bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine Learning Models for the Seasonal Forecast of Winter Surface Air Temperature in North America
Authors: Qian Qi Feng , Jia Xiao Jing , Lin Hai
Published: August 2020

In this study, two machine learning (ML) models (support vector regression (SVR) and extreme gradient boosting (XGBoost)) are developed to perform seasonal forecasts of the surface air temperature (SAT) in winter (December‐January‐February, DJF) in North America (NA). The seasonal forecast skills of the two ML models are evaluated via cross validation. The forecast results from one linear regression (LR) model, and two dynamic climate models are used for comparison. In the take‐one‐out hindcast experiment, the two ML models and the LR model show reasonable seasonal forecast skills for winter SAT in NA. Compared to the two dynamic models, the two ML models and the LR model have better forecast skill for the winter SAT over central NA, which is mainly derived from a skillful forecast of the second empirical orthogonal function (EOF) mode of winter SAT over NA. In general, the SVR model and XGBoost model hindcasts show better forecast performances than the LR model. However, the LR model shows less dependence on the size of the training data set than the SVR and XGBoost models. In the real forecast experiments during the period of 2011–2017, the two ML models exhibit better forecasting skills for the winter SAT over northern and central NA than do the two dynamic models. The results of this study suggest that the ML models may provide improved forecasting skill for seasonal forecasts of the winter climate in NA.
Quantifying the Effects of EMIC Wave Scattering and Magnetopause Shadowing in the Outer Electron Radiation Belt by Means of Data Assimilation
Authors: Cervantes S. , Shprits Y. Y. , Aseev N. A. , Allison H. J.
Published: August 2020

In this study we investigate two distinct loss mechanisms responsible for the rapid dropouts of radiation belt electrons by assimilating data from Van Allen Probes A and B and Geostationary Operational Environmental Satellites (GOES) 13 and 15 into a 3‐D diffusion model. In particular, we examine the respective contribution of electromagnetic ion cyclotron (EMIC) wave scattering and magnetopause shadowing for values of the first adiabatic invariant μ ranging from 300 to 3,000 MeV G−1. We inspect the innovation vector and perform a statistical analysis to quantitatively assess the effect of both processes as a function of various geomagnetic indices, solar wind parameters, and radial distance from the Earth. Our results are in agreement with previous studies that demonstrated the energy dependence of these two mechanisms. We show that EMIC wave scattering tends to dominate loss at lower L shells, and it may amount to between 10%/hr and 30%/hr of the maximum value of phase space density (PSD) over all L shells for fixed first and second adiabatic invariants. On the other hand, magnetopause shadowing is found to deplete electrons across all energies, mostly at higher L shells, resulting in loss from 50%/hr to 70%/hr of the maximum PSD. Nevertheless, during times of enhanced geomagnetic activity, both processes can operate beyond such location and encompass the entire outer radiation belt.
Preconditioned Crank‐Nicolson Markov Chain Monte Carlo Coupled With Parallel Tempering: An Efficient Method for Bayesian Inversion of Multi‐Gaussian Log‐Hydraulic Conductivity Fields
Authors: Xu Teng , Reuschen Sebastian , Nowak Wolfgang , Hendricks Franssen Harrie‐Jan
Published: August 2020

Geostatistical inversion with quantified uncertainty for nonlinear problems requires techniques for providing conditional realizations of the random field of interest. Many first‐order second‐moment methods are being developed in this field, yet almost impossible to critically test them against high‐accuracy reference solutions in high‐dimensional and nonlinear problems. Our goal is to provide a high‐accuracy reference solution algorithm. Preconditioned Crank‐Nicolson Markov chain Monte Carlo (pCN‐MCMC) has been proven to be more efficient in the inversion of multi‐Gaussian random fields than traditional MCMC methods; however, it still has to take a long chain to converge to the stationary target distribution. Parallel tempering aims to sample by communicating between multiple parallel Markov chains at different temperatures. In this paper, we develop a new algorithm called pCN‐PT. It combines the parallel tempering technique with pCN‐MCMC to make the sampling more efficient, and hence converge to a stationary distribution faster. To demonstrate the high‐accuracy reference character, we test the accuracy and efficiency of pCN‐PT for estimating a multi‐Gaussian log‐hydraulic conductivity field with a relative high variance in three different problems: (1) in a high‐dimensional, linear problem; (2) in a high‐dimensional, nonlinear problem and with only few measurements; and (3) in a high‐dimensional, nonlinear problem with sufficient measurements. This allows testing against (1) analytical solutions (kriging), (2) rejection sampling, and (3) pCN‐MCMC in multiple, independent runs, respectively. The results demonstrate that pCN‐PT is an asymptotically exact conditional sampler and is more efficient than pCN‐MCMC in geostatistical inversion problems.
The role of histone methylation in the development of digestive cancers: a potential direction for cancer management
Authors: Chen Yuan , Ren Bo , Yang Jinshou , Wang Huanyu , Yang Gang , Xu Ruiyuan , You Lei , Zhao Yupei
Published: August 2020

Digestive cancers are the leading cause of cancer-related death worldwide and have high risks of morbidity and mortality. Histone methylation, which is mediated mainly by lysine methyltransferases, lysine demethylases, and protein arginine methyltransferases, has emerged as an essential mechanism regulating pathological processes in digestive cancers. Under certain conditions, aberrant expression of these modifiers leads to abnormal histone methylation or demethylation in the corresponding cancer-related genes, which contributes to different processes and phenotypes, such as carcinogenesis, proliferation, metabolic reprogramming, epithelial–mesenchymal transition, invasion, and migration, during digestive cancer development. In this review, we focus on the association between histone methylation regulation and the development of digestive cancers, including gastric cancer, liver cancer, pancreatic cancer, and colorectal cancer, as well as on its clinical application prospects, aiming to provide a new perspective on the management of digestive cancers.
Application of exosomes as liquid biopsy in clinical diagnosis
Authors: Zhou Biting , Xu Kailun , Zheng Xi , Chen Ting , Wang Jian , Song Yongmao , Shao Yingkuan , Zheng Shu
Published: August 2020

Liquid biopsy refers to the sampling and molecular analysis of the biofluids of circulating tumor cells, extracellular vesicles, nucleic acids, and so forth. Exosomes are small extracellular vesicles with sizes between 30–150 nm. They are secreted by multivesicular bodies through exocytosis in live cells and can participate in intercellular communication due to their contents, including nucleic acids, proteins, and lipids. Herein, we investigate publication frequencies on exosomes over the past 10 years, and review recent clinical studies on liquid biopsy of exosomes in the fields of oncology, pregnancy disorders, cardiovascular diseases, and organ transplantation. We also describe the advantages of exosomes as an effective liquid biopsy tool and the progression of exosome extraction methods. Finally, we depict the commercial development of exosome research and discuss the future role of exosomes in liquid biopsy.
A deep learning model to predict RNA-Seq expression of tumours from whole slide images
Authors: Schmauch Benoît , Romagnoni Alberto , Pronier Elodie , Saillard Charlie , Maillé Pascale , Calderaro Julien , Kamoun Aurélie , Sefta Meriem , Toldo Sylvain , Zaslavskiy Mikhail , Clozel Thomas , Moarii Matahi , Courtiol Pierre , Wainrib Gilles
Published: August 2020

Deep learning methods for digital pathology analysis are an effective way to address multiple clinical questions, from diagnosis to prediction of treatment outcomes. These methods have also been used to predict gene mutations from pathology images, but no comprehensive evaluation of their potential for extracting molecular features from histology slides has yet been performed. We show that HE2RNA, a model based on the integration of multiple data modes, can be trained to systematically predict RNA-Seq profiles from whole-slide images alone, without expert annotation. Through its interpretable design, HE2RNA provides virtual spatialization of gene expression, as validated by CD3- and CD20-staining on an independent dataset. The transcriptomic representation learned by HE2RNA can also be transferred on other datasets, even of small size, to increase prediction performance for specific molecular phenotypes. We illustrate the use of this approach in clinical diagnosis purposes such as the identification of tumors with microsatellite instability.
Blind spots in global soil biodiversity and ecosystem function research
Authors: Guerra Carlos A. , Heintz-Buschart Anna , Sikorski Johannes , Chatzinotas Antonis , Guerrero-Ramírez Nathaly , Cesarz Simone , Beaumelle Léa , Rillig Matthias C. , Maestre Fernando T. , Delgado-Baquerizo Manuel , Buscot François , Overmann Jörg , Patoine Guillaume , Phillips Helen R. P. , Winter Marten , Wubet Tesfaye , Küsel Kirsten , Bardgett Richard D. , Cameron Erin K. , Cowan Don , Grebenc Tine , Marín César , Orgiazzi Alberto , Singh Brajesh K. , Wall Diana H. , Eisenhauer Nico
Published: August 2020

Soils harbor a substantial fraction of the world’s biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.
Acoustic phonon recycling for photocarrier generation in graphene-WS2 heterostructures
Authors: Wei Ke , Sui Yizhen , Xu Zhongjie , Kang Yan , You Jie , Tang Yuxiang , Li Han , Ma Yating , Ouyang Hao , Zheng Xin , Cheng Xiangai , Jiang Tian
Published: August 2020

Electron-phonon scattering is the key process limiting the efficiency of modern nanoelectronic and optoelectronic devices, in which most of the incident energy is converted to lattice heat and finally dissipates into the environment. Here, we report an acoustic phonon recycling process in graphene-WS2 heterostructures, which couples the heat generated in graphene back into the carrier distribution in WS2. This recycling process is experimentally recorded by spectrally resolved transient absorption microscopy under a wide range of pumping energies from 1.77 to 0.48 eV and is also theoretically described using an interfacial thermal transport model. The acoustic phonon recycling process has a relatively slow characteristic time (>100 ps), which is beneficial for carrier extraction and distinct from the commonly found ultrafast hot carrier transfer (~1 ps) in graphene-WS2 heterostructures. The combination of phonon recycling and carrier transfer makes graphene-based heterostructures highly attractive for broadband high-efficiency electronic and optoelectronic applications.
Author Correction: Mutations in COMP cause familial carpal tunnel syndrome
Authors: Li Chunyu , Wang Ni , Schäffer Alejandro A. , Liu Xilin , Zhao Zhuo , Elliott Gene , Garrett Lisa , Choi Nga Ting , Wang Yueshu , Wang Yufa , Wang Cheng , Wang Jin , Chan Danny , Su Peiqiang , Cui Shusen , Yang Yingzi , Gao Bo
Published: August 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Emergence and clonal expansion of in vitro artemisinin-resistant Plasmodium falciparum kelch13 R561H mutant parasites in Rwanda
Authors: Uwimana Aline , Legrand Eric , Stokes Barbara H. , Ndikumana Jean-Louis Mangala , Warsame Marian , Umulisa Noella , Ngamije Daniel , Munyaneza Tharcisse , Mazarati Jean-Baptiste , Munguti Kaendi , Campagne Pascal , Criscuolo Alexis , Ariey Frédéric , Murindahabi Monique , Ringwald Pascal , Fidock David A. , Mbituyumuremyi Aimable , Menard Didier
Published: August 2020

Artemisinin resistance (delayed P. falciparum clearance following artemisinin-based combination therapy), is widespread across Southeast Asia but to date has not been reported in Africa1–4. Here we genotyped the P. falciparum K13 (Pfkelch13) propeller domain, mutations in which can mediate artemisinin resistance5,6, in pretreatment samples collected from recent dihydroarteminisin-piperaquine and artemether-lumefantrine efficacy trials in Rwanda7. While cure rates were >95% in both treatment arms, the Pfkelch13 R561H mutation was identified in 19 of 257 (7.4%) patients at Masaka. Phylogenetic analysis revealed the expansion of an indigenous R561H lineage. Gene editing confirmed that this mutation can drive artemisinin resistance in vitro. This study provides evidence for the de novo emergence of Pfkelch13-mediated artemisinin resistance in Rwanda, potentially compromising the continued success of antimalarial chemotherapy in Africa.
Dorsal posterior cingulate cortex encodes the informational value of feedback in human–computer interaction
Authors: Wolff Susann , Kohrs Christin , Angenstein Nicole , Brechmann André
Published: August 2020

In communication between humans as well as in human–computer interaction, feedback is ubiquitous. It is essential for keeping up the dialogue between interaction partners, evaluating the adequacy of an action, or improving task performance. While the neuroscientific view on feedback has largely focused on its function as reward, more general definitions also emphasise its function as information about aspects of one’s task performance. Using fMRI in a computer-controlled auditory categorisation task, we studied the neural correlates of the informational value of computer-given feedback independent of reward. Feedback about the correctness of a decision, compared with feedback only indicating the registration of a decision, increases activation of the dorsal posterior cingulate cortex, supporting this region’s role in adapting to behaviourally relevant information. Both conditions elicit equally strong activation of the dorsal striatum which does not support an interpretation of feedback information as a type of reward. Instead, we suggest that it reflects a more fundamental aspect of human interaction behaviour, namely the establishment of a state that enables us to continue with the next step of the interaction.
Preoperative handgrip strength is not associated with complications and health-related quality of life after surgery for colorectal cancer
Authors: van Heinsbergen M. , Konsten J. L. , Bours M. J. L. , Bouvy N. D. , Weijenberg M. P. , Janssen-Heijnen M. L.
Published: August 2020

Colorectal cancer (CRC) treatment is associated with a high morbidity which may result in a reduced health-related quality of life (HRQoL). The pre-operative measurement of handgrip strength (HGS) might be a tool to predict the patient’s outcome after CRC surgery. The aim of this study was to evaluate the association of pre-operative HGS with the occurrence of postoperative complications and postoperative HRQoL. Stage I to III CRC patients ≥ 18 years were included at diagnosis. Demographic and clinical data as well as HGS were collected before start of treatment. HGS was classified as weak if it was below the gender-specific 25th percentile of our study population; otherwise HGS was classified as normal. The occurrence of postoperative complications within 30 days after surgery was collected from medical records. Cancer-specific HRQoL was measured 6 weeks after treatment using the EORTC QLQ-C30 and the EORTC QLQ-CR29 questionnaire. Of 295 patients who underwent surgical treatment for CRC, 67 (23%) patients had a weak HGS while 228 (77%) patients had normal HGS. 118 patients (40%) developed a postoperative complication. Complications occurred in 37% of patients with a weak HGS and in 41% of patients with a normal HGS (p = 0.47). After adjustment for age, sex, ASA, BMI and TNM, no significant associations between pre-operative HGS and the occurrence of postoperative complications and between HGS and HRQoL were found. We conclude that a single pre-operative HGS measurement was not associated with the occurrence of postoperative complications or post-treatment HRQoL in stage I–III CRC patients.
Publisher Correction: Mice repeatedly exposed to Group-A β-Haemolytic Streptococcus show perseverative behaviors, impaired sensorimotor gating, and immune activation in rostral diencephalon
Authors: Macrì Simone , Ceci Chiara , Proietti Onori Martina , Invernizzi Roberto William , Bartolini Erika , Altabella Luisa , Canese Rossella , Imperi Monica , Orefici Graziella , Creti Roberta , Margarit Immaculada , Magliozzi Roberta , Laviola Giovanni
Published: August 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
A framework based on deep neural networks to extract anatomy of mosquitoes from images
Authors: Minakshi Mona , Bharti Pratool , Bhuiyan Tanvir , Kariev Sherzod , Chellappan Sriram
Published: August 2020

We design a framework based on Mask Region-based Convolutional Neural Network to automatically detect and separately extract anatomical components of mosquitoes-thorax, wings, abdomen and legs from images. Our training dataset consisted of 1500 smartphone images of nine mosquito species trapped in Florida. In the proposed technique, the first step is to detect anatomical components within a mosquito image. Then, we localize and classify the extracted anatomical components, while simultaneously adding a branch in the neural network architecture to segment pixels containing only the anatomical components. Evaluation results are favorable. To evaluate generality, we test our architecture trained only with mosquito images on bumblebee images. We again reveal favorable results, particularly in extracting wings. Our techniques in this paper have practical applications in public health, taxonomy and citizen-science efforts.
Quantitative T2 MRI is predictive of neurodegeneration following organophosphate exposure in a rat model
Authors: Lee Kevin , Bohnert Sara , Bouchard Matthew , Vair Cory , Farrell Jordan S. , Teskey G. Campbell , Mikler John , Dunn Jeff F.
Published: August 2020

Organophosphorus compounds, such as chemical warfare nerve agents and pesticides, are known to cause neurological damage. This study measured nerve agent-related neuropathology and determined whether quantitative T2 MRI could be used as a biomarker of neurodegeneration. Quantitative T2 MRI was performed using a 9.4 T MRI on rats prior to and following soman exposure. T2 images were taken at least 24 h prior, 1 h and 18–24 h after soman exposure. Rats were pre- and post-treated with HI-6 dimethanesulfonate and atropine methyl nitrate. A multicomponent T2 acquisition and analysis was performed. Brains were stained with Fluoro-Jade C to assess neurodegeneration. Rats exposed to soman developed behavioral expression of electrographic seizures. At 18–24 h after soman exposure, significant increases in T2, a possible marker of edema, were found in multiple regions. The largest changes were in the piriform cortex (before: 47.7 ± 1.4 ms; 18–24 h: 82.3 ± 13.4 ms). Fluoro-Jade C staining showed significant neurodegeneration 18–24 h post exposure. The piriform cortex had the strongest correlation between the change in relaxation rate and percent neurodegeneration (r = 0.96, p < 0.001). These findings indicate there is regionally specific neurodegeneration 24 h after exposure to soman. The high correlation between T2 relaxivity and histopathology supports the use of T2 as a marker of injury.
Influence of kiwifruit on gastric and duodenal inflammation-related gene expression in aspirin-induced gastric mucosal damage in rats
Authors: Bentley-Hewitt Kerry L. , Perrott Matthew , Butts Christine A. , Hedderley Duncan I. , Stoklosinski Halina M. , Parkar Shanthi G.
Published: August 2020

Kiwifruit (KF) contains bioactive compounds with potential anti-inflammatory properties. In this study, we investigated the protective effects of KF on gastric and duodenal damage induced by soluble aspirin in healthy rats. Sixty-four male Sprague Dawley rats were allocated to eight experimental treatments (n = 8) and the experimental diets were fed for 14 days ad libitum. The experimental diets were 20% fresh pureed KF (green-fleshed and gold-fleshed) or 10% glucose solution (control diet). A positive anti-inflammatory control treatment (ranitidine) was included. At the end of the 14-day feeding period, the rats were fasted overnight, and the following morning soluble aspirin (400 mg/kg aspirin) or water (control) was administered by oral gavage. Four hours after aspirin administration, the rats were euthanized and samples taken for analysis. We observed no significant ulcer formation or increase in infiltration of the gastric mucosal inflammatory cells in the rats with the aspirin treatment. Despite this, there were significant changes in gene expression, such as in the duodenum of aspirin-treated rats fed green KF where there was increased expression of inflammation-related genes NOS2 and TNF-alpha. We also observed that gold and green KF diets had a number of contrasting effects on genes related to inflammation and gastro-protective effects.
Fabrication of flexible self-powered humidity sensor based on super-hydrophilic titanium oxide nanotube arrays
Authors: Farahani Elham , Mohammadpour Raheleh
Published: August 2020

Stable and flexible super-hydrophilic nanotubular-based titanium oxide electrode has been utilized as the active electrode of self-powered humidity sensor. TiO2 nanotubular electrodes fabricated through anodization method and utilized in combination with Kapton electrode as the triboelectric nanogenerator (TENG). Vertical contact-separation mode TENG performance has been examined in various range of frequencies and the maximum output voltage and current more than 300 V and 40 μA respectively with maximum power of 1.25 ± 0.67 mW has been achieved at 4 Hz. The fabricated TENG has been employed as the active self-powered humidity sensor. Super-hydrophilic feature of TiO2 nanotubes resulted in full absorption of water molecules, and noticeable decrease in charge transfer across two triboelectric materials upon increasing humidity. The TiO2-based TENG sensor was exposed to various relative humidity (RH) and the results showed that by increasing the humidity the output voltage and output current decreased from 162.24 ± 35.99 V and 20.4 ± 4.93 μA at RH = 20% to 37.92 ± 1.54 V at RH = 79% and 40.87 88 6.88 ± 1.7 μA at RH = 84%, respectively, Which shows the responsivity more than 300%. This method of measuring humidity has a simple and cost-effective fabrication that has various applications in many fields such as industry and medicine.
Normalized power variance of eLORETA at high-convexity area predicts shunt response in idiopathic normal pressure hydrocephalus
Authors: Aoki Yasunori , Kazui Hiroaki , Bruña Ricardo , Pascual-Marqui Roberto D. , Yoshiyama Kenji , Wada Tamiki , Kanemoto Hideki , Suzuki Yukiko , Suehiro Takashi , Matsumoto Takuya , Kakeda Kyosuke , Hata Masahiro , Canuet Leonides , Ishii Ryouhei , Iwase Masao , Ikeda Manabu
Published: August 2020

Idiopathic normal pressure hydrocephalus (iNPH) is a neuropsychiatric disease characterized by gait disturbance, cognitive deterioration and urinary incontinence associated with excessive accumulation of cerebrospinal fluid (CSF) in the brain ventricles. These symptoms, in particular gait disturbance, can be potentially improved by shunt operation in the early stage of the disease, and the intervention associates with a worse outcome when performed late during the course of the disease. Despite the variable outcome of shunt operation, noninvasive presurgical prediction methods of shunt response have not been established yet. In the present study, we used normalized power variance (NPV), a sensitive measure of the instability of cortical electrical activity, to analyze cortical electrical activity derived from EEG data using exact-low-resolution-electromagnetic-tomography (eLORETA) in 15 shunt responders and 19 non-responders. We found that shunt responders showed significantly higher NPV values at high-convexity areas in beta frequency band than non-responders. In addition, using this difference, we could discriminate shunt responders from non-responders with leave-one-subject-out cross-validation accuracy of 67.6% (23/34) [positive predictive value of 61.1% (11/18) and negative predictive value of 75.0% (12/16)]. Our findings indicate that eLORETA-NPV can be a useful tool for noninvasive prediction of clinical response to shunt operation in patients with iNPH.
Author Correction: Analog Coding in Emerging Memory Systems
Authors: Zarcone Ryan V. , Engel Jesse H. , Eryilmaz S. Burc , Wan Weier , Kim SangBum , BrightSky Matthew , Lam Chung , Lung Hsiang-Lan , Olshausen Bruno A. , Wong H.-S. Philip
Published: August 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
The comparison of bone mineral density of femoral head between non-hip fracture side and hip fracture side
Authors: Li Xianlong , Xu Yueyang , Lin Weilong , Fan Yongqian
Published: August 2020

We aimed to analyze the associations of bone mineral density (BMD) of femoral heads, age and gender, and compare the differences in BMD between fracture side and non-fracture side by “3D Spine Exam Analysis” module in QCT Pro software. In this study, we identified patients who had undergone quantitative computed tomography (QCT) examinations between March 2016 and July 2018 and measured their trabecular volumetric BMD (vBMD) of femoral heads. This retrospective study enrolled 367 subjects. A total of 149 participants with images were randomly selected to verify the repeatability of this method. The relationship among the vBMD, age and gender was analyzed (n = 367), and the difference of vBMD between non-fracture side and fracture side were studied in subjects (n = 75) with low-energy hip fracture on one side and compared the image quality of bilateral hip joints. The intraclass correlation coefficients (ICCs) between the results measured by 2 operators and the results measured by the same operator showed excellent agreement (ICCs > 0.9). Multivariate regression equation of vBMD of femoral head, age and gender showed statistical significance (P < 0.05). vBMD showed negative correlation with age (P < 0.05), and showed no statistically significant relation with gender (P > 0.05). vBMD of non-fracture side was higher than that of fracture side, but the difference was statistically significant only at the middle layer (Pmiddle < 0.05). In conclusions, the vBMD of femoral head as measured by "3D Spine Exam Analysis" module in QCT Pro software showed good repeatability. The trabecular vBMD of femoral head was negatively correlated with age, and not related with gender. The vBMD of femoral head was higher on non-fracture side than that on the fracture side.
MethylResolver—a method for deconvoluting bulk DNA methylation profiles into known and unknown cell contents
Authors: Arneson Douglas , Yang Xia , Wang Kai
Published: August 2020

Bulk tissue DNA methylation profiling has been used to examine epigenetic mechanisms and biomarkers of complex diseases such as cancer. However, heterogeneity of cellular content in tissues complicates result interpretation and utility. In silico deconvolution of cellular fractions from bulk tissue data offers a fast and inexpensive alternative to experimentally measuring such fractions. In this study, we report the design, implementation, and benchmarking of MethylResolver, a Least Trimmed Squares regression-based method for inferring leukocyte subset fractions from methylation profiles of tumor admixtures. Compared to previous approaches MethylResolver is more accurate as unknown cellular content in the mixture increases and is able to resolve tumor purity-scaled immune cell-type fractions without a cancer-specific signature. We also present a pan-cancer deconvolution of TCGA, recapitulating that high eosinophil fraction predicts improved cervical carcinoma survival and identifying elevated B cell fraction as a previously unreported predictor of poor survival for papillary renal cell carcinoma.
Molecular basis of the lipid-induced MucA-MucB dissociation in Pseudomonas aeruginosa
Authors: Li Tao , He Lihui , Li Changcheng , Kang Mei , Song Yingjie , Zhu Yibo , Shen Yalin , Zhao Ninglin , Zhao Chang , Yang Jing , Huang Qin , Mou Xingyu , Tong Aiping , Yang Jinliang , Wang Zhenling , Ji Chengjie , Li Hong , Tang Hong , Bao Rui
Published: August 2020

MucA and MucB are critical negative modulators of sigma factor AlgU and regulate the mucoid conversion of Pseudomonas aeruginosa. Previous studies have revealed that lipid signals antagonize MucA-MucB binding. Here we report the crystal structure of MucB in complex with the periplasmic domain of MucA and polyethylene glycol (PEG), which unveiled an intermediate state preceding the MucA-MucB dissociation. Based on the biochemical experiments, the aliphatic side chain with a polar group was found to be of primary importance for inducing MucA cleavage. These results provide evidence that the hydrophobic cavity of MucB is a primary site for sensing lipid molecules and illustrates the detailed control of conformational switching within MucA-MucB in response to lipophilic effectors.
Ligand-bound glutamine binding protein assumes multiple metastable binding sites with different binding affinities
Authors: Zhang Lu , Wu Shaowen , Feng Yitao , Wang Dan , Jia Xilin , Liu Zhijun , Liu Jianwei , Wang Wenning
Published: August 2020

Protein dynamics plays key roles in ligand binding. However, the microscopic description of conformational dynamics-coupled ligand binding remains a challenge. In this study, we integrate molecular dynamics simulations, Markov state model (MSM) analysis and experimental methods to characterize the conformational dynamics of ligand-bound glutamine binding protein (GlnBP). We show that ligand-bound GlnBP has high conformational flexibility and additional metastable binding sites, presenting a more complex energy landscape than the scenario in the absence of ligand. The diverse conformations of GlnBP demonstrate different binding affinities and entail complex transition kinetics, implicating a concerted ligand binding mechanism. Single molecule fluorescence resonance energy transfer measurements and mutagenesis experiments are performed to validate our MSM-derived structure ensemble as well as the binding mechanism. Collectively, our study provides deeper insights into the protein dynamics-coupled ligand binding, revealing an intricate regulatory network underlying the apparent binding affinity.
Molecular spectroscopy of aqueous solutions: a theoretical perspective
Authors: Giovannini Tommaso , Egidi Franco , Cappelli Chiara
Published: August 2020

We review a mixed quantum-classical theoretical model and computational technique designed to accurately reproduce spectral signals of aqueous systems and provide a rationalization for the underlying physics.
Stimuli-responsive polymer/nanomaterial hybrids for sensing applications
Authors: Shu Tong , Shen Qiming , Zhang Xueji , Serpe Michael J.
Published: August 2020

Stimuli-responsive polymer (SRP)-based nanoparticles and SRP/nanomaterial hybrids have myriad applications, we review their uses for chemical sensing and biosensing.
3D-printed phantoms for characterizing SERS nanoparticle detectability in turbid media
Authors: Fales Andrew M. , Strobbia Pietro , Vo-Dinh Tuan , Ilev Ilko K. , Pfefer T. Joshua
Published: August 2020

A 3D-printed phantom showed that SERS tag detectability in solution and turbid media are dissimilar and illustrated fiber-probe depth sensitivity.
β-Lactoglobulin amyloid fibril-templated gold nanoclusters for cellular multicolor fluorescence imaging and colorimetric blood glucose assay
Authors: Suo Zhiguang , Hou Xialing , Liu Yu , Xing Feifei , Chen Yingying , Feng Lingyan
Published: August 2020

β-Lactoglobulin amyloid fibril-templated superior multicolor gold nanoclusters for cell imaging and colorimetric blood glucose assay.
Hierarchical assembly of dual-responsive biomineralized polydopamine–calcium phosphate nanocomposites for enhancing chemo-photothermal therapy by autophagy inhibition
Authors: Wang Xuan , Li Yunhao , Cui Yankun , Deng Xiongwei , Lu Jianqing , Jia Fan , Pan Zian , Cui Xinyue , Hu Fanqi , Hu Wenhao , Zhang Xuesong , Wu Yan
Published: August 2020

Hierarchically assembled biomineralized nanocomposites would be used to sensitize chemo-photothermal therapy by complementary autophagy inhibition.
Correction: Nanoscale insight into the degradation mechanisms of the cartilage articulating surface preceding OA
Authors: Shoaib Tooba , Yuh Catherine , Wimmer Markus A. , Schmid Thomas M. , Espinosa-Marzal Rosa M.
Published: August 2020

Correction for ‘Nanoscale insight into the degradation mechanisms of the cartilage articulating surface preceding OA’ by Tooba Shoaib, et al., Biomater. Sci., 2020, 8, 3944–3955, DOI: 10.1039/D0BM00496K.
Fluorescent small-molecule agonists as follicle-stimulating hormone receptor imaging tools
Authors: Hoogendoorn Sascha , van Puijvelde Gijs H. M. , van der Marel Gijs A. , van Koppen Chris J. , Timmers C. Marco , Overkleeft Herman S.
Published: August 2020

Discovery of a potent, small-molecule, fluorescent agonist of the follicle-stimulating hormone receptor (FSHR) for selective staining of FSHR-expressing cells.
Facile carbon fiber-sewed high areal density electrode for lithium sulfur batteries
Authors: He Mengxue , Li Yaqi , Liu Songsong , Guo Rui , Ma Yulin , Xie Jingying , Huo Hua , Cheng Xinqun , Yin Geping , Zuo Pengjian
Published: August 2020

Carbon fiber-sewed electrode with sulfur loading over 10 mg cm−2 is achieved via typical coating method.
Organelle-localized radiosensitizers
Authors: Chen Yuanyuan , Gao Peng , Wu Tong , Pan Wei , Li Na , Tang Bo
Published: August 2020

This feature article highlights the recent advances of organelle-localized radiosensitizers and discusses the current challenges and future directions.
Robust bi-directional photoswitching of thiomethyl substituted arylazopyrazoles under visible light
Authors: Bhunia Supriya , Dolai Anirban , Samanta Subhas
Published: August 2020

Mono-ortho- and para-thiomethyl substituted arylazopyrazoles display excellent isomerization in both directions under visible light, and show long cis half-lives. These switches are also resistant to photobleaching and reduction by glutathione.
Negative and zero thermal expansion in α-(Cu2−xZnx)V2O7 solid solutions
Authors: Shi Naike , Sanson Andrea , Venier Alessandro , Fan Longlong , Sun Chengjun , Xing Xianran , Chen Jun
Published: August 2020

The thermal expansion of α-Cu2−xZnxV2O7 (x = 0, 0.1, 0.2) series has been controlled from negative to zero with increasing content of Zn. The transverse vibrations of V–O dominant the contraction the overall volume NTE in α-Cu2V2O7.
Krypton-derivatization highlights O2-channeling in a four-electron reducing oxidase
Authors: Engilberge Sylvain , Wagner Tristan , Carpentier Philippe , Girard Eric , Shima Seigo
Published: August 2020

Kr-derivatization and X-ray structures indicated O2-channel and gating-loop that prevent side-reaction in reduction of O2 to water in F420H2 oxidase.
Construction of Sn–P–graphene microstructure with Sn–C and P–C co-bonding as anodes for lithium-ion batteries
Authors: Zhang Yuanxing , Sun Li , Zhao Xiaoxue , Wu Lin , Wang Ke , Si Haochen , Gu Jialin , Sun Chao , Shi Yan , Zhang Yihe
Published: August 2020

Using an HEBM method, few layered graphene (FLG) isin situformed and composited with an Sn–P-based material, establishing strong Sn–C/P–C co-bonding and excellent electrochemical properties, as anodes for lithium-ion batteries.
Formation of nanocrystalline manganese oxide in flames: oxide phase governed by classical nucleation and size-dependent equilibria
Authors: Dasappa Shruthi , Camacho Joaquin
Published: August 2020

Particle nucleation and growth of crystalline manganese oxide nanoparticles was examined in a complementary experimental and modelling study.
Plasmon catalytic PATP coupling reaction on Ag-NPs/graphite studied via in situ electrochemical surface-enhanced Raman spectroscopy
Authors: Zhong Hang , Chen Jun , Chen Jinfan , Tao Ran , Jiang Jiaolai , Hu Yi , Xu Jingsong , Zhang Tianzhu , Liao Junsheng
Published: August 2020

Plasmon-induced hot holes and electrons play different roles in the PATP coupling reaction, resulting in two different catalytic reaction paths.
Surface charging parameters of charged particles in symmetrical electrolyte solutions
Authors: Saboorian-Jooybari Hadi , Chen Zhangxin
Published: August 2020

This research work is directed at development of accurate physics-based formulas for quantification of curvature-dependence of surface potential, surface charge density, and total surface charge for cylindrical and spherical charged particles immersed in a symmetrical electrolyte solution.
Multicolored fluorescence variation of a new carbazole-based AIEE molecule by external stimuli
Authors: Liu Yan , Li Aisen , Ma Zhimin , Xu Weiqing , Ma Zhiyong , Jia Xinru
Published: August 2020

Here, we obtained a new carbazole-based molecule, Cz2CN, with a twisted D–A structure. Cz2CN is a rare carbazole-based molecule that shows simultaneous AIEE, solvatochromism and force-induced multicolored variation.
Amyloid β fibril disruption by oleuropein aglycone: long-time molecular dynamics simulation to gain insight into the mechanism of action of this polyphenol from extra virgin olive oil
Authors: Brogi Simone , Sirous Hajar , Calderone Vincenzo , Chemi Giulia
Published: August 2020

Insight into the mechanism of action of oleuropein aglycone as a potent anti-amyloidogenic agent.
Hydrosilylation and hydroboration in a sustainable manner: from Earth-abundant catalysts to catalyst-free solutions
Authors: Kuciński Krzysztof , Hreczycho Grzegorz
Published: August 2020

Hydroelementation enables a facile reduction or functionalization of several unsaturated systems, and thus activation of such bonds like B–H and Si–H is a powerful synthetic tool.
Super protective anti-bacterial coating development with silica–titania nano core–shells
Authors: Verma Jaya , Khanna A. S. , Sahney Rachana , Bhattacharya Arpita
Published: August 2020

In the present study, we have developed an anti-bacterial as well as mechanically-strengthened super protective coating material, which can be used as a marine antifouling paint.
Inorganic–organic core/shell nanoparticles: progress and applications
Authors: Chiozzi Viola , Rossi Filippo
Published: August 2020

In recent decades a great deal of research has been dedicated to the development of core–shell nanoparticles (NPs).
The scaffold-forming steps of plant alkaloid biosynthesis
Authors: Lichman Benjamin R.
Published: August 2020

Plant alkaloids are central to both modern and traditional medicines. This review describes the progress made towards understanding the metabolic origins of these compounds, focussing on the common features of different biosynthetic pathways.
Strongly coupled exciton–plasmon nanohybrids reveal extraordinary resistance to harsh environmental stressors: temperature, pH and irradiation
Authors: Hendel Thomas , Krivenkov Victor , Sánchez-Iglesias Ana , Grzelczak Marek , Rakovich Yury P.
Published: August 2020

Outstanding resistance of the strength of light-matter coupling in plexciton nanostructures to environmental stressors such as temperature, pH and exposure to radiation is demonstrated. New insights into the design of plexciton systems are provided.
Cobalt doped BiVO4 with rich oxygen vacancies for efficient photoelectrochemical water oxidation
Authors: Liu Guoquan , Li Fei , Zhu Yong , Li Jiayuan , Sun Licheng
Published: August 2020

A facile electrodeposition method was developed to prepare Co-BiVO4 thin films with rich oxygen vacancies.
Studies on interstitial carbon doping from a Ti precursor in a hierarchical TiO2 nanostructured photoanode by a single step hydrothermal route
Authors: Burungale V. V. , Bae Hyojung , Kamble A. S. , Kim J.-H. , Patil P. S. , Ha J.-S.
Published: August 2020

Interstitial carbon doping is possible directly from a Ti precursor (titanium(iv) isopropoxide) without using any other carbon source.
Influence of solvent mixture on nucleophilicity parameters: the case of pyrrolidine in methanol–acetonitrile
Authors: Souissi Salma , Gabsi Wahiba , Echaieb Abderraouf , Roger Julien , Hierso Jean-Cyrille , Fleurat-Lessard Paul , Boubaker Taoufik
Published: August 2020

Combined experiments and modelling rationalize the large influence of solvent composition on pyrrolidine nucleophilicity.
Electronic and vibrational surface-enhanced Raman scattering: from atomically defined Au(111) and (100) to roughened Au
Authors: Inagaki Motoharu , Isogai Taichi , Motobayashi Kenta , Lin Kai-Qiang , Ren Bin , Ikeda Katsuyoshi
Published: August 2020

Both electronic and vibrational information at the metal/dielectric interface were explicitly extracted from surface-enhanced Raman spectra.
A unified understanding of the cononsolvency of polymers in binary solvent mixtures
Authors: Zhang Xiangyu , Zong Jing , Meng Dong
Published: August 2020

The parameter region in the Δχ−χSC plane where cononsolvency will (the shaded area) and will not (the blank area) occur with ϕP = 0.1.
Layering of magnetic nanoparticles at amorphous magnetic templates with perpendicular anisotropy
Authors: Saini Apurve , Borchers Julie A. , George Sebastian , Maranville Brian B. , Krycka Kathryn L. , Dura Joseph A. , Theis-Bröhl Katharina , Wolff Max
Published: August 2020

