bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conditional generative adversarial network for 3D rigid‐body motion correction in MRI
Authors: Johnson Patricia M. , Drangova Maria 
Published: April 2019

PurposeSubject motion in MRI remains an unsolved problem; motion during image acquisition may cause blurring and artifacts that severely degrade image quality. In this work, we approach motion correction as an image‐to‐image translation problem, which refers to the approach of training a deep neural network to predict an image in 1 domain from an image in another domain. Specifically, the purpose of this work was to develop and train a conditional generative adversarial network to predict artifact‐free brain images from motion‐corrupted data.MethodsAn open source MRI data set comprising T2*‐weighted, FLASH magnitude, and phase brain images for 53 patients was used to generate complex image data for motion simulation. To simulate rigid motion, rotations and translations were applied to the image data based on randomly generated motion profiles. A conditional generative adversarial network, comprising a generator and discriminator networks, was trained using the motion‐corrupted and corresponding ground truth (original) images as training pairs.ResultsThe images predicted by the conditional generative adversarial network have improved image quality compared to the motion‐corrupted images. The mean absolute error between the motion‐corrupted and ground‐truth images of the test set was 16.4% of the image mean value, whereas the mean absolute error between the conditional generative adversarial network‐predicted and ground‐truth images was 10.8% The network output also demonstrated improved peak SNR and structural similarity index for all test‐set images.ConclusionThe images predicted by the conditional generative adversarial network have quantitatively and qualitatively improved image quality compared to the motion‐corrupted images.
Proton exchange in aqueous urea solutions measured by water‐exchange (WEX) NMR spectroscopy and chemical exchange saturation transfer (CEST) imaging in vitro
Authors: Stabinska Julia , Neudecker Philipp , Ljimani Alexandra , Wittsack Hans‐Jörg , Lanzman Rotem Shlomo , Müller‐Lutz Anja 
Published: April 2019

PurposeTo characterize the proton exchange in aqueous urea solutions using a modified version of the WEX II filter at high magnetic field, and to assess the feasibility of performing quantitative urea CEST MRI on a 3T clinical MR system.MethodsIn order to study the dependence of the exchange‐rate constant of urea as a function of pH and T, the WEX‐spectra were acquired at 600 MHz from urea solutions in a pH range from 6.4 to 8.0 and a temperature range from to . The CEST experiments were performed on a 3T MRI scanner by applying a train of 50 Gaussian‐shaped pulses, each 100‐millisecond long with a spacing of 100 milliseconds, for saturation. Exchange rates of urea were calculated using the (extended) AREX metric.ResultsThe results showed that proton exchange in aqueous urea solutions is acid and base catalyzed with the rate constants: l/(mol·s) and l/(mol·s), respectively. Since the urea protons undergo a slow exchange with water protons, the CEST effect of urea can be observed efficiently at 3T. However, in neutral solutions the exchange rate of urea is minimal and cannot be estimated using the quantitative CEST approach.ConclusionsBy means of the WEX‐spectroscopy, the kinetic parameters of the proton exchange in urea solutions have been determined. It was also possible to estimate the exchange rates of urea in a broad range of pH values using the CEST method at a clinical scanner.
A Statewide Evaluation of Florida Bass Genetic Introgression in Tennessee
Authors: Hargrove John S. , Rogers Mark W. , Kacmar Phillip T. , Black Pat 
Published: April 2019

Abstract
The Largemouth Bass (LMB) Micropterus salmoides is one of the most popular freshwater sport fish in the United States, and managers in southeastern states have stocked its subspecies, the Florida Bass (FLB) M. salmoides floridanus, outside of the subspecies’ natural range to increase the size structure of existing LMB populations. In Tennessee, fisheries for LMB are concentrated in reservoirs of the Cumberland and Tennessee River systems; however, FLB stockings have to date been restricted to two reservoirs of the Tennessee River and have varied significantly in extent and duration. We quantified levels of genetic admixture between FLB and LMB by using 38 species-diagnostic single-nucleotide polymorphisms for 979 fish sampled from 14 reservoirs within the Cumberland and Tennessee River systems. We tested for differences in genetic admixture across river systems and evaluated the relative importance of fish stockings in explaining observed levels of genetic admixture. Levels of admixture and associated variation were higher in Tennessee River reservoirs (average percentage of FLB alleles: range = 6.3–30.4%) than in Cumberland River reservoirs (range = 5.7–13.4%), but admixture was not solely related to stocking rates. The highest levels of FLB introgression were detected in Chickamauga Reservoir, the most extensively stocked reservoir in the state. Linear models identified fish stocked as a significant overall predictor of admixture, but we also observed stocked and unstocked reservoirs with similar levels of admixture, suggesting that factors other than stocking influence population genetics. Our statewide assessment of reservoir-level patterns of hybridization among black bass was performed prior to the recent expansion of FLB stocking efforts in Tennessee and thus represents a baseline for evaluation of future stocking.
Metabolic Risk Factors Associated with Visceral and Subcutaneous Adipose Tissue in a Sex‐Specific Manner in Seven‐Year‐Olds
Authors: Kjellberg Emma , Roswall Josefine , Andersson Jonathan , Bergman Stefan , Karlsson Ann‐Katrine , Svensson Pär‐Arne , Kullberg Joel , Dahlgren Jovanna 
Published: April 2019

