bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multispectral near infrared absorption imaging for histology of skin cancer
Authors: Spreinat Alexander , Selvaggio Gabriele , Erpenbeck Luise , Kruss Sebastian 
Published: October 2019

AbstractMultispectral imaging combines the spectral resolution of spectroscopy with the spatial resolution of imaging and is therefore very useful for biomedical applications. Currently, histological diagnostics use mainly stainings with standard dyes (eg, hematoxylin + eosin) to identify tumors. This method is not applicable in vivo and provides low amounts of chemical information. Biomolecules absorb near infrared light (NIR, 800‐1700 nm) at different wavelengths, which could be used to fingerprint tissue. Here, we built a NIR multispectral absorption imaging setup to study skin tissue samples. NIR light (900‐1500 nm) was used for homogenous wide‐field transmission illumination and detected by a cooled InGaAs camera. In this setup, images I(x, y, λ) from dermatological samples (melanoma, nodular basal‐cell carcinoma, squamous‐cell carcinoma) were acquired to distinguish healthy from diseased tissue regions. In summary, we show the potential of multispectral NIR imaging for cancer diagnostics.
Synthesis, antimicrobial, and antioxidant activities of new pyridyl‐ and thiazolyl‐bearing carbohydrazides
Authors: Muluk Mahesh B. , Phatak Pramod S. , Pawar Shriram B. , Dhumal Sambhaji T. , Rehman Naziya N. M. A. , Dixit Prashant P. , Choudhari Prafulla B. , Haval Kishan P. 
Published: October 2019

AbstractA series of novel substituted (E)‐N′‐benzylidene‐4‐methyl‐2‐(2‐propylpyridin‐4‐yl)thiazole‐5‐carbohydrazide derivatives (6a‐l) have been synthesized by following the multistep synthetic route starting from prothionamide. The resulting compounds were characterized via 1H, 13C NMR, and HRMS spectral data. The synthesized carbohydrazides were evaluated for their in vitro antimicrobial and antioxidant activities. Tested molecules have displayed moderate to good growth inhibition activity. Among the screened compounds, 6b, 6e, 6j, and 6k are found to be the more promising antimicrobial agents. A 2,2‐diphenyl‐1‐picrylhydrazyl assay was used to test the antioxidant activity of the carbohydrazides. The carbohydrazide derivatives 6b and 6i have shown better free‐radical scavenging ability than the other investigated compounds.
Study of FABP's interactome and detecting new molecular targets in clear cell renal cell carcinoma
Authors: Wu Guangzhen , Zhang Zhiwei , Tang Qizhen , Liu Lei , Liu Wei , Li Quanlin , Wang Qifei 
Published: October 2019

AbstractFatty acids (FAs) play a crucial role in the development of clear cell renal cell carcinoma (ccRCC), FAs function requires the participation of fatty‐acid‐binding protein (FABP). Current studies have shown that different members of the FABP's family play different roles in the tumorigenesis of ccRCC. Therefore, the systematic analysis of FABPs will be of great significance. However, the diverse expression patterns and prognostic values of nine FABPs have yet to be elucidated. In this study, through multiple analysis and verification of multiple databases, such as ONCOMINE, The Human Protein Atlas, UALCAN, Gene Expression Profiling Interactive Analysis, and cBioPortal, we found that the expression of FABP1 was significantly downregulated and the expression of FABP5/6/7 was significantly upregulated in ccRCC compared with renal tissues, and the patients with high messenger RNA (mRNA) levels of the FABP5/6/7 or low mRNA levels of FABP1 were predicted to have a lower overall survival or disease‐free survival. Further analysis by the protein–protein interaction (PPI), Gene Ontology pathway, and Kyoto Encyclopedia of Genes and Genomes pathway showed that FABPs were mainly involved in the peroxisome proliferator‐activated receptor (PPAR) pathway. In coexpression analysis, we found that FABP1/5/6/7 was coexpressed with transforming growth factor‐β1 (TGF‐β1), PPARA, and LPL. This study implied that FABP1/5/6/7 could act as an important tumor biomarker of ccRCC; the role of FABPs may be related to PPAR or TGF‐β pathway.
CRISPR‐Cas9‐mediated knockout of the Prkdc in mouse embryonic stem cells leads to the modulation of the expression of pluripotency genes
Authors: Soleimani Farzad , Babaei Esmaeil , H. Feizi Mohammad A. , Fathi Fardin 
Published: October 2019

