bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of maternal diet on offspring gut microbiota development: A review
Authors: Al Rubaye Hiba , Adamson Chelsea C. , Jadavji Nafisa M.
Published: February 2020

In offspring, an adequate maternal diet is important for neurodevelopment. One mechanism by which maternal diet impacts neurodevelopment is through its dynamic role in the development of the gut microbiota. Communication between the gut, and its associated microbiota, and the brain is facilitated by the vagus nerve, in addition to other routes. Currently, the mechanisms through which maternal diet impacts offspring microbiota development are not well‐defined. Therefore, this review aims to investigate the relationship between maternal diet during pregnancy and offspring microbiota development and its impact on neurodevelopment. Both human and animal model studies were reviewed to understand the impact of maternal diet on offspring microbiota development and potential consequences on neurodevelopment. In the period after birth, as reported in both human and model system studies, maternal diet impacts offspring bacterial colonization (e.g., decreased presence of Lactobacillus reuteri as a result of a high‐fat maternal diet). It remains unknown whether these changes persist into adulthood and whether they impact vulnerability to disease. Therefore, further long‐term studies are required in both human and model systems to study these changes. Our survey of the literature indicates that maternal diet influences early postnatal microbiota development, which in turn, may serve as a mechanism through which maternal diet impacts neurodevelopment.
Human serum mast cell tryptase levels in elbow fractures or dislocations and its association with injury severity
Authors: Liu Crystal S. , Ademola Ayoola , Zhang Mei , Garven Alexandra , Kopka Michaela , Salo Paul T. , Hart David A. , Befus A. Dean , Hildebrand Kevin A.
Published: February 2020

Mast cells contain an abundance of tryptase, and preclinical models have shown elevated serum mast cell tryptase (SMCT) in the setting of posttraumatic joint contractures. Therefore, SMCT emerged as a potential biomarker to help recognize patients with more severe injuries and a higher likelihood of developing contractures. The objective of this study is to assess SMCT levels in participants with varying severity of elbow fractures and/or dislocations. A prospective cohort including 13 participants with more severe injuries that required an operation and 28 participants with less severe injuries managed nonoperatively were evaluated. A control group of eight individuals without elbow injuries was also evaluated. The SMCT levels were measured using an enzyme‐linked immunosorbent assay kit specific for human mast cell tryptase. A one‐way analysis of variance and Tukey's Honest Significance test was used to assess for statistical significance among and between the three groups. The average time from injury to the collection of the blood samples was 4 ± 2 days. Highly significant differences were identified between the operative, nonoperative, and control groups (P = .0005). In the operative group, SMCT levels were significantly higher than the nonoperative group (P = .0005) and the control group (P = .009), suggesting a correlation between SMCT levels and injury severity. There was no statistically significant difference in SMCT levels between the nonoperative and control groups. The SMCT levels were elevated in participants with acute elbow injuries requiring operative intervention, suggesting that SMCT levels were higher in injuries regarded as more severe.
Freeze‐dried immobilized kefir culture in cider‐making
Authors: Nikolaou Anastasios , Nelios Grigorios , Kanellaki Maria , Kourkoutas Yiannis
Published: February 2020

BACKGROUND

The aim of the present study was to evaluate the fermentation efficiency of freeze‐dried immobilized kefir culture on natural supports (apple pieces, delignified cellulosic material) in cider making at various temperatures (5–45 °C) in comparison with freeze‐dried free cells. Freeze‐dried cells were initially tested in apple juice fermentations at 30 °C, and then the freeze‐dried cultures produced with no cryoprotectants were assessed in repeated batch fermentations.

RESULTS

Repeated batch fermentations lasted for longer than 5 months. High malic acid conversion rates (up to 78.5%) and ethanol productivity values (up to 37.9 g L−1 day−1) were recorded for freeze‐dried immobilized cells. Polymerase chain reaction – denaturing gradient gel electrophoresis (PCR‐DGGE) analysis showed that freeze‐drying had no effect on the microbial diversity of kefir culture. Higher alcohols were significantly reduced at low fermentation temperatures. Application of principal component analysis (PCA) revealed that both the fermentation temperature and the nature of the freeze‐dried kefir culture affected significantly the minor volatiles determined by gas chromatography/mass spectrometry (GC/MS). Notably, all ciders produced were of high quality and were accepted by the tasting panel.

CONCLUSIONS

Freeze‐dried immobilized kefir culture on natural supports with no cryoprotectants was found to be suitable for simultaneous alcoholic and malolactic cider fermentation at various temperatures (5–45 °C). The high operational stability of the systems was confirmed and the results obtained are of great interest for the industrial sector as they could be exploited for cider, low‐alcohol cider, or ‘soft’ cider production. © 2020 Society of Chemical Industry
Changes in markers of lipid oxidation and thermal treatment in feed‐grade fats and oils
Authors: Winkler–Moser Jill K , Hwang Hong‐Sik , Kerr Brian J
Published: February 2020

BACKGROUND

Oxidized feed lipids have been shown to have detrimental effects on food animal growth and metabolism. The present study aimed to measure classes of lipid oxidation products (LOP) in feed‐grade oils at temperatures representing production and storage conditions.

