bluuebunny/crossref_metadata_2025 huggingface dataset:
Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase
Authors: Gamiz-Arco Gloria , Gutierrez-Rus Luis I. , Risso Valeria A. , Ibarra-Molero Beatriz , Hoshino Yosuke , Petrović Dušan , Justicia Jose , Cuerva Juan Manuel , Romero-Rivera Adrian , Seelig Burckhard , Gavira Jose A. , Kamerlin Shina C. L. , Gaucher Eric A. , Sanchez-Ruiz Jose M.
Published: January 2021

Glycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed.
Inositol pyrophosphates promote the interaction of SPX domains with the coiled-coil motif of PHR transcription factors to regulate plant phosphate homeostasis
Authors: Ried Martina K. , Wild Rebekka , Zhu Jinsheng , Pipercevic Joka , Sturm Kristina , Broger Larissa , Harmel Robert K. , Abriata Luciano A. , Hothorn Ludwig A. , Fiedler Dorothea , Hiller Sebastian , Hothorn Michael
Published: January 2021

Phosphorus is an essential nutrient taken up by organisms in the form of inorganic phosphate (Pi). Eukaryotes have evolved sophisticated Pi sensing and signaling cascades, enabling them to stably maintain cellular Pi concentrations. Pi homeostasis is regulated by inositol pyrophosphate signaling molecules (PP-InsPs), which are sensed by SPX domain-containing proteins. In plants, PP-InsP-bound SPX receptors inactivate Myb coiled-coil (MYB-CC) Pi starvation response transcription factors (PHRs) by an unknown mechanism. Here we report that a InsP8–SPX complex targets the plant-unique CC domain of PHRs. Crystal structures of the CC domain reveal an unusual four-stranded anti-parallel arrangement. Interface mutations in the CC domain yield monomeric PHR1, which is no longer able to bind DNA with high affinity. Mutation of conserved basic residues located at the surface of the CC domain disrupt interaction with the SPX receptor in vitro and in planta, resulting in constitutive Pi starvation responses. Together, our findings suggest that InsP8regulates plant Pi homeostasis by controlling the oligomeric state and hence the promoter binding capability of PHRs via their SPX receptors.
Sensing the future of bio-informational engineering
Authors: Dixon Thomas A. , Williams Thomas C. , Pretorius Isak S.
Published: January 2021

The practices of synthetic biology are being integrated into ‘multiscale’ designs enabling two-way communication across organic and inorganic information substrates in biological, digital and cyber-physical system integrations. Novel applications of ‘bio-informational’ engineering will arise in environmental monitoring, precision agriculture, precision medicine and next-generation biomanufacturing. Potential developments include sentinel plants for environmental monitoring and autonomous bioreactors that respond to biosensor signaling. As bio-informational understanding progresses, both natural and engineered biological systems will need to be reimagined as cyber-physical architectures. We propose that a multiple length scale taxonomy will assist in rationalizing and enabling this transformative development in engineering biology.
TreeMap, a tree-level model of conterminous US forests circa 2014 produced by imputation of FIA plot data
Authors: Riley Karin L. , Grenfell Isaac C. , Finney Mark A. , Wiener Jason M.
Published: January 2021

A 30 × 30m-resolution gridded dataset of forest plot identifiers was developed for the conterminous United States (CONUS) using a random forests machine-learning imputation approach. Forest plots from the US Forest Service Forest Inventory and Analysis program (FIA) were imputed to gridded c2014 landscape data provided by the LANDFIRE project using topographic, biophysical, and disturbance variables. The output consisted of a raster map of plot identifiers. From the plot identifiers, users of the dataset can link to a number of tree- and plot-level attributes stored in the accompanying tables and in the publicly available FIA DataMart, and then produce maps of any of these attributes, including number of trees per acre, tree species, and forest type. Of 67,141 FIA plots available, 62,758 of these (93.5%) were utilized at least once in imputation to 2,841,601,981 forested pixels in CONUS. Continuous high-resolution forest structure data at a national scale will be invaluable for analyzing carbon dynamics, habitat distributions, and fire effects.
The ISN/RPS 2016 classification predicts renal prognosis in patients with first-onset class III/IV lupus nephritis
Authors: Hachiya Asaka , Karasawa Munetoshi , Imaizumi Takahiro , Kato Noritoshi , Katsuno Takayuki , Ishimoto Takuji , Kosugi Tomoki , Tsuboi Naotake , Maruyama Shoichi
Published: January 2021

Lupus nephritis (LN) is a life-threatening complication of systemic lupus erythematosus. The 2003 pathological classification of LN was revised in 2016; it quantitatively evaluates the interstitium in addition to the glomeruli. We performed a retrospective multi-centre cohort study and investigated the utility of the 2016 classification—including the activity index (AI), chronicity index (CI), and each pathological component to predict complete remission or renal function decline, defined as 1.5-fold increase in serum creatinine levels—and compare with that of the 2003 classification. Ninety-one consecutive adult patients with first-onset class III/IV LN who were newly prescribed any immunosuppressants were enrolled and followed up for a median of 51 months from January 2004. Cox regression analysis demonstrated the subclasses based on the 2003 classification, which mainly evaluate glomerular lesions, were not associated with clinical outcomes. After adjustments for estimated glomerular filtration rate and urinary protein levels, higher CI and higher interstitial fibrosis and lower hyaline deposit scores were associated with renal functional decline. Similarly, higher CI and interstitial inflammation scores were associated with failure to achieve complete remission. Therefore, the 2016 classification can predict the clinical outcomes more precisely than the 2003 classification.
The effects of flooding and weather conditions on leptospirosis transmission in Thailand
Authors: Chadsuthi Sudarat , Chalvet-Monfray Karine , Wiratsudakul Anuwat , Modchang Charin
Published: January 2021

The epidemic of leptospirosis in humans occurs annually in Thailand. In this study, we have developed mathematical models to investigate transmission dynamics between humans, animals, and a contaminated environment. We compared different leptospire transmission models involving flooding and weather conditions, shedding and multiplication rate in a contaminated environment. We found that the model in which the transmission rate depends on both flooding and temperature, best-fits the reported human data on leptospirosis in Thailand. Our results indicate that flooding strongly contributes to disease transmission, where a high degree of flooding leads to a higher number of infected individuals. Sensitivity analysis showed that the transmission rate of leptospires from a contaminated environment was the most important parameter for the total number of human cases. Our results suggest that public education should target people who work in contaminated environments to preventLeptospirainfections.
Low BMI and weight loss aggravate COPD mortality in men, findings from a large prospective cohort: the JACC study
Authors: Wada Hiroo , Ikeda Ai , Maruyama Koutatsu , Yamagishi Kazumasa , Barnes Peter J. , Tanigawa Takeshi , Tamakoshi Akiko , Iso Hiroyasu
Published: January 2021

To clarify how low BMI and weight loss were associated with risk of chronic obstructive pulmonary disease (COPD) mortality, in a large prospective cohort of the general population across Japan, the Japan Collaborative Cohort Study, conducted between 1988 and 2009. A total of 45,837 male residents were observed for a median period of 19.1 years. Self-administered questionnaires, collecting information on BMI, weight loss since the age of 20, lifestyles, history of diseases, as well as records of COPD mortality, were analysed at 2019. During follow-up, 268 participants died from COPD. The multivariate-adjusted hazard ratio (95% confidence interval) of COPD mortality associated with a 1-SD increment of body mass index (BMI) was 0.48 (0.41–0.57), while for weight change from age of 20 (+ 2.0 kg) it was 0.63 (0.59–0.68). These associations were persistently observed after stratifications with smoking status, excluding those having airway symptoms in the baseline survey, and excluding early COPD deaths within 5, 10 and 15 years. Our study suggests that BMI and weight change since the age of 20 could be markers for COPD prognosis, indicated by risk of COPD mortality.
Plasma tissue plasminogen activator and plasminogen activator inhibitor-1 in hospitalized COVID-19 patients
Authors: Zuo Yu , Warnock Mark , Harbaugh Alyssa , Yalavarthi Srilakshmi , Gockman Kelsey , Zuo Melanie , Madison Jacqueline A. , Knight Jason S. , Kanthi Yogendra , Lawrence Daniel A.
Published: January 2021

Patients with coronavirus disease-19 (COVID-19) are at high risk for thrombotic arterial and venous occlusions. However, bleeding complications have also been observed in some patients. Understanding the balance between coagulation and fibrinolysis will help inform optimal approaches to thrombosis prophylaxis and potential utility of fibrinolytic-targeted therapies. 118 hospitalized COVID-19 patients and 30 healthy controls were included in the study. We measured plasma antigen levels of tissue-type plasminogen activator (tPA) and plasminogen activator inhibitor-1 (PAI-1) and performed spontaneous clot-lysis assays. We found markedly elevated tPA and PAI-1 levels in patients hospitalized with COVID-19. Both factors demonstrated strong correlations with neutrophil counts and markers of neutrophil activation. High levels of tPA and PAI-1 were associated with worse respiratory status. High levels of tPA, in particular, were strongly correlated with mortality and a significant enhancement in spontaneous ex vivo clot-lysis. While both tPA and PAI-1 are elevated among COVID-19 patients, extremely high levels of tPA enhance spontaneous fibrinolysis and are significantly associated with mortality in some patients. These data indicate that fibrinolytic homeostasis in COVID-19 is complex with a subset of patients expressing a balance of factors that may favor fibrinolysis. Further study of tPA as a biomarker is warranted.
Comparative analysis of nuclear, chloroplast, and mitochondrial genomes of watermelon and melon provides evidence of gene transfer
Authors: Cui Haonan , Ding Zhuo , Zhu Qianglong , Wu Yue , Qiu Boyan , Gao Peng
Published: January 2021

During plant evolution, there is genetic communication between organelle and nuclear genomes. A comparative analysis was performed on the organelle and nuclear genomes of the watermelon and melon. In the watermelon, chloroplast-derived sequences accounted for 7.6% of the total length of the mitochondrial genome. In the melon, chloroplast-derived sequences accounted for approximately 2.73% of the total mitochondrial genome. In watermelon and melon, the chloroplast-derived small-fragment sequences are either a subset of large-fragment sequences or appeared multiple times in the mitochondrial genome, indicating that these fragments may have undergone multiple independent migration integrations or emerged in the mitochondrial genome after migration, replication, and reorganization. There was no evidence of migration from the mitochondria to chloroplast genome. A sequence with a total length of about 73 kb (47%) in the watermelon chloroplast genome was homologous to a sequence of about 313 kb in the nuclear genome. About 33% of sequences in the watermelon mitochondrial genome was homologous with a 260 kb sequence in the nuclear genome. A sequence with a total length of about 38 kb (25%) in the melon chloroplast genome was homologous with 461 sequences in the nuclear genome, with a total length of about 301 kb. A 3.4 Mb sequence in the nuclear genome was homologous with a melon mitochondrial sequence. These results indicate that, during the evolution of watermelon and melon, a large amount of genetic material was exchanged between the nuclear genome and the two organelle genomes in the cytoplasm.
Experimental and computational investigation on underlying factors promoting high coke resistance in NiCo bimetallic catalysts during dry reforming of methane
Authors: Saelee Tinnakorn , Lerdpongsiripaisarn Mongkol , Rittiruam Meena , Somdee Siriwimol , Liu Anchittha , Praserthdam Supareak , Praserthdam Piyasan
Published: January 2021