AbstractPrkdc encodes for the catalytic subunit of the DNA‐dependent protein kinase (DNA‐PKcs) playing a key role in nonhomologous end joining pathway during DNA double‐strand break repair and also influencing the homologous recombination (HR) repair system by phosphorylation of proteins involved in HR. In addition, Prkdc has other critical functions in biological processes, such as transcriptional regulation, telomere stability, apoptosis, and metabolism. DNA‐PKcs upregulates during in vitro differentiation of mouse embryonic stem cells (mESCs). To address the potential role of Prkdc in mESCs pluripotency and in vitro differentiation into ectoderm, mesoderm, and endoderm germ layers under normal physiological conditions, a bi‐allelic Prkdc‐knockout cell line was generated in the present study by employing CRISPR/Cas9 system, and subsequently, its potential role in stemness and development was studied. The results of the study showed that the expression of pluripotency‐associated genes, including Nanog and Sox‐2 were overexpressed in the bi‐allelic Prkdc‐knockout cell line. Also, bi‐allelic Prkdc‐knockout cell line was shown to have typical mESCs cell morphology, cell cycle distribution, and alkaline phosphatase activity. Furthermore, the results of the study revealed that the expression of several germ layer markers is modulated in Prkdc‐knockout lines. In conclusion, the findings of our study demonstrated the role of Prkdc during differentiation and development of ESCs.
Effect of Plasma Protein Binding on the Pharmacokinetics of Erdafitinib: Results of an Integrated Cross‐Study Analysis
Authors: Li Lilian Y. , Guo Yue , Gonzalez Martha , Ouellet Daniele 
Published: October 2019

AbstractErdafitinib, a potent oral fibroblast growth factor receptor inhibitor, is a low extraction ratio drug highly bound to alpha‐1‐acid glycoprotein (AGP) with free fraction (fu) varying across populations. This analysis aimed to characterize the impact of plasma protein binding on erdafitinib pharmacokinetics (PK). Plasma protein‐binding data (fu, AGP, albumin) and PK parameters were pooled from 6 phase 1 studies in healthy participants and 1 first‐in‐human study in patients with cancer. Binding kinetics were characterized using a nonlinear mixed‐effects model. Mean (coefficient of variation, CV%) fu was 0.510% (39.4%) for healthy participants and 0.316% (64.0%) for patients, with a 2.1‐fold higher AGP and 10% lower albumin. Linear binding of erdafitinib to AGP and albumin was observed, with >1000‐fold higher binding constant for AGP than albumin (17.6 vs 0.017 µM‐1). The fu decreased with increasing AGP in a nonlinear relationship. Despite its abundance in plasma relative to AGP, albumin contributed to <4% of the overall binding of erdafitinib (1.8% in patients; 4.0% in healthy participants). The AGP‐binding constant was 68.0% lower in predose (spiked) versus postdose (ex vivo) samples. Total oral clearance was generally proportional to the fu and higher in healthy participants than in patients, consistent with the differences in AGP. Correcting for fu accounted for the majority of the relationship between oral clearance and fu as expected with a low extraction ratio drug. Characterizing free erdafitinib concentrations is critical to accounting for differences in fu and to further investigating its clinical relevance.
A rapid colloidal gold‐based immunochromatographic strip assay for monitoring nitroxynil in milk
Authors: Na Guanqiong , Hu Xiaofei , Yang Jifei , Sun Yaning , Kwee Sharon , Tang Liang , Xing Guangxu , Xing Yunrui , Zhang Gaiping 
Published: October 2019

