bluuebunny/crossref_metadata_2025 huggingface dataset:
Anti-cancer effect of LINC00478 in bladder cancer correlates with KDM1A-dependent MMP9 demethylation
Authors: Yang Han-Jie , Liu Tian , Xiong Yang
Published: May 2022

Accumulating evidence has highlighted the important roles of long intergenic non-coding RNAs (lincRNAs) during cancer progression. However, the involvement of LINC00478 in bladder cancer remains largely unclear. Accordingly, the current study sought to investigate the function of LINC00478 on malignant phenotypes of bladder cancer cells as well as the underlying mechanism. By integrating data from in silico analysis, we uncovered that LINC00478 was differentially expressed in bladder cancer. We further analyzed the expression of LINC00478 and matrix metalloprotein 9 (MMP9) in bladder cancer tissues and cell lines and observed a significant decline in LINC00478 expression and an elevation in MMP9 expression. In addition, chromatin immunoprecipitation, RNA-binding protein immunoprecipitation, and RNA pull-down assays predicted and validated that LINC00478 targeted lysine-specific demethylase-1 (KDM1A) and down-regulated the expression of MMP9 by decreasing the monomethylation on lysine 4 of histone H3 (H3K4me1) of MMP9 promoter. Treatment with KDM1A inhibitor tranylcypromine (TCP) also led to an increase in the enrichment of H3K4me1 in the MMP9 promoter region. Through gain- and loss-of-function approaches, we found that LINC00478 up-regulation diminished the malignant phenotype of bladder cancer cells in vitro, and further inhibited xenograft tumor growth and metastasis in vivo by repressing MMP9. Collectively, our findings unraveled a LINC00478-mediated inhibitory mechanism in bladder cancer via the recruitment of histone demethylation transferase KDM1A to the MMP9 promoter region, which can provide potential implications for novel therapeutic targets against bladder cancer.
circDHTKD1 promotes lymphatic metastasis of bladder cancer by upregulating CXCL5
Authors: Lu Qun , Yin Haoli , Deng Yongming , Chen Wei , Diao Wenli , Ding Meng , Cao Wenmin , Fu Yao , Mo Wenjing , Chen Xiaoqing , Zhang Qing , Zhao Xiaozhi , Guo Hongqian
Published: May 2022

Lymph node (LN) metastasis is associated with unfavorable prognosis of bladder cancer (BCa). Although lymphangiogenesis is functionally important in LN metastasis of tumors, the potential mechanism in BCa remains unclear. Here, we clarified a regulatory mechanism of circRNA-mediated lymphangiogenesis and LN metastasis in BCa based on next-generation sequencing data. We revealed that circDHTKD1 was positively associated with LN metastasis and significantly upregulated in BCa. By analyzing the co-expression patterns of circDHTKD1 and differentially expressed mRNAs, we identified that circDHTKD1 facilitated lymphangiogenesis by upregulating CXCL5. Mechanistically, circDHTKD1 directly interacted with miR-149-5p, and antagonized the repression of miR-149-5p on CXCL5. Furthermore, circDHTKD1-induced CXCL5 expression recruited and activated neutrophils, which participated in lymphangiogenesis by secreting VEGF-C. Our study supports circDHTKD1 as a promising diagnostic and therapeutic target for LN metastasis in BCa.
Dynamic O-GlcNAcylation coordinates ferritinophagy and mitophagy to activate ferroptosis
Authors: Yu Fan , Zhang Qianping , Liu Hanyu , Liu Jinming , Yang Song , Luo Xiaofan , Liu Wei , Zheng Hao , Liu Qiqi , Cui Yunxi , Chen Guo , Li Yanjun , Huang Xinglu , Yan Xiyun , Zhou Jun , Chen Quan
Published: May 2022

