy to learn as it interactively guides the user through the data extraction process. Notably, it enables large-scale extraction by automatically loading image files, letting the user stop processing, edit and add to the resulting data-frame at any point.Digitised data can be easily re-plotted and checked, facilitating reproducible data extraction from plots with little inter-observer bias. We hope that by making the process of figure extraction more flexible and easy to conduct it will improve the transparency and quality of meta-analyses in the future.
HEx: a heterologous expression platform for the discovery of fungal natural products
Authors: Harvey Colin JB , Tang Mancheng , Schlecht Ulrich , Horecka Joe , Fischer Curt R , Lin Hsiao-ching , Li Jian , Naughton Brian , Cherry James , Miranda Molly , Fuga Li Yong , Chu Angela M , Hennessy James R , Vandova Gergana A , Inglis Diane , Aiyar Raeka , Steinmetz Lars M. , Davis Ronald W. , Medema Marnix H. , Sattely Elizabeth , Khosla Chaitan , St.Onge Robert P , Tang Yi , Hillenmeyer Maureen E. 
Published: January 2018

AbstractFor decades, fungi have been a source of FDA-approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molecules are difficult or impossible to access because the organisms are uncultivable or the genes are transcriptionally silent. To overcome this bottleneck in natural product discovery, we developed the HEx (Heterologous EXpression) synthetic biology platform for rapid, scalable expression of fungal biosynthetic genes and their encoded metabolites in Saccharomyces cerevisiae. We applied this platform to 41 fungal biosynthetic gene clusters from diverse fungal species from around the world, 22 of which produced detectable compounds. These included novel compounds with unexpected biosynthetic origins, particularly from poorly studied species. This result establishes the HEx platform for rapid discovery of natural products from any fungal species, even those that are uncultivable, and opens the door to discovery of the next generation of natural products.SummaryHere we present the largest scale effort reported to date toward the complete refactoring and heterologous expression of fungal biosynthetic gene clusters utilizing HEx, a novel synthetic biology platform.
Lempel-Ziv complexity of the EEG predicts long-term functional recovery after stroke in rats
Authors: Leemburg Susan , Bassetti Claudio L. 
Published: January 2018

AbstractNon-linear complexity of the EEG signal can be used to detect abnormal brain function relating to behavioral deficits. Here, we compare the effects of experimental stroke on EEG complexity using Lempel-Ziv complexity analysis (LZC) and multiscale entropy analysis (SampEn).EEG was recorded in bilateral motor cortex at baseline and during a 30-day recovery period after distal middle cerebral artery occlusion in rats. Motor function was assessed using a single pellet reaching task. Stroke caused an acute drop in both LZC and SampEn in the ipsilesional hemisphere in wakefulness, NREM and REM sleep, as well as reduced pellet reaching success. SampEn reductions persisted for at least 10 days post-stroke, whereas LZC had returned to baseline levels by day 4. EEG complexity in the contralesional hemisphere and in sham-operated animals were unaffected.If EEG complexity reflects post-stroke brain function, post-stroke asymmetry could be used to predict behavioral recovery. In rats, acute LZC asymmetry was significantly correlated with the amount of motor function recovery by post-stroke day 31, but SampEn asymmetry was not. EEG LZC may thus be a useful tool for predicting functional recovery after stroke. MSE could be effective in identifying cortical dysfunction, but does not reflect behavioral outcomes.
Improved cortical boundary registration for locally distorted fMRI scans
Authors: van Mourik Tim , Koopmans Peter J , Norris David G 
Published: January 2018

AbstractWith continuing advances in MRI techniques and the emergence of higher static field strengths, submillimetre spatial resolution is now possible in human functional imaging experiments. This has opened up the way for more specific types of analysis, for example investigation of the cortical layers of the brain. With this increased specificity, it is important to correct for the geometrical distortions that are inherent to echo planar imaging (EPI). Inconveniently, higher field strength also increases these distortions. The resulting displacements can easily amount to several millimetres and as such pose a serious problem for laminar analysis. We here present a method, Recursive Boundary Registration (RBR), that corrects distortions between an anatomical and an EPI volume. By recursively applying Boundary Based Registration (BBR) on progressively smaller subregions of the brain we generate an accurate whole-brain registration, based on the grey-white matter contrast. Explicit care is taken that the deformation does not break the topology of the cortical surface, which is an important requirement for several of the most common subsequent steps in laminar analysis. We show that RBR obtains submillimetre accuracy with respect to a manually distorted gold standard, and apply it to a set of human in vivo scans to show a clear increase in spacial specificity. RBR further automates the process of non-linear distortion correction. This is an important step towards routine human laminar fMRI. We provide the code for the RBR algorithm, as well as a variety of functions to better investigate registration performance in a public GitHub repository, https://github.com/TimVanMourik/OpenFmriAnalysis, under the GPL 3.0 license.
Chronic inflammation delays cell migration to villi in the intestinal epithelium
Authors: Muraro Daniele , Parker Aimee , Vaux Laura , Filippi Sarah , Fletcher Alexander G. , Watson Alastair J. , Pin Carmen , Maini Philip K. , Byrne Helen M. 
Published: January 2018

