bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dosage‐dependent effects of monensin on the rumen microbiota of lactating dairy cattle
Authors: McGarvey Jeffery A. , Place Sara , Palumbo Jeffrey , Hnasko Robert , Mitloehner Frank 
Published: December 2018

AbstractWe examined the dose‐dependent effects of feeding lactating dairy cows a standard diet supplemented with monensin at 175, 368, or 518 mg cow‐1 day‐1on the rumen microbiota. For each dosage, 3 animals were randomly assigned into groups and fed the same basal total mixed ration diet supplemented with monensin, at the respective dose. After 20 days, rumen samples were taken and the effect on the microbiota was examined by 16S rRNA gene sequence analysis and qPCR. At the lowest dose no significant change in 16S rRNA gene sequences associated with any bacterial phyla was observed; however, at the medium and high dosages, we observed significant reductions in sequences associated with gram‐positive bacteria and significant increases in those associated with gram‐negative bacteria that were dosage dependent. All dosages reduced the levels of sequences associated with methanogenic archaea in the rumen, with the medium dosage showing the largest decline. No significant difference was observed for the 18S rRNA gene sequences associated with protozoa in any of the libraries. Our results indicate that with this diet the medium dosage of monensin was most efficacious for the reduction in methanogenic archaea in the rumen of lactating dairy.
Insertional translocation involving an additional nonchromothriptic chromosome in constitutional chromothripsis: Rule or exception?
Authors: Kurtas Nehir Edibe , Xumerle Luciano , Giussani Ursula , Pansa Alessandra , Cardarelli Laura , Bertini Veronica , Valetto Angelo , Liehr Thomas , Clara Bonaglia Maria , Errichiello Edoardo , Delledonne Massimo , Zuffardi Orsetta 
Published: December 2018

AbstractBackgroundChromothripsis, which is the local massive shattering of one or more chromosomes and their reassembly in a disordered array with frequent loss of some fragments, has been mainly reported in association with abnormal phenotypes. We report three unrelated healthy persons, two of which parenting a child with some degree of intellectual disability, carrying a chromothripsis involving respectively one, two, and three chromosomes, which was detected only after whole‐genome sequencing. Unexpectedly, in all three cases a fragment from one of the chromothripsed chromosomes resulted to be inserted within a nonchromothripsed one.MethodsConventional cytogenetic techniques, paired‐end whole‐genome sequencing, polymerase chain reaction, and Sanger sequencing were used to characterize complex rearrangements, copy‐number variations, and breakpoint sequences in all three families.ResultsIn two families, one parent was carrier of a balanced chromothripsis causing in the index case a deletion and a noncontiguous duplication at 3q in case 1, and a t(6;14) translocation associated with interstitial 14q deletion in case 2. In the third family, an unbalanced chromothripsis involving chromosomes 6, 7, and 15 was inherited to the proband by the mosaic parent. In all three parents, the chromothripsis was concurrent with an insertional translocation of a portion of one of the chromothriptic chromosomes within a further chromosome that was not involved in the chromothripsis event.ConclusionOur findings show that (a) both simple and complex unbalanced rearrangements may result by the recombination of a cryptic parental balanced chromothripsis and that (b) insertional translocations are the spy of more complex rearrangements and not simply a three‐breakpoint event.
A high gain 60 GHz antipodal Fermi‐tapered slot antenna based on robust synthesized dielectric
Authors: Loo Xi Sung , Win Moe Z. , Yeo Kiat Seng 
Published: December 2018

AbstractA high performance antipodal Fermi taper slot antenna based on unique synthesized dielectric is presented for ultra‐wideband radar applications at 60 GHz band. Specifically, the synthesized dielectric is implemented based on machined holes concentrates only at aperture area to improve its mechanical robustness for lengthy antenna. Further, it is able to suppress back lobe level by 2.5 dB through curving tapered end of the antenna. Concurrently, sine corrugations and dielectric loading are adopted to improve radiation pattern and gain of the antenna for over 20 dB.
Is the dose‐averaged LET a reliable predictor for the relative biological effectiveness?
Authors: Grün Rebecca , Friedrich Thomas , Traneus Erik , Scholz Michael 
Published: December 2018