Ferroptosis is a regulated iron-dependent cell death characterized by the accumulation of lipid peroxidation. A myriad of facets linking amino acid, lipid, redox, and iron metabolisms were found to drive or to suppress the execution of ferroptosis. However, how the cells decipher the diverse pro-ferroptotic stress to activate ferroptosis remains elusive. Here, we report that protein O-GlcNAcylation, the primary nutrient sensor of glucose flux, orchestrates both ferritinophagy and mitophagy for ferroptosis. Following the treatment of ferroptosis stimuli such as RSL3, a commonly used ferroptosis inducer, there exists a biphasic change of protein O-GlcNAcylation to modulate ferroptosis. Pharmacological or genetic inhibition of O-GlcNAcylation promoted ferritinophagy, resulting in the accumulation of labile iron towards mitochondria. Inhibition of O-GlcNAcylation resulted in mitochondria fragmentation and enhanced mitophagy, providing an additional source of labile iron and rendering the cell more sensitive to ferroptosis. Mechanistically, we found that de-O-GlcNAcylation of the ferritin heavy chain at S179 promoted its interaction with NCOA4, the ferritinophagy receptor, thereby accumulating labile iron for ferroptosis. Our findings reveal a previously uncharacterized link of dynamic O-GlcNAcylation with iron metabolism and decision-making for ferroptosis, thus offering potential therapeutic intervention for fighting disease.
DNA methylation signature of chronic low-grade inflammation and its role in cardio-respiratory diseases
Authors: Wielscher Matthias , Mandaviya Pooja R. , Kuehnel Brigitte , Joehanes Roby , Mustafa Rima , Robinson Oliver , Zhang Yan , Bodinier Barbara , Walton Esther , Mishra Pashupati P. , Schlosser Pascal , Wilson Rory , Tsai Pei-Chien , Palaniswamy Saranya , Marioni Riccardo E. , Fiorito Giovanni , Cugliari Giovanni , Karhunen Ville , Ghanbari Mohsen , Psaty Bruce M. , Loh Marie , Bis Joshua C. , Lehne Benjamin , Sotoodehnia Nona , Deary Ian J. , Chadeau-Hyam Marc , Brody Jennifer A. , Cardona Alexia , Selvin Elizabeth , Smith Alicia K. , Miller Andrew H. , Torres Mylin A. , Marouli Eirini , Gào Xin , van Meurs Joyce B. J. , Graf-Schindler Johanna , Rathmann Wolfgang , Koenig Wolfgang , Peters Annette , Weninger Wolfgang , Farlik Matthias , Zhang Tao , Chen Wei , Xia Yujing , Teumer Alexander , Nauck Matthias , Grabe Hans J. , Doerr Macus , Lehtimäki Terho , Guan Weihua , Milani Lili , Tanaka Toshiko , Fisher Krista , Waite Lindsay L. , Kasela Silva , Vineis Paolo , Verweij Niek , van der Harst Pim , Iacoviello Licia , Sacerdote Carlotta , Panico Salvatore , Krogh Vittorio , Tumino Rosario , Tzala Evangelia , Matullo Giuseppe , Hurme Mikko A. , Raitakari Olli T. , Colicino Elena , Baccarelli Andrea A. , Kähönen Mika , Herzig Karl-Heinz , Li Shengxu ,   BIOS consortium, Conneely Karen N. , Kooner Jaspal S. , Köttgen Anna , Heijmans Bastiaan T. , Deloukas Panos , Relton Caroline , Ong Ken K. , Bell Jordana T. , Boerwinkle Eric , Elliott Paul , Brenner Hermann , Beekman Marian , Levy Daniel , Waldenberger Melanie , Chambers John C. , Dehghan Abbas , Järvelin Marjo-Riitta
Published: May 2022

We performed a multi-ethnic Epigenome Wide Association study on 22,774 individuals to describe the DNA methylation signature of chronic low-grade inflammation as measured by C-Reactive protein (CRP). We find 1,511 independent differentially methylated loci associated with CRP. These CpG sites show correlation structures across chromosomes, and are primarily situated in euchromatin, depleted in CpG islands. These genomic loci are predominantly situated in transcription factor binding sites and genomic enhancer regions. Mendelian randomization analysis suggests altered CpG methylation is a consequence of increased blood CRP levels. Mediation analysis reveals obesity and smoking as important underlying driving factors for changed CpG methylation. Finally, we find that an activated CpG signature significantly increases the risk for cardiometabolic diseases and COPD.
Indigenous oyster fisheries persisted for millennia and should inform future management
Authors: Reeder-Myers Leslie , Braje Todd J. , Hofman Courtney A. , Elliott Smith Emma A. , Garland Carey J. , Grone Michael , Hadden Carla S. , Hatch Marco , Hunt Turner , Kelley Alice , LeFebvre Michelle J. , Lockman Michael , McKechnie Iain , McNiven Ian J. , Newsom Bonnie , Pluckhahn Thomas , Sanchez Gabriel , Schwadron Margo , Smith Karen Y. , Smith Tam , Spiess Arthur , Tayac Gabrielle , Thompson Victor D. , Vollman Taylor , Weitzel Elic M. , Rick Torben C.
Published: May 2022

