bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autoantibody Specificities and Type I Interferon Pathway Activation in Idiopathic Inflammatory Myopathies
Authors: Ekholm L. , Vosslamber S. , Tjärnlund A. , de Jong T. D. , Betteridge Z. , McHugh N. , Plestilova L. , Klein M. , Padyukov L. , Voskuyl A. E. , Bultink I. E. M. , Pegtel D. Michiel , Mavragani C. P. , Crow M. K. , Vencovsky J. , Lundberg I. E. , Verweij C. L. 
Published: May 2016

AbstractMyositis is a heterogeneous group of autoimmune diseases, with different pathogenic mechanisms contributing to the different subsets of disease. The aim of this study was to test whether the autoantibody profile in patients with myositis is associated with a type I interferon (IFN) signature, as in patients with systemic lupus erythematous (SLE). Patients with myositis were prospectively enrolled in the study and compared to healthy controls and to patients with SLE. Autoantibody status was analysed using an immunoassay system and immunoprecipitation. Type I IFN activity in whole blood was determined using direct gene expression analysis. Serum IFN‐inducing activity was tested using peripheral blood cells from healthy donors. Blocking experiments were performed by neutralizing anti‐IFNAR or anti‐IFN‐α antibodies. Patients were categorized into IFN high and IFN low based on an IFN score. Patients with autoantibodies against RNA‐binding proteins had a higher IFN score compared to patients without these antibodies, and the IFN score was related to autoantibody multispecificity. Patients with dermatomyositis (DM) and inclusion body myositis (IBM) had a higher IFN score compared to the other subgroups. Serum type I IFN bioactivity was blocked by neutralizing anti‐IFNAR or anti‐IFN‐α antibodies. To conclude, a high IFN score was not only associated with DM, as previously reported, and IBM, but also with autoantibody monospecificity against several RNA‐binding proteins and with autoantibody multispecificity. These studies identify IFN‐α in sera as a trigger for activation of the type I IFN pathway in peripheral blood and support IFN‐α as a possible target for therapy in these patients.
Outliers and Model Selection: Discussion of the Paper by Søren Johansen and Bent Nielsen
Authors: Doornik Jurgen A. , Hendry David F. 
Published: May 2016

AbstractIt is argued that model selection and robust estimation should be handled jointly. Impulse indicator saturation makes that possible, but leads to the situation where there are more variables than observations. This is illustrated by revisiting the analysis of Tobin's food data.
A Parallel Scheme for Large‐scale Polygon Rasterization on CUDA‐enabled GPUs
Authors: Zhou Chen , Chen Zhenjie , Pian Yuzhe , Xiao Ningchuan , Li Manchun 
Published: May 2016

AbstractThis research develops a parallel scheme to adopt multiple graphics processing units (GPUs) to accelerate large‐scale polygon rasterization. Three new parallel strategies are proposed. First, a decomposition strategy considering the calculation complexity of polygons and limited GPU memory is developed to achieve balanced workloads among multiple GPUs. Second, a parallel CPU/GPU scheduling strategy is proposed to conceal the data read/write times. The CPU is engaged with data reads/writes while the GPU rasterizes the polygons in parallel. This strategy can save considerable time spent in reading and writing, further improving the parallel efficiency. Third, a strategy for utilizing the GPU's internal memory and cache is proposed to reduce the time required to access the data. The parallel boundary algebra filling (BAF) algorithm is implemented using the programming models of compute unified device architecture (CUDA), message passing interface (MPI), and open multi‐processing (OpenMP). Experimental results confirm that the implemented parallel algorithm delivers apparent acceleration when a massive dataset is addressed (50.32 GB with approximately 1.3 × 108 polygons), reducing conversion time from 25.43 to 0.69 h, and obtaining a speedup ratio of 36.91. The proposed parallel strategies outperform the conventional method and can be effectively extended to a CPU‐based environment.
MRI texture features as biomarkers to predict MGMT methylation status in glioblastomas
Authors: Korfiatis Panagiotis , Kline Timothy L. , Coufalova Lucie , Lachance Daniel H. , Parney Ian F. , Carter Rickey E. , Buckner Jan C. , Erickson Bradley J. 
Published: May 2016