RESULTS

There were significant oil type × time interactions in the accumulation of primary and secondary LOP. At 22.5 °C, peroxide value (PV), a marker for the primary phase of lipid oxidation, increased most in fish oil (FO), followed by tallow (TL), soybean oil (SO), linseed oil (LO) and modified algae oil (MAO), whereas palm oil (PO) showed no appreciable increase in PV. Secondary LOP, such as p‐anisidine value, hexanal, 2,4,‐decadienal, polymerized triacylglycerols and total polar compounds, increased only in FO. At 45 °C, FO and SO produced both primary and secondary LOP, whereas MAO, PO and TL had slower rates of PV increase and no secondary LOP. At 90 °C and 180 °C, all oils except for FO accumulated both primary and secondary LOP.

Conclusions

Higher polyunsaturated fatty acid:saturated fatty acid oils and higher temperatures produced greater quantities of primary and secondary LOP. However, unrefined TL was more prone to oxidation at 22.5 °C than predicted, whereas LO was more stable than predicted, indicating that pro‐oxidant and antioxidant compounds can markedly influence the rate of oxidation. Measuring both primary and secondary LOP will provide better information about the oxidative status of feed oils and provide better information about which classes of LOP are responsible for detrimental health effects in animals. Published 2020. This article is a U.S. Government work and is in the public domain in the USA.
Simultaneous determination of ferulic acid, paeoniflorin, and albiflorin in rat plasma by ultra‐high performance liquid chromatography with tandem mass spectrometry: Application to a pharmacokinetic study of Danggui‐Shaoyao‐San
Authors: Zhu Heyun , Guan Jiao , Zhang Hui , Chang Sheng , Wang Liming , Shi Jianyi , Feng Bo , Gu Jingkai
Published: February 2020

A rapid, selective, and sensitive ultra‐high performance liquid chromatography‐tandem mass spectrometry method was developed for simultaneous determination of ferulic acid, paeoniflorin, and albiflorin, the major active constituents of Danggui‐Shaoyao‐San, in rat plasma using geniposide as the internal standard. The plasma samples were processed by protein precipitation with acetonitrile, and then separated on a Shim‐Pack XR‐ODS C18 column (75 mm × 3.0 mm, 2.2 μm) using gradient elution program with a mobile phase consisting of 0.1% aqueous formic acid and acetonitrile at a flow rate of 0.4 mL/min. The detection was achieved on a 3200 QTRAP mass spectrometer equipped with electrospray ionization source in negative ionization mode. Quantification was performed using multiple reaction monitoring mode by monitoring the fragmentation of m/z 192.9→134.0 for ferulic acid, m/z 525.0→120.9 for paeoniflorin, m/z 525.2→121.0 for albiflorin, and m/z 433.1→225.1 for the internal standard, respectively. The calibration curve was linear in the range of 5–2500 ng/mL for all the three analytes (r ≥ 0.9972) with the lower limit of quantitation of 5 ng/mL. The intraday and interday precisions were below 12.1% for all the analytes in terms of relative standard deviation, and the accuracy was within ±11.5% in terms of relative error. The extraction recovery, matrix effect and stability were satisfactory in rat plasma. The validated method was successfully applied to a pharmacokinetic study of ferulic acid, paeoniflorin, and albiflorin after oral administration of Danggui‐Shaoyao‐San to rats.
Binding modes identification through molecular dynamic simulations: A case study with carnosine enantiomers and the Teicoplanin A2‐2‐based chiral stationary phase
Authors: Sardella Roccaldo , Ianni Federica , Cossignani Lina , Aldini Giancarlo , Carotti Andrea
Published: February 2020

In the present study, an in silico methodology able to define the binding modes adopted by carnosine enantiomers in the setting of the chiral recognition process is described. The inter‐ and intramolecular forces involved in the enantioseparation process with the Teicoplanin A2‐2 chiral selector and carnosine as model compound are successfully identified. This approach fully rationalizes, at a molecular level, the (S) < (R) enantiomeric elution order obtained under reversed‐phase conditions. Consistent explanations were achieved by managing molecular dynamics results with advanced techniques of data analysis. As a result, the time‐dependent identification of all the interactions simultaneously occurring in the chiral selector‐enantiomeric analyte binding process was obtained. Accordingly, it was found that only (R)‐carnosine is able to engage a stabilizing charge–charge interaction through its ionized imidazole ring with the carboxylate counter‐part on the chiral selector. Instead, (S)‐carnosine establishes intramolecular contacts between its ionized functional groups, that limit its conformational freedom and impair the association with the chiral selector unit.
A capillary electrophoresis strategy to sensitively detect dynamic properties of coiled coil polypeptides
Authors: Yang Jie , Zhao Sun‐Duo , Zhao Dong‐Hui , Huang Yan , Liu Xiao‐Xia , Hu Wei , Liu Bo
Published: February 2020

The self‐assembly behavior of polypeptides plays an essential role to form biological and functional macromolecules, which have attracted a lot of attention due to their excellent characters. Understanding the polypeptide self‐assembly systems and dynamic behaviors is fundamental to improve the potential of biomedical applications. In this work, coiled coil polypeptides PC10 and PC10P were designed and biosynthesized. PC10 and PC10P could form nanogels when the concentration of polypeptides was less than 2% (m/v). The dynamic behaviors of PC10 and PC10P were measured by Förster resonance energy transfer method based on a capillary electrophoresis system. The Förster resonance energy transfer efficiency of this system was 60.4%, and the distance of self‐assembled domains in the polypeptides was calculated as 6.14 nm, demonstrating that the exchange behavior occurred between two different polypeptides containing the same coiled coil region.
The Prognostic Role of Programmed Death‐Ligand 1 in Nasopharyngeal Carcinoma
Authors: Wotman Michael , Herman Saori W. , Costantino Peter , Tham Tristan
Published: February 2020

Objectives

Programmed death‐ligand 1 (PD‐L1) is an immune checkpoint protein that may be a useful prognostic biomarker in nasopharyngeal cancer (NPC). The purpose of this systematic review and meta‐analysis was to investigate the relationship between PD‐L1 expression and survival in NPC.