ObjectiveThis study aimed to investigate how visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) volumes were associated with metabolic risk factors in 7‐year‐old children.MethodsA total of 81 children (52% girls) from a Swedish birth cohort were studied. At 6 years of age, anthropometric data, fasting insulin, glucose, cholesterol, and blood pressure were collected on 53 children with normal weight and 28 children with overweight or obesity, and insulin resistance was estimated. At 7 years of age, magnetic resonance imaging quantified VAT and SAT. Sex and regression analyses were conducted.ResultsSAT was more strongly associated with metabolic risk factors than VAT. The associations between VAT and metabolic risk factors were stronger in girls (P < 0.05). When VAT was adjusted for birth weight and maternal BMI and education, it accounted for 51% of insulin variance (β = 11.72; P = 0.001) but only in girls. The key finding of this study was that adjusted SAT accounted for 63% of the fasting insulin variance in girls (β = 2.76; P < 0.001). Waist circumference was the best anthropometric marker for insulin resistance.ConclusionsInsulin resistance was associated with abdominal adipose tissue and its associated metabolic risk factors in children as young as 7 years old.
Adipose Tissue CTGF Expression is Associated with Adiposity and Insulin Resistance in Humans
Authors: Yoshino Jun , Patterson Bruce W. , Klein Samuel 
Published: April 2019

ObjectiveConnective tissue growth factor (CTGF) is an important regulator of fibrogenesis in many organs. This study evaluated the interrelationship among adipose tissue CTGF expression, fat mass, and insulin resistance in humans.MethodsThis study examined (1) CTGF gene expression in human subcutaneous preadipocytes before and after inducing adipogenesis; (2) relationships among abdominal subcutaneous adipose tissue CTGF gene expression, body fat mass, and indices of insulin sensitivity, including the hepatic insulin sensitivity index and the hyperinsulinemic‐euglycemic clamp procedure in conjunction with stable isotope glucose tracer infusion, in 72 people who had marked differences in adiposity and insulin sensitivity; (3) localization of CTGF protein in subcutaneous adipose tissue; and (4) effect of progressive (5%, 11%, and 16%) weight loss on adipose tissue CTGF gene expression.ResultsCTGF was highly expressed in preadipocytes, not adipocytes. Adipose tissue CTGF expression was strongly correlated with body fat mass and both skeletal muscle and liver insulin sensitivity, and CTGF‐positive cells were predominantly found in areas of fibrosis. Progressive weight loss caused a stepwise decrease in adipose tissue CTGF expression.ConclusionsIt was concluded that increased CTGF expression is associated with adipose tissue expansion, adipose tissue fibrosis, and multi‐organ insulin resistance in people with obesity.
Role of Leptin in the Association Between Body Adiposity and Persistent Asthma: A Longitudinal Study
Authors: Li Zhen , Leynaert Bénédicte , Dumas Orianne , Diaz Gil Oscar , Garcia‐Aymerich Judith , Fito Colomer Montserrat , Le Moual Nicole , Pison Christophe , Romieu Isabelle , Siroux Valérie , Camargo Carlos A. , Varraso Raphaëlle , Nadif Rachel 
Published: April 2019