Purpose:Imaging biomarker research focuses on discovering relationships between radiological features and histological findings. In glioblastoma patients, methylation of the O6‐methylguanine methyltransferase (MGMT) gene promoter is positively correlated with an increased effectiveness of current standard of care. In this paper, the authors investigate texture features as potential imaging biomarkers for capturing the MGMT methylation status of glioblastoma multiforme (GBM) tumors when combined with supervised classification schemes.Methods:A retrospective study of 155 GBM patients with known MGMT methylation status was conducted. Co‐occurrence and run length texture features were calculated, and both support vector machines (SVMs) and random forest classifiers were used to predict MGMT methylation status.Results:The best classification system (an SVM‐based classifier) had a maximum area under the receiver‐operating characteristic (ROC) curve of 0.85 (95% CI: 0.78–0.91) using four texture features (correlation, energy, entropy, and local intensity) originating from the T2‐weighted images, yielding at the optimal threshold of the ROC curve, a sensitivity of 0.803 and a specificity of 0.813.Conclusions:Results show that supervised machine learning of MRI texture features can predict MGMT methylation status in preoperative GBM tumors, thus providing a new noninvasive imaging biomarker.
Dosimetric comparison of stopping power calibration with dual‐energy CT and single‐energy CT in proton therapy treatment planning
Authors: Zhu Jiahua , Penfold Scott N. 
Published: May 2016

Purpose:The accuracy of proton dose calculation is dependent on the ability to correctly characterize patient tissues with medical imaging. The most common method is to correlate computed tomography (CT) numbers obtained via single‐energy CT (SECT) with proton stopping power ratio (SPR). CT numbers, however, cannot discriminate between a change in mass density and change in chemical composition of patient tissues. This limitation can have consequences on SPR calibration accuracy. Dual‐energy CT (DECT) is receiving increasing interest as an alternative imaging modality for proton therapy treatment planning due to its ability to discriminate between changes in patient density and chemical composition. In the current work we use a phantom of known composition to demonstrate the dosimetric advantages of proton therapy treatment planning with DECT over SECT.Methods:A phantom of known composition was scanned with a clinical SECT radiotherapy CT‐simulator. The phantom was rescanned at a lower X‐ray tube potential to generate a complimentary DECT image set. A set of reference materials similar in composition to the phantom was used to perform a stoichiometric calibration of SECT CT number to proton SPRs. The same set of reference materials was used to perform a DECT stoichiometric calibration based on effective atomic number. The known composition of the phantom was used to assess the accuracy of SPR calibration with SECT and DECT. Intensity modulated proton therapy (IMPT) treatment plans were generated with the SECT and DECT image sets to assess the dosimetric effect of the imaging modality. Isodose difference maps and root mean square (RMS) error calculations were used to assess dose calculation accuracy.Results:SPR calculation accuracy was found to be superior, on average, with DECT relative to SECT. Maximum errors of 12.8% and 2.2% were found for SECT and DECT, respectively. Qualitative examination of dose difference maps clearly showed the dosimetric advantages of DECT imaging, compared to SECT imaging for IMPT dose calculation for the case investigated. Quantitatively, the maximum dose calculation error in the SECT plan was 7.8%, compared to a value of 1.4% in the DECT plan. When considering the high dose target region, the root mean square (RMS) error in dose calculation was 2.1% and 0.4% for SECT and DECT, respectively.Conclusions:DECT‐based proton treatment planning in a commercial treatment planning system was successfully demonstrated for the first time. DECT is an attractive imaging modality for proton therapy treatment planning owing to its ability to characterize density and chemical composition of patient tissues. SECT and DECT scans of a phantom of known composition have been used to demonstrate the dosimetric advantages obtainable in proton therapy treatment planning with DECT over the current approach based on SECT.
Grating‐based x‐ray differential phase contrast imaging with twin peaks in phase‐stepping curves—phase retrieval and dewrapping
Authors: Yang Yi , Xie Huiqiao , Cai Weixing , Mao Hui , Tang Xiangyang 
Published: May 2016

