bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated River Plastic Monitoring Using Deep Learning and Cameras
Authors: van Lieshout Colin , van Oeveren Kees , van Emmerik Tim , Postma Eric
Published: July 2020

Quantifying plastic pollution on surface water is essential to understand and mitigate the impact of plastic pollution to the environment. Current monitoring methods such as visual counting are labor intensive. This limits the feasibility of scaling to long‐term monitoring at multiple locations. We present an automated method for monitoring plastic pollution that overcomes this limitation. Floating macroplastics are detected from images of the water surface using deep learning. We perform an experimental evaluation of our method using images from bridge‐mounted cameras at five different river locations across Jakarta, Indonesia. The four main results of the experimental evaluation are as follows. First, we realize a method that obtains a reliable estimate of plastic density (68.7% precision). Our monitoring method successfully distinguishes plastics from environmental elements, such as water surface reflection and organic waste. Second, when trained on one location, the method generalizes well to new locations with relatively similar conditions without retraining (≈50% average precision). Third, generalization to new locations with considerably different conditions can be boosted by retraining on only 50 objects of the new location (improving precision from ≈20% to ≈42%). Fourth, our method matches visual counting methods and detects ≈35% more plastics, even more so during periods of plastic transport rates of above 10 items per meter per minute. Taken together, these results demonstrate that our method is a promising way of monitoring plastic pollution. By extending the variety of the data set the monitoring method can be readily applied at a larger scale.
Relationships Among Decadal Changes in Nitrate and Salinity in the Eastern and Western North Pacific Ocean After 2000
Authors: Kouketsu Shinya , Sasano Daisuke , Osafune Satoshi , Aoyama Michio
Published: July 2020

Decadal changes in nitrate and preformed nitrate, as detected by the most accurate observations possible, were small in the subsurface layer around the subarctic front in the North Pacific Ocean. However, the patterns of differences in vertical sections were similar to those in repeat observations along survey Line P and were caused mainly by decadal rather than year‐to‐year changes. The changes in nitrate and preformed nitrate along Line P after 1996 were correlated with those based on high‐accuracy observational data along 165°E (with lags of a few years). Whereas similar relationships at bidecadal timescales were reported previously based on more long‐term historical data, the high‐accuracy methods in this study allowed us to detect smaller decade‐scale differences and compare the amplitudes of the changes. Furthermore, the patterns of changes were correlated with those for salinity, which a previous study considered to be formed mainly by eastward propagation of the decadal changes observed in the western part of the northern North Pacific. The time lags between the time series for nitrate and preformed nitrate were similar to the time required for the salinity anomalies to reach the Alaska Gyre from the western part of the subarctic front, which suggests that changes in the western part of the northern North Pacific Ocean affect those in the eastern part.
Heat Production and Tidally Driven Fluid Flow in the Permeable Core of Enceladus
Authors: Liao Yang , Nimmo Francis , Neufeld Jerome A.
Published: July 2020

Saturn's moon Enceladus has a global subsurface ocean and a porous rocky core in which water‐rock reactions likely occur; it is thus regarded as a potentially habitable environment. For icy moons like Enceladus, tidal heating is considered to be the main heating mechanism, which has generally been modeled using viscoelastic solid rheologies in existing studies. Here we provide a new framework for calculating tidal heating based on a poroviscoelastic model in which the porous solid and interstitial fluid deformation are coupled. We show that the total heating rate predicted for a poroviscoelastic core is significantly larger than that predicted using a classical viscoelastic model for intermediate to large (>1014 Pa·s) rock viscosities. The periodic deformation of the porous rock matrix is accompanied by interstitial pore fluid flow, and the combined effects through viscous dissipation result in high heat fluxes particularly at the poles. The heat generated in the rock matrix is also enhanced due to the high compressibility of the porous matrix structure. For a sufficiently compressible core and high permeability, the total heat production can exceed 10 GW—a large fraction of the moon's total heat budget—without requiring unrealistically low solid viscosities. The partitioning of heating between rock and fluid constituents depends most sensitively on the viscosity of the rock matrix. As the core of Enceladus warms and weakens over time, pore fluid motion likely shifts from pressure‐driven local oscillations to buoyancy‐driven global hydrothermal convection, and the core transitions from fluid‐dominated to rock‐dominated heating.
Accelerated Multilevel Monte Carlo With Kernel‐Based Smoothing and Latinized Stratification
Authors: Taverniers Søren , Bosma Sebastian B. M. , Tartakovsky Daniel M.
Published: July 2020

Heterogeneity and a paucity of measurements of key material properties undermine the veracity of quantitative predictions of subsurface flow and transport. For such model forecasts to be useful as a management tool, they must be accompanied by computationally expensive uncertainty quantification, which yields confidence intervals, probability of exceedance, and so forth. We design and implement novel multilevel Monte Carlo (MLMC) algorithms that accelerate estimation of the cumulative distribution functions (CDFs) of quantities of interest, for example, water breakthrough time or oil production rate. Compared to standard non‐smoothed MLMC, the new estimators achieve a significant variance reduction at each discretization level by smoothing the indicator function with a Gaussian kernel or replacing standard Monte Carlo (MC) with the recently developed hierarchical Latinized stratified sampling (HLSS). After validating the kernel‐smoothed MLMC and HLSS‐enhanced MLMC methods on a single‐phase flow test bed, we demonstrate that they are orders of magnitude faster than standard MC for estimating the CDF of breakthrough times in multiphase flow problems.
Forced Changes in the Arctic Freshwater Budget Emerge in the Early 21st Century
Authors: Jahn Alexandra , Laiho Rory
Published: July 2020