ObjectiveObesity is a likely risk factor for asthma. However, underlying mechanisms by which obesity affects asthma activity remain poorly understood. This study aimed to investigate the role of leptin, an adipocyte‐derived proinflammatory protein, as a mediator in the association between body adiposity (assessed using BMI, waist circumference, and body fat percentage) and persistent asthma.MethodsA causal approach to mediation analysis was used to disentangle total and direct effects and the indirect effect mediated by leptin, using data from the French prospective French Epidemiological Study on the Genetics and Environment of Asthma (EGEA) (baseline: 2003‐2007; follow‐up: 2011‐2013; mean follow‐up time: 7 years). A total of 331 participants with current asthma at baseline were included.ResultsPer 1‐SD increment in BMI, waist circumference, and body fat percentage, the adjusted odds ratios of the total effect were 1.59 (95% CI: 0.95‐2.97), 2.06 (1.06‐4.00), and 3.25 (1.01‐9.41), respectively; the odds ratios of the indirect effect mediated by leptin were 1.68 (1.09‐2.46), 1.55 (0.99‐2.57), and 1.99 (0.94‐4.83), respectively.ConclusionsLeptin partly (> 60%) mediated the association between high body adiposity and persistent asthma over time. Using a newly developed analytic approach, this longitudinal study brought new insight into one mechanism by which obesity may affect asthma activity.
Pressure support ventilation, sigh adjunct to pressure support ventilation, and neurally adjusted ventilatory assist in infants after cardiac surgery: A physiologic crossover randomized study
Authors: Bonacina Daniele , Bronco Alfio , Nacoti Mirco , Ferrari Floriana , Fazzi Francesco , Bonanomi Ezio , Bellani Giacomo 
Published: April 2019

AbstractObjectivesWe sought to compare gas exchange, respiratory mechanics, and asynchronies during pressure support ventilation (PSV), sigh adjunct to PSV (PSV SIGH), and neurally adjusted ventilatory assist (NAVA) in hypoxemic infants after cardiac surgery.DesignProspective, single‐center, crossover, randomized physiologic study.SettingTertiary‐care pediatric intensive care unit.PatientsFourteen hypoxemic infants (median age 11.5 days [8.7‐74]).InterventionsThe protocol begins with a 1 hour step of PSV, followed by two consecutive steps in PSV SIGH and NAVA in random order, with a washout period of 30 minutes (PSV) between them.Main ResultsThree infants presented an irregular Eadi signal because of diaphragmatic paralysis and were excluded from analysis. For the remaining 11 infants, PaO2/FiO
2 and oxygenation index improved in PSV SIGH compared with PSV (P < 0.05) but not in NAVA compared with PSV. PSV SIGH showed increased tidal volumes and lower respiratory rate than PSV (P < 0.05), as well as a significant improvement in compliance with respiratory system indexed to body weight when compared with both PSV and NAVA (P < 0.01). No changes in mean airway pressure was registered among steps. Inspiratory time resulted prolonged for both PSV SIGH and NAVA than PSV (P < 0.05). NAVA showed the higher coefficient of variability in respiratory parameters and a significative decrease in asynchrony index when compared with both PSV and PSV SIGH (P < 0.01).ConclusionsThe adjunct of one SIGH per minute to PSV improved oxygenation and lung mechanics while NAVA provided the best patient‐ventilator synchrony in infants after cardiac surgery.
Function and solution structure of the Arabidopsis thaliana RALF8 peptide
Authors: Frederick Ronnie O. , Haruta Miyoshi , Tonelli Marco , Lee Woonghee , Cornilescu Gabriel , Cornilescu Claudia C. , Sussman Michael R. , Markley John L. 
Published: April 2019

AbstractWe report the recombinant preparation from Escherichia coli cells of samples of two closely related, small, secreted cysteine‐rich plant peptides: rapid alkalinization factor 1 (RALF1) and rapid alkalinization factor 8 (RALF8). Purified samples of the native sequence of RALF8 exhibited well‐resolved nuclear magnetic resonance (NMR) spectra and also biological activity through interaction with a plant receptor kinase, cytoplasmic calcium mobilization, and in vivo root growth suppression. By contrast, RALF1 could only be isolated from inclusion bodies as a construct containing an N‐terminal His‐tag; its poorly resolved NMR spectrum was indicative of aggregation. We prepared samples of the RALF8 peptide labeled with 15N and 13C for NMR analysis and obtained near complete 1H, 13C, and 15N NMR assignments; determined the disulfide pairing of its four cysteine residues; and examined its solution structure. RALF8 is mostly disordered except for the two loops spanned by each of its two disulfide bridges.
Optimal Scheduling of Bevacizumab and Pemetrexed/Cisplatin Dosing in Non‐Small Cell Lung Cancer
Authors: Schneider Benjamin K. , Boyer Arnaud , Ciccolini Joseph , Barlesi Fabrice , Wang Kenneth , Benzekry Sebastien , Mochel Jonathan P. 
Published: April 2019

Bevacizumab‐pemetrexed/cisplatin (BEV‐PEM/CIS) is a first‐line therapeutic for advanced nonsquamous non‐small cell lung cancer. Bevacizumab potentiates PEM/CIS cytotoxicity by inducing transient tumor vasculature normalization. BEV‐PEM/CIS has a narrow therapeutic window. Therefore, it is an attractive target for administration schedule optimization. The present study leverages our previous work on BEV‐PEM/CIS pharmacodynamic modeling in non‐small cell lung cancer–bearing mice to estimate the optimal gap in the scheduling of sequential BEV‐PEM/CIS. We predicted the optimal gap in BEV‐PEM/CIS dosing to be 2.0 days in mice and 1.2 days in humans. Our simulations suggest that the efficacy loss in scheduling BEV‐PEM/CIS at too great of a gap is much less than the efficacy loss in scheduling BEV‐PEM/CIS at too short of a gap.
Theoretical study of the photophysical processes of a styryl‐bodipy derivative eliciting an AND molecular logic gate response
Authors: Tzeli Demeter , Petsalakis Ioannis D. , Theodorakopoulos Giannoula 
Published: April 2019

AbstractWe study, via density functional theory and time dependent DFT calculations, the photophysical processes of a styryl‐bodipy derivative, which acts as a three metal‐cation‐receptor fluorophore in order to (a) gain information on the appropriate computational approach for successful prediction of molecular logic gate candidates, (b) rationalize the available experimental data and (c) understand how the given combination of three different receptors with the BODIPY fluorophore presents such interesting optoelectronic responses. The fluorophore (1), its monometallic complexes (1‐Ca
2+, 1‐Zn
2+, and 1‐Hg
2+), and its trimetallic complex (2) are studied. The calculated λmax values for absorption and emission are in excellent agreement with experimental data. It was found that the observed quenching of emission of 1 and of the monometallic complexes is attributed to the fact that their first excited state is a charge‐transfer state whereas this does not happen for the complex 2. It should be noted that for the correct ordering of the excited states, the inclusion of corrections to the excitation energies for nonequilibrium solvent effects is required; while in the case of 1‐Ca
2+, the additional explicit inclusion of the solvent is necessary for the quenching of the emission spectra.
Mapping the underside of an iceberg with a modified underwater glider
Authors: Zhou Mingxi , Bachmayer Ralf , deYoung Brad 
Published: April 2019

AbstractIcebergs pose many challenges to offshore operations in the Arctic Ocean and sub‐arctic regions. They could damage underwater infrastructure such as pipelines, and disrupt marine transportation. The below‐water shape of an iceberg is a key factor for iceberg management in the North Atlantic Ocean because it affects the iceberg towing plans and iceberg drift patterns. In recent years, unmanned platforms have been proposed as potential candidates for underwater iceberg mapping. Compared to a conventional ship‐based iceberg survey, using unmanned platforms is more efficient and safer. In this paper, we present research using a hybrid underwater glider to measure the underwater shape of an iceberg. The vehicle is equipped with a mechanical scanning sonar for range sensing and iceberg mapping, and a guidance system is designed to use the sonar measurements for guiding the vehicle to circumnavigate an iceberg at the desired standoff distance. Several field experiments have been conducted on an iceberg to evaluate the system performance. With repeated observations, the underside of the target iceberg was successfully reconstructed, and iceberg shape comparisons are presented.
Optimizing Donor Cellular Dissociation and Subretinal Injection Parameters for Stem Cell-Based Treatments
Authors: Scruggs Brittni A. , Jiao Chunhua , Cranston Cathryn M. , Kaalberg Emily , Wang Kai , Russell Stephen R. , Wiley Luke A. , Mullins Robert F. , Stone Edwin M. , Tucker Budd A. , Sohn Elliott H. 
Published: April 2019

Abstract
Subretinal delivery of stem cell-derived retinal cells as a strategy to treat retinal degenerative blindness holds great promise. Currently, two clinical trials are underway in which human fetal retinal progenitor cells (RPCs) are being delivered to patients by intravitreal or subretinal injection to preserve or restore vision, respectively. With the advent of the induced pluripotent stem cell (iPSC), and in turn three-dimensional derivation of retinal tissue, it is now possible to generate autologous RPCs for cell replacement. The purpose of this study was to evaluate the effect of commonly used cell isolation and surgical manipulation strategies on donor cell viability. iPSC-RPCs were subjected to various conditions, including different dissociation and isolation methods, injection cannula sizes, and preinjection storage temperatures and times. The effects of commonly used surgical techniques on both host and donor cell viability were evaluated in Yucatan mini-pigs (n = 61 eyes). We found a significant increase in cell viability when papain was used for RPC isolation. In addition, a significant decrease in cell viability was detected when using the 41G cannula compared with 31G and at storage times of 4 hours compared with 30 minutes. Although 96.4% of all eyes demonstrated spontaneous retinal reattachment following injection, retinal pigment epithelium (RPE) abnormalities were seen more frequently in eyes receiving injections via a 31G cannula; interestingly, eyes that received cell suspensions were relatively protected against such RPE changes. These findings indicate that optimization of donor cell isolation and delivery parameters should be considered when developing a subretinal cell replacement strategy. Stem Cells Translational Medicine 2019;8:797–809
Fates of antibiotic resistance genes in a distributed swine wastewater treatment plant
Authors: Yuan Qing‐Bin , Zhai Yi‐Fan , Mao Bu‐Yun , Schwarz Cory , Hu Nan 
Published: April 2019

AbstractThis study explores the prevalence, emission, and reduction of five ARGs (sulI, tetA, mphB, qnrD, and mcr‐1) and integron (intI) through a distributed swine wastewater purification facility and the effluent‐receiving environment. Typical metal resistance genes (MRGs), pathogenic bacterial indicators, the bacterial community, and wastewater properties were also explored to determine their effects on the fates of ARGs. Results indicated that the purification process could hardly effectively remove ARGs’ prevalence. 3.1 × 104–7.1 × 108 copies/L were present after purification, and 4%–57% of them persisted in the subsequent creek and adjacent soil. 16S rRNA sequencing suggested that the discharge of wastewater significantly changed the bacterial community in receiving creek and soil. Molecular ecological networks analysis detected the wide co‐occurrence among ARGs, MRGs, and PBGs, which could further facilitate the propagation of antibiotic resistance. ARG incidence and specific bacterial genera were closely correlated, suggesting an extensive hosting relationship. Redundancy analyses showed wastewater organics and nutrients showed positive correlation to most ARGs’ abundance, but negatively correlated to their relative abundance.Practitioner points

Fate of five ARGs and intI was studied in a swine wastewater treatment system.

The treatment process could not effectively reduce ARGs’ abundance.

ARGs and pathogens in wastewater were transferred to the receiving creek and soil.

The network analysis found wide co‐occurrence among ARGs, metal resistance genes, and pathogens.

Wastewater nutrients positively correlated to ARG's abundance but negatively correlated to their relative abundance.
A Methodology for Global Sensitivity Analysis of Activated Sludge Models: Case Study with Activated Sludge Model No. 3 (ASM3)
Authors: Fortela Dhan Lord B. , Farmer Kyle , Zappi Alex , Sharp Wayne W. , Revellame Emmanuel , Gang Daniel , Zappi Mark 
Published: April 2019

AbstractThe main objective of this study was to demonstrate a computational approach of global sensitivity analysis (GSA) integrated with functional principal component analysis (fPCA) for activated sludge models through aggregation of time‐dependent model response patterns into time‐independent coefficients of functional principal components (PCs). This proposed approach addresses the main issue of time‐varying character of GSA indices when calculated solely on the time‐dependent model outputs. The GSA‐fPCA methodology was implemented using the rigorous model Activated Sludge Model No. 3 (ASM3) as case study. The approach transforms the time‐dependent model outputs into functional PCs prior to calculation of GSA indices to remove the time‐varying character of the calculated GSA indices. This work focused on the evaluation of the following key computational factors that may significantly influence the performance of the GSA‐fPCA methodology: (a) model parameter sampling range, (b) model simulation period, (c) basis functions system, and (d) state of the system being modeled—batch or continuous activated sludge process. Results show that first few functional PCs capture up to 100% of the curve patterns in the time‐dependent model outputs. The sensitivity indices calculated from the PC scores via Morris’ GSA technique elucidated parameter sensitivity patterns inherent to the complex mathematical structure of ASM3.Practitioner points

Functional principal components‐mediated GSA technique to remove time‐varying character of sensitivity indices derived from time‐dependent dynamical models.

Technique amenable to improving efficiency of capturing response patterns into few functional principal components through various basis functions.

Identifying priority parameters for ASM3 model calibration requires specification of target model outputs to which parameter sensitivities are calculated.

GSA‐fPCA offers a comprehensive numerical approach to manipulating models depending on the intended applications: simple fast‐responding models to complex models.