PurposeThe dose‐averaged linear energy transfer (LETD) is frequently used as representative quantity for the biological effectiveness of a radiation field. Moreover, relative biological effectiveness (RBE) values measured or calculated in mixed radiation fields are typically plotted vs the LETD. In this study, we will investigate whether the LETD is an appropriate quantity to describe the RBE of any mixed radiation field of protons and heavier ions and discuss potential limitations.MethodsTo study the reliability of LETD, we investigate model predictions of RBE in monoenergetic beams under track segment conditions and pristine Bragg peaks as well as spread out Bragg peaks (SOBP) in water. Both, the pristine Bragg peaks and the SOBPs are regarded as mixed radiation fields in this analysis, that is, they are characterized by a certain width of the energy spectrum of the projectile, although the underlying energy distribution is much broader in the case of an SOBP as compared to a pristine peak. For both cases, the corresponding RBE values are compared to those of strictly monoenergetic particles under track segment conditions, characterized by a single LET value. For the planning we use the treatment planning software TRiP98 together with the Local Effect Model to predict the RBE of protons, helium, and carbon ions. We further compare our model predictions for protons with a simplistic linear RBE‐LET relationship representative for the phenomenological models in literature.ResultsRegarding pristine Bragg peaks in water, the deviations in RBE compared to monoenergetic particles under track segment conditions for the same LET value are low (mostly 0–5%), except for the distal fall‐off region. The situation changes in SOBPs for which we found deviations in the order of up to 25% for the lighter particles and even more pronounced deviations for heavier particles like carbon ions.ConclusionsThe analysis showed that LETD is a sufficiently accurate predictor for RBE only in regions with comparably narrow, but not in regions with broad, LET distribution as in a single SOBP or in multiple overlapping fields. The deviations are caused by the nonlinearity of the RBE(LET) relationship in the case of track segment conditions. Thus, independent of the underlying RBE model and the particle type regarded, as long as the RBE(LET) relationship deviates from being purely linear, LETD is not a good predictor for RBE, and especially for heavier particles like carbon ions knowledge of the underlying LET distribution is mandatory to describe the RBE in mixed radiation fields.
Fast high‐resolution brain metabolite mapping on a clinical 3T MRI by accelerated H‐FID‐MRSI and low‐rank constrained reconstruction
Authors: Klauser Antoine , Courvoisier Sebastien , Kasten Jeffrey , Kocher Michel , Guerquin‐Kern Matthieu , Van De Ville Dimitri , Lazeyras Francois 
Published: December 2018

PurposeEpitomizing the advantages of ultra short echo time and no chemical shift displacement error, high‐resolution‐free induction decay magnetic resonance spectroscopic imaging (FID‐MRSI) sequences have proven to be highly effective in providing unbiased characterizations of metabolite distributions. However, its merits are often overshadowed in high‐resolution settings by reduced signal‐to‐noise ratios resulting from the smaller voxel volumes procured by extensive phase encoding and the related acquisition times.MethodsTo address these limitations, we here propose an acquisition and reconstruction scheme that offers both implicit dataset denoising and acquisition acceleration. Specifically, a slice selective high‐resolution FID‐MRSI sequence was implemented. Spectroscopic datasets were processed to remove fat contamination, and then reconstructed using a total generalized variation (TGV) regularized low‐rank model. We further measured reconstruction performance for random undersampled data to assess feasibility of a compressed‐sensing SENSE acceleration scheme. Performance of the lipid suppression was assessed using an ad hoc phantom, while that of the low‐rank TGV reconstruction model was benchmarked using simulated MRSI data. To assess real‐world performance, 2D FID‐MRSI acquisitions of the brain in healthy volunteers were reconstructed using the proposed framework.ResultsResults from the phantom and simulated data demonstrate that skull lipid contamination is effectively removed and that data reconstruction quality is improved with the low‐rank TGV model. Also, we demonstrated that the presented acquisition and reconstruction methods are compatible with a compressed‐sensing SENSE acceleration scheme.ConclusionsAn original reconstruction pipeline for 2D H‐FID‐MRSI datasets was presented that places high‐resolution metabolite mapping on 3T MR scanners within clinically feasible limits.
Non‐contrast myocardial infarct scar assessment using a hybrid native T1 and magnetization transfer imaging sequence at 1.5T
Authors: Duan Chong , Zhu Yanjie , Jang Jihye , Rodriguez Jennifer , Neisius Ulf , Fahmy Ahmed S. , Nezafat Reza 
Published: December 2018