Methods

PubMed, Cochrane, Embase, Scopus, and Web of Science were searched from inception to present. A predefined inclusion and exclusion criteria were used to select articles. Hazard ratios (HRs) and 95% confidence intervals (CIs) were pooled for overall survival (OS), disease‐free survival (DFS), and disease metastasis‐free survival (DMFS).

Results

Eleven studies published from 2014 to 2018 were included, with 1,356 total participants. PD‐L1 expression was not associated with OS (HR = 1.10, 95% CI: 0.79‐1.55), DFS (HR = 1.66, 95% CI: 0.68‐4.03), or DMFS (HR = 1.18, 95% CI: 0.44‐3.20).

Conclusions

The prognostic role of PD‐L1 in NPC remains unsubstantiated. Future research is needed. Laryngoscope, 130:2598–2606, 2020
Partitioning the impacts of land use/land cover change and climate variability on water supply over the source region of the Blue Nile Basin
Authors: Belete Marye , Deng Jinsong , Abubakar Ghali A. , Teshome Menberu , Wang Ke , Woldetsadik Muluneh , Zhu Enyan , Comber Alexis , Gudo Adam
Published: February 2020

Water plays a vital role in sustaining the natural functioning of the entire ecosystem that supports life on Earth. It plays key roles in the well‐being of society in numerous ways. However, climate variability and land use land cover (LULC) change have caused spatiotemporal water supply variation. Disentangling the effects of climate variability from LULC change on water supply is crucial for sustainable water resource management. The main purpose of this study is, therefore, to disentangle the relative contribution of LULC change and climate variability to the overall average annual water supply variation. Residual trends analysis combined with Integrated Valuation of Environmental Services and Tradeoffs (InVEST) annual water yield model was adopted to perform simulations and disentangle the relative impacts of climate variability and LULC change. Ground and satellite data were used in this study. The study area has experienced a significant increasing wetness trend and significant LULC dynamics between 2003 and 2017. As a result, an increasing water supply was observed due to the joint effects of climate variability and LULC change in the watershed (203 mm). The contribution of climate variability was 94%, whereas LULC contributes only 6% from 2003 to 2017. Climate variability negatively led to water supply variation while LULC change contributed positively from 2010 to 2017. Although the ongoing soil and water conservation (SWC) practices improved vegetation cover and water retention of the watershed, climate variability is the main driver of water supply variation. Therefore, SWC practices should incorporate ecosystem‐based climate change adaptation strategies and scale up to community‐based integrated watershed management to sustain water supply.
Pantoea sp. P37 as a novel nonpathogenic host for the heterologous production of rhamnolipids
Authors: Nawrath Margarete Monika , Ottenheim Christoph , Wu Jin Chuan , Zimmermann Wolfgang
Published: February 2020

Microbially derived surfactants, so‐called biosurfactants, have attracted significant attention as an environmentally friendly alternative to their chemically synthesized counterparts. Particularly, rhamnolipids offer a large potential with their outstanding surfactant properties such as complete biodegradability, low toxicity, and stability. Rhamnolipids are naturally synthesized by the opportunistic human pathogen Pseudomonas aeruginosa under the tight regulation of a highly complex quorum‐sensing system. The heterologous production of mono‐rhamnolipids by a newly isolated nonpathogenic strain of the genus Pantoea was investigated. Analysis of the genome obtained by a chimeric assembly of Nanopore long reads and high‐quality Illumina reads suggested that the strain has evolved to an epiphytic rather than a pathogenic lifestyle. Functional heterologous expression of the mono‐rhamnolipid operon rhlAB derived from a P. aeruginosa strain was established and confirmed by HPLC analysis. Transcriptome analysis indicated destabilizing effects of the produced rhamnolipids on the cell envelope of the host resulting in the induction of molecular stress responses. After integration of the rmlBCDA operon, extracellular rhamnolipids in amounts up to 0.4 g/L could be detected and were identified as a mono‐rhamnolipid Rha‐C10‐C10 by MALDI‐TOF mass spectrometry.
Three‐dimensional in vitro cell culture devices using patient‐derived cells for high‐throughput screening of drug combinations
Authors: Kwon Seok‐Joon , Lee Dongwoo , Gopal Sneha , Ku Ashlyn , Moon Hosang , Dordick Jonathan S.
Published: February 2020