We reveal the assembly of magnetite nanoparticles of sizes 5 nm, 15 nm and 25 nm from dilute water-based ferrofluids onto an amorphous magnetic template with out-of-plane anisotropy.
The effect of chemically preintercalated alkali ions on the structure of layered titanates and their electrochemistry in aqueous energy storage systems
Authors: Mukherjee Santanu , Quilty Calvin D. , Yao Shanshan , Stackhouse Chavis A. , Wang Lei , Takeuchi Kenneth J. , Takeuchi Esther S. , Wang Feng , Marschilok Amy C. , Pomerantseva Ekaterina
Published: August 2020

We introduce a novel chemical preintercalation synthesis technique based on a hydrogen peroxide induced sol–gel process to obtain alkali ion containing ternary layered titanates (MTO, where M = Li, Na, K).
Coupling of triporosity and strong Au–Li interaction to enable dendrite-free lithium plating/stripping for long-life lithium metal anodes
Authors: Liang Yaohua , Chen Yuanmao , Ke Xi , Zhang Zouxin , Wu Wenli , Lin Guide , Zhou Zhen , Shi Zhicong
Published: August 2020

Coupling of triporosity and strong Au–Li interaction leads to dendrite-free and long-life LMAs.
Chemical relaxation in porous ionic–electronic conducting materials represented by the distribution of characteristic times
Authors: Zhang Yanxiang , Yan Fuyao , Hu Bobing , Xia Changrong , Yan Mufu
Published: August 2020

Distribution of characteristic times (DCT) is proposed to resolve chemical relaxation in porous MIECs and to estimate kinetic parameters.
A novel perylene diimide-based zwitterion as the cathode interlayer for high-performance perovskite solar cells
Authors: Wang Helin , Song Jun , Qu Junle , Lian Jiarong , Qian Peng-Cheng , Wong Wai-Yeung
Published: August 2020

A novel perylene diimide-based zwitterion (QAPDI) is developed as a cathode interlayer and can enhance electron injection, reduce energy losses, and improve interface contacts, thus achieving excellent device performance.
A flexible composite solid electrolyte with a highly stable interphase for dendrite-free and durable all-solid-state lithium metal batteries
Authors: Zhang Dechao , Xu Xijun , Huang Xinyue , Shi Zhicong , Wang Zhuosen , Liu Zhengbo , Hu Renzong , Liu Jun , Zhu Min
Published: August 2020

A flexible composite solid electrolyte has been successfully designed. Benefitting from the synergistic effect of the organic–inorganic complex, such PBL-CSE membrane shows superior electrochemical properties and interface stability.
A facile route for constructing Cu–N–C peroxidase mimics
Authors: Lin Zhen , Zheng Linlin , Yao Wensong , Liu Shijun , Bu Yemei , Zeng Qi , Zhang Xiaomin , Deng Haohua , Lin Xinhua , Chen Wei
Published: August 2020

Cu–N–C single-atom nanozymes were successfully designedviaa one-pot solvothermal method and their excellent peroxidase-mimicking activity has been investigated and applied for H2O2and glucose determination.
Molecular doping in few-molecule polymer-dopant complexes shows reduced Coulomb binding
Authors: Dong Chuan-ding , Schumacher Stefan
Published: August 2020

Coulomb binding energy is reduced when a few-molecule integer charge transfer complex (ICTC) is formed.
Correction: Solid solutions of M2−2xIn2xS3 (M = Bi or Sb) by solventless thermolysis
Authors: Alqahtani Tahani , Dilshad Khan Malik , Cernik Robert J. , O’Brien Paul , Lewis David J.
Published: August 2020

Correction for ‘Solid solutions of M2−2xIn2xS3 (M = Bi or Sb) by solventless thermolysis’ by Tahani Alqahtani et al., J. Mater. Chem. C, 2019, 7, 5112–5121, DOI: 10.1039/C9TC00148D.
Analysis of the prognostic significance of solute carrier (SLC) family 39 genes in breast cancer
Authors: Liu Limei , Yang Jiaomin , Wang Chao
Published: August 2020

Background: Breast cancer (BC) is the most common malignancy in females and remains a main cause of cancer-associated death worldwide. The solute carrier (SLC) groups of membrane transport proteins, which control the influx of zinc, participate in ranging of physiological processes and may provide novel therapeutic targets of cancers. However, the prognostic values of individual SLC family 39 (SLC39A) genes in patients with BC are not clarified.

Materials and Methods: The mRNA expression of SLC family 39 genes in BC was evaluated by using the UALCAN database. The prognostic values of overall survival (OS) of SLC family 39 genes in patients with BC were investigated by Kaplan–Meier plotter. The survival analysis of cells was determined by Project Achilles.

Results: The analytic results suggested that SLC39A1, SLC39A3, SLC39A4, SLC39A5, SLC39A6, SLC39A7, SLC39A9, SLC39A10, SLC39A11 and SLC39A13 were significantly up-regulated in BC tissues compared with normal breast tissues. However, SLC39A8 and SLC39A14 were expressed higher in normal tissues than in BC tissues. High expression of SLC39A2, SLC39A3, SLC39A4, SLC39A5, SLC39A7, SLC39A12 and SLC39A13 was significantly associated with worse OS in patients with BC. In contrast, high mRNA levels of SLC39A6 and SLC39A14 indicated favorable OS. Through subgroup analysis, all abnormal expressed SLC family members were correlated with prognoses of patients with specific BC. Moreover, SLC39A7 was associated with proliferation and cloning of BC.

Conclusions: Our results suggested that SLC family 39 members were promising prognostic biomarkers of BC. The SLC39A7 played a key role in growth and survival of BC cells.