Arctic liquid freshwater (FW) storage has shown a large increase over the past decades, posing the question: Is the Arctic FW budget already showing clear signs of anthropogenic climate change, or are the observed changes the result of multidecadal variability? We show that the observed change in liquid and solid Arctic FW storage is likely already driven by the changing climate, based on ensemble simulations from a state‐of‐the‐art climate model. Generally, the emergence of forced changes in Arctic FW fluxes occurs earlier for oceanic fluxes than for atmospheric or land fluxes. Nares Strait liquid FW flux is the first flux to show emergence outside the range of background variability, with this change potentially already occurring. Other FW fluxes have likely started to shift but have not yet emerged into a completely different regime. Future emissions reductions have the potential to avoid the emergence of some FW fluxes beyond the background variability.
Integrating Perspectives to Understand Lake Ice Dynamics in a Changing World
Authors: Sharma Sapna , Meyer Michael F. , Culpepper Joshua , Yang Xiao , Hampton Stephanie , Berger Stella A. , Brousil Matthew R. , Fradkin Steven C. , Higgins Scott N. , Jankowski Kathi Jo , Kirillin Georgiy , Smits Adrianne P. , Whitaker Emily C. , Yousef Foad , Zhang Shuai
Published: July 2020

Ice cover plays a critical role in physical, biogeochemical, and ecological processes in lakes. Despite its importance, winter limnology remains relatively understudied. Here, we provide a primer on the predominant drivers of freshwater lake ice cover and the current methodologies used to study lake ice, including in situ and remote sensing observations, physical based models, and experiments. We highlight opportunities for future research by integrating these four disciplines to address key knowledge gaps in our understanding of lake ice dynamics in changing winters. Advances in technology, data integration, and interdisciplinary collaboration will allow the field to move toward developing global forecasts of lake ice cover for small to large lakes across broad spatial and temporal scales, quantifying ice quality and ice thickness, moving from binary to continuous ice records, and determining how winter ice conditions and quality impact ecosystem processes in lakes over winter. Ultimately, integrating disciplines will improve our ability to understand the impacts of changing winters on lake ice.
A spore quality–quantity tradeoff favors diverse sporulation strategies in Bacillus subtilis
Authors: Mutlu Alper , Kaspar Charlotte , Becker Nils , Bischofs Ilka B
Published: July 2020

Quality–quantity tradeoffs govern the production of propagules across taxa and can explain variability in life-history traits in higher organisms. A quality–quantity tradeoff was recently discovered in spore forming bacteria, but whether it impacts fitness is unclear. Here we show both theoretically and experimentally that the nutrient supply during spore revival determines the fitness advantage associated with different sporulation behaviors in Bacillus subtilis. By tuning sporulation rates we generate spore-yield and spore-quality strategists that compete with each other in a microscopic life-cycle assay. The quality (yield) strategist is favored when spore revival is triggered by poor (rich) nutrients. We also show that natural isolates from the gut and soil employ different life-cycle strategies that result from genomic variations in the number of rap-phr signaling systems. Taken together, our results suggest that a spore quality–quantity tradeoff contributes to the evolutionary adaptation of sporulating bacteria.
Active particle feedback control with a single-shot detection convolutional neural network
Authors: Fränzl Martin , Cichos Frank
Published: July 2020

The real-time detection of objects in optical microscopy allows their direct manipulation, which has recently become a new tool for the control, e.g., of active particles. For larger heterogeneous ensembles of particles, detection techniques are required that can localize and classify different objects with strongly inhomogeneous optical contrast at video rate, which is often difficult to achieve with conventional algorithmic approaches. We present a convolutional neural network single-shot detector which is suitable for real-time applications in optical microscopy. The network is capable of localizing and classifying multiple microscopic objects at up to 100 frames per second in images as large as $$416 \times 416$$

416
×
416

pixels, even at very low signal-to-noise ratios. The detection scheme can be easily adapted and extended, e.g., to new particle classes and additional parameters as demonstrated for particle orientation. The developed framework is shown to control self-thermophoretic active particles in a heterogeneous ensemble selectively. Our approach will pave the way for new studies of collective behavior in active matter based on artificial interaction rules.
Hepatocytic transcriptional signatures predict comparative drug interaction potential of rifamycin antibiotics
Authors: Dyavar Shetty Ravi , Mykris Timothy M. , Winchester Lee C. , Scarsi Kimberly K. , Fletcher Courtney V. , Podany Anthony T.
Published: July 2020

Current strategies to treat tuberculosis (TB) and co-morbidities involve multidrug combination therapies. Rifamycin antibiotics are a key component of TB therapy and a common source of drug–drug interactions (DDIs) due to induction of drug metabolizing enzymes (DMEs). Management of rifamycin DDIs are complex, particularly in patients with co-morbidities, and differences in DDI potential between rifamycin antibiotics are not well established. DME profiles induced in response to tuberculosis antibiotics (rifampin, rifabutin and rifapentine) were compared in primary human hepatocytes. We identified rifamycin induced DMEs, cytochrome P450 (CYP) 2C8/3A4/3A5, SULT2A, and UGT1A4/1A5 and predicted lower DDIs of rifapentine with 58 clinical drugs used to treat co-morbidities in TB patients. Transcriptional networks and upstream regulator analyses showed FOXA3, HNF4α, NR1I2, NR1I3, NR3C1 and RXRα as key transcriptional regulators of rifamycin induced DMEs. Our study findings are an important resource to design effective medication regimens to treat common co-conditions in TB patients.
Ehrlichia spp. and Anaplasma spp. in Xenarthra mammals from Brazil, with evidence of novel ‘Candidatus Anaplasma spp.’
Authors: Calchi Ana Cláudia , Vultão Juliana Gaboardi , Alves Mario Henrique , Yogui Débora Regina , Desbiez Arnaud Leonard Jean , De Santi Mariele , Santana Matheus de Souza , da Silva Thiago Merighi Vieira , Werther Karin , Teixeira Marta Maria Geraldes , Machado Rosangela Zacarias , André Marcos Rogério
Published: July 2020