Drug discovery using traditional animal models is often inefficient because test animal models cannot accurately represent human responses, particularly in terms of toxicology and pathophysiology. For these reasons, there is an urgent need to develop in vitro human disease models to accelerate new drug development. This is especially the case for precision medicine, where current in vitro and ex vivo models are not sufficient to predict individual drug efficacy and safety across the enormous heterogeneity of populations and individuals. In addition, model cell lines cultured under non‐physiological conditions do not recapitulate the complex microenvironment of patient tissues. Precision medicine using patient‐derived cells and drug combination therapies may be a promising solution to overcome these limitations. Three‐dimensional (3D) cell culture models can simultaneously simulate complex in vivo tissue microenvironments and be miniaturized for large‐scale screening of drug combinations using limited available patient‐derived cells. Recently, microfluidic and microarray platforms have been developed to mimic multiple human organs and human‐specific disease states, and are becoming more commonly used in high‐throughput drug screening. Herein, we highlight the current status of microfluidic‐based 3D cell culture devices, such as organ/body‐on‐chip systems, as well as microarray‐based 3D cell culture platforms, which can be combined with patient‐derived cells. Miniaturized cell culture systems using patient‐derived cells represent promising tools for identifying new drug combinations and also biological mechanisms that underlie drug synergies.
Certain fractional calculus and integral transform results of incomplete ℵ‐functions with applications
Authors: Kumar Bansal Manish , Kumar Devendra , Nisar K. S. , Singh Jagdev
Published: February 2020

In this paper, we study certain interesting and useful properties of incomplete
‐functions. The incomplete
‐function is an extension of the
‐function. We find several useful classical integral transforms of these functions. Further, we examine the fractional calculus with the incomplete
‐functions and point out several special cases. Finally, we give the applications of incomplete
‐functions in detecting glucose supply in human blood.
Dose‐Dependent Increases in Ellagitannin Metabolites as Biomarkers of Intake in Humans Consuming Standardized Black Raspberry Food Products Designed for Clinical Trials
Authors: Roberts Kristen M. , Grainger Elizabeth M. , Thomas‐Ahner Jennifer M. , Hinton Alice , Gu Junnan , Riedl Ken , Vodovotz Yael , Abaza Ronney , Schwartz Steven J. , Clinton Steven K.
Published: February 2020

Scope

Black raspberry (BRB) phytochemicals demonstrate anti‐carcinogenic properties in experimental models, including prostate cancer. Two BRB foods, a confection and nectar, providing a consistent and reproducible product for human clinical studies are designed and characterized.

Methods and results

Men with clinically localized prostate cancer are sequentially enrolled to a control group or one of four intervention groups (confection or nectar, 10 or 20 g dose; n = 8 per group) for 4 weeks prior to prostatectomy. Primary outcomes include: safety, adherence, and ellagitannin metabolism. Adherence to the intervention is >96%. No significant (≥grade II) toxicities are detected. Urinary urolithins (A, B, C, and D) and dimethyl ellagic acid (DMEA) quantified by Ultra high performance liquid chromatography tandem mass spectroscopy (UPLC/MS/MS) indicate a dose‐dependent excretion yet heterogeneous patterns among men. Men in the BRB confection groups have greater urinary excretion of the microbial urinary metabolites urolithin A and DMEA, suggesting that this food matrix provides greater colonic microflora exposure.

Conclusion

Fully characterized BRB confections and nectar are ideal for food‐based large phase III human clinical studies. BRB products provide a bioavailable source of BRB phytochemicals, however large inter individual variation in polyphenol metabolism suggests that host genetics, microflora, and other factors are critical to understanding bioactivity and metabolism.
A high power CMOS cascode power amplifier with adaptive dynamic bias control for linearity enhancement
Authors: Ren Jiangchuan , Dai Ruofan , He Jun , Zhang Zhengxuan , Zou Shichang
Published: February 2020

This work presents both high power and high linearity CMOS cascode power amplifier (PA) with adaptive dynamic bias (ADB) circuit. The ADB circuit sets appropriate gate bias for the common source and common gate (CG) amplifiers according to the input envelope signal, significantly improving the linearity. Meanwhile, harmonic termination circuits are introduced at the gate of the CG amplifier and the center‐tap node of the output transformer to short the second harmonic component to ground, further improving the linearity. In addition, this work utilizes an on‐chip series‐connected transformer‐based power combiner to enhance output power. A fully integrated differential PA including the ADB circuit is fabricated in 0.13 μm radio frequency silicon‐on‐insulator technology. From 2.5 V supply voltage, the proposed PA produces a saturated output power of 30.3 dBm with a peak power‐added efficiency of 43.1%. Thanks to the linearization techniques, the proposed PA transmits 23.5 dBm average linear output power with 3% error vector magnitude for a 20‐MHz 64‐QAM orthogonal frequency division multiplexing modulated signal without any digital predistortion circuits.
Design and simulation of all optical shift registers using D flip‐flop
Authors: Ramachandran Manohari , Prince Shanthi , Kambham Archana , Maruthi Naga
Published: February 2020

All optical memory elements are considered to be essential building components for optical networks with high practicality and utility. In this paper, a feasible integrable scheme is presented for the realization of all optical shift register, which is basically a memory device, where the information is transferred from input to output based on the configurations either in serial or parallel upon a clock pulse. Shift registers are classified based on input‐output configuration as serial input‐serial output, serial input‐parallel output, parallel input‐serial output (PISO), and parallel input‐parallel output. All optical shift register is designed using interconnected D flip‐flop (DFF) memories that are driven by standard clock pulses. DFF is built using Mach‐Zehnder interferometer‐semiconductor optical amplifier based on all optical logic gates, which is then cascaded accordingly to design different types of 4‐bit shift registers except for PISO which is designed as a 2‐bit shift register. The entire design is simulated in optisystem and verified the data transfer through DFFs in various configurations. The speed of the circuit is the same as data rate. The proposed circuits are simulated up to data rate of 100 Gbps.
How to write a research article for MRC
Authors: Trevorrow Paul , Martin Gary E.
Published: February 2020