Purpose:X‐ray differential phase contrast CT implemented with Talbot interferometry employs phase‐stepping to extract information of x‐ray attenuation, phase shift, and small‐angle scattering. Since inaccuracy may exist in the absorption grating G2 due to an imperfect fabrication, the effective period of G2 can be as large as twice the nominal period, leading to a phenomenon of twin peaks that differ remarkably in their heights. In this work, the authors investigate how to retrieve and dewrap the phase signal from the phase‐stepping curve (PSC) with the feature of twin peaks for x‐ray phase contrast imaging.Methods:Based on the paraxial Fresnel–Kirchhoff theory, the analytical formulae to characterize the phenomenon of twin peaks in the PSC are derived. Then an approach to dewrap the retrieved phase signal by jointly using the phases of the first‐ and second‐order Fourier components is proposed. Through an experimental investigation using a prototype x‐ray phase contrast imaging system implemented with Talbot interferometry, the authors evaluate and verify the derived analytic formulae and the proposed approach for phase retrieval and dewrapping.Results:According to theoretical analysis, the twin‐peak phenomenon in PSC is a consequence of combined effects, including the inaccuracy in absorption grating G2, mismatch between phase grating and x‐ray source spectrum, and finite size of x‐ray tube's focal spot. The proposed approach is experimentally evaluated by scanning a phantom consisting of organic materials and a lab mouse. The preliminary data show that compared to scanning G2 over only one single nominal period and correcting the measured phase signal with an intuitive phase dewrapping method that is being used in the field, stepping G2 over twice its nominal period and dewrapping the measured phase signal with the proposed approach can significantly improve the quality of x‐ray differential phase contrast imaging in both radiograph and CT.Conclusions:Using the phase retrieval and dewrapping methods proposed to deal with the phenomenon of twin peaks in PSCs and phase wrapping, the performance of grating‐based x‐ray differential phase contrast radiography and CT can be significantly improved.
Physical Activity and Cognitive Trajectories in Schoolchildren
Authors: López-Vicente Mónica , Forns Joan , Esnaola Mikel , Suades-González Elisabet , Álvarez-Pedrerol Mar , Robinson Oliver , Júlvez Jordi , Garcia-Aymerich Judith , Sunyer Jordi 
Published: May 2016

Purpose:The evidence regarding the role of physical activity (PA) habits on cognitive development in children is still scarce. Our study aimed to assess the association between PA habits and cognitive growth patterns, including working memory (WM) and inattentiveness in a large sample of primary schoolchildren.Method:This study included 2,897 children between 7 and 10 years old. WM was measured using the n-back task (2- and 3-back) and inattentiveness was measured using the attentional network task (ANT) on four occasions during one year. Parents completed a questionnaire with data about the extracurricular exercise of their child, commuting to school and other sociodemographic information at the first visit.Results:Exercising twice per week or more was associated with better 2-back, 3-back and inattentiveness scores at baseline, as compared with the once per week or less category. Active commuting for more than 50 min was associated with better 3-back scores at baseline, as compared with passive commuting. No consistent associations were found between PA and cognitive growth.Conclusion:Overall, although children with high levels of PA performed better in cognitive tasks at baseline, PA levels had no clear effects on cognitive growth trajectories.
The CHANGE! Project: Changes in Body Composition and Cardiorespiratory Fitness in 10- to 11-Year-Old Children After Completing the CHANGE! Intervention
Authors: Dagger Rebecca M. , Davies Ian G. , Mackintosh Kelly A. , Stone Genevieve L. , George Keith P. , Fairclough Stuart J. , Boddy Lynne M. 
Published: May 2016

Purpose: To assess the effects of the Children’s Health, Activity and Nutrition: Get Educated! intervention on body size, body composition, and peak oxygen uptake in a subsample of 10- to 11-year-old children. Methods: Sixty children were recruited from 12 schools (N = 6 intervention) to take part in the CHANGE! subsample study. Baseline, postintervention, and follow-up measures were completed in October 2010, March–April 2011, and June–July 2011, respectively. Outcome measures were body mass index z score, waist circumference, body composition assessed using dual-energy X-ray absorptiometry (baseline and follow-up only), and peak oxygen uptake. Results: Significant differences in mean trunk fat mass (control = 4.72 kg, intervention = 3.11 kg, P = .041) and trunk fat % (control = 23.08%, intervention = 17.75%, P = .022) between groups were observed at follow-up. Significant differences in waist circumference change scores from baseline to follow-up were observed between groups (control = 1.3 cm, intervention = −0.2 cm, P = .023). Favorable changes in body composition were observed in the intervention group; however, none of these changes reached statistical significance. No significant differences in peak oxygen uptake were observed. Conclusions: The results of the present study suggest the multicomponent curriculum intervention had small to medium beneficial effects on body size and composition health outcomes.
Impact of a School-Based Intervention Protocol—ACORDA Project—On Adipokines in an Overweight and Obese Pediatric Population
Authors: Nascimento Henrique , Alves Ana Inês , Medeiros Ana Filipa , Coimbra Susana , Catarino Cristina , Bronze-da-Rocha Elsa , Costa Elísio , Rocha-Pereira Petronila , Silva Gustavo , Aires Luísa , Seabra André , Mota Jorge , Mansilha Helena Ferreira , Rêgo Carla , Santos-Silva Alice , Belo Luis 
Published: May 2016

