bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cluster of rotavirus enteritis in pediatric liver recipients
Authors: Cui H. , Bai S. , Huo Z. , Li J. , Sun J. , An X. 
Published: March 2015

AbstractWe observed a cluster of 4 pediatric liver recipients who developed diarrhea in a liver transplant unit within 5 days. Feces from these 4 patients were rotavirus positive when tested with Colloidal Gold Diagnostic Kit. Nucleic acid from 3 fecal specimens was extracted and reverse transcribed. Two were amplified positively. The complementary DNAs were sequenced. Alignment and phylogenetic analysis were performed with MEGA 6.06. Although involving only 4 pediatric liver recipients, this cluster was caused by at least 2 distinct G9P[8] rotavirus strains and included community infection and nosocomial infection.
Adaptive beamlet‐based finite‐size pencil beam dose calculation for independent verification of IMRT and VMAT
Authors: Park Justin C. , Li Jonathan G. , Arhjoul Lahcen , Yan Guanghua , Lu Bo , Fan Qiyong , Liu Chihray 
Published: March 2015

Purpose:The use of sophisticated dose calculation procedure in modern radiation therapy treatment planning is inevitable in order to account for complex treatment fields created by multileaf collimators (MLCs). As a consequence, independent volumetric dose verification is time consuming, which affects the efficiency of clinical workflow. In this study, the authors present an efficient adaptive beamlet‐based finite‐size pencil beam (AB‐FSPB) dose calculation algorithm that minimizes the computational procedure while preserving the accuracy.Methods:The computational time of finite‐size pencil beam (FSPB) algorithm is proportional to the number of infinitesimal and identical beamlets that constitute an arbitrary field shape. In AB‐FSPB, dose distribution from each beamlet is mathematically modeled such that the sizes of beamlets to represent an arbitrary field shape no longer need to be infinitesimal nor identical. As a result, it is possible to represent an arbitrary field shape with combinations of different sized and minimal number of beamlets. In addition, the authors included the model parameters to consider MLC for its rounded edge and transmission.Results:Root mean square error (RMSE) between treatment planning system and conventional FSPB on a 10 × 10 cm2 square field using 10 × 10, 2.5 × 2.5, and 0.5 × 0.5 cm2 beamlet sizes were 4.90%, 3.19%, and 2.87%, respectively, compared with RMSE of 1.10%, 1.11%, and 1.14% for AB‐FSPB. This finding holds true for a larger square field size of 25 × 25 cm2, where RMSE for 25 × 25, 2.5 × 2.5, and 0.5 × 0.5 cm2 beamlet sizes were 5.41%, 4.76%, and 3.54% in FSPB, respectively, compared with RMSE of 0.86%, 0.83%, and 0.88% for AB‐FSPB. It was found that AB‐FSPB could successfully account for the MLC transmissions without major discrepancy. The algorithm was also graphical processing unit (GPU) compatible to maximize its computational speed. For an intensity modulated radiation therapy (∼12 segments) and a volumetric modulated arc therapy fields (∼90 control points) with a 3D grid size of 2.0 × 2.0 × 2.0 mm3, dose was computed within 3–5 and 10–15 s timeframe, respectively.Conclusions:The authors have developed an efficient adaptive beamlet‐based pencil beam dose calculation algorithm. The fast computation nature along with GPU compatibility has shown better performance than conventional FSPB. This enables the implementation of AB‐FSPB in the clinical environment for independent volumetric dose verification.
Spectra of clinical CT scanners using a portable Compton spectrometer
Authors: Duisterwinkel H. A. , van Abbema J. K. , van Goethem M. J. , Kawachimaru R. , Paganini L. , van der Graaf E. R. , Brandenburg S. 
Published: March 2015