Historical ecology has revolutionized our understanding of fisheries and cultural landscapes, demonstrating the value of historical data for evaluating the past, present, and future of Earth’s ecosystems. Despite several important studies, Indigenous fisheries generally receive less attention from scholars and managers than the 17th–20th century capitalist commercial fisheries that decimated many keystone species, including oysters. We investigate Indigenous oyster harvest through time in North America and Australia, placing these data in the context of sea level histories and historical catch records. Indigenous oyster fisheries were pervasive across space and through time, persisting for 5000–10,000 years or more. Oysters were likely managed and sometimes “farmed,” and are woven into broader cultural, ritual, and social traditions. Effective stewardship of oyster reefs and other marine fisheries around the world must center Indigenous histories and include Indigenous community members to co-develop more inclusive, just, and successful strategies for restoration, harvest, and management.
Structural basis for the synthesis of the core 1 structure by C1GalT1
Authors: González-Ramírez Andrés Manuel , Grosso Ana Sofia , Yang Zhang , Compañón Ismael , Coelho Helena , Narimatsu Yoshiki , Clausen Henrik , Marcelo Filipa , Corzana Francisco , Hurtado-Guerrero Ramon
Published: May 2022

C1GalT1 is an essential inverting glycosyltransferase responsible for synthesizing the core 1 structure, a common precursor for mucin-type O-glycans found in many glycoproteins. To date, the structure of C1GalT1 and the details of substrate recognition and catalysis remain unknown. Through biophysical and cellular studies, including X-ray crystallography of C1GalT1 complexed to a glycopeptide, we report that C1GalT1 is an obligate GT-A fold dimer that follows a SN2 mechanism. The binding of the glycopeptides to the enzyme is mainly driven by the GalNAc moiety while the peptide sequence provides optimal kinetic and binding parameters. Interestingly, to achieve glycosylation, C1GalT1 recognizes a high-energy conformation of the α-GalNAc-Thr linkage, negligibly populated in solution. By imposing this 3D-arrangement on that fragment, characteristic of α-GalNAc-Ser peptides, C1GalT1 ensures broad glycosylation of both acceptor substrates. These findings illustrate a structural and mechanistic blueprint to explain glycosylation of multiple acceptor substrates, extending the repertoire of mechanisms adopted by glycosyltransferases.
Ambient-pressure hydrogenation of CO2 into long-chain olefins
Authors: Li Zhongling , Wu Wenlong , Wang Menglin , Wang Yanan , Ma Xinlong , Luo Lei , Chen Yue , Fan Kaiyuan , Pan Yang , Li Hongliang , Zeng Jie
Published: May 2022

The conversion of CO2 by renewable power-generated hydrogen is a promising approach to a sustainable production of long-chain olefins (C4+=) which are currently produced from petroleum resources. The decentralized small-scale electrolysis for hydrogen generation requires the operation of CO2 hydrogenation in ambient-pressure units to match the manufacturing scales and flexible on-demand production. Herein, we report a Cu-Fe catalyst which is operated under ambient pressure with comparable C4+= selectivity (66.9%) to that of the state-of-the-art catalysts (66.8%) optimized under high pressure (35 bar). The catalyst is composed of copper, iron oxides, and iron carbides. Iron oxides enable reverse-water-gas-shift to produce CO. The synergy of carbide path over iron carbides and CO insertion path over interfacial sites between copper and iron carbides leads to efficient C-C coupling into C4+=. This work contributes to the development of small-scale low-pressure devices for CO2 hydrogenation compatible with sustainable hydrogen production.
Design of a two-dimensional interplanar heterojunction for catalytic cancer therapy
Authors: Kang Yong , Mao Zhuo , Wang Ying , Pan Chao , Ou Meitong , Zhang Hanjie , Zeng Weiwei , Ji Xiaoyuan
Published: May 2022