Anaplasmataceae agents are obligatory intracellular Gram-negative α-proteobacteria that are transmitted mostly by arthropod vectors. Although mammals of the Superorder Xenarthra (sloths, anteaters, and armadillos) have been implicated as reservoirs for several zoonotic agents, only few studies have sought to detect Anaplasmataceae agents in this group of mammals. This study aimed to investigate the occurrence and genetic diversity ofAnaplasmaspp. andEhrlichiaspp. in blood and spleen samples of free-living Xenarthra from four different states in Brazil (São Paulo, Mato Grosso do Sul, Rondônia, and Pará). Nested and conventional PCR screening assays were performed to detect therrsanddsbgenes ofAnaplasmaspp. andEhrlichiaspp., respectively. The assays were positive in 27.57% (91/330) of theAnaplasmaspp. and 24.54% (81/330) of theEhrlichiaspp. Of the 91 positiveAnaplasmaspp. samples, 56.04% were positive in a conventional PCR assay targeting the 23S–5S intergenic region. Phylogenetic and distance analyses based on therrsgene allocatedAnaplasmasequences from sloths captured in Rondônia and Pará states in a single clade, which was closely related to theA. marginale,A. ovis,andA. capraclades. The sequences detected in southern anteaters from São Paulo were allocated in a clade closely related to sequences ofAnaplasmaspp. detected inNasua nasua,Leopardus pardalis, andCerdocyon thousin Brazil. These sequences were positioned close toA. odocoileisequences. Genotype analysis corroborated previous findings and demonstrated the circulation of two distinctAnaplasmagenotypes in animals from north and southeast Brazil. The first genotype was new. The second was previously detected inN. nasuain Mato Grosso do Sul state. The intergenic region analyses also demonstrated two distinct genotypes ofAnaplasma. The sequences detected in Xenarthra from Pará and Rondônia states were closely related to those inA. marginale,A. ovis,andA. capra.Anaplasmaspp. sequences detected in Xenarthra from São Paulo and were allocated close to those inA. phagocytophilum. The analyses based on thedsbgene grouped theEhrlichiaspp. sequences with sequences ofE. canis(São Paulo, Mato Grosso do Sul, and Pará) andE. minasensis(Rondônia and Pará). The data indicate the occurrence ofE. canisandE. minasensisand two possible newCandidatusspecies ofAnaplasmaspp. in free-living mammals of the Superorder Xenarthra in Brazil.
Elevated troponin levels are associated with early neurological worsening in ischemic stroke with atrial fibrillation
Authors: Nam Ki-Woong , Kim Chi Kyung , Yu Sungwook , Chung Jong-Won , Bang Oh Young , Kim Gyeong-Moon , Jung Jin-Man , Song Tae-Jin , Kim Yong-Jae , Kim Bum Joon , Heo Sung Hyuk , Park Kwang-Yeol , Kim Jeong-Min , Park Jong-Ho , Choi Jay Chol , Park Man-Seok , Kim Joon-Tae , Choi Kang-Ho , Hwang Yang Ha , Seo Woo-Keun , Oh Kyungmi
Published: July 2020

Serum cardiac troponin I (cTnI) is often elevated in patients with ischemic stroke, and is associated with their prognosis. Since cTnI is also closely related to atrial fibrillation (AF), cTnI may be a sensitive prognostic indicator in patients with AF-related stroke. This study aimed to evaluate the association between serum cTnI and early neurological deterioration (END) in patients with AF-related stroke. We included consecutive AF-related stroke patients between 2013 and 2015. END was defined as an increase ≥ 2 in the total NIHSS score or ≥ 1 in the motor NIHSS score within the first 72 h of admission. A total of 1,133 patients with AF-related stroke were evaluated. In multivariable analysis, cTnI [adjusted odds ratio (aOR) = 1.16, 95% confidence interval (CI) 1.00–1.34; P = 0.047] remained significant after adjusting for confounders. Initial NIHSS score (aOR = 1.03, 95% CI 1.00–1.06; P = 0.043) was also positively associated with END; meanwhile, the use of anticoagulants was negatively associated in both vitamin K antagonists (aOR = 0.35, 95% CI 0.23–0.54; P < 0.001) and new oral anticoagulants (aOR = 0.41, 95% CI 0.19–0.89; P = 0.024). In conclusion, higher serum cTnI was associated with END in patients with AF-related stroke.
Structural analysis of 70S ribosomes by cross-linking/mass spectrometry reveals conformational plasticity
Authors: Tüting Christian , Iacobucci Claudio , Ihling Christian H. , Kastritis Panagiotis L. , Sinz Andrea
Published: July 2020