AbstractBACKGROUNDNitroxynil (NIT) is a veterinary drug against hepatic fluke disease for food‐producing cattle and sheep. NIT has a long half‐life time in animals since it is highly bound to plasma protein. Therefore NIT possibly remains in animal edible tissues or milk due to drug abuse. In this study, a specific murine monoclonal antibody (mAb) against NIT was prepared and an immunochromatographic strip assay based on the mAb was developed for screening NIT in milk.RESULTSThe affinity constant of the anti‐NIT mAb was 2.93 × 1010 and the anti‐NIT mAb had almost no cross‐reactivity with other analogs, so that it showed good specificity. The cutoff value of this test strip was considered to be 50 ng mL−1 by the naked eye. When detected by the strip reader, the half maximum inhibition concentration (IC50) of the immunoassay strip was calculated to be 5.716 ng mL−1 and the limit of detection (LOD) was 1.146 ng mL−1. Intra‐assay recoveries from 88.80 to 97.13% were obtained, with the highest coefficient of variation (CV) at 9.01%; inter‐assay recoveries ranged from 84.60 to 106.87%, with the highest CV at 9.93%.CONCLUSIONThe operative procedure of the proposed method can be completed within 10 min. The strip developed in this study was a practical tool for rapid semiquantitative and quantitative detection of NIT in milk. This study suggested great potential for analytically monitoring NIT in other food samples. © 2019 Society of Chemical Industry
The carbonic anhydrase activity of sinking and suspended particles in the North Pacific Ocean
Authors: Subhas Adam V. , Adkins Jess F. , Dong Sijia , Rollins Nick E. , Berelson William M. 
Published: October 2019

AbstractThe enzyme carbonic anhydrase (CA) is crucial to many physiological processes involving CO2, from photosynthesis and respiration, to calcification and CaCO3 dissolution. We present new measurements of CA activity along a North Pacific transect, on samples from in situ pumps, sediment traps, discreet plankton samples from the ship's underway seawater line, plankton tows, and surface sediment samples from multicores. CA activity is highest in the surface ocean and decreases with depth, both in suspended and sinking particles. Subpolar gyre surface particles exhibit 10× higher CA activity per liter of seawater compared to subtropical gyre surface particles. Activity persists to 4700 m in the subpolar gyre, but only to 1000 m in the subtropics. All sinking CA activity normalized to particulate organic carbon (POC) follows a single relationship (CA/POC = 1.9 ± 0.2 × 10−7 mol mol−1). This relationship is consistent with CA/POC values in subpolar plankton tow material, suspended particles, and core top sediments. We hypothesize that most subpolar CA activity is associated with rapidly sinking diatom blooms, consistent with a large mat of diatomaceous material identified on the seafloor. Compared to the basin‐wide sinking CA/POC relationship, a lower subtropical CA/POC suggests that the inventory of subtropical biomass is different in composition from exported material. Pteropods also demonstrate substantial CA activity. Scaled to the volume within pteropod shells, first‐order CO2 hydration rate constants are elevated ≥ 1000× above background. This kinetic enhancement is large enough to catalyze carbonate dissolution within microenvironments, providing observational evidence for CA‐catalyzed, respiration‐driven CaCO3 dissolution in the shallow North Pacific.
Low‐profile circularly polarized planar antenna for GPS L1, L2, and L5 bands
Authors: Mishra Shailesh , Das Sushrut , Pattnaik Shyam Sunder , Kumar Sachin , Kanaujia Binod Kumar 
Published: October 2019

AbstractIn this paper, a circularly polarized (CP) planar antenna covering global positioning system (GPS) L1 (1575.42 MHz), L2 (1227.6 MHz), and L5 (1176.45 MHz) bands is presented. The antenna consists of an elliptical patch excited through the inset feed line. A pair of concentric ring slots is etched on the ground plane to achieve dual‐band response that covers L5/L2 and L1 bands. The circular polarization is achieved by integrating a quarter‐wavelength arc with the inset feed and loading a pair of slits on the elliptical patch. In addition, the quarter‐wavelength arc improves the impedance bandwidth of the lower resonant band to cover the GPS L5 band. The antenna shows right‐hand circular polarization (RHCP) in all the three bands. The antenna also satisfies the ±1 dBi gain flatness criteria of the GPS antenna. A prototype antenna is fabricated and experimental results are found in a good match with the simulated results.
A phase‐field method for modeling cracks with frictional contact
Authors: Fei Fan , Choo Jinhyun 
Published: October 2019