AbstractThe intestinal epithelium is a single layer of cells which provides the first line of defence of the intestinal mucosa to bacterial infection. Cohesion of this physical barrier is supported by renewal of epithelial stem cells, residing in invaginations called crypts, and by crypt cell migration onto protrusions called villi; dysregulation of such mechanism may render the gut susceptible to chronic inflammation. The impact that excessive or misplaced epithelial cell death may have on villus cell migration is currently unknown. We integrated cell-tracking methods with computational models to determine how epithelial homeostasis is affected by acute and chronic inflammatory cell death. Parameter inference reveals that acute inflammatory cell death has a transient effect on epithelial cell dynamics, whereas cell death caused by chronic inflammation causes a delay in the accumulation of labelled cells onto the villus compared to control. Such a delay may be reproduced by using a cell-based model to simulate the dynamics of each cell in a crypt-villus geometry, showing that a prolonged increase in cell death slows the migration of cells from the crypt to the villus. This investigation highlights which injuries (acute or chronic) may be regenerated and which cause disruption of healthy epithelial homeostasis.
Spindly is Required for Rapid Migration of Human Cells
Authors: Conte Claudia , Baird Michelle A. , Davidson Michael W. , Griffis Eric R. 
Published: January 2018

AbstractDynein is the sole minus-end directed microtubule motor found in animals. It has roles in cell division, membrane trafficking, and cell migration. Together with dynactin, dynein regulates centrosomal orientation to establish and maintain cell polarity, controls focal adhesion turnover and anchors microtubules at the leading edge. In higher eukaryotes, dynein/dynactin requires additional components such as Bicaudal D to form an active motor complex and for regulating its cellular localization. Spindly is a protein that targets dynein/dynactin to kinetochores in mitosis and can activate its motility in vitro. However, no role for Spindly in interphase dynein/dynactin function has been found. We show that Spindly binds to the cell cortex and microtubule tips and colocalizes with dynein/dynactin at the leading edge of migrating U2OS cells and primary fibroblasts. U2OS cells that lack Spindly migrated slower in 2D than control cells, although centrosome polarization appeared to happen properly in the absence of Spindly. Re-expression of Spindly rescues migration, but the expression of a mutant, which is defective for dynactin binding, failed to rescue this defect. Taken together, these data demonstrate that Spindly plays an important role in mediating a subset of dynein/dynactin’s function in cell migration.
A framework for business model with strategic innovation in ICT firms
Authors: Faghih Nezameddin , Dastourian Banafsheh , Sajadi Seyyed Mojtaba , Henten Andres , Foroudi Pantea 
Published: January 2018

Purpose
The purpose of this study is to help gain an accurate and distinct understanding of information-based business concepts and critical steps in designing an appropriate business model, by providing a framework for designing an innovative information-based business to help fledgling businesses development in the information and communication technology (ICT) industry of Iran. What is a business model framework with the strategic innovation approach in the small and medium enterprises (SMEs) of ICT industry? What are the components of this model and the relations between them? Business model is a logical response to how a business can create value. Changing business environment means that business models are rapidly growing; accordingly, innovation is no longer optional. However, innovation is important in general, but the kind of innovation that is widely and directly dependent on business model will be quite critical for all parts of the organization. In fact, business model innovation is an exquisite technic to create, deliver and earn value by changing one or more components of a typical business model. Business model innovation needs information and form business environment based on dynamic information system.

Design/methodology/approach
The present paper focuses upon SMEs in ICT. Grounded theory has been used for this purpose, with 15 interviews conducted.

Findings
An emerging market is one in which commercial exchanges of a particular industry between the countries are relatively new but possess great investment attractiveness and a high potential to grow (such as Iran).As the ICT industry of Iran is a leading industry, and the country itself is an emerging market, the main purpose of this study is to provide a framework for designing an innovative information-based business to help fledgling businesses development in the ICT industry of Iran.

Originality/value
The purpose of this paper is to help accurate and distinct understanding of the business model concept and critical steps in designing an appropriate business model. Studies conducted to simultaneously deal with the business model and strategic innovations are few, and by the time the proposal was written, there was no research observed from Persian sources.