This nonscientific tutorial proposes best practice for authors publishing research articles in Magnetic Resonance in Chemistry (MRC). It offers authors essential insights into writing eye‐catching article titles, author/co‐author names and hierarchy, IMRaD and IRDaM article structures, referencing and the composition of abstracts, introductions, experimental, results and discussion, and conclusions together with the all‐important covering letter. This arsenal of insights aims to provide tools for authors to maximize the chance of success for their research articles.
Optimizing 3D EPI for rapid T1‐weighted imaging
Authors: Norbeck Ola , Sprenger Tim , Avventi Enrico , Rydén Henric , Kits Annika , Berglund Johan , Skare Stefan
Published: February 2020

Purpose

To investigate the use of 3D EPI for rapid T1‐weighted brain imaging, focusing on the RF pulse’s influence on the contrast between gray and white matter.

Methods

An interleaved 3D EPI sequence use partial Fourier and CAIPIRINHA sampling was used to acquire T1‐weighted brain volumes with isotropic resolution, low echo times, and low geometric distortions. Five different RF pulses were evaluated in terms of fat suppression performance and gray–white matter contrast. Two binomial RF pulses were compared to a single rectangular (WE‐rect) RF pulse exciting only water, and two new RF pulses developed in this work, where one was an extension of the WE‐rect, and the other was an SLR pulse. The technique was demonstrated in three clinical cases, where brain tumor patients were imaged before and after gadolinium administration.

Results

A fat‐suppressed 3D EPI sequence with a phase encoding bandwidth of around 100 Hz was found to exhibit a good trade‐off between geometrical distortions and scan duration. Whole‐brain T1‐weighted 3D EPI images with 1.2 mm isotropic voxel size could be acquired in 24 seconds. The WE‐rect, its extension, and the SLR RF pulses resulted in reduced magnetization transfer effects and provided a 20% mean increase in gray–white matter contrast.

Conclusion

Using a high phase encoding bandwidth and RF pulses that reduce magnetization transfer effects, a fat‐suppressed multi‐shot 3D EPI sequence can be used to rapidly acquire isotropic T1‐weighted volumes.
MRI‐visible liquid crystal thermometer
Authors: Keenan Kathryn E. , Stupic Karl F. , Russek Stephen E. , Mirowski Elizabeth
Published: February 2020

Purpose

MRI parameters, such as T1, T2, and ADC, of tissue‐mimicking materials in MRI phantoms can exhibit temperature dependence, and bore temperatures can vary over a 10°C range across different MRI systems. If this variation is not accurately corrected for, the quantitative nature of reference or phantom measurements is irrelevant. Available thermometers require opening the phantoms to probe the temperature, which can introduce contaminants that may affect the stability and accuracy of the phantom. An integrated, MRI‐visible thermometer that can be read using typical imaging protocols is needed.

Theory and Methods

An MRI‐compatible thermometer was designed using liquid crystals (LCs) that exhibit rapid transitions between the LC cholesteric state and isotropic state in the room temperature range spanning 17°C to 23°C in 1.0°C increments. The LC thermometer was assessed visually and using superconducting quantum interference device magnetometry, NMR, and MRI techniques.

Results

The signal generated from the LC thermometer was visible with spin‐echo and gradient‐echo MRI images. The LC state transition temperatures were visually referenced to a National Institute of Standards and Technology‐traceable thermometer, and these LC state transitions were confirmed using superconducting quantum interference device magnetometry and NMR.

Conclusions

The LC MR‐visible thermometer had measurable changes in relative signal with temperature, which were invariant to a variety of imaging sequences used.
Translating pH‐sensitive PROgressive saturation for QUantifying Exchange rates using Saturation Times (PRO‐QUEST) MRI to a 3T clinical scanner
Authors: Kim Mina , Kujawa Aaron , Battiston Marco , Demetriou Eleni , Schneider Torben , Collorone Sara , Tur Carmen , Evans Vincent , Okuchi Sachi , Atkinson David , Gandini Wheeler‐Kingshott Claudia A. M. , Golay Xavier
Published: February 2020

Purpose

To translate the recently developed PRO‐QUEST (Progressive saturation for quantifying exchange rates using saturation times) sequence from preclinical 9.4T to 3T clinical magnetic field strength.

Methods

Numerical simulations were performed to define the optimal saturation flip angles for PRO‐QUEST saturation pulses at 3T and demonstrate the effect of a ∆T2 error on the exchange rate (kex) estimation at various field strengths. Exchange‐dependent relaxation rate (Rex) was measured for glutamate solutions in various pH, healthy volunteers and patients with multiple sclerosis (MS). Additionally, concentration‐independent ratiometric Rex maps were produced to evaluate regional signal variations across the brain of human volunteers.

Results

The calculated Rex significantly correlates with pH in glutamate samples, however, kex values are underestimated as compared to those previously obtained at 9.4T. In the ratiometric Rex map of healthy volunteers, no significant differences are found between grey matter, white matter, and basal ganglia. In patients with MS, white matter lesions are visible in single saturation power Rex maps whereas only a periventricular lesion is apparent in the ratiometric Rex map.