Limited substrates content is a major hurdle dampening the antitumor effect of catalytic therapy. Herein, a two-dimensional interplanar heterojunction (FeOCl/FeOOH NSs) with ·OH generation under ultrasound irradiation is fabricated and utilized for catalytic cancer therapy. This interplanar heterojunction is prepared through replacing chlorine from iron oxychloride with hydroxyl. Benefiting from the longer hydroxyl bond length and enhanced affinity with water, the alkali replacement treatment integrates interplanar heterojunction synthesis and exfoliation in one step. In particular, a build-in electric field facilitated Z-scheme interplanar heterojunction is formed due to the aligning Fermi levels. The holes on the valence band of FeOCl have great ability to catalyze O2 evolution from H2O, meanwhile, the generated O2 is immediately and directly reduced to H2O2 by the electrons on the conductive band of FeOOH. The self-supplying H2O2 ability guarantees efficient ·OH generation via the Fenton-like reaction catalyzed by FeOCl/FeOOH NSs, which exhibits excellent anti-tumor performance.
High-throughput analysis of single human cells reveals the complex nature of DNA replication timing control
Authors: Massey Dashiell J. , Koren Amnon
Published: May 2022

DNA replication initiates from replication origins firing throughout S phase. Debate remains about whether origins are a fixed set of loci, or a loose agglomeration of potential sites used stochastically in individual cells, and about how consistent their firing time is. We develop an approach to profile DNA replication from whole-genome sequencing of thousands of single cells, which includes in silico flow cytometry, a method for discriminating replicating and non-replicating cells. Using two microfluidic platforms, we analyze up to 2437 replicating cells from a single sample. The resolution and scale of the data allow focused analysis of replication initiation sites, demonstrating that most occur in confined genomic regions. While initiation order is remarkably similar across cells, we unexpectedly identify several subtypes of initiation regions in late-replicating regions. Taken together, high throughput, high resolution sequencing of individual cells reveals previously underappreciated variability in replication initiation and progression.
Fast-growing species shape the evolution of reef corals
Authors: Siqueira Alexandre C. , Kiessling Wolfgang , Bellwood David R.
Published: May 2022

Ecological interactions are ubiquitous on tropical coral reefs, where sessile organisms coexist in limited space. Within these high-diversity systems, reef-building scleractinian corals form an intricate interaction network. The role of biotic interactions among reef corals is well established on ecological timescales. However, its potential effect on macroevolutionary patterns remains unclear. By analysing the rich fossil record of Scleractinia, we show that reef coral biodiversity experienced marked evolutionary rate shifts in the last 3 million years, possibly driven by biotic interactions. Our models suggest that there was an overwhelming effect of staghorn corals (family Acroporidae) on the fossil diversity trajectories of other coral groups. Staghorn corals showed an unparalleled spike in diversification during the Pleistocene. But surprisingly, their expansion was linked with increases in both extinction and speciation rates in other coral families, driving a nine-fold increase in lineage turnover. These results reveal a double-edged effect of diversity dependency on reef evolution. Given their fast growth, staghorn corals may have increased extinction rates via competitive interactions, while promoting speciation through their role as ecosystem engineers. This suggests that recent widespread human-mediated reductions in staghorn coral cover, may be disrupting the key macroevolutionary processes that established modern coral reef ecosystems.
MatSciBERT: A materials domain language model for text mining and information extraction
Authors: Gupta Tanishq , Zaki Mohd , Krishnan N. M. Anoop , Mausam
Published: May 2022

A large amount of materials science knowledge is generated and stored as text published in peer-reviewed scientific literature. While recent developments in natural language processing, such as Bidirectional Encoder Representations from Transformers (BERT) models, provide promising information extraction tools, these models may yield suboptimal results when applied on materials domain since they are not trained in materials science specific notations and jargons. Here, we present a materials-aware language model, namely, MatSciBERT, trained on a large corpus of peer-reviewed materials science publications. We show that MatSciBERT outperforms SciBERT, a language model trained on science corpus, and establish state-of-the-art results on three downstream tasks, named entity recognition, relation classification, and abstract classification. We make the pre-trained weights of MatSciBERT publicly accessible for accelerated materials discovery and information extraction from materials science texts.
Antinodal kink in the band dispersion of electron-doped cuprate La2−xCexCuO4±δ
Authors: Tang C. Y. , Lin Z. F. , Zhang J. X. , Guo X. C. , Zhong Y. G. , Guan J. Y. , Gao S. Y. , Rao Z. C. , Zhao J. , Huang Y. B. , Qian T. , Weng Z. Y. , Jin K. , Sun Y. J. , Ding H.
Published: May 2022