Purpose:There are few reliable studies assessing the effect of physical exercise (PE) on adipokines levels at young ages. Our objective was to study the effects of regular PE on plasma adipokines in pediatric overweight and obesity.Method:117 overweight and obese children and adolescents (47% females; 10.2 years) participated in an 8-month longitudinal study divided in two groups: PE group (n = 80), engaged in an after-school PE program; control group (n = 37), with no PE program. Plasma lipids, C-reactive protein (CRP), adiponectin, resistin, leptin, IL-6, IL-1beta, TNF-alpha, insulin and glucose levels were determined.Results:contrarily to the control group, the PE group presented reductions in body mass index z-score (BMIzsc) and body fat percentage that were accompanied by an improvement in lipid profile and insulin resistance, a reduction in CRP and TNF-alpha and an increase in adiponectin levels. The reductions in BMIzsc were inversely correlated with changes in adiponectin (r=−0.329, p = .003) and positively correlated with changes in percentage body fat (r = .262, p = .032), triglycerides (r = .228, p = .042) and leptin (r = .285, p = .010).Conclusion:Moderate reductions in adiposity improve proinflammatory status in obese children and adolescents. A more substantial reduction in BMIzsc was associated with a greater increment in adiponectin and reduction in leptin.
Waist-to-Height Ratio, Aerobic Fitness, and Cardiometabolic Risk in Hispanic Children From Low-Income U.S. Schools
Authors: Burns Ryan D. , Brusseau Timothy A. , Fang Yi , Fu You , Hannon James C. 
Published: May 2016

Purpose:The purpose of this study was to examine the relationships among waist-to-height ratio (WHtR), aerobic fitness, and cardio-metabolic risk factors in Hispanic children from low-income U.S. schools.Method:Participants were 198 Hispanic children from low-income schools (Mean age = 10.3 ± 0.5 years; 119 girls, 79 boys). Waist circumference, height, and cardio-metabolic blood markers were collected in a fasted state. Estimated VO2 Peak scores were also collected. Multilevel generalized mixed effects models were employed to examine the independent effect of WHtR and aerobic fitness classification on a child meeting recommended levels for each cardio-metabolic blood marker.Results:A child having a WHtR < 0.5 related to meeting recommended levels for HDL cholesterol (OR = 3.25, p < .01), triglycerides (OR = 2.94, p < .01), glucose (OR = 3.42, p < .01), and related to a lower continuous Mean Arterial Pressure (MAP) score (β = −8.5 mmHg, p < .01). Aerobic fitness classification only independently related to meeting recommended levels for HDL cholesterol (OR = 2.94, p = .010).Conclusion:Having a WHtR < 0.5 independently associated with favorable cardio-metabolic blood markers and thus serves as an effective screening tool for cardio-metabolic risk in Hispanic children from low-income schools.
The Effect of Handcycle Ergometer Exercise on Glucose Tolerance in Ambulatory and Non-Ambulatory Adolescents
Authors: Short Kevin R. , Teague April M. , Klein Jake C. , Malm-Buatsi Elizabeth , Frimberger Dominic 
Published: May 2016

Purpose:Whole body or leg exercise before a meal can increase insulin sensitivity, but it is unclear whether the same can occur with upper body exercise since a smaller muscle mass is activated. We measured the impact of a single session of handcycle exercise on glucose tolerance and insulin sensitivity.Methods:Nonambulatory (Non-Amb) adolescents with spina bifida or cerebral palsy (4F/3M), or ambulatory peers (Control, 4F/7M) completed 2 glucose tolerance tests on separate days, preceded by either rest or a 35-min bout of moderate-to-vigorous intermittent handcycle exercise.Results:The Non-Amb group had higher body fat (mean ± SD: 38 ± 12%, Control: 24 ± 9, p = .041) but similar VO2peak (17.7 ± 6.1 ml/kg/min, Control: 21.1 ± 7.9). Fasting glucose and insulin were normal for all participants. Compared with the rest trial, exercise resulted in a reduction in glucose area under the curve (11%, p = .008) without a significant group x trial interaction and no difference in the magnitude of change between groups. Insulin sensitivity was increased 16% (p = .028) by exercise in the Control group but was not significantly changed in the Non-Amb group.Conclusion:A single bout of handcycle exercise improves glucose tolerance in adolescents with and without mobility limitations and could therefore help maintain or improve metabolic health.
Draft Genome Sequence of Bacillus megaterium BHG1.1, a Strain Isolated from Bar-Headed Goose (
Anser indicus
) Feces on the Qinghai-Tibet Plateau
Authors: Wang Wen , Zheng Si-Si , Sun Hao , Cao Jian , Yang Fang , Wang Xue-Lian , Li Lai-Xing 
Published: May 2016