SummaryWe introduce a phase‐field method for continuous modeling of cracks with frictional contacts. Compared with standard discrete methods for frictional contacts, the phase‐field method has two attractive features: (i) it can represent arbitrary crack geometry without an explicit function or basis enrichment, and (ii) it does not require an algorithm for imposing contact constraints. The first feature, which is common in phase‐field models of fracture, is attained by regularizing a sharp interface geometry using a surface density functional. The second feature, which is a unique advantage for contact problems, is achieved by a new approach that calculates the stress tensor in the regularized interface region depending on the contact condition of the interface. Particularly, under a slip condition, this approach updates stress components in the slip direction using a standard contact constitutive law, while making other stress components compatible with stress in the bulk region to ensure nonpenetrating deformation in other directions. We verify the proposed phase‐field method using stationary interface problems simulated by discrete methods in the literature. Subsequently, by allowing the phase field to evolve according to brittle fracture theory, we demonstrate the proposed method's capability for modeling crack growth with frictional contact.
The concept of representative crack elements for phase‐field fracture: Anisotropic elasticity and thermo‐elasticity
Authors: Storm J. , Supriatna D. , Kaliske M. 
Published: October 2019

SummaryThe realistic representation of material degradation at a fully evolved crack is still one of the main challenges of the phase‐field method for fracture. An approach with realistic degradation behavior is only available for isotropic elasticity in the small deformation framework. In this paper, a variational framework is presented for the standard phase‐field formulation, which allows to derive the kinematically consistent material degradation. For this purpose, the concept of representative crack elements (RCE) is introduced to analyze the fully degraded material state. The realistic material degradation is further tested using the self‐consistency condition, where the behavior of the phase‐field model is compared to a discrete crack model. The framework is applied to isotropic elasticity, anisotropic elasticity and thermo‐elasticity, but not restricted to these constitutive formulations.
A stiffness parameter and truncation error criterion for adaptive path following in structural mechanics
Authors: Maghami Ali , Schillinger Dominik 
Published: October 2019

SummaryWe explore a truncation error criterion to steer adaptive step length refinement and coarsening in incremental‐iterative path following procedures, applied to problems in large‐deformation structural mechanics. Elaborating on ideas proposed by Bergan and collaborators in the 1970s, we first describe an easily computable scalar stiffness parameter whose sign and rate of change provide reliable information on the local behavior and complexity of the equilibrium path. We then derive a simple scaling law that adaptively adjusts the length of the next step based on the rate of change of the stiffness parameter at previous points on the path. We show that this scaling is equivalent to keeping a local truncation error constant in each step. We demonstrate with numerical examples that our adaptive method follows a path with a significantly reduced number of points compared to an analysis with uniform step length of the same fidelity level. A comparison with Abaqus illustrates that the truncation error criterion effectively concentrates points around the smallest‐scale features of the path, which is generally not possible with automatic incrementation solely based on local convergence properties.
Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)
Authors: Senior Andrew W. , Evans Richard , Jumper John , Kirkpatrick James , Sifre Laurent , Green Tim , Qin Chongli , Žídek Augustin , Nelson Alexander W. R. , Bridgland Alex , Penedones Hugo , Petersen Stig , Simonyan Karen , Crossan Steve , Kohli Pushmeet , Jones David T. , Silver David , Kavukcuoglu Koray , Hassabis Demis 
Published: October 2019

AbstractWe describe AlphaFold, the protein structure prediction system that was entered by the group A7D in CASP13. Submissions were made by three free‐modeling (FM) methods which combine the predictions of three neural networks. All three systems were guided by predictions of distances between pairs of residues produced by a neural network. Two systems assembled fragments produced by a generative neural network, one using scores from a network trained to regress GDT_TS. The third system shows that simple gradient descent on a properly constructed potential is able to perform on par with more expensive traditional search techniques and without requiring domain segmentation. In the CASP13 FM assessors' ranking by summed z‐scores, this system scored highest with 68.3 vs 48.2 for the next closest group (an average GDT_TS of 61.4). The system produced high‐accuracy structures (with GDT_TS scores of 70 or higher) for 11 out of 43 FM domains. Despite not explicitly using template information, the results in the template category were comparable to the best performing template‐based methods.
Protein structure prediction assisted with sparse NMR data in CASP13
Authors: Sala Davide , Huang Yuanpeng Janet , Cole Casey A. , Snyder David A. , Liu Gaohua , Ishida Yojiro , Swapna G.V.T. , Brock Kelly P. , Sander Chris , Fidelis Krzysztof , Kryshtafovych Andriy , Inouye Masayori , Tejero Roberto , Valafar Homayoun , Rosato Antonio , Montelione Gaetano T. 
Published: October 2019

AbstractCASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and 15N‐1H residual dipolar coupling data, typical of that obtained for 15N,13C‐enriched, perdeuterated proteins up to about 40 kDa, were simulated for 11 CASP13 targets ranging in size from 80 to 326 residues. For several targets, two prediction groups generated models that are more accurate than those produced using baseline methods. Real NMR data collected for a de novo designed protein were also provided to predictors, including one data set in which only backbone resonance assignments were available. Some NMR‐assisted prediction groups also did very well with these data. CASP13 also assessed whether incorporation of sparse NMR data improves the accuracy of protein structure prediction relative to nonassisted regular methods. In most cases, incorporation of sparse, noisy NMR data results in models with higher accuracy. The best NMR‐assisted models were also compared with the best regular predictions of any CASP13 group for the same target. For six of 13 targets, the most accurate model provided by any NMR‐assisted prediction group was more accurate than the most accurate model provided by any regular prediction group; however, for the remaining seven targets, one or more regular prediction method provided a more accurate model than even the best NMR‐assisted model. These results suggest a novel approach for protein structure determination, in which advanced prediction methods are first used to generate structural models, and sparse NMR data is then used to validate and/or refine these models.
Hypovirulent effect of theCryphonectria hypovirus 1in British isolates ofCryphonectria parasitica
Authors: Romon‐Ochoa Pedro , Gorton Caroline , Lewis Alex , van der Linde Sietse , Webber Joan , Pérez‐Sierra Ana 
Published: October 2019

AbstractBackgroundChestnut blight, caused byCryphonectria parasitica, is controlled in many European countries by the naturally occurring mycovirusCryphonectria hypovirus 1(CHV‐1). During surveys of recently identified chestnut blight outbreak in England, CHV‐1 was detected in several individuals of the pathogen isolated from affected trees. We investigated two of these CHV‐1‐infected isolates (L‐6 and Db‐1) as potential biocontrol agents for deployment in the UK comparing their virulence against virus‐free (M1275) and hypovirulent (M784) European isolates by inoculating sweet chestnut seedlings.ResultsBoth the European CHV‐1 M784 hypovirulent isolate and UK L‐6 isolate formed significantly smaller lesions in sweet chestnut seedling bark than the other three isolates (Db‐1, and virulent isolates FTC121 and M1275). The highest virus concentration was detected in isolate M784, followed by L‐6, with the lowest concentration in isolate Db‐1. White colony colouration indicative of hypovirulence was common in colonies re‐isolated from smaller lesions, and the same isolates also tended to be slower growing in culture, have a higher virus concentration, and caused less epicormic growth and fewer stromata to be present in plants. L‐6 and Db‐1 virus sequences, respectively, matched the virus haplotype E‐5 detected previously in Switzerland and a mutation of the same subtype I haplotype.ConclusionIsolate L‐6 could potentially act as biocontrol for chestnut blight outbreaks in the UK but further laboratory and field experiments are needed. © 2019 Crown copyright.Pest Management Science© 2019 Society of Chemical Industry
Advanced Technologies for Quantum Photonic Devices Based on Epitaxial Quantum Dots
Authors: Zhao Tian Ming , Chen Yan , Yu Ying , Li Qing , Davanco Marcelo , Liu Jin 
Published: October 2019

AbstractQuantum photonic devices are candidates for realizing practical quantum computers and networks. The development of integrated quantum photonic devices can greatly benefit from the ability to incorporate different types of materials with complementary, superior optical or electrical properties on a single chip. Semiconductor quantum dots (QDs) serve as a core element in the emerging modern photonic quantum technologies by allowing on‐demand generation of single‐photons and entangled photon pairs. During each excitation cycle, there is one and only one emitted photon or photon pair. QD photonic devices are on the verge of unfolding for advanced quantum technology applications. This review is focused on the latest significant progress of QD photonic devices. First, advanced technologies in QD growth are discussed, with special attention to droplet epitaxy and site‐controlled QDs. Then, the wavelength engineering of QDs via strain tuning and quantum frequency conversion techniques is overviewed. The discussion is extended to advanced optical excitation techniques recently developed for achieving the desired emission properties of QDs. Finally, the advances in heterogeneous integration of active quantum light‐emitting devices and passive integrated photonic circuits are reviewed, in the context of realizing scalable quantum information processing chips.