bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractIn 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

AbstractThe 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

ObjectivesProgrammed 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.MethodsPubMed, 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).ResultsEleven 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).ConclusionsThe 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

AbstractWater 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

AbstractMicrobially 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

AbstractDrug 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.
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

ScopeBlack 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 resultsMen 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.ConclusionFully 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

AbstractThis 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

AbstractAll 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

AbstractThis 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

PurposeTo 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.MethodsAn 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.ResultsA 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.ConclusionUsing 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

PurposeMRI 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 MethodsAn 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.ResultsThe 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.ConclusionsThe 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

PurposeTo 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.MethodsNumerical 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.ResultsThe 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.ConclusionWe 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

PurposeSeveral 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.MethodsThis 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.ResultsThe 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.ConclusionThe 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

AbstractConstrained 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.