The ribosome is not only a highly complex molecular machine that translates the genetic information into proteins, but also an exceptional specimen for testing and optimizing cross-linking/mass spectrometry (XL-MS) workflows. Due to its high abundance, ribosomal proteins are frequently identified in proteome-wide XL-MS studies of cells or cell extracts. Here, we performed in-depth cross-linking of the E. coli ribosome using the amine-reactive cross-linker disuccinimidyl diacetic urea (DSAU). We analyzed 143 E. coli ribosomal structures, mapping a total of 10,771 intramolecular distances for 126 cross-link-pairs and 3,405 intermolecular distances for 97 protein pairs. Remarkably, 44% of intermolecular cross-links covered regions that have not been resolved in any high-resolution E. coli ribosome structure and point to a plasticity of cross-linked regions. We systematically characterized all cross-links and discovered flexible regions, conformational changes, and stoichiometric variations in bound ribosomal proteins, and ultimately remodeled 2,057 residues (15,794 atoms) in total. Our working model explains more than 95% of all cross-links, resulting in an optimized E. coli ribosome structure based on the cross-linking data obtained. Our study might serve as benchmark for conducting biochemical experiments on newly modeled protein regions, guided by XL-MS. Data are available via ProteomeXchange with identifier PXD018935.
Machine learning for predicting pathological complete response in patients with locally advanced rectal cancer after neoadjuvant chemoradiotherapy
Authors: Huang Chun-Ming , Huang Ming-Yii , Huang Ching-Wen , Tsai Hsiang-Lin , Su Wei-Chih , Chang Wei-Chiao , Wang Jaw-Yuan , Shi Hon-Yi
Published: July 2020

For patients with locally advanced rectal cancer (LARC), achieving a pathological complete response (pCR) after neoadjuvant chemoradiotherapy (CRT) provides them with the optimal prognosis. However, no reliable prediction model is presently available. We evaluated the performance of an artificial neural network (ANN) model in pCR prediction in patients with LARC. Predictive accuracy was compared between the ANN, k-nearest neighbor (KNN), support vector machine (SVM), naïve Bayes classifier (NBC), and multiple logistic regression (MLR) models. Data from two hundred seventy patients with LARC were used to compare the efficacy of the forecasting models. We trained the model with an estimation data set and evaluated model performance with a validation data set. The ANN model significantly outperformed the KNN, SVM, NBC, and MLR models in pCR prediction. Our results revealed that the post-CRT carcinoembryonic antigen is the most influential pCR predictor, followed by intervals between CRT and surgery, chemotherapy regimens, clinical nodal stage, and clinical tumor stage. The ANN model was a more accurate pCR predictor than other conventional prediction models. The predictors of pCR can be used to identify which patients with LARC can benefit from watch-and-wait approaches.
Model-based optimization of combination protocols for irradiation-insensitive cancers
Authors: Hat Beata , Jaruszewicz-Błońska Joanna , Lipniacki Tomasz
Published: July 2020

Alternations in the p53 regulatory network may render cancer cells resistant to the radiation-induced apoptosis. In this theoretical study we search for the best protocols combining targeted therapy with radiation to treat cancers with wild-type p53, but having downregulated expression of PTEN or overexpression of Wip1 resulting in resistance to radiation monotherapy. Instead of using the maximum tolerated dose paradigm, we exploit stochastic computational model of the p53 regulatory network to calculate apoptotic fractions for both normal and cancer cells. We consider combination protocols, with irradiations repeated every 12, 18, 24, or 36 h to find that timing between Mdm2 inhibitor delivery and irradiation significantly influences the apoptotic cell fractions. We assume that uptake of the inhibitor is higher by cancer than by normal cells and that cancer cells receive higher irradiation doses from intersecting beams. These two assumptions were found necessary for the existence of protocols inducing massive apoptosis in cancer cells without killing large fraction of normal cells neighboring tumor. The best found protocols have irradiations repeated every 24 or 36 h with two inhibitor doses per irradiation cycle, and allow to induce apoptosis in more than 95% of cancer cells, killing less than 10% of normal cells.
Cancer-associated fibroblasts stimulate primary tumor growth and metastatic spread in an orthotopic prostate cancer xenograft model
Authors: Linxweiler Johannes , Hajili Turkan , Körbel Christina , Berchem Carolina , Zeuschner Philip , Müller Andreas , Stöckle Michael , Menger Michael D. , Junker Kerstin , Saar Matthias
Published: July 2020

The unique microenvironment of the prostate plays a crucial role in the development and progression of prostate cancer (PCa). We examined the effects of cancer-associated fibroblasts (CAFs) on PCa progression using patient-derived fibroblast primary cultures in a representative orthotopic xenograft model. Primary cultures of CAFs, non-cancer-associated fibroblasts (NCAFs) and benign prostate hyperplasia-associated fibroblasts (BPHFs) were generated from patient-derived tissue specimens. These fibroblasts were coinjected together with cancer cells (LuCaP136 spheroids or LNCaP cells) in orthotopic PCa xenografts to investigate their effects on local and systemic tumor progression. Primary tumor growth as well as metastatic spread to lymph nodes and lungs were significantly stimulated by CAF coinjection in LuCaP136 xenografts. When NCAFs or BPHFs were coinjected, tumor progression was similar to injection of tumor cells alone. In LNCaP xenografts, all three fibroblast types significantly stimulated primary tumor progression compared to injection of LNCaP cells alone. CAF coinjection further increased the frequency of lymph node and lung metastases. This is the first study using an orthotopic spheroid culture xenograft model to demonstrate a stimulatory effect of patient-derived CAFs on PCa progression. The established experimental setup will provide a valuable tool to further unravel the interacting mechanisms between PCa cells and their microenvironment.
Rod function deficit in retained photoreceptors of patients with class B Rhodopsin mutations
Authors: Cideciyan Artur V. , Jacobson Samuel G. , Roman Alejandro J. , Sumaroka Alexander , Wu Vivian , Charng Jason , Lisi Brianna , Swider Malgorzata , Aguirre Gustavo D. , Beltran William A.
Published: July 2020

A common inherited retinal disease is caused by mutations in RHO expressed in rod photoreceptors that provide vision in dim ambient light. Approximately half of all RHO mutations result in a Class B phenotype where mutant rods are retained in some retinal regions but show severe degeneration in other regions. We determined the natural history of dysfunction and degeneration of retained rods by serially evaluating patients. Even when followed for more than 20 years, rod function and structure at some retinal locations could remain unchanged. Other locations showed loss of both vision and photoreceptors but the rate of rod vision loss was greater than the rate of photoreceptor degeneration. This unexpected divergence in rates with disease progression implied the development of a rod function deficit beyond loss of cells. The divergence of progression rates was also detectable over a short interval of 2 years near the health-disease transition in the superior retina. A model of structure–function relationship supported the existence of a large rod function deficit which was also most prominent near regions of health-disease transition. Our studies support the realistic therapeutic goal of improved night vision for retinal regions specifically preselected for rod function deficit in patients.
Detection of femtosecond spin injection into a thin gold layer by time and spin resolved photoemission
Authors: Bühlmann K. , Saerens G. , Vaterlaus A. , Acremann Y.
Published: July 2020

The ultrafast demagnetization effect allows for the generation of femtosecond spin current pulses, which is expected to extend the fields of spin transport and spintronics to the femtosecond time domain. Thus far, directly observing the spin polarization induced by spin injection on the femtosecond time scale has not been possible. Herein, we present time- and spin-resolved photoemission results of spin injection from a laser-excited ferromagnet into a thin gold layer. The injected spin polarization is aligned along the magnetization direction of the underlying ferromagnet. Its decay time depends on the thickness of the gold layer, indicating that transport as well as storage of spins are relevant. This capacitive aspect of spin transport may limit the speed of future spintronic devices.
Lead sulphide colloidal quantum dots for room temperature NO2 gas sensors
Authors: Mitri Federica , De Iacovo Andrea , De Luca Massimiliano , Pecora Alessandro , Colace Lorenzo
Published: July 2020

Colloidal quantum dots (CQDs) have been recently investigated as promising building blocks for low-cost and high-performance gas sensors due to their large effective surface-to-volume ratio and their suitability for versatile functionalization through surface chemistry. In this work we report on lead sulphide CQDs based sensors for room temperature NO2 detection. The sensor response has been measured for different pollutant gases including NO2, CH4, CO and CO2 and for different concentrations in the 2.8–100 ppm range. For the first time, the influence of the QDs film thickness on the sensor response has been investigated and optimized. Upon 30 ppm NO2 release, the best room temperature gas response is about 14 Ω/Ω, with response and recovery time of 12 s and 26 min, respectively. A detection limit of about 0.15 ppb was estimated from the slope of the sensor response and its electric noise. The gas sensors exhibit high sensitivity to NO2, remarkable selectivity, repeatability and full recovery after exposure.
α-Hemolysin of uropathogenic E. coli regulates NLRP3 inflammasome activation and mitochondrial dysfunction in THP-1 macrophages
Authors: Verma Vivek , Kumar Parveen , Gupta Surbhi , Yadav Sonal , Dhanda Rakesh Singh , Thorlacius Henrik , Yadav Manisha
Published: July 2020

Hemolysin expressing UPEC strains have been associated with severe advanced kidney pathologies, such as cystitis and pyelonephritis, which are associated with an inflammatory response. Macrophages play an important role in regulating an inflammatory response during a urinary tract infection. We have studied the role of purified recombinant α-hemolysin in inducing inflammatory responses and cell death in macrophages. Acylation at lysine residues through HlyC is known to activate proHlyA into a fully functional pore-forming toxin, HlyA. It was observed that active α-hemolysin (HlyA) induced cleavage of caspase-1 leading to the maturation of IL-1β, while inactive α-hemolysin (proHlyA) failed to do so in THP-1 derived macrophages. HlyA also promotes deubiquitination, oligomerization, and activation of the NLRP3 inflammasome, which was found to be dependent on potassium efflux. We have also observed the co-localization of NLRP3 within mitochondria during HlyA stimulations. Moreover, blocking of potassium efflux improved the mitochondrial health in addition to a decreased inflammatory response. Our study demonstrates that HlyA stimulation caused perturbance in potassium homeostasis, which led to the mitochondrial dysfunction followed by an acute inflammatory response, resulting in cell death. However, the repletion of intracellular potassium stores could avoid HlyA induced macrophage cell death. The findings of this study will help to understand the mechanism of α-hemolysin induced inflammatory response and cell death.
Cell spheroid fusion: beyond liquid drops model
Authors: Kosheleva Nastasia V. , Efremov Yuri M. , Shavkuta Boris S. , Zurina Irina M. , Zhang Deying , Zhang Yuanyuan , Minaev Nikita V. , Gorkun Anastasiya A. , Wei Shicheng , Shpichka Anastasia I. , Saburina Irina N. , Timashev Peter S.
Published: July 2020

Biological self-assembly is crucial in the processes of development, tissue regeneration, and maturation of bioprinted tissue-engineered constructions. The cell aggregates—spheroids—have become widely used model objects in the study of this phenomenon. Existing approaches describe the fusion of cell aggregates by analogy with the coalescence of liquid droplets and ignore the complex structural properties of spheroids. Here, we analyzed the fusion process in connection with structure and mechanical properties of the spheroids from human somatic cells of different phenotypes: mesenchymal stem cells from the limbal eye stroma and epithelial cells from retinal pigment epithelium. A nanoindentation protocol was applied for the mechanical measurements. We found a discrepancy with the liquid drop fusion model: the fusion was faster for spheroids from epithelial cells with lower apparent surface tension than for mesenchymal spheroids with higher surface tension. This discrepancy might be caused by biophysical processes such as extracellular matrix remodeling in the case of mesenchymal spheroids and different modes of cell migration. The obtained results will contribute to the development of more realistic models for spheroid fusion that would further provide a helpful tool for constructing cell aggregates with required properties both for fundamental studies and tissue reparation.
Characterization of skin surface and dermal microbiota in dogs with mast cell tumor
Authors: Zamarian Valentina , Catozzi Carlotta , Cuscó Anna , Stefanello Damiano , Ferrari Roberta , Ceciliani Fabrizio , Francino Olga , Sánchez Armand , Grieco Valeria , Zani Davide , Talenti Andrea , Crepaldi Paola , Lecchi Cristina
Published: July 2020

The skin microbiota interacts with the host immune response to maintain the homeostasis. Changes in the skin microbiota are linked to the onset and the progression of several diseases, including tumors. We characterized the skin surface and dermal microbiota of 11 dogs affected by spontaneous mast cell tumor (MCT), using skin contralateral sites as intra-animal healthy controls. The microbial profile differed between healthy and tumor skin surfaces and dermis, demonstrating that the change in microbiota composition is related to the presence of MCT. The number of observed taxa between MCT and healthy skin surfaces was detected, showing a decrease in number and heterogeneity of taxa over the skin surface of MCT, at both inter- and intra-individual level. Preliminary data on bacterial population of MCT dermis, obtained only on three dogs, demonstrated an intra-individual reduction of taxa number when compared to the skin surface. Taxonomy reveals an increase of Firmicutes phylum and Corynebacteriaceae family in MCT skin surface when compared to the healthy contralateral. In conclusion, we demonstrate that microbial population of skin surface and dermis is related to mast cell tumor. Our study provides the basis for future investigations aiming to better define the interaction between mast cell tumors, microbiota and host immune response.
Laparoscopic complete mesocolic excision with D3 lymph node dissection for right colon cancer in elderly patients
Authors: Hwang Duk Yeon , Lee Gyeo Ra , Kim Ji Hoon , Lee Yoon Suk
Published: July 2020

Complete mesocolic excision (CME) with D3 lymph node dissection is considered an oncological surgery for right colon cancer. However, there is still controversy for extensive oncological surgery in elderly patients. The aim of this study is to evaluate the safety and oncological outcomes of laparoscopic CME with D3 lymph node dissection for right colon cancer in elderly patients. Patients who underwent laparoscopic right colectomy, from 2004 to 2014, were divided into Groups A (age ≥ 70 years, n = 80) or B (age < 70 years, n = 127). Short and long-term outcomes were analysed. Basic demographics and short-term surgical outcomes were similar between groups. Among pathological outcomes, the mean number of harvested lymph nodes was significantly less in Group A. Adjuvant chemotherapy refusal rate was significantly higher in Group A. Overall and recurrence-free survival were similar between groups. We found laparoscopic CME with D3 lymph node dissection is a safe and feasible surgical option for right colon cancer in elderly patients.
High gain, wide-angle QCTO-enabled modified Luneburg lens antenna with broadband anti-reflective layer
Authors: Biswas Soumitra , Mirotznik Mark
Published: July 2020

The gradient-index (GRIN) Luneburg lens antenna offers significant benefits, e.g. high aperture efficiency, low-power, minimal cost, wide beam scanning angle and broad bandwidth, over phased array antennas and reflector antennas. However, the spherical shape of the Luneburg lens geometry complicates the integration of standard planar feed sources and poses significant implementation challenge. To eliminate the feed mismatch problem, the quasi-conformal transformation optics (QCTO) method can be adopted to modify the lens’ spherical feed surface into a planar one. However, Luneburg lenses designed with QCTO method are limited to poor performance due to the presence of the reflections and beam broadening arising from the quasi-conformal mapping. In this paper, we present a new method of implementing QCTO-enabled modified Luneburg lens antenna by designing a broadband anti-reflective layer along with the modified lens’s planar excitation surface. The proposed anti-reflector layer is inherently broadband in nature, has a continuously tapered inhomogeneous dielectric permittivity profile along its thickness, and ensures broadband impedance matching. To show the new QCTO modified Luneburg lens antenna, an example lens antenna was designed at Ka-band (26–40 GHz) and fabricated using fused deposition modeling (FDM) based additive manufacturing technique. Electromagnetic performance of the lens antenna was experimentally demonstrated.
Large-scale controls of propagation of the Madden-Julian Oscillation
Authors: Jiang Xianan , Maloney Eric , Su Hui
Published: July 2020

With widespread influence on global climate and weather extremes, the Madden-Julian Oscillation (MJO) plays a crucial role in subseasonal prediction. Our latest global climate models (GCMs), however, have great difficulty in realistically simulating the MJO. This model inability is largely due to problems in representation of MJO’s cumulus organization. This study, based on a series of idealized aqua-planet model experiments using an atmospheric-only GCM, clearly demonstrates that MJO propagation is strongly modulated by the large-scale background state in which the lower-tropospheric mean moisture gradient and zonal winds are critical. Therefore, when tuning climate models to achieve improved MJO simulations, particular attention needs to be placed on the model large-scale mean state that is also significantly affected by cumulus parameterizations. This study indicates that model biases in representing MJO propagation may be related to the widely reported double-ITCZ (intertropical convergence zone) problem in climate models.
Correction: The recent advances in surface antibacterial strategies for biomedical catheters
Authors: Liu Lin , Shi Hengchong , Yu Huan , Yan Shunjie , Luan Shifang
Published: July 2020

Correction for ‘The recent advances in surface antibacterial strategies for biomedical catheters’ by Lin Liu et al., Biomater. Sci., 2020, DOI: 10.1039/d0bm00659a.
Bi(nanoparticles)/CNx(nanosheets) nanocomposites as high capacity and stable electrode materials for supercapacitors: the role of urea
Authors: Butenko Denys S. , Zhang Xinyu , Zatovsky Igor V. , Fesych Igor V. , Li Shilin , Chen Ruoyu , Chufarov Marian , Symonenko Oleksii , Klyui N. I. , Han Wei
Published: July 2020

A facile method was developed to prepare Bi/CNx nanocomposites for high performance energy storage devices.
Photoformation of persistent free radicals on a montmorillonite-humic acid complex simulated as particulate organic matter in an aqueous solution
Authors: Li Xintong , Shen Chen , Zhao Hongxia , Jiang Jingqiu , Ban Zixin , Chen Zhenyu , Qu Baocheng
Published: July 2020

This study investigates the formation of persistent free radicals (PFRs) on simulated particulate organic matter (POM) under irradiation in water.
Correction: 4D synchrotron microtomography and pore-network modelling for direct in situ capillary flow visualization in 3D printed microfluidic channels
Authors: Piovesan Agnese , Van De Looverbosch Tim , Verboven Pieter , Achille Clement , Parra Cabrera Cesar , Boller Elodie , Cheng Yin , Ameloot Rob , Nicolai Bart
Published: July 2020

Correction for ‘4D synchrotron microtomography and pore-network modelling for direct in situ capillary flow visualization in 3D printed microfluidic channels’ by Agnese Piovesan et al., Lab Chip, 2020, 20, 2403–2411, DOI: 10.1039/D0LC00227E.
A novel benzothiadiazole-based and NIR-emissive fluorescent sensor for detection of Hg2+ and its application in living cell and zebrafish imaging
Authors: He Haifeng , Meng Xiangying , Deng Lili , Sun Qi , Huang Xuelong , Lan Ning , Zhao Feng
Published: July 2020

The probe TBBA exhibited excellent analytical properties with a remarkably large Stokes shift (195 nm), rapid response, high selectivity and sensitivity, good binding constant (2.37 × 104 M−1) and low LOD (13.10 nM).
Thermo-responsive light-emitting metal complexes and related materials
Authors: Li Rui , Xu Fa-Feng , Gong Zhong-Liang , Zhong Yu-Wu
Published: July 2020

This review discusses the fundamentals and design strategies for the development of thermo-responsive metal–ligand coordination materials and the applications of these materials in temperature sensing, bioimaging, information security, etc.
Photo-induced preparation of unnatural α-amino acids: synthesis and characterization of novel Leu5-enkephalin analogues
Authors: Xue Hongxiang , Guo Mengzhun , Wang Chao , Shen Yuxuan , Qi Rupeng , Wu Yifei , Xu Zhaoqing , Chang Min
Published: July 2020

2.6-Fold more long-lasting compared to Leu5-enkephalin.
Interfacial engineering by creating Cu-based ternary heterostructures on C3N4 tubes towards enhanced photocatalytic oxidative coupling of benzylamines
Authors: Fu Yunqi , Zheng Mang , Li Qi , Zhang Liping , Wang Shuai , Kondratiev V. V. , Jiang Baojiang
Published: July 2020

Cu/Cu2O/Cu3N heterostructures supported C3N4 tubes were synthesized by one-step hydrothermal treatment followed by calcination, which showed enhanced photocatalytic activity for oxidative self-coupling of benzylamine under visible-light.
Structure–activity relationships in well-defined conjugated oligomer photocatalysts for hydrogen production from water
Authors: Aitchison Catherine M. , Sachs Michael , Little Marc A. , Wilbraham Liam , Brownbill Nick J. , Kane Christopher M. , Blanc Frédéric , Zwijnenburg Martijn A. , Durrant James R. , Sprick Reiner Sebastian , Cooper Andrew I.
Published: July 2020

Oligomer chain length and backbone twisting were found to have a strong effect on optoelectronic properties but a trimer of dibenzo[b,d]thiophene sulfone was found to have high photocatalytic activity approaching that of its polymer analogue.
Two-dimensional CuAg/Ti3C2 catalyst for electrochemical synthesis of ammonia under ambient conditions: a combined experimental and theoretical study
Authors: Liu Anmin , Yang Qiyue , Ren Xuefeng , Gao Mengfan , Yang Yanan , Gao Liguo , Li Yanqiang , Zhao Yingyuan , Liang Xingyou , Ma Tingli
Published: July 2020

With preferable adsorption of N2, desorption of NH3, and suppression of the HER, CuAg/Ti3C2 is a promising catalyst for the NRR.
Role of phosphate source in improving the proton conductivity of tin pyrophosphate and its composite electrolytes
Authors: Ramaiyan Kannan P. , Herrera Sergio , Workman Michael J. , Semelsberger Troy A. , Atanasov Vladimir , Kerres Jochen , Maurya Sandip , Kim Yu Seung , Kreller Cortney R. , Mukundan Rangachary
Published: July 2020