Conclusion

We demonstrate that quantification of pH sensitive indices using PRO‐QUEST is feasible at 3T within clinically acceptable acquisition times. Our initial findings in patients with MS show that pH sensitive indices varied with the type of lesion examined whereas no significant difference was found in healthy volunteers between tissue types, suggesting that it would be worthwhile to apply PRO‐QUEST in a larger cohort of patients to better understand its distinct imaging features relative to conventional techniques.
Test–retest reliability and long‐term stability of three‐tissue constrained spherical deconvolution methods for analyzing diffusion MRI data
Authors: Newman Benjamin T. , Dhollander Thijs , Reynier Kristen A. , Panzer Matthew B. , Druzgal T. Jason
Published: February 2020

Purpose

Several recent studies have used a three‐tissue constrained spherical deconvolution pipeline to obtain quantitative metrics of brain tissue microstructure from diffusion‐weighted MRI data. The three tissue compartments, consisting of white matter, gray matter, and CSF‐like (free water) signals, are potentially useful in the evaluation of brain microstructure in a range of pathologies. However, the reliability and long‐term stability of these metrics have not yet been evaluated.

Methods

This study examined estimates of whole‐brain microstructure for the three tissue compartments, in three separate test–retest cohorts. Each cohort had different lengths of time between baseline and retest, ranging from within the same scanning session in the shortest interval to 3 months in the longest interval. Each cohort was also collected with different acquisition parameters.

Results

The CSF‐like compartment displayed the greatest reliability across all cohorts, with intraclass correlation coefficient (ICC) values being above 0.95 in each cohort. White matter–like and gray matter–like compartments both demonstrated very high reliability in the immediate cohort (both ICC > 0.90); however, this declined in the 3‐month interval cohort to both compartments having ICC > 0.80. Regional CSF‐like signal fraction was examined in bilateral hippocampus and had an ICC > 0.80 in each cohort.

Conclusion

The three‐tissue constrained spherical deconvolution techniques provide reliable and stable estimates of tissue‐microstructure composition, up to 3 months longitudinally in a control population. This forms an important basis for further investigations using three‐tissue constrained spherical deconvolution techniques to track changes in microstructure across a variety of brain pathologies.
Two‐class constrained optimization with applications to queueing control
Authors: Girard Cory , Green Linda V. , Lewis Mark E. , Xie Jingui
Published: February 2020

Constrained Markov decision process (CMDP) is a methodology that has not seen wide applications in the literature, but is a more natural specification for modeling preferences in modern service systems. In this paper we present a general framework for solving two‐class CMDPs. In particular, we show that CMDPs can be solved by using the Lagrangian dual to specify a particular unconstrained problem. If an appropriate Lagrange multiplier can be discerned, structural results can be exploited to solve the original CMDP with the appropriate structure. We show that for two queues in parallel or two queues in series, the framework leads to simple threshold‐like optimal policies. The results in each case are used to develop heuristics for analogous problems with abandonments with applications to health care, call centers, and manufacturing systems. The efficacy of the heuristics is verified in each case via a detailed numerical study.
An efficient auxiliary projection‐based multigrid isogeometric reanalysis method and its application in an optimization framework
Authors: Liu Juanjuan , Li Enying , Wu Yunqiang , Wang Hu
Published: February 2020

An efficient optimization framework is developed in this study by integrating auxiliary projection‐based multigrid isogeometric reanalysis (MG‐IGR) and metaheuristic searching techniques. It is well known that the inherent characteristics of isogeometric analysis (IGA) are superior in shape optimization problems. Inheriting the characteristics of IGA, an auxiliary projection‐based MG reanalysis (MGR) is proposed to construct mapping between the mesh before modification and after modification during the optimization process. Subsequently, MG‐IGR is utilized to reanalyze the modified design efficiently by reusing the initial evaluated results. Moreover, the proposed MG‐IGR also eliminates the restriction of mesh consistency. In this framework, the structure can be designed directly through parameterized control of the non‐uniform rational B‐spline (NURBS) model, and the MG‐IGR fast solver enables any metaheuristic algorithm to perform the optimization procedure. Moreover, the accuracy of the simulation can be guaranteed by the NURBS model and the convergence criterion of the MG. Finally, two geometric optimization examples are presented to validate the performance of the developed framework.
Characterization of silty to fine‐sandy sediments with SH waves: full waveform inversion in comparison with other geophysical methods
Authors: Schwardt Michaela , Köhn Daniel , Wunderlich Tina , Wilken Dennis , Seeliger Martin , Schmidts Thomas , Brückner Helmut , Başaran Sait , Rabbel Wolfgang
Published: February 2020