PurposeTo develop a gadolinium‐free cardiac MR technique that simultaneously exploits native T1 and magnetization transfer (MT) contrast for the imaging of myocardial infarction.MethodsA novel hybrid T one and magnetization transfer (HYTOM) method was developed based on the modified look‐locker inversion recovery (MOLLI) sequence, with a train of MT‐prep pulses placed before the balanced SSFP (bSSFP) readout pulses. Numerical simulations, based on Bloch‐McConnell equations, were performed to investigate the effects of MT induced by (1) the bSSFP readout pulses, and (2) the MT‐prep pulses, on the measured, “apparent,” native T1 values. The HYTOM method was then tested on 8 healthy adult subjects, 6 patients, and a swine with prior myocardial infarction (MI). The resulting imaging contrast between normal myocardium and infarcted tissues was compared with that of MOLLI. Late gadolinium enhancement (LGE) images were also obtained for infarct assessment in patients and swine.ResultsNumerical simulation and in vivo studies in healthy volunteers demonstrated that MT effects, resulting from on‐resonance bSSFP excitation pulses and off‐resonance MT‐prep pulses, reduce the measured T1 in both MOLLI and HTYOM. In vivo studies in patients and swine showed that the HYTOM sequence can identify locations of MI, as seen on LGE. Furthermore, the HYTOM method yields higher myocardium‐to‐scar contrast than MOLLI (contrast‐to‐noise ratio: 7.33 ± 1.67 vs. 3.77 ± 0.66, P < 0.01).ConclusionThe proposed HYTOM method simultaneously exploits native T1 and MT contrast and significantly boosts the imaging contrast for myocardial infarction.
Internal erosion in dike‐on‐foundation modeled by a coupled hydromechanical approach
Authors: Yang Jie , Yin Zhen‐Yu , Laouafa Farid , Hicher Pierre‐Yves 
Published: December 2018

SummaryOne of the major causes of instability in geotechnical structures such as dikes or earth dams is internal erosion, an insidious process that occurs over a long period of time. Research on this topic is still fairly new and much more needs to be understood in order to solve the problems posed by this phenomenon. This paper proposes a hydromechanical model based on porous continuous medium theory to assess how internal erosion impacts the safety of earthen structures. The saturated soil is considered as a mixture of four interacting constituents: soil skeleton, erodible fines, fluidized fine particles, and fluid. The detachment and transport of the fine particles are described by a mass exchange model between the solid and the fluid phases. An elastoplastic constitutive model for sand‐silt mixtures has been developed to monitor the effect of the evolution of both porosity and fines content induced by internal erosion upon the behavior of the soil skeleton. The model has been numerically solved with the finite element method. It has then been applied to the specific case study of a dike foundation subjected to internal erosion induced by the presence of a karstic cavity beneath the alluvium layer. The numerical results show the onset of erosion, the time‐space evolution of the eroded zone, and the hydromechanical response of the soil constituting the dike, all of which highlights the effects of the cavity location, the erosion rate, and the fines content.
Percutaneous Endoscopic Gastrostomy Tubes May Be Associated With Preservation of Lung Function in Patients With Cystic Fibrosis
Authors: Khalaf Racha T. , Green Deanna , Amankwah Ernest K. , Peck Jacquelin , Carr Vanessa , Goldenberg Neil A. , Wilsey Michael 
Published: December 2018

AbstractBackgroundImproving nutrition status of patients with cystic fibrosis (CF) has a positive effect on pulmonary function.MethodsWe conducted a retrospective case‐control study evaluating the effect of percutaneous endoscopic gastrostomy (PEG) placement on body mass index (BMI) and forced expiratory volume in 1 second percent predicted (FEV1) between matched subjects with CF who received PEG (n = 20) and controls who did not (n = 40).ResultsWe observed that after adjusting for mutation class and baseline BMI, BMI percentile increased per month for those with PEG (0.51, 95% confidence interval (CI) = −0.05–1.08, P = .08), but decreased for those without PEG (−0.03, 95% CI = −0.33–0.28, P = .86); however, the difference (0.54; 95% CI = −0.10–1.18, P = .10) was not statistically significant. FEV1 change with time showed a decrease for patients with PEG (−0.04; 95% CI = −0.30–0.22, P = .74) and those without PEG (−.22; 95% CI = −0.45–0.01, P = .06). Although the decrease for those without PEG was higher than those with PEG, the difference between the groups was not statistically significant (0.18; 95% CI = −0.17–0.52, P = .32)ConclusionLung function trajectory showed a trend towards preservation among patients with CF who receive PEG despite lack of significant difference in BMI. There may be a favorable effect of PEG on lung function independent of changes in BMI.
Lower knowledge about diabetes among foreign‐born compared to Swedish‐born persons with diabetes—A descriptive study
Authors: Pettersson Sara , Hadziabdic Emina , Marklund Helén , Hjelm Katarina 
Published: December 2018

AbstractAimTo compare foreign‐ and Swedish‐born persons, diagnosed with type 2 diabetes, to study whether there are dissimilarities in knowledge about diabetes and to study determinants of knowledge.DesignA cross‐sectional descriptive study was conducted.MethodData were collected between September 2014 and March 2016, using the standardized Diabetes Knowledge Test (DKT), statistically analysed.ResultsThe results showed dissimilarities in knowledge between foreign‐ and Swedish‐born persons, supporting the hypothesis that foreign‐born persons had lower knowledge about diabetes than Swedish‐born persons. There was a relationship between poor knowledge and country of birth, marital status and employment status. Country of birth was the strongest independent determinant of knowledge about diabetes. The risk of poor knowledge was ten times higher among persons born in the Middle East or in another country outside Europe compared with Swedish‐born persons. Other influencing factors for poor knowledge about diabetes were being not gainfully employed and living alone.
Cost‐Effectiveness Comparison of Ustekinumab, Infliximab, or Adalimumab for the Treatment of Moderate‐Severe Crohn's Disease in Biologic‐Naïve Patients
Authors: Aliyev Elmar R. , Hay Joel W. , Hwang Caroline 
Published: December 2018

Study ObjectiveUstekinumab was recently approved by the United States U.S. Food and Drug Administration for the treatment of Crohn's disease. In this analysis, we aimed to compare the cost‐effectiveness of ustekinumab, infliximab, or adalimumab for the treatment of moderate‐severe Crohn's disease in patients who failed conventional therapy (i.e., corticosteroids and immunomodulators) but were naïve to tumor necrosis factor antagonists (i.e., biologic drugs).DesignCost‐effectiveness analysis using a hybrid model structure (decision tree and Markov model).Measurements and Main ResultsA decision tree simulated biologic induction, and a Markov model simulated biologic and conventional therapy maintenance. Cycle length was 2 weeks with a discounted 5‐year time horizon and a limited U.S. societal perspective in the base case; results from a payer perspective are also reported. Transition probabilities, direct costs, indirect costs, and utilities were obtained from the literature. To measure relative treatment value (i.e., order of treatment cost‐effectiveness), net monetary benefits were reported for a $150,000 willingness‐to‐pay threshold per quality‐adjusted life‐year in the base case. Infliximab dominated both adalimumab and ustekinumab, with a net monetary benefit (NMB) of $9943 and $29,798, respectively, in the base case. Adalimumab dominated ustekinumab, with an NMB of $19,855. All biologics yielded similar quality‐adjusted life‐years (~3.5), whereas costs varied substantially ($50,510, $54,985, and $72,921 for infliximab, adalimumab, and ustekinumab, respectively). The payer perspective, alternate time horizons, and scenario analyses consistently showed infliximab dominance. One‐way, threshold, and probabilistic sensitivity analyses confirmed the robustness of these results with respect to all parameters. Although biosimilars were not explicitly modeled as comparators, one‐way sensitivity analysis showed that drug acquisition costs could alter relative treatment value but would have to be varied by at least 50%.ConclusionFor moderate‐severe Crohn's disease, infliximab yields significantly more NMBs compared with both adalimumab and ustekinumab. Additional clinical (e.g., empiric dosing, biologic cycling) and quality‐of‐life (e.g., lost productivity, disutility of home injections) research is needed to allow for model frameworks and parameters that more accurately reflect the nuances of Crohn's disease treatment.
Structure Analysis of Solid Lipid Nanoparticles for Drug Delivery: A Combined USANS/SANS Study
Authors: Shah Rohan M. , Mata Jitendra P. , Bryant Gary , de Campo Liliana , Ife Alexander , Karpe Avinash V. , Jadhav Snehal R. , Eldridge Daniel S. , Palombo Enzo A. , Harding Ian H. 
Published: December 2018

AbstractSuspensions of solid lipid nanoparticles (SLNs) stabilized with emulsifiers have been extensively investigated (since the 1990s) as drug carriers, although details of their ultrastructure are poorly defined. Previously, a novel microwave‐assisted microemulsion‐based technique to prepare SLNs was reported. To understand the detailed internal structure of these SLNs, ultra‐small angle neutron scattering (USANS) and small angle neutron scattering (SANS) experiments are conducted on suspensions of hydrogenated stearic acid SLNs stabilized with hydrogenated Tween 20 surfactant in D2O. Together, SANS and USANS gives a combined Q range of 0.000047 to 0.6 Å−1 (corresponding to a size range of ≈1 nm–15 µm). This extended Q range allows a comprehensive understanding of the hierarchical structure of SLNs. The data are consistent with the multi‐length scale structure of SLNs having polydispersed large particles with roughened surfaces at the microscale level. At the nanoscale level, the results are consistent with the SLNs having an ellipsoidal shape intermediate between spheres and rods, with a crossover from mass fractals to surface fractals. The elucidation of this structure is particularly important given that the structure influences the stability and drug release properties of the nanoparticles. These results assist in the development of systems with desired shape and properties.
Probabilistic forecasts of tropical cyclone tracks and intensities in the southwest Indian Ocean basin
Authors: Bonnardot Francois , Quetelard Hubert , Jumaux Guillaume , Leroux Marie‐Dominique , Bessafi Miloud 
Published: December 2018

Under the responsibility of the Regional Specialized Meteorological Centre (RSMC) of La Réunion, the southwest Indian Ocean (SWIO) has tropical cyclone activity close to that of the North Atlantic. Like most territories of the SWIO basin, La Réunion island is highly vulnerable to cyclone‐induced hazards and the potential impact of nearby storms is closely related to their track and intensity evolution. Although storm track and intensity forecasts have been steadily improving in the last decades, a great amount of uncertainty remains. Operational centres have therefore developed probabilistic products such as uncertainty cones for the prediction of storm track and intensity over the different cyclone basins. Unfortunately, the cone approach does not fully match the end‐user needs for efficient decision‐making.This article provides a method to generate alternate probabilistic scenarios of tropical system track and intensity forecasts around an official forecast. The method has been calibrated and evaluated to answer the needs of the Système de Prévision des Inondations en contexte Cyclonique (SPICy) project that aimed to explore new probabilistic forecast products for tropical system induced hazards such as coastal inundations. A hybrid method has been developed to benefit from both climatological and dynamical existing approaches. A first set of climatology‐built scenarios is generated using the statistical distribution of RSMC La Réunion forecast errors. This initial set is then modulated using real‐time information provided by the ensemble prediction system of the European Centre for Medium‐range Weather Forecasts (ECMWF). The final product is a set of about 20 scenarios that are built around the official deterministic forecast with some associated probabilities. Performance scores demonstrate the efficiency of the method against other evaluated systems especially in the first 2 days of the forecast. The reasonable number of defined scenarios is cost efficient and makes it possible to perform further impact‐oriented applications such as wave and storm surge simulations.
OpenMP in VASP: Threading and SIMD
Authors: Wende Florian , Marsman Martijn , Kim Jeongnim , Vasilev Fedor , Zhao Zhengji , Steinke Thomas 
Published: December 2018

AbstractThe Vienna Ab initio Simulation Package (VASP) is a widely used electronic structure code that originally exploits process‐level parallelism through the Message Passing Interface (MPI) for work distribution within and across nodes. Architectural changes of modern parallel processors urge programmers to address thread‐ and data‐level parallelism as well to benefit most from the available compute resources within a node. We describe for VASP how to approach for an MPI + OpenMP parallelization including data‐level parallelism through OpenMP SIMD constructs together with a generic high‐level vector coding scheme. We can demonstrate an improved scalability of VASP and more than 20% gain over the MPI‐only version as well as a 2× increased performance of collective operations using the multiple‐endpoint MPI feature. The high‐level vector coding scheme applied to VASP's general gradient approximation routine gives up 9× performance gain on AVX512 platforms with the Intel compiler.