Proper phosphorus precursor selection during synthesis could help produce better tin-pyrophosphate powder and composite membranes with improved fuel cell performance.
Towards the understanding of acetonitrile suppressing salt precipitation mechanism in a water-in-salt electrolyte for low-temperature supercapacitors
Authors: Sun Yinglun , Wang Yue , Liu Lingyang , Liu Bao , Zhang Qingnuan , Wu Dandan , Zhang Hongzhang , Yan Xingbin
Published: July 2020

Acetonitrile suppressing precipitation of NaClO4 originates from transforming the cation–anion aggregate structure to contact ion pairs and/or solvent separated ion pairs.
Challenges and opportunities in the bottom-up mechanochemical synthesis of noble metal nanoparticles
Authors: de Oliveira Paulo F. M. , Torresi Roberto M. , Emmerling Franziska , Camargo Pedro H. C.
Published: July 2020

This review covers the fundamentals and recent developments on the mechanochemical synthesis of noble metal nanoparticles.
Dual-responsive TPGS crosslinked nanocarriers to overcome multidrug resistance
Authors: Li Li , Liu Tao , Liao Jia-Xin , Zhang Zhe-Yi , Song Dai-Bo , Wang Guan-Hai
Published: July 2020

Efficient delivery of chemotherapeutic agents into tumor cells and reversal of chemoresistance are crucially important to enhance cancer therapy.
Highly adhesive, washable and stretchable on-skin electrodes based on polydopamine and silk fibroin for ambulatory electrocardiography sensing
Authors: Du Xiaohui , Niu Zhikai , Li Rongjin , Yang Hui , Hu Wenping
Published: July 2020

Highly skin-adhesive, washable and stretchable electrodes were fabricated by combining polydopamine, silk fibroin, and SEBS/Au films for ambulatory electrocardiography sensing.
Heavy Mn2+-doped near-infrared photon upconversion luminescence in fluoride RbZnF3:Yb3+,Mn2+ guided by dopant distribution simulation
Authors: Han Xinxin , Song Enhai , Zhang Shuai , Ye Shi , Yang Xiao-Bao , Zhang Qinyuan
Published: July 2020

NIR UC emission was observed in heavy Mn2+-doped RbZnF3:Yb3+,Mn2+ designed by the dopant-distribution prediction simulation. The GSA/ESA and GSA/ETU models of the super-exchange-coupled Yb3+–Mn2+–Mn2+ trimer are proposed for the NIR UC emission.
Double threshold construction method for attribute‐induced three‐way concept lattice in incomplete fuzzy formal context
Authors: Long Binghan , Xu Weihua , Zhang Xiaoyan
Published: July 2020

Concept lattice theory is the basis of formal concept analysis. It is an effective tool for knowledge representation and discovery. Three‐way decision theory is a new decision theory based on rough sets and decision rough sets. In this study, a method is proposed for constructing attribute‐induced three‐way concept lattices in an incomplete fuzzy formal context. First, the authors introduce the related knowledge of the classical formal context, the fuzzy formal context and incomplete fuzzy formal context in detail. They put forward a method to fill the incomplete formal context. Secondly, they propose a double threshold operation, which divides the relationship between objects and attributes into three parts: belonging, not belonging and undetermined. Thirdly, they propose three methods to complement incomplete formal context and introduce their advantages and disadvantages. Fourthly, they deal with incomplete formal context by special symbol completion method and get related algorithms of attribute‐induced three‐way concept lattice. Finally, a case is given to verify the effectiveness of the algorithm for constructing attribute‐induced three‐way concept lattices.
Single‐shot detector with enriched semantics for PCB tiny defect detection
Authors: Shi Wei , Lu Zhisheng , Wu Wei , Liu Hong
Published: July 2020

Printed circuit board (PCB) defect detection is one of the primary problems in quality control of the most electronic products. Usually, the industrial PCB imagery has high resolution, but defects take up a small proportion (often only ∼10 pixels in size), which makes it difficult to use traditional machine vision methods. To this end, a novel single shot object detector (SSDT) is proposed for tiny defect detection in PCBs in this study. Specifically, a semantic ascending module, which propagates the semantic property of deep layers to shallow layers, is presented by fusing features of different levels. An attention mechanism is utilised to learn the relationship of the features to be fused across channels and a shuffle module is used to eliminate the aliasing effect after fusion. Moreover, the improved non‐maximum suppression is proposed to extenuate the overlap effect for testing the whole PCB image. The proposed detector can rapidly detect tiny defects and the results of SSD and SSDT are further compared not only in PCB defect dataset but also the object detection public dataset PASCAL VOC2007 where SSDT achieves 81.3% mAP, better than SSD (79.5%). In final, the proposed detector is validated to be robust to rotation and blur.
Using normal dictionaries to extract multiple semantic relationships
Authors: Liang Li , Tian Fang
Published: July 2020

This article proposes a rule‐based semantic relationship extraction method for Chinese sentiment lexicon to solve the problem that words in the sentiment dictionary cannot be updated in time, and expand the lexicon and the semantic relationship in the dictionary. Using the massive information on the Internet, the modern Chinese dictionary and sentiment dictionary and other resources, based on the interpretation of words and the characteristics of semantic relationships between words, sentiment lexicon are automatically extracted and their semantic relationships are annotated. At the same time, the semantic relationship extraction rules are defined, and the sentiment lexicon with synonymous relationship and antisense relationship is extracted recursively. The extraction rules and algorithms of emotional intensity relationship are also improved, and the lexicon is extracted according to the level of degree adverbs and their emotional weights are calculated. Compare the extraction effect before and after the improved algorithm and the change of the number of lexicon extracted after increasing the corpus. The experimental results show the effectiveness and accuracy of the proposed method.