We apply seismic full waveform inversion to SH‐ and Love‐wave data for investigating the near‐surface lithology at an archaeological site. We evaluate the resolution of the applied full waveform inversion algorithm through ground truthing in the form of an excavation and sediment core studies. Thereby, we investigate the benefits of full waveform inversion in comparison with other established methods of near‐surface prospecting in terms of resolution capabilities and interpretation security. The study is performed in a presumed harbour area of the ancient Thracian city of Ainos. The exemplary target is the source of a linear magnetic anomaly oriented perpendicular to the coast, which was found in a previous magnetic gradiometry survey, suggesting a mole. The SH‐wave full waveform inversion recovered a subsurface SH‐wave velocity model with submeter resolution showing lateral and vertical velocity variation between 40 and 150 m/s. To tame the non‐linearity of the full waveform inversion, a sequential inversion of frequency bands has to be combined with time‐windowing in order to separate the Love wave from the reflected SH wavefield. We compare the full waveform inversion results with multichannel analysis of surface waves, standard seismic reflection imaging, electrical resistivity tomography and electromagnetic induction. It turns out that the respective depth sections are correlated to a certain degree with the full waveform inversion results. However, the structural resolution of the other geophysical methods is significantly lower than for the full waveform inversion. An exception is the reflection seismic imaging, which shows the same resolution as full waveform inversion but can only be interpreted together with the full waveform inversion–based velocity model. An archaeological excavation as well as coring data allows ground truthing and a direct understanding of the geophysical structures. The results show that the target was a sort of near‐surface trench of about 3–4 m width and 0.8 m to 1.0 m depth, filled with silty sediment, which differs from the layered surrounding in colour and composition. The ground truthing revealed that only SH‐wave full waveform inversion and seismic reflection imaging could image the trench and sediment structure with satisfying lateral and depth resolution. We emphasize that the velocity distribution from SH‐wave full waveform inversion agrees closely with the excavated subsurface structures, and that the discovered changes in seismic velocity correlate with changes in the sand content in the respective sediment facies sequences. The study demonstrated that SH‐wave full waveform inversion is capable to image structural and lithological changes in the near subsurface at scales as low as 0.5 m, thus providing the high resolution needed for archaeological and geoarchaeological prospection.
Differences in stability and calcium sensitivity of the Ig domains in titin's N2A region
Authors: Kelly Colleen M. , Manukian Sophia , Kim Emily , Gage Matthew J.
Published: February 2020

Titin is a large filamentous protein that spans half a sarcomere, from Z‐disk to M‐line. The N2A region within the titin molecule exists between the proximal immunoglobulin (Ig) region and the PEVK region and protein–protein interactions involving this region are required for normal muscle function. The N2A region consists of four Ig domains (I80–I83) with a 105 amino acid linker region between I80 and I81 that has a helical nature. Using chemical stability measurements, we show that predicted differences between the adjacent Ig domains (I81–I83) correlate with experimentally determined differences in chemical stability and refolding kinetics. Our work further shows that I83 has the lowest ΔGunfolding, which is increased in the presence of calcium (pCa 4.3), indicating that Ca2+ plays a role in stabilizing this immunoglobulin domain. The characteristics of N2A's three Ig domains provide insight into the stability of the binding sites for proteins that interact with the N2A region. This work also provides insights into how Ca2+ might influence binding events involving N2A.
FiRES: A computational method for the de novo identification of internal structure similarity in proteins
Authors: Alvarez‐Carreño Claudia , Coello Gerardo , Arciniega Marcelino
Published: February 2020

Internal structure similarity in proteins can be observed at the domain and subdomain levels. From an evolutionary perspective, structurally similar elements may arise divergently by gene duplication and fusion events but may also be the product of convergent evolution under physicochemical constraints. The characterization of proteins that contain repeated structural elements has implications for many fields of protein science including protein domain evolution, structure classification, structure prediction, and protein engineering. FiRES (Find Repeated Elements in Structure) is an algorithm that relies on a topology‐independent structure alignment method to identify repeating elements in protein structure. FiRES was tested against two hand curated databases of protein repeats: MALIDUP, for very divergent duplicated domains; and RepeatsDB for short tandem repeats. The performance of FiRES was compared to that of lalign, RADAR, HHrepID, CE‐symm, ReUPred, and Swelfe. FiRES was the method that most accurately detected proteins either with duplicated domains (accuracy = 0.86) or with multiple repeated units (accuracy = 0.92). FiRES is a new methodology for the discovery of proteins containing structurally similar elements. The FiRES web server is publicly available at http://fires.ifc.unam.mx. The scripts, results, and benchmarks from this study can be downloaded from https://github.com/Claualvarez/fires.
Tracking wireworm burrowing behaviour in soil over time using 3D X‐ray computed tomography
Authors: Booth Samuel , Kurtz Benedikt , de Heer Martine I , Mooney Sacha J , Sturrock Craig J
Published: February 2020

BACKGROUND

Wireworms (larvae of the click beetle, Elateridae) are a significant agricultural pest, causing crop damage and reducing yields globally. Owing to the complex nature and opacity of the soil environment, research to investigate wireworm behaviour in situ has been scarce. X‐ray computed tomography (CT) has previously been demonstrated as a powerful tool to independently visualise the 3D root system architecture, macroinvertebrate movement and distribution of burrow systems in soil, but not simultaneously within the same sample. In this study, we apply X‐ray CT to visualise and quantify wireworms, their burrow systems and the root architecture of two contrasting crop species (Hordeum vulgare and Zea mays) in a soil pot experiment scanned at different time intervals.

RESULTS

The majority of wireworm burrows were produced within the first 20 h post inoculation, suggesting that burrow systems are established quickly and persist at a similar volume. There was a significant difference in the volume of burrow systems produced by wireworms between the two crop species suggesting differences in wireworm behaviour elicited by crop species. There was no significant correlation between burrow volume and either root volume or surface area, indicating this behavioural difference is caused by factor(s) other than the mass of root systems.

CONCLUSION

X‐ray CT shows potential as a non‐destructive technique to quantify the interaction of wireworms in the natural soil environment with crop roots, and aid the development of effective pest management strategies to minimise their negative impact on crop production. © 2020 Society of Chemical Industry
Epitaxial Graphene Growth on the Step‐Structured Surface of Off‐Axis C‐Face 3C‐SiC(1¯1¯1¯)
Authors: Shi Yuchen , Zakharov Alexei A. , Ivanov Ivan Gueorguiev , Yazdi Gholamreza , Syväjärvi Mikael , Yakimova Rositsa , Sun Jianwu
Published: February 2020

Graphene layers grown on the C‐face SiC exhibit quite different structural and electronic properties compared with those grown on the Si‐face SiC. Herein, the growth and structural properties of graphene on the off‐axis C‐face 3C‐SiC() are studied. The as‐grown 4° off‐axis 3C‐SiC() exhibits highly periodic steps with step height of ≈0.75 nm and terrace width of ≈50 nm. After annealing at 1800 °C under 850 mbar argon atmosphere, relatively uniform large graphene domains can be grown. The low‐energy electron microscopy (LEEM) results demonstrate that one monolayer (ML) to four‐ML graphene domains are grown over several micrometers square, which enables us to measure micro low‐energy electron diffraction (μ‐LEED) on the single graphene domain. The μ‐LEED pattern collected on the monolayer domain mainly exhibits four sets of graphene (1 × 1) spots, indicating the presence of graphene grains with different azimuthal orientations in the same graphene sheet. Raman spectra collected on the graphene domains show rather small D peaks, indicating the presence of less defects and higher crystalline quality of the graphene layers grown on the C‐face off‐axis 3C‐SiC().
Simultaneous confidence interval for assessing non‐inferiority with assay sensitivity in a three‐arm trial with binary endpoints
Authors: Tang Niansheng , Yu Bin
Published: February 2020

A three‐arm trial including an experimental treatment, an active reference treatment and a placebo is often used to assess the non‐inferiority (NI) with assay sensitivity of an experimental treatment. Various hypothesis‐test‐based approaches via a fraction or pre‐specified margin have been proposed to assess the NI with assay sensitivity in a three‐arm trial. There is little work done on confidence interval in a three‐arm trial. This paper develops a hybrid approach to construct simultaneous confidence interval for assessing NI and assay sensitivity in a three‐arm trial. For comparison, we present normal‐approximation‐based and bootstrap‐resampling‐based simultaneous confidence intervals. Simulation studies evidence that the hybrid approach with the Wilson score statistic performs better than other approaches in terms of empirical coverage probability and mesial‐non‐coverage probability. An example is used to illustrate the proposed approaches.
Local and non‐local controls on a persistent cold‐air pool in the Arve River Valley
Authors: Arduini G. , Chemel C. , Staquet C.
Published: February 2020

A numerical model is used to simulate a persistent cold‐air pool (PCAP) event that occurred in the section of the Arve River Valley around Passy in the French Alps. During this period, an upper‐level ridge from the Atlantic moved over Europe, allowing a PCAP to form and persist over time. The impact of the upper‐level ridge on the PCAP and on the dynamics within the valley section is quantified by examining the mass and heat budgets of the valley atmosphere. During the persistent stage, the magnitude of the flow through the tributary valleys is enhanced by the large‐scale flow. Also, the direction of the flow through one of the tributaries is found to be determined by the height of the PCAP with respect to that of the tributary above the valley floor. The tributary flows, together with subsiding motions at the valley top, control by and large the night‐time valley‐scale circulation and the thermal structure of the upper part of the PCAP, whereas thermally driven valley flows control its lower part. When the upper‐level ridge passes over the Arve River Valley, warm air advection through the tributaries continuously erodes the upper part of the PCAP during night‐time, thereby reducing its depth, while down‐valley flows export the air mass out of the valley. As the ridge moves away from the valley, the near‐surface air is found to be trapped within the valley. This trapping results from the advection of warm air in the upper part of the PCAP by the large‐scale flow channelled through one of the tributaries. This reduces the thermally induced pressure difference in the down‐valley direction, thereby suppressing the near‐surface down‐valley flow. The study therefore highlights the interplay between the large‐scale flow, the tributary flows and the thermal structure of the
PCAP.
Atmospheric rivers and water fluxes in precipitating quasi‐geostrophic turbulence
Authors: Edwards Thomas K. , Smith Leslie M. , Stechmann Samuel N.
Published: February 2020

Most of the poleward transport of water can be accounted for by long narrow corridors known as Atmospheric Rivers (ARs). ARs are typically associated with extratropical cyclones and, for dry extratropical cyclones, an idealized prototype has previously been provided by quasi‐geostrophic (QG) dynamics. However, there are few if any studies that investigate ARs in a QG framework. Here, the overarching question is: do idealized ARs appear in moist QG dynamics? A precipitating quasi‐geostrophic (PQG) model is explored as a possible prototype for ARs and associated water transport. The set‐up uses numerical simulations of geostrophic turbulence with precipitation, in a single phase. The simulations are shown to produce idealized ARs, and they have reasonably realistic statistics for such a simple set‐up. For instance, the model ARs occur roughly as frequently as in nature, based on commonly used AR identification algorithms. To produce ARs in this model, it is found that two key ingredients are needed beyond the dry QG framework: precipitation and a meridional moisture gradient. If either of these two ingredients is too weak, then less realistic ARs are produced. In addition, for a range of precipitation rates, a large fraction of the meridional moisture transport is due to
ARs.