Purpose:Spectral information of the output of x‐ray tubes in (dual source) computer tomography (CT) scanners can be used to improve the conversion of CT numbers to proton stopping power and can be used to advantage in CT scanner quality assurance. The purpose of this study is to design, validate, and apply a compact portable Compton spectrometer that was constructed to accurately measure x‐ray spectra of CT scanners.Methods:In the design of the Compton spectrometer, the shielding materials were carefully chosen and positioned to reduce background by x‐ray fluorescence from the materials used. The spectrum of Compton scattered x‐rays alters from the original source spectrum due to various physical processes. Reconstruction of the original x‐ray spectrum from the Compton scattered spectrum is based on Monte Carlo simulations of the processes involved. This reconstruction is validated by comparing directly and indirectly measured spectra of a mobile x‐ray tube. The Compton spectrometer is assessed in a clinical setting by measuring x‐ray spectra at various tube voltages of three different medical CT scanner x‐ray tubes.Results:The directly and indirectly measured spectra are in good agreement (their ratio being 0.99) thereby validating the reconstruction method. The measured spectra of the medical CT scanners are consistent with theoretical spectra and spectra obtained from the x‐ray tube manufacturer.Conclusions:A Compton spectrometer has been successfully designed, constructed, validated, and applied in the measurement of x‐ray spectra of CT scanners. These measurements show that our compact Compton spectrometer can be rapidly set‐up using the alignment lasers of the CT scanner, thereby enabling its use in commissioning, troubleshooting, and, e.g., annual performance check‐ups of CT scanners.
The Intracellular Scots Pine Shoot Symbiont Methylobacterium extorquens DSM13060 Aggregates around the Host Nucleus and Encodes Eukaryote-Like Proteins
Authors: Koskimäki Janne J. , Pirttilä Anna Maria , Ihantola Emmi-Leena , Halonen Outi , Frank A. Carolin 
Published: March 2015

ABSTRACT

Endophytes are microbes that inhabit plant tissues without any apparent signs of infection, often fundamentally altering plant phenotypes. While endophytes are typically studied in plant roots, where they colonize the apoplast or dead cells,
Methylobacterium extorquens
strain DSM13060 is a facultatively intracellular symbiont of the meristematic cells of Scots pine (Pinus sylvestris L.) shoot tips. The bacterium promotes host growth and development without the production of known plant growth-stimulating factors. Our objective was to examine intracellular colonization by M. extorquens DSM13060 of Scots pine and sequence its genome to identify novel molecular mechanisms potentially involved in intracellular colonization and plant growth promotion. Reporter construct analysis of known growth promotion genes demonstrated that these were only weakly active inside the plant or not expressed at all. We found that bacterial cells accumulate near the nucleus in intact, living pine cells, pointing to host nuclear processes as the target of the symbiont's activity. Genome analysis identified a set of eukaryote-like functions that are common as effectors in intracellular bacterial pathogens, supporting the notion of intracellular bacterial activity. These include ankyrin repeats, transcription factors, and host-defense silencing functions and may be secreted by a recently imported type IV secretion system. Potential factors involved in host growth include three copies of phospholipase A2, an enzyme that is rare in bacteria but implicated in a range of plant cellular processes, and proteins putatively involved in gibberellin biosynthesis. Our results describe a novel endophytic niche and create a foundation for postgenomic studies of a symbiosis with potential applications in forestry and agriculture.

IMPORTANCE
All multicellular eukaryotes host communities of essential microbes, but most of these interactions are still poorly understood. In plants, bacterial endophytes are found inside all tissues. M. extorquens DSM13060 occupies an unusual niche inside cells of the dividing shoot tissues of a pine and stimulates seedling growth without producing cytokinin, auxin, or other plant hormones commonly synthesized by plant-associated bacteria. Here, we tracked the bacteria using a fluorescent tag and confocal laser scanning microscopy and found that they localize near the nucleus of the plant cell. This prompted us to sequence the genome and identify proteins that may affect host growth by targeting processes in the host cytoplasm and nucleus. We found many novel genes whose products may modulate plant processes from within the plant cell. Our results open up new avenues to better understand how bacteria assist in plant growth, with broad implications for plant science, forestry, and agriculture.
The Number of Alphaherpesvirus Particles Infecting Axons and the Axonal Protein Repertoire Determines the Outcome of Neuronal Infection
Authors: Koyuncu Orkide O. , Song Ren , Greco Todd M. , Cristea Ileana M. , Enquist Lynn W. 
Published: March 2015