Angle-resolved photoemission spectroscopy (ARPES) measurements have established the phenomenon of kink in band dispersion of high-Tc cuprate superconductors. However, systematic studies of the kink in electron-doped cuprates are still lacking experimentally. We performed in situ ARPES measurements on La2−xCexCuO4±δ (LCCO) thin films over a wide electron doping (n) range from 0.05 to 0.23. While the nodal kink is nearly invisible, an antinodal kink around 45 meV, surviving above 200 K, is observed for n ~ 0.05–0.19, whose position is roughly independent of doping. The fact that the antinodal kink observed at high temperatures and in the highly overdoped region favors the phonon mechanism with contributions from the Cu–O bond-stretching mode and the out-of-plane oxygen buckling mode.
Symmetry-enforced nodal chain phonons
Authors: Zhu Jiaojiao , Wu Weikang , Zhao Jianzhou , Chen Hao , Zhang Lifa , Yang Shengyuan A.
Published: May 2022

Topological phonons in crystalline materials have been attracting great interest. Most cases studied so far are direct generalizations of the topological states from electronic systems. Here, we reveal a class of topological phonons - the symmetry-enforced nodal-chain phonons, which manifest the characteristic of phononic systems. We show that in five space groups with D2d little co-group at a non-time-reversal-invariant-momentum point, the phononic nodal chain is guaranteed to exist owing to the vector basis symmetry of phonons, which is a character distinct from electronic and other systems. In other words, this symmetry enforcement feature of the proposed nodal chain is limited to phononic systems. Interestingly, the chains in these five space groups exhibit two different patterns: for tetragonal systems, they are one-dimensional along the fourfold axis; for cubic systems, they form a three-dimensional network structure. Based on first-principles calculations, we identify K2O as a realistic material hosting the proposed nodal-chain phonons. We show that the effect of LO-TO splitting helps to expose the nodal-chain phonons in a large frequency window. In addition, the nodal chains may lead to drumhead surface phonon modes on multiple surfaces of a sample.
MASCDB, a database of images, descriptors and microphysical properties of individual snowflakes in free fall
Authors: Grazioli Jacopo , Ghiggi Gionata , Billault-Roux Anne-Claire , Berne Alexis
Published: May 2022

Snowfall information at the scale of individual particles is rare, difficult to gather, but fundamental for a better understanding of solid precipitation microphysics. In this article we present a dataset (with dedicated software) of in-situ measurements of snow particles in free fall. The dataset includes gray-scale (255 shades) images of snowflakes, co-located surface environmental measurements, a large number of geometrical and textural snowflake descriptors as well as the output of previously published retrieval algorithms. These include: hydrometeor classification, riming degree estimation, identification of melting particles, discrimination of wind-blown snow, as well as estimates of snow particle mass and volume. The measurements were collected in various locations of the Alps, Antarctica and Korea for a total of 2’555’091 snowflake images (or 851’697 image triplets). As the instrument used for data collection was a Multi-Angle Snowflake Camera (MASC), the dataset is named MASCDB. Given the large amount of snowflake images and associated descriptors, MASCDB can be exploited also by the computer vision community for the training and benchmarking of image processing systems.
Genome-wide analysis of basic helix–loop–helix (bHLH) transcription factors in Aquilaria sinensis
Authors: Sun Pei-Wen , Gao Zhi-Hui , Lv Fei-Fei , Yu Cui-Cui , Jin Yue , Xu Yan-Hong , Wei Jian-He
Published: May 2022