ABSTRACT

Bacillus megaterium
is a soil-inhabiting Gram-positive bacterium that is routinely used in industrial applications for recombinant protein production and bioremediation. Studies involving
Bacillus megaterium
isolated from waterfowl are scarce. Here, we report a 6.26-Mbp draft genome sequence of
Bacillus megaterium
BHG1.1, which was isolated from feces of a bar-headed goose.
Complete Genome Sequence of a CTX-M-15-Producing Escherichia coli Strain from the
H
30Rx Subclone of Sequence Type 131 from a Patient with Recurrent Urinary Tract Infections, Closely Related to a Lethal Urosepsis Isolate from the Patient's Sister
Authors: Johnson Timothy J. , Aziz Maliha , Liu Cindy M. , Sokurenko Evgeni , Kisiela Dagmara I. , Paul Sandip , Andersen Paal , Johnson James R. , Price Lance B. 
Published: May 2016

ABSTRACT

We report here the complete genome sequence, including five plasmid sequences, of
Escherichia coli
sequence type 131 (ST131) strain JJ1887. The strain was isolated in 2007 in the United States from a patient with recurrent cystitis, whose caregiver sister died from urosepsis caused by a nearly identical strain.
Whole-Genome Sequence of Salmonella enterica Serovar Enteritidis Phage Type 4, Isolated from a Brazilian Poultry Farm
Authors: Milanez Guilherme Paier , Nascimento Leandro Costa , Tirabassi Adriane Holtz , Zuanaze Marcelo , Rodrigues Dália Prazeres , Pereira Gonçalo Amarante Guimarães , Brocchi Marcelo 
Published: May 2016

ABSTRACT

The draft genome of
Salmonella enterica
serovar Enteritidis phage type 4 (PT4) strain IOC4647/2004, isolated from a poultry farm in São Paulo state, was obtained with high-throughput Illumina sequencing platform, generating 4,173,826 paired-end reads with 251 bp. The assembly of 4,804,382 bp in 27 scaffolds shows strong similarity to other
S
. Enteritidis strains.
Complete Genome Sequence of
Algoriphagus
sp. Strain M8-2, Isolated from a Brackish Lake
Authors: Muraguchi Yusuke , Kushimoto Koya , Ohtsubo Yoshiyuki , Suzuki Tomohiro , Dohra Hideo , Kimbara Kazuhide , Shintani Masaki 
Published: May 2016

ABSTRACT

Algoriphagus
sp. strain M8-2 was isolated from a brackish lake, Lake Sanaru, in Hamamatsu, Japan, as a filterable bacterium through a 0.22-µm-pore-size membrane filter. We report here the complete nucleotide sequence of the M8-2 genome (a 3,882,610-bp chromosome).
Complete Genome Sequence of a Chicken Embryo Fibroblast-Adapted Attenuated Infectious Bursal Disease Virus Isolate from India
Authors: Senthilkumar T. M. A. , Priyadharsini C. V. , Raja P. , Kumanan K. 
Published: May 2016

ABSTRACT
Infectious bursal disease virus is an avian pathogen that causes huge morbidity and mortality in the poultry sector all over the world. Here, we report the full-length genome sequence of an Indian strain, MB11/ABT/MVC/2016, isolated from a commercial broiler flock. This is a first report of a complete genome sequence of infectious bursal disease virus from India.
Genome Sequencing of Foot-and-Mouth Disease Virus Type O Isolate GRE/23/94
Authors: King David J. , Knowles Nick J. , Freimanis Graham L. , King Donald P. 
Published: May 2016

ABSTRACT
The complete genome of a foot-and-mouth disease type O virus originating from an epidemic in Greece in 1994 is reported. This virus belongs to the Middle East-South Asia topotype.
Complete Genome Sequence of
Labrenzia
sp. Strain CP4, Isolated from a Self-Regenerating Biocathode Biofilm
Authors: Wang Zheng , Eddie Brian J. , Malanoski Anthony P. , Hervey W. Judson , Lin Baochuan , Strycharz-Glaven Sarah M. 
Published: May 2016

ABSTRACT

Here, we present the complete genome sequence of
Labrenzia
sp. strain CP4, isolated from an electricity-consuming marine biocathode biofilm.
Labrenzia
sp. strain CP4 consists of a circular 5.2 Mbp chromosome and an 88 Kbp plasmid.
Complete Mitochondrial Genome Sequence of the Pezizomycete
Pyronema confluens
Authors: Nowrousian Minou 
Published: May 2016

ABSTRACT

The complete mitochondrial genome of the ascomycete
Pyronema confluens
has been sequenced. The circular genome has a size of 191 kb and contains 48 protein-coding genes, 26 tRNA genes, and two rRNA genes. Of the protein-coding genes, 14 encode conserved mitochondrial proteins, and 31 encode predicted homing endonuclease genes.