ABSTRACT
Infection by alphaherpesviruses invariably results in invasion of the peripheral nervous system (PNS) and establishment of either a latent or productive infection. Infection begins with long-distance retrograde transport of viral capsids and tegument proteins in axons toward the neuronal nuclei. Initial steps of axonal entry, retrograde transport, and replication in neuronal nuclei are poorly understood. To better understand how the mode of infection in the PNS is determined, we utilized a compartmented neuron culturing system where distal axons of PNS neurons are physically separated from cell bodies. We infected isolated axons with fluorescent-protein-tagged pseudorabies virus (PRV) particles and monitored viral entry and transport in axons and replication in cell bodies during low and high multiplicities of infection (MOIs of 0.01 to 100). We found a threshold for efficient retrograde transport in axons between MOIs of 1 and 10 and a threshold for productive infection in the neuronal cell bodies between MOIs of 1 and 0.1. Below an MOI of 0.1, the viral genomes that moved to neuronal nuclei were silenced. These genomes can be reactivated after superinfection by a nonreplicating virus, but not by a replicating virus. We further showed that viral particles at high-MOI infections compete for axonal proteins and that this competition determines the number of viral particles reaching the nuclei. Using mass spectrometry, we identified axonal proteins that are differentially regulated by PRV infection. Our results demonstrate the impact of the multiplicity of infection and the axonal milieu on the establishment of neuronal infection initiated from axons.

IMPORTANCE
Alphaherpesvirus genomes may remain silent in peripheral nervous system (PNS) neurons for the lives of their hosts. These genomes occasionally reactivate to produce infectious virus that can reinfect peripheral tissues and spread to other hosts. Here, we use a neuronal culture system to investigate the outcome of axonal infection using different numbers of viral particles and coinfection assays. We found that the dynamics of viral entry, transport, and replication change dramatically depending on the number of virus particles that infect axons. We demonstrate that viral genomes are silenced when the infecting particle number is low and that these genomes can be reactivated by superinfection with UV-inactivated virus, but not with replicating virus. We further show that viral invasion rapidly changes the profiles of axonal proteins and that some of these axonal proteins are rate limiting for efficient infection. Our study provides new insights into the establishment of silent versus productive alphaherpesvirus infections in the PNS.
The Soil Microbiome Influences Grapevine-Associated Microbiota
Authors: Zarraonaindia Iratxe , Owens Sarah M. , Weisenhorn Pamela , West Kristin , Hampton-Marcell Jarrad , Lax Simon , Bokulich Nicholas A. , Mills David A. , Martin Gilles , Taghavi Safiyh , van der Lelie Daniel , Gilbert Jack A. 
Published: March 2015

ABSTRACT

Grapevine is a well-studied, economically relevant crop, whose associated bacteria could influence its organoleptic properties. In this study, the spatial and temporal dynamics of the bacterial communities associated with grapevine organs (leaves, flowers, grapes, and roots) and soils were characterized over two growing seasons to determine the influence of vine cultivar, edaphic parameters, vine developmental stage (dormancy, flowering, preharvest), and vineyard. Belowground bacterial communities differed significantly from those aboveground, and yet the communities associated with leaves, flowers, and grapes shared a greater proportion of taxa with soil communities than with each other, suggesting that soil may serve as a bacterial reservoir. A subset of soil microorganisms, including root colonizers significantly enriched in plant growth-promoting bacteria and related functional genes, were selected by the grapevine. In addition to plant selective pressure, the structure of soil and root microbiota was significantly influenced by soil pH and C:N ratio, and changes in leaf- and grape-associated microbiota were correlated with soil carbon and showed interannual variation even at small spatial scales. Diazotrophic bacteria, e.g.,
Rhizobiaceae
and Bradyrhizobium spp., were significantly more abundant in soil samples and root samples of specific vineyards. Vine-associated microbial assemblages were influenced by myriad factors that shape their composition and structure, but the majority of organ-associated taxa originated in the soil, and their distribution reflected the influence of highly localized biogeographic factors and vineyard management.

IMPORTANCE
Vine-associated bacterial communities may play specific roles in the productivity and disease resistance of their host plant. Also, the bacterial communities on grapes have the potential to influence the organoleptic properties of the wine, contributing to a regional terroir. Understanding that factors that influence these bacteria may provide insights into management practices to shape and craft individual wine properties. We show that soil serves as a key source of vine-associated bacteria and that edaphic factors and vineyard-specific properties can influence the native grapevine microbiome preharvest.
Web search activity data accurately predict population chronic disease risk in the USA
Authors: Nguyen Thin , Tran Truyen , Luo Wei , Gupta Sunil , Rana Santu , Phung Dinh , Nichols Melanie , Millar Lynne , Venkatesh Svetha , Allender Steve 
Published: March 2015

BackgroundThe WHO framework for non-communicable disease (NCD) describes risks and outcomes comprising the majority of the global burden of disease. These factors are complex and interact at biological, behavioural, environmental and policy levels presenting challenges for population monitoring and intervention evaluation. This paper explores the utility of machine learning methods applied to population-level web search activity behaviour as a proxy for chronic disease risk factors.MethodsWeb activity output for each element of the WHO's Causes of NCD framework was used as a basis for identifying relevant web search activity from 2004 to 2013 for the USA. Multiple linear regression models with regularisation were used to generate predictive algorithms, mapping web search activity to Centers for Disease Control and Prevention (CDC) measured risk factor/disease prevalence. Predictions for subsequent target years not included in the model derivation were tested against CDC data from population surveys using Pearson correlation and Spearman's r.ResultsFor 2011 and 2012, predicted prevalence was very strongly correlated with measured risk data ranging from fruits and vegetables consumed (r=0.81; 95% CI 0.68 to 0.89) to alcohol consumption (r=0.96; 95% CI 0.93 to 0.98). Mean difference between predicted and measured differences by State ranged from 0.03 to 2.16. Spearman's r for state-wise predicted versus measured prevalence varied from 0.82 to 0.93.ConclusionsThe high predictive validity of web search activity for NCD risk has potential to provide real-time information on population risk during policy implementation and other population-level NCD prevention efforts.
Stagnation of treatment times over a decade: results of a pooled analysis from the MERCI registry, MERCI, TREVO, and TREVO 2 trials
Authors: Gupta Rishi , Xiang Bin , Ge Sijian , Sun Chung-Huan J , Yoo Albert J , Mehta Brijesh P 
Published: March 2015

BackgroundThere has been a growing interest in improving systems of care for the endovascular treatment of acute ischemic stroke. We analyzed data from previous registries and studies to determine if there has been an improvement in times to reperfusion with increasing experience.MethodsWe analyzed the pooled data from the Multi Mechanical Embolus Removal in Cerebral Ischemia (MERCI), MERCI Registry and Thrombectomy Revascularization of Large Vessel Occlusions (TREVO), and TREVO 2 trials and assessed times from last known normal to puncture, from hospital arrival to puncture, and procedure duration by year to determine if there has been a reduction in times. Demographic, radiographic, and clinical information were also assessed in a multivariate regression analysis to determine the predictors of good outcomes defined as a modified Rankin Scale score of 0–2 at 3 months.Results1248 patients of mean age 68±14 years and median NIH Stroke Scale score 18 were analyzed from 2001 to 2011. Procedure times showed a significant improvement while last known normal to puncture times remained static. In multivariate logistic regression analysis, longer last known normal to puncture time and longer procedure duration were associated with a decreased chance of a good outcome (OR 0.84, 95% CI 0.76 to 0.92, p=0.0004 and OR 0.75, 95% CI 0.61 to 0.91, p=0.0040, respectively).ConclusionsDespite a reduction in procedure times, there has not been a corresponding improvement in overall last known normal to puncture times over a 10-year period. The current study shows that there are many opportunities to create more efficient endovascular stroke systems of care in trials.
Size Bounds for Factorised Representations of Query Results
Authors: Olteanu Dan , Závodný Jakub 
Published: March 2015

We study two succinct representation systems for relational data based on relational algebra expressions with unions, Cartesian products, and singleton relations: f-representations, which employ algebraic factorisation using distributivity of product over union, and d-representations, which are f-representations where further succinctness is brought by explicit sharing of repeated subexpressions.
In particular we study such representations for results of conjunctive queries. We derive tight asymptotic bounds for representation sizes and present algorithms to compute representations within these bounds. We compare the succinctness of f-representations and d-representations for results of equi-join queries, and relate them to fractional edge covers and fractional hypertree decompositions of the query hypergraph.
Recent work showed that f-representations can significantly boost the performance of query evaluation in centralised and distributed settings and of machine learning tasks.
Bioinspired Fingertip for Anthropomorphic Robotic Hands
Authors: Controzzi Marco , D'Alonzo Marco , Peccia Carlo , Oddo Calogero Maria , Carrozza Maria Chiara , Cipriani Christian 
Published: March 2015

Background: An artificial fingertip with mechanical features and appearance similar to the human fingertip could represent a significant step forward towards the development of the next generation artificial hands. However, so far, a fingertip showing a good trade-off among mechanical features, appearance and anthropomorphism, along with its 3D computational model, is still missing.Objective: To explore and develop an artificial fingertip demonstrating a mechanical response similar to the human fingertip, in order to improve the grasp stability of robotic hands.Methods: Taking inspiration from the multi-layered structure of the human finger, novel artificial fingertips, composed of a rigid core and covered by layers of polymeric materials with different degrees of stiffness and topped by a hard nail were developed. An accurate 3D finite element (FE) model was also developed in order to simulate and evaluate the internal mechanical behavior of the prototypes under external indentations. The mechanical response of the prototypes was assessed and compared with that of the human fingertip and the FE model results, under different experimental conditions. Finally, the artificial fingertips were integrated into an anthropomorphic robotic hand and evaluated in grip tests, in order to compare the grasp stability with respect to conventional stiff (metal) fingertips.Results: The developed prototypes demonstrated a response to compression tests similar to the human finger and the FE model showed a discrete accuracy (mean error 7%). Finally, an increased ability (by 96%) in stably holding objects during precision grips with respect to conventional stiff fingers was demonstrated.Conclusion: Multi-layered biomimetic fingertips can improve grasp stability and cosmetic appearance of anthropomorphic robot hands.
Possible Usage of Cannulated Pedicle Screws without Cement Augmentation
Authors: Demir Teyfik 
Published: March 2015

Background: The use of pedicle screws is becoming increasingly popular for spinal surgery practice as the technology advances. Screw pullout due to bone quality and loading conditions is one of the most common problems observed after pedicle screw fixation. Several solutions were studied to prevent screw pullout. These can be investigated under three main categories: screw design, expandable screws and cement augmentation.Objective: This study aimed to investigate the pullout performance of cannulated screws without cement augmentation on synthetic foams.Methods: Artificial fusion process for PU is described and validated in our previous studies. For this study six newly designed cannulated pedicle screws were artificially fused to PU foam and pullout test were conducted according to ASTM F543 standard testing protocols.Results: According to the results of post-fusion pullout tests, worst performed cannulated screw design was S3H on healthy bone simulating PU foam. However, pullout strength of unilaterally three holes including (S3H) design was purchased with two times higher loads when compared to control group. Solid cored screws were purchased with 671 N where this value was 1450 N for S3H design.Conclusions: This study provided that using cannulated pedicle screws without cement augmentation for the cases with healthy bone can be a reliable alternative to classical screws. To the knowledge of the authors this is the first post-fusion study investigating cannulated pedicle screws without cement augmentation.