Global warming remains one of the greatest challenges. One of the most prominent solutions is to close the carbon cycle by utilizing the greenhouse gas: CO2, and CH4, as a feedstock via the dry reforming of methane (DRM). This work provided an insight into how the NiCo bimetallic catalyst can perform with high stability against coking during DRM compared to the Ni and Co monometallic catalysts, in which the experimental and computational techniques based on density functional theory were performed. It was found that the high stability against coking found on the NiCo surface can be summarized into two key factors: (1) the role of Co weakening the bond between a Ni active site and coke (2) significantly high surface coke diffusion rate on NiCo. Moreover, the calculation of the surface fraction weighted rate of coke diffusion which modeled the real NiCo particle into four regions: Ni-dominant, Co-dominant, NiCo-dominant, and the mixed region consisting a comparable amount of the former there regions, have shown that the synthesis of a NiCo particle should be dominated with NiCo region while keeping the Ni-dominant, and Co-dominant regions to be as low as possible to facilitate coke diffusion and removal. Thus, to effectively utilize the coke-resistant property of NiCo catalyst for DRM, one should together combine its high coke diffusion rate with coke removal mechanisms such as oxidation or hydrogenation, especially at the final diffusion site, to ensure that there will not be enough coke at the final site that will cause back-diffusion.
Quantum Szilard engine for the fractional power-law potentials
Authors: Aydiner Ekrem
Published: January 2021

In this study, we consider the quantum Szilárd engine with a single particle under the fractional power-law potential. We suggest that such kind of the Szilárd engine works a Stirling-like cycle. We obtain energy eigenvalues and canonical partition functions for the degenerate and non-degenerate cases in this cycle process. By using these quantities we numerically compute work and efficiency for this thermodynamic cycle for various power-law potentials with integer and non-integer exponents. We show that the presented simple engine also yields positive work and efficiency. We discuss the importance of fractional dynamics in physics and finally, we conclude that fractional calculus should be included in the fields of quantum information and thermodynamics.
Coupling machine learning and crop modeling improves crop yield prediction in the US Corn Belt
Authors: Shahhosseini Mohsen , Hu Guiping , Huber Isaiah , Archontoulis Sotirios V.
Published: January 2021

This study investigates whether coupling crop modeling and machine learning (ML) improves corn yield predictions in the US Corn Belt. The main objectives are to explore whether a hybrid approach (crop modeling + ML) would result in better predictions, investigate which combinations of hybrid models provide the most accurate predictions, and determine the features from the crop modeling that are most effective to be integrated with ML for corn yield prediction. Five ML models (linear regression, LASSO, LightGBM, random forest, and XGBoost) and six ensemble models have been designed to address the research question. The results suggest that adding simulation crop model variables (APSIM) as input features to ML models can decrease yield prediction root mean squared error (RMSE) from 7 to 20%. Furthermore, we investigated partial inclusion of APSIM features in the ML prediction models and we found soil moisture related APSIM variables are most influential on the ML predictions followed by crop-related and phenology-related variables. Finally, based on feature importance measure, it has been observed that simulated APSIM average drought stress and average water table depth during the growing season are the most important APSIM inputs to ML. This result indicates that weather information alone is not sufficient and ML models need more hydrological inputs to make improved yield predictions.
Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage
Authors: Strange Josephine E. S. , Leekitcharoenphon Pimlapas , Møller Frederik Duus , Aarestrup Frank M.
Published: January 2021

Bacteriophages, or phages, are ubiquitous bacterial and archaeal viruses with an estimated total global population of 1031. It is well-known that wherever there are bacteria, their phage counterparts will be found, aiding in shaping the bacterial population. The present study used metagenomic data from global influent sewage in 79 cities in 60 countries to identify phages associated with bacteria and to explore their potential role in antimicrobial resistance gene (ARG) dissemination. The reads were mapped to known databases for bacteriophages and their abundances determined and correlated to geographic origin and the countries socio-economic status, as well as the abundances of bacterial species and ARG. We found that some phages were not equally distributed on a global scale, but their distribution was rather dictated by region and the socioeconomic status of the specific countries. This study provides a preliminary insight into the global and regional distribution of phages and their potential impact on the transmission of ARGs between bacteria. Moreover, the findings may indicate that phages in sewage could have adopted a lytic lifestyle, meaning that most may not be associated with bacteria and instead may be widely distributed as free-living phages, which are known to persist longer in the environment than their hosts. In addition, a significant correlation between phages and ARGs was obtained, indicating that phages may play a role in ARG dissemination. However, further analyses are needed to establish the true relationship between phages and ARGs due to a low abundance of the phages identified.
Biodistribution and radiation dosimetry of the positron emission tomography probe for AMPA receptor, [11C]K-2, in healthy human subjects
Authors: Hatano Mai , Miyazaki Tomoyuki , Ishiwata Yoshinobu , Nakajima Waki , Arisawa Tetsu , Kuroki Yoko , Kobayashi Ayako , Takada Yuuki , Ogawa Matsuyoshi , Kawamura Kazunori , Zhang Ming-Rong , Higuchi Makoto , Taguri Masataka , Kimura Yasuyuki , Takahashi Takuya
Published: January 2021

[11C]K-2, a radiotracer exhibiting high affinity and selectivity for α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors (AMPARs), is suitable for the quantification of AMPARs in living human brains and potentially useful in the identification of epileptogenic foci in patients. This study aimed to estimate the radiation doses of [11C]K-2 in various organs and calculate the effective dose after injection of [11C]K-2 in healthy human subjects. Twelve healthy male subjects were registered and divided into two groups (370 or 555 MBq of [11C]K-2), followed by 2 h whole-body scans. We estimated the radiation dose of each organ and then calculated the effective dose for each subject. The highest uptake of [11C]K-2 was observed in the liver, while the brain also showed relatively high uptake. The urinary bladder exhibited the highest radiation dose. The kidneys and liver also showed high radiation doses after [11C]K-2 injections. The effective dose of [11C]K-2 ranged from 5.0 to 5.2 μSv/MBq. Our findings suggest that [11C]K-2 is safe in terms of the radiation dose and adverse effects. The injection of 370–555 MBq (10 to 15 mCi) for PET studies using this radiotracer is applicable in healthy human subjects and enables serial PET scans in a single subject.
Evidence for a spin acoustic surface plasmon from inelastic atom scattering
Authors: Benedek G. , Bernasconi M. , Campi D. , Silkin I. V. , Chernov I. P. , Silkin V. M. , Chulkov E. V. , Echenique P. M. , Toennies J. P. , Anemone G. , Al Taleb A. , Miranda R. , Farías D.
Published: January 2021

Closed-shell atoms scattered from a metal surface exchange energy and momentum with surface phonons mostly via the interposed surface valence electrons, i.e., via the creation of virtual electron-hole pairs. The latter can then decay into surface phonons via electron-phonon interaction, as well as into acoustic surface plasmons (ASPs). While the first channel is the basis of the current inelastic atom scattering (IAS) surface-phonon spectroscopy, no attempt to observe ASPs with IAS has been made so far. In this study we provide evidence of ASP in Ni(111) with both Ne atom scattering and He atom scattering. While the former measurements confirm and extend so far unexplained data, the latter illustrate the coupling of ASP with phonons inside the surface-projected phonon continuum, leading to a substantial reduction of the ASP velocity and possibly to avoided crossing with the optical surface phonon branches. The analysis is substantiated by a self-consistent calculation of the surface response function to atom collisions and of the first-principle surface-phonon dynamics of Ni(111). It is shown that in Ni(111) ASP originate from the majority-spin Shockley surface state and are therefore collective oscillation of surface electrons with the same spin, i.e. it represents a new kind of collective quasiparticle: a Spin Acoustic Surface Plasmon (SASP).
Quantitative MRI phenotypes capture biological heterogeneity in multiple sclerosis patients
Authors: Smets Ide , Goris An , Vandebergh Marijne , Demeestere Jelle , Sunaert Stefan , Dupont Patrick , Dubois Bénédicte
Published: January 2021

Magnetization transfer ratio (MTR) and brain volumetric imaging are (semi-)quantitative MRI markers capturing demyelination, axonal degeneration and/or inflammation. However, factors shaping variation in these traits are largely unknown. In this study, we collected a longitudinal cohort of 33 multiple sclerosis (MS) patients and extended it cross-sectionally to 213. We measured MTR in lesions, normal-appearing white matter (NAWM), normal-appearing grey matter (NAGM) and total brain, grey matter, white matter and lesion volume. We also calculated the polygenic MS risk score. Longitudinally, inter-patient differences at inclusion and intra-patient changes during follow-up together explained > 70% of variance in MRI, with inter-patient differences at inclusion being the predominant source of variance. Cross-sectionally, we observed a moderate correlation of MTR between NAGM and NAWM and, less pronounced, with lesions. Age and gender explained about 30% of variance in total brain and grey matter volume. However, they contributed less than 10% to variance in MTR measures. There were no significant associations between MRI traits and the genetic risk score. In conclusion, (semi-)quantitative MRI traits change with ongoing disease activity but this change is modest in comparison to pre-existing inter-patient differences. These traits reflect individual variation in biological processes, which appear different from those involved in genetic MS susceptibility.
Development of antisense-mediated myostatin knockdown for the treatment of insulin resistance
Authors: Eilers Wouter , Cleasby Mark , Foster Keith
Published: January 2021

Myostatin is a negative regulator of muscle mass and its inhibition represents a promising strategy for the treatment of muscle disorders and type 2 diabetes. However, there is currently no clinically effective myostatin inhibitor, and therefore novel methods are required. We evaluated the use of antisense phosphorodiamidate morpholino oligomers (PMO) to reduce myostatin expression in skeletal muscle and measured their effects on muscle mass and glucose uptake. C57/Bl6 mice received intramuscular or intravenous injections of anti-myostatin PMOs. Repeated intramuscular administration lead to a reduction in myostatin transcript levels (~ 20–40%), and an increase in muscle mass in chow and high-fat diet (HFD)-fed mice, but insulin-stimulated glucose uptake was reduced in PMO-treated muscles of HFD-fed mice. Five weekly intravenous administrations of 100 nmol PMO did not reduce myostatin expression, and therefore had no significant physiological effects. Unexpectedly, exon skipping levels were higher after intramuscular administration of PMO in HFD- than chow-fed mice. These results suggest that a modest PMO-induced reduction in myostatin transcript levels is sufficient to induce an increase in muscle mass, but that a greater degree of inhibition may be required to improve muscle glucose uptake.
Fecal transplantation alleviates acute liver injury in mice through regulating Treg/Th17 cytokines balance
Authors: Liu Yongmei , Fan Linda , Cheng Zhuo , Yu Lei , Cong Shuo , Hu Yaxin , Zhu Lili , Zhang Baofang , Cheng Yiju , Zhao Peiling , Zhao Xueke , Cheng Mingliang
Published: January 2021

Changes in intestinal microecology during acute liver failure (ALF) directly affect the occurrence and development of the disease. The study aimed to investigate the relationship between the intestinal microbiota and the key immune cells. Fecal microbiota transplantation (FMT) was used to determine whether ALF can balance Th17/Treg cytokines. The relationship between gut microbiota and clinical indicators was analyzed. BALB/c mice were treated with d-galactosamine (d-GalN) to induce a murine ALF model. FMT to d-GalN mice was conducted to test for liver function indicators. Results showed that the proportions of Lachnospiraceae, Prevotella, S24-7, Odoribacter and Rikenellaceae in d-GalN mice with intestinal microbiota disorder were restored after FMT. Further, CIA analysis showed that bacteria had a covariant relationship with clinical indicators. Microbiota could account for changes in 49.9% of the overall clinical indicators. Adonis analysis showed that Ruminococcus, and Enterococcus have a greater impact on clinical indicators. FMT down-regulated the expression of IL-17A, TNF-α, and TGF-β, while up-regulated IL-10 and IL-22. Transplantation of feces from Saccharomyces boulardii donor mice improved GalN-induced liver damage. These findings indicate that FMT attenuates d-GalN-induced liver damage in mice, and a clinical trial is required to validate the relevance of our findings in humans, and to test whether this therapeutic approach is effective for patients with ALF.
Vulnerability to shear stress caused by altered peri-endothelial matrix is a key feature of Moyamoya disease
Authors: Matsuo Muneaki , Nadanaka Satomi , Soga Minami , Sugiyama Taku , Serigano Shota , Shimano Kenjiro , Ichinose Fumio , Nakamura Takuji , Maeda Toshiyuki , Houkin Kiyohiro , Era Takumi , Kitagawa Hiroshi
Published: January 2021

Moyamoya disease (MMD) is characterized by progressive bilateral stenotic changes in the terminal portion of the internal carotid arteries. Although RNF213 was identified as a susceptibility gene for MMD, the exact pathogenesis remains unknown. Immunohistochemical analysis of autopsy specimens from a patient with MMD revealed marked accumulation of hyaluronan and chondroitin sulfate (CS) in the thickened intima of occlusive lesions of MMD. Hyaluronan synthase 2 was strongly expressed in endothelial progenitor cells in the thickened intima. Furthermore, MMD lesions showed minimal staining for CS and hyaluronan in the endothelium, in contrast to control endothelium showing positive staining for both. Glycosaminoglycans of endothelial cells derived from MMD and control induced pluripotent stem cells demonstrated a decreased amount of CS, especially sulfated CS, in MMD. A computational fluid dynamics model showed highest wall shear stress values in the terminal portion of the internal carotid artery, which is the predisposing region in MMD. Because the peri-endothelial extracellular matrix plays an important role in protection, cell adhesion and migration, an altered peri-endothelial matrix in MMD may contribute to endothelial vulnerability to wall shear stress. Invading endothelial progenitor cells repairing endothelial injury would produce excessive hyaluronan and CS in the intima, and cause vascular stenosis.
Co-introduction of precipitate hardening and TRIP in a TWIP high-entropy alloy using friction stir alloying
Authors: Wang Tianhao , Shukla Shivakant , Gwalani Bharat , Sinha Subhasis , Thapliyal Saket , Frank Michael , Mishra Rajiv S.
Published: January 2021

Tuning deformation mechanisms is imperative to overcome the well-known strength-ductility paradigm. Twinning-induced plasticity (TWIP), transformation-induced plasticity (TRIP) and precipitate hardening have been investigated separately and have been altered to achieve exceptional strength or ductility in several alloy systems. In this study, we use a novel solid-state alloying method—friction stir alloying (FSA)—to tune the microstructure, and a composition of a TWIP high-entropy alloy by adding Ti, and thus activating site-specific deformation mechanisms that occur concomitantly in a single alloy. During the FSA process, grains of the as-cast face-centered cubic matrix were refined by high-temperature severe plastic deformation and, subsequently, a new alloy composition was obtained by dissolving Ti into the matrix. After annealing the FSA specimen at 900 °C, hard Ni–Ti rich precipitates formed to strengthen the alloy. An additional result was a Ni-depleted region in the vicinity of newly-formed precipitates. The reduction in Ni locally reduced the stacking fault energy, thus inducing TRIP-based deformation while the remaining matrix still deformed as a result of TWIP. Our current approach presents a novel microstructural architecture to design alloys, an approach that combines and optimizes local compositions such that multiple deformation mechanisms can be activated to enhance engineering properties.
Decorin-mediated suppression of tumorigenesis, invasion, and metastasis in inflammatory breast cancer
Authors: Hu Xiaoding , Villodre Emilly S. , Larson Richard , Rahal Omar M. , Wang Xiaoping , Gong Yun , Song Juhee , Krishnamurthy Savitri , Ueno Naoto T. , Tripathy Debu , Woodward Wendy A. , Debeb Bisrat G.
Published: January 2021

Inflammatory breast cancer (IBC) is a clinically distinct and highly aggressive form of breast cancer with rapid onset and a strong propensity to metastasize. The molecular mechanisms underlying the aggressiveness and metastatic propensity of IBC are largely unknown. Herein, we report that decorin (DCN), a small leucine-rich extracellular matrix proteoglycan, is downregulated in tumors from patients with IBC. Overexpression of DCN in IBC cells markedly decreased migration, invasion, and cancer stem cells in vitro and inhibited tumor growth and metastasis in IBC xenograft mouse models. Mechanistically, DCN functioned as a suppressor of invasion and tumor growth in IBC by destabilizing E-cadherin and inhibiting EGFR/ERK signaling. DCN physically binds E-cadherin in IBC cells and accelerates its degradation through an autophagy-linked lysosomal pathway. We established that DCN inhibits tumorigenesis and metastasis in IBC cells by negatively regulating the E-cadherin/EGFR/ERK axis. Our findings offer a potential therapeutic strategy for IBC, and provide a novel mechanism for IBC pathobiology.
A ratiometric electrochemiluminescent cytosensor based on polyaniline hydrogel electrodes in spatially separated electrochemiluminescent systems
Authors: Liu Gen , Chen Zixuan , Jin Bao-Kang , Jiang Li-Ping
Published: January 2021

A three-channel ratiometric ECL platform for MCF-7 cells detection using potential-resolved ECL probes.
Identification of black microplastics using long-wavelength infrared hyperspectral imaging with imaging-type two-dimensional Fourier spectroscopy
Authors: Nogo Kosuke , Ikejima Kou , Qi Wei , Kawashima Natsumi , Kitazaki Tomoya , Adachi Satoru , Wada Kenji , Nishiyama Akira , Ishimaru Ichiro
Published: January 2021

We constructed a palm-sized LWIR hyperspectral camera with a microbolometer and successfully measured the absorbance of black microplastics.
Bypassing the requirement for aminoacyl-tRNA by a cyclodipeptide synthase enzyme
Authors: Harding Christopher J. , Sutherland Emmajay , Hanna Jane G. , Houston Douglas R. , Czekster Clarissa M.
Published: January 2021

Cyclodipeptide synthases recognize a minimalistic substrate to produce cyclic dipeptides in a tRNA-independent manner.
Revision in the first steps of the biosynthesis of the red antibiotic prodigiosin: use of a synthetic thioester to validate a new intermediate
Authors: Couturier Maxime , Bhalara Hiral D. , Monson Rita E. , Salmond George P. C. , Leeper Finian J.
Published: January 2021

A revision is proposed to the biosynthetic pathway to the well-known red pigment prodigiosin via a new thioester intermediate.
Site-specific single point mutation by anthranilic acid in hIAPP8–37 enhances anti-amyloidogenic activity
Authors: Kalita Sourav , Kalita Sujan , Paul Ashim , Shah Manisha , Kumar Sachin , Mandal Bhubaneswar
Published: January 2021

β-Amino acid based peptidomimetics are attractive scaffolds for therapeutics design towards T2D. They prevent amyloid formation of hIAPP by forming non-fibrillar non-toxic aggregates.
Substituted meso-vinyl-BODIPY as thiol-selective fluorogenic probes for sensing unfolded proteins in the endoplasmic reticulum
Authors: Mu Huiying , Miki Koji , Kubo Takuya , Otsuka Koji , Ohe Kouichi
Published: January 2021

Thiol-selective probes based on BODIPY scaffold were developed for sensing small-molecule thiols and unfolded proteins. The good organelle specificity of probe enables its utility for reporting the protein unfolding under ER stress in living cells.
Insights on the catalytic behaviour of sulfonic acid-functionalized ionic liquids (ILs) in transesterification reactions – voltammetric characterization of sulfonic task-specific ILs with bisulfate anions
Authors: Martini María B. , Fernández José L. , Adam Claudia G.
Published: January 2021

Cyclic voltammetry measurements on imidazolic ionic liquids with sulfonic acid groups and bisulfate counterions revealed that they work as efficient reservoirs of sulfuric acid and are able to dose it on demand to uphold an efficient acid catalysis.
Boosting electrochemical nitrogen reduction reaction performance of two-dimensional Mo porphyrin monolayers via turning the coordination environment
Authors: Liu Shiqiang , Cheng Zhiwen , Liu Yawei , Gao Xiaoping , Tan Yujia , Ren Yuanyang , Shen Zhemin
Published: January 2021

Designing atomically dispersed metal catalysts for the nitrogen reduction reaction (NRR) is an effective approach to achieve better energy conversion efficiencies.
Nanostructured manganese oxides as highly active catalysts for enhanced hydrolysis of bis(4-nitrophenyl)phosphate and catalytic decomposition of methanol
Authors: Šťastný Martin , Issa Gloria , Popelková Daniela , Ederer Jakub , Kormunda Martin , Kříženecká Sylvie , Henych Jiří
Published: January 2021

The nanostructured manganese oxides (MnOx) exhibited high catalytic activities for hydrolysis of phosphate diester-based substrate bis(4-nitrophenyl)phosphate and decomposition of methanol to carbon monoxide and hydrogen as a potential alternative fuel.
Review of the current state of protein aggregation inhibition from a materials chemistry perspective: special focus on polymeric materials
Authors: Rajan Robin , Ahmed Sana , Sharma Neha , Kumar Nishant , Debas Alisha , Matsumura Kazuaki
Published: January 2021

This review discusses various aspects of protein aggregation and inhibition strategies, emphasizing the use of polymers, which is one of the most promising approaches to combat various aggregation-induced complications in neurodegenerative diseases and protein therapeutics.
Reduced graphene oxide integrated poly(ionic liquid) functionalized nano-fibrillated cellulose composite paper with improved toughness, ductility and hydrophobicity
Authors: Layek Rama K. , Parihar Vijay Singh , Seppälä Jukka , Efimov Alexander , Palola Sarianna , Kanerva Mikko , Annurakshita Shambhavee , Kellomäki Minna , Sarlin Essi
Published: January 2021

Reduced graphene oxide/poly (ionic liquid) functionalized nano-fibrillated cellulose composite paper with significant enhancement of mechanical strength, ductility, toughness and hydrophobicity was fabricated by vacuum filtration assisted assembly.
Investigation of spectral output of Er3+ and Yb3+/Er3+ doped TeO2–ZnO–BaO glasses for photonic applications
Authors: Doğan Anıl , Yıldırım Saniye Merve , Erdem Murat , Esmer Kadir , Eryürek Gönül
Published: January 2021

Er3+ and Yb3+/Er3+ doped TeO2–ZnO–BaO glasses were synthesized using the melt quenching technique with two different Er3+ concentrations for photonic applications.
Quantitative mapping of magnetic properties at the nanoscale with bimodal AFM
Authors: Gisbert Victor G. , Amo Carlos A. , Jaafar Miriam , Asenjo Agustina , Garcia Ricardo
Published: January 2021

We demonstrate that a force microscope operated in a bimodal configuration enables the mapping of magnetic interactions with high quantitative accuracy and high-spatial resolution (∼30 nm).
The colorimetric and microfluidic paper-based detection of cysteine and homocysteine using 1,5-diphenylcarbazide-capped silver nanoparticles
Authors: Shariati Sattar , Khayatian Gholamreza
Published: January 2021

A simple and novel portable method for the quantitative measurement of cysteine and homocysteine in human urine samples is presented.
Hydrogen-driven dramatically improved mechanical properties of amorphized ITO–Ag–ITO thin films
Authors: Park Sungmin , Yoon Janghee , Kim Seohan , Song Pungkeun
Published: January 2021

An oxide/metal/oxide (OMO) multi-structure, which has good electrical, optical, and mechanical stability, was studied as a potential replacement of polycrystalline In–Sn–O (ITO).
Oxidative esterification of renewable furfural on cobalt dispersed on ordered porous nitrogen-doped carbon
Authors: Yin Defeng , Zheng Yanxia , Yang Lixi , Li Shuyue , Zhu Daqing , Guo Yafei , Zuo Cuncun , Li Yuchao , Huang Haofei , Wang Ming
Published: January 2021

Catalytic oxidative esterification of furfural to methyl 2-furoate with cobalt-dispersed N-doped ordered porous carbon.
An efficient synthesis of 4-phenoxy-quinazoline, 2-phenoxy-quinoxaline, and 2-phenoxy-pyridine derivatives using aryne chemistry
Authors: Zilla Mahesh K. , Mahajan Sheena , Khajuria Rajni , Gupta Vivek K. , Kapoor Kamal K. , Ali Asif
Published: January 2021

Efficient synthesis of 4-phenoxyquinazoline, 2-phenoxyquinoxaline, 2-phenoxypyridine derivatives were generated of aryne from 2-(trimethylsilyl)phenyltrifluoromethanesulfonate with cesium fluoride.
Low photoactive phase temperature all-inorganic, tin–lead mixed perovskite solar cell
Authors: Kuan Chun-Hsiao , Shen Hui-Hung , Lin Ching-Fuh
Published: January 2021

In Cs-based all inorganic perovskite solar cells based, doping Sn can cause lattice shrinkage, which reduces annealing temperature of forming photoactive phase.
CRISPR base editing applications for identifying cancer-driving mutations
Authors: Pal Martin , Herold Marco J.
Published: January 2021

CRISPR base editing technology is a promising genome editing tool as (i) it does not require a DNA template to introduce mutations and (ii) it avoids creating DNA double-strand breaks, which can lead to unintended chromosomal alterations or elicit an unwanted DNA damage response. Given many cancers originate from point mutations in cancer-driving genes, the application of base editing for either modelling tumour development, therapeutic editing, or functional screening is of great promise. In this review, we summarise current DNA base editing technologies and will discuss recent advancements and existing hurdles for its usage in cancer research.
DVC‐Net: A deep neural network model for dense video captioning
Authors: Lee Sujin , Kim Incheol
Published: January 2021

Dense video captioning (DVC) detects multiple events in an input video and generates natural language sentences to describe each event. Previous studies predominantly used convolutional neural networks to extract visual features from videos but failed to employ high‐level semantics to effectively explain video content such as people, objects, actions, and places, and utilized only limited context information in generating natural language. To overcome these deficiencies, DVC‐Net is proposed, a new deep neural network model that uses high‐level semantics to efficiently represent important events as well as visual features. Additionally, DVC‐Net uses a bidirectional long short‐term memory network, a type of recurrent neural network, to detect events over time. Furthermore, DVC‐Net applies an attention mechanism and context gating to effectively exploit context information in a caption generation step. In experiments conducted versus state‐of‐the‐art models, DVC‐Net presented relative gains of over 1.72% (BLEU@1 score increases from 12.22 to 13.94) and 3.19% (CIDEr score increases from 12.61 to 15.80) on the large‐scale benchmark datasets, namely ActivityNet Captions and MSR‐VTT, respectively.
A BCS microwave imaging algorithm for object detection and shape reconstruction tested with experimental data
Authors: Zilberstein Nicolás , Maya Juan Augusto , Altieri Andrés
Published: January 2021

An approach based on the Green function and the Born approximation is used for impulsive radio ultra‐wideband microwave imaging, in which a permittivity map of the illuminated scenario is estimated using the scattered fields measured at several positions. Two algorithms are applied to this model and compared: the first one solves the inversion problem using a linear operator. The second one is based on the Bayesian compressive sensing technique, where the sparseness of the contrast function is introduced as a priori knowledge in order to improve the inverse mapping. In order to compare both methods, measurements in real scenarios are taken using an ultra‐wideband radar prototype. The results with real measurements illustrate that, for the considered scenarios, the Bayesian compressive sensing imaging algorithm has a better performance in terms of range and cross‐range resolution allowing object detection and shape reconstruction, with a reduced computational burden, and fewer space and frequency measurements, as compared to the linear operator.
Miniaturized inverted ultra‐wideband multiple‐input multiple‐output antenna with high isolation
Authors: Nan Jing‐Chang , Wang Ming‐Huan , Gao Ming‐Ming , Liu Jing
Published: January 2021

For the ultra‐wideband (UWB) transmission requirements in wireless communication systems and better miniaturization of mobile terminal antennas, a compact UWB multiple‐input multiple‐output (MIMO) antenna with higher isolation between units is proposed. The MIMO antenna consists of two semi‐circular antenna units and a defective ground structure. By improving the structure of the ground plane, the antenna units are placed upside down by taking advantage of the inherent directional radiation characteristics of the antenna units, thereby achieving higher isolation. The proposed antenna size is 15 × 22 × 1.6 mm3. The measurement results show that the proposed UWB MIMO antenna satisfies the port reflection coefficient S11 < −10 dB in the 3.4–12.9 GHz band, and the isolation is all greater than 25 dB, which has high isolation. The allowable limit of the envelope correlation coefficient ensures good MIMO performance, which can meet the requirements of UWB wireless communication in practical engineering applications.
Effect of the gate structure on the kink phenomenon in of AlGaN/GaN HEMT
Authors: Osmanoglu Sinan , Ozbay Ekmel
Published: January 2021

For the first time, the effect of the gate structure on the kink phenomenon in of the AlGaN/GaN HEMT is investigated in this study. To provide critical understanding into the kink effect, the kink effect in of the AlGaN/GaN HEMTs is investigated with transistors that have various gate lengths () and gate connected field plate lengths (). The HEMTs are fabricated and characterised at the same conditions, and the equivalent circuit models are used to get consistent results. The experimental results show that the gate structure can play an important role on kink effect in . The results present valuable information on the development of the AlGaN/GaN HEMT technology and the MMIC design regarding kink effect.
A robust tracking algorithm for a human‐following mobile robot
Authors: Tsai Tsung‐Han , Yao Chia‐Hsiang
Published: January 2021

The capability of recognizing and tracking a specific human is considered a key technique for serving mobile robots. This paper proposes a real‐time tracker that uses a stereo camera to track specific people in different environments. A tracker has been designed to detect the selected target from multiple people by use of block matching algorithm, human detection, and colour histogram comparison. Considering the similar colour of the objects, the predictor of the Kalman filter determines the position of the object. Finally, the mobile robot is moved according to the tracking results with a relative distance between the robot and the target. The effectiveness of the proposed method is demonstrated by experiments on many video sequences and real environments.
Level set method with Retinex‐corrected saliency embedded for image segmentation
Authors: Liu Dongmei , Chang Faliang , Zhang Huaxiang , Liu Li
Published: January 2021

It can be a very challenging task when using level set method segmenting natural images with high intensity inhomogeneity and complex background scenes. A new synthesis level set method for robust image segmentation based on the combination of Retinex‐corrected saliency region information and edge information is proposed in this work. First, the Retinex theory is introduced to correct the saliency information extraction. Second, the Retinex‐corrected saliency information is embedded into the level set method due to its advantageous quality which makes a foreground object stand out relative to the backgrounds. Combined with the edge information, the boundary of segmentation will be more precise and smooth. Experiments indicate that the proposed segmentation algorithm is efficient, fast, reliable, and robust.