The basic helix–loop–helix (bHLH) transcription factors are involved in several biological processes both in plant development and stress responses. Agarwood, a major active and economical product, is only induced and accumulated when the roots, stems, or branches are wounded in Aquilaria sinensis. Although genome-wide comprehensive analyses of the bHLH family have been identified in many plants, no systematic study of the genes in this family has been conducted in A. sinensis. In this study, 105 bHLH genes were identified in A. sinensis through genome-wide analysis and named according to their chromosomal locations. Based on a phylogenetic tree, AsbHLH family proteins were classified into 18 subfamilies. Most of them were distributed on eight chromosomes, with the exception of two genes. Based on the tissue-specific expression characteristics and expression patterns in response to methyl jasmonate (MeJA) treatment, seven AsbHLH genes were likely involved in wound-induced agarwood formation. The results provide comprehensive information on AsbHLHs that can be used to elucidate the molecular functions and physiological roles of these proteins in A. sinensis.
Neuropsychiatric symptoms and seizure related with serum cytokine in epilepsy patients
Authors: Shin Hye-Rim , Chu Kon , Lee Woo-Jin , Lee Han Sang , Kim Eun Young , Son Hyoshin , Moon Jangsup , Kim Narae , Jung Ki-Young , Jung Keun-Hwa , Lee Soon-Tae , Park Kyung-Il , Lee Sang Kun
Published: May 2022

Neuroinflammation contributes to epileptogenesis and ictogenesis. Various signals of neuroinflammation lead to neuronal hyper-excitability. Since an interplay between epilepsy, psychiatric comorbidities and neuroinflammation has been suggested, we explored psychiatric symptoms in epilepsy patients, and the relationship with neuroinflammation. We screened epilepsy patients who were admitted for video-EEG monitoring between July 2019 and December 2020. Enrolled patients were asked to respond to neuropsychiatric questionnaires (Hospital Anxiety and Depression Scale (HADS) and Neuropsychiatric Inventory-Questionnaire (NPI-Q)) on admission. Serum cytokines (IL-1β, IL-2, IL-6, IFN-γ, CCL2, and CCL5) were measured by ELISA on admission, and within 6 h after a seizure. We enrolled 134 patients, and 32 patients (23.9%) had seizures during monitoring. Cytokine levels did not change after seizures, but IL-2 and IL-6 increased in cases of generalized tonic–clonic seizures. The HADS-A score was lower in Q4 of CCL5 (p-value = 0.016) and anxiety was also less common in Q4 of CCL5 (p-value = 0.042). NPI-Q question 4 (depression) severity was higher in CCL2 (p-value = 0.024). This suggested that psychiatric symptoms may also be related to inflammatory processes in epilepsy patients. Further large, standardized studies are necessary to underpin the inflammatory mechanisms in epilepsy and psychiatric symptoms.
Imaging evolution of Cascadia slow-slip event using high-rate GPS
Authors: Itoh Yuji , Aoki Yosuke , Fukuda Junichi
Published: May 2022

The slip history of short-term slow slip event (SSE) is typically inferred from daily Global Positioning System (GPS) data, which, however, cannot image the sub-daily processes, leaving the underlying mechanisms of SSEs elusive. To address the temporal resolution issue, we attempted to employ the kinematic subdaily GPS analysis, which has never been applied to SSE studies because its signal-to-noise ratio has been believed too low. By carefully post-processing sub-daily positions to remove non-tectonic position fluctuation, our 30-min kinematic data clearly exhibits the transient motion of a few mm during one Cascadia SSE. A spatiotemporal slip image by inverting the 30-min data exhibits a multi-stage evolution; it consists of an isotropic growth of SSE followed by an along-strike migration and termination within the rheologically controlled down-dip width. This transition at the slip growth mode is similar to the rupture growth of regular earthquakes, implying the presence of common mechanical factors behind the two distinct slip phenomena. The comparison with a slip inversion of the daily GPS demonstrates the current performance and limitation of the subdaily data in the SSE detection and imaging. Better understanding of the non-tectonic noise in the kinematic GPS analysis will further improve the temporal resolution of SSE.
Optimization study of plasmonic cell fusion
Authors: Belansky Julia , Yelin Dvir
Published: May 2022

Artificial cell fusion often serves as a valuable tool for studying different applications in biology and medicine, including natural development, immune response, cancer metastasis and production of therapeutic molecules. Plasmonic cell fusion, a technique that uses specific cell labeling by gold nanoparticles and resonant femtosecond pulse irradiation for fusing neighboring cells, has been demonstrated useful for such applications, allowing high cell specificity and an overall low toxicity. Despite these advantages, the numerous experimental factors contributing to plasmonic fusion have often led to subpar fusion efficiencies, requiring repeated experiments and extensive calibration protocols for achieving optimal results. In this work we present a study that aims to improve the overall performance of plasmonic cell fusion in terms of fusion efficiency and cell viability. By varying the pulse fluence, nanoparticle concentration, incubation times, and culture handling protocols, we demonstrate up to 100% fusion of malignant epithelial cells across the entire irradiated area of the culture. We also show that some of the smaller cells may stay viable for up to several days. The results would allow plasmonic fusion to play a key role in numerous studies and applications that require specific, high-efficiency cell–cell fusion.
PCA-based sub-surface structure and defect analysis for germanium-on-nothing using nanoscale surface topography
Authors: Jeong Jaewoo , Kim Taeyeong , Lee Bong Jae , Lee Jungchul
Published: May 2022

Empty space in germanium (ESG) or germanium-on-nothing (GON) are unique self-assembled germanium structures with multiscale cavities of various morphologies. Due to their simple fabrication process and high-quality crystallinity after self-assembly, they can be applied in various fields including micro-/nanoelectronics, optoelectronics, and precision sensors, to name a few. In contrast to their simple fabrication, inspection is intrinsically difficult due to buried structures. Today, ultrasonic atomic force microscopy and interferometry are some prevalent non-destructive 3-D imaging methods that are used to inspect the underlying ESG structures. However, these non-destructive characterization methods suffer from low throughput due to slow measurement speed and limited measurable thickness. To overcome these limitations, this work proposes a new methodology to construct a principal-component-analysis based database that correlates surface images with empirically determined sub-surface structures. Then, from this database, the morphology of buried sub-surface structure is determined only using surface topography. Since the acquisition rate of a single nanoscale surface micrograph is up to a few orders faster than a thorough 3-D sub-surface analysis, the proposed methodology benefits from improved throughput compared to current inspection methods. Also, an empirical destructive test essentially resolves the measurable thickness limitation. We also demonstrate the practicality of the proposed methodology by applying it to GON devices to selectively detect and quantitatively analyze surface defects. Compared to state-of-the-art deep learning-based defect detection schemes, our method is much effortlessly finetunable for specific applications. In terms of sub-surface analysis, this work proposes a fast, robust, and high-resolution methodology which could potentially replace the conventional exhaustive sub-surface inspection schemes.
Improved methods for the detection and quantification of SARS-CoV-2 RNA in wastewater
Authors: Peinado Beatriz , Martínez-García Lorena , Martínez Francisco , Nozal Leonor , Sánchez Maria Blanca
Published: May 2022

Since the start of the COVID-19 pandemic, different methods have been used to detect the presence of genetic material of SARS-CoV-2 in wastewater. The use of wastewater for SARS-CoV-2 RNA detection and quantification showed different problems, associated to the complexity of the matrix and the lack of standard methods used to analyze the presence of an enveloped virus, such as coronavirus. Different strategies for the concentration process were selected to carry out the detection and quantification of SARS-CoV-2 RNA in wastewater: (a) aluminum hydroxide adsorption–precipitation, (b) pre-treatment with glycine buffer and precipitation with polyethylene-glycol (PEG) and (c) ultrafiltration (Centricon). Our results showed that the reduction of organic matter, using the pre-treatment with glycine buffer before the concentration with Centricon or aluminum hydroxide adsorption–precipitation, improved the recovery percentage of the control virus, Mengovirus (MgV) (8.37% ± 5.88 n = 43; 6.97% ± 6.51 n = 20, respectively), and the detection of SARS-CoV-2 in comparison with the same methodology without a pre-treatment. For the concentration with Centricon, the use of 100 mL of wastewater, instead of 200 mL, increased the MgV recovery, and allowed a positive detection of SARS-CoV-2 with N1 and N2 targets. The quantity of SARS-CoV-2 RNA detected in wastewater did not show a direct correlation with the number of confirmed cases, but the study of its upwards or downwards trend over time enabled the detection of an increase of epidemiological data produced in September 2020, January 2021 and April 2021.
Multi-state MRAM cells for hardware neuromorphic computing
Authors: Rzeszut Piotr , Chȩciński Jakub , Brzozowski Ireneusz , Ziȩtek Sławomir , Skowroński Witold , Stobiecki Tomasz
Published: May 2022

Magnetic tunnel junctions (MTJ) have been successfully applied in various sensing application and digital information storage technologies. Currently, a number of new potential applications of MTJs are being actively studied, including high-frequency electronics, energy harvesting or random number generators. Recently, MTJs have been also proposed in designs of new platforms for unconventional or bio-inspired computing. In the current work, we present a complete hardware implementation design of a neural computing device that incorporates serially connected MTJs forming a multi-state memory cell can be used in a hardware implementation of a neural computing device. The main purpose of the multi-cell is the formation of quantized weights in the network, which can be programmed using the proposed electronic circuit. Multi-cells are connected to a CMOS-based summing amplifier and a sigmoid function generator, forming an artificial neuron. The operation of the designed network is tested using a recognition of hand-written digits in 20$$\times $$×20 pixels matrix and shows detection ratio comparable to the software algorithm, using weights stored in a multi-cell consisting of four MTJs or more. Moreover, the presented solution has better energy efficiency in terms of energy consumed per single image processing, as compared to a similar design.
Nanoscale copper and silver thin film systems display differences in antiviral and antibacterial properties
Authors: Meister Toni Luise , Fortmann Jill , Breisch Marina , Sengstock Christina , Steinmann Eike , Köller Manfred , Pfaender Stephanie , Ludwig Alfred
Published: May 2022

The current Coronavirus Disease 19 (COVID-19) pandemic has exemplified the need for simple and efficient prevention strategies that can be rapidly implemented to mitigate infection risks. Various surfaces have a long history of antimicrobial properties and are well described for the prevention of bacterial infections. However, their effect on many viruses has not been studied in depth. In the context of COVID-19, several surfaces, including copper (Cu) and silver (Ag) coatings have been described as efficient antiviral measures that can easily be implemented to slow viral transmission. In this study, we detected antiviral properties against Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) on surfaces, which were coated with Cu by magnetron sputtering as thin Cu films or as Cu/Ag ultrathin bimetallic nanopatches. However, no effect of Ag on viral titers was observed, in clear contrast to its well-known antibacterial properties. Further enhancement of Ag ion release kinetics based on an electrochemical sacrificial anode mechanism did not increase antiviral activity. These results clearly demonstrate that Cu and Ag thin film systems display significant differences in antiviral and antibacterial properties which need to be considered upon implementation.
Growth factor dependency in mammary organoids regulates ductal morphogenesis during organ regeneration
Authors: Sahu Sounak , Albaugh Mary E. , Martin Betty K. , Patel Nimit L. , Riffle Lisa , Mackem Susan , Kalen Joseph D. , Sharan Shyam K.
Published: May 2022

Signaling pathways play an important role in cell fate determination in stem cells and regulate a plethora of developmental programs, the dysregulation of which can lead to human diseases. Growth factors (GFs) regulating these signaling pathways therefore play a major role in the plasticity of adult stem cells and modulate cellular differentiation and tissue repair outcomes. We consider murine mammary organoid generation from self-organizing adult stem cells as a tool to understand the role of GFs in organ development and tissue regeneration. The astounding capacity of mammary organoids to regenerate a gland in vivo after transplantation makes it a convenient model to study organ regeneration. We show organoids grown in suspension with minimal concentration of Matrigel and in the presence of a cocktail of GFs regulating EGF and FGF signaling can recapitulate key epithelial layers of adult mammary gland. We establish a toolkit utilizing in vivo whole animal imaging and ultrasound imaging combined with ex vivo approaches including tissue clearing and confocal imaging to study organ regeneration and ductal morphogenesis. Although the organoid structures were severely impaired in vitro when cultured in the presence of individual GFs, ex vivo imaging revealed ductal branching after transplantation albeit with significantly reduced number of terminal end buds. We anticipate these imaging modalities will open novel avenues to study mammary gland morphogenesis in vivo and can be beneficial for monitoring mammary tumor progression in pre-clinical and clinical settings.
Characterizing the diversity of MHC conserved extended haplotypes using families from the United Arab Emirates
Authors: Alnaqbi Halima , Tay Guan K. , Chehadeh Sarah El Hajj , Alsafar Habiba
Published: May 2022

Aside from its anthropological relevance, the characterization of the allele frequencies of genes in the human Major Histocompatibility Complex (MHC) and the combination of these alleles that make up MHC conserved extended haplotypes (CEHs) is necessary for histocompatibility matching in transplantation as well as mapping disease association loci. The structure and content of the MHC region in Middle Eastern populations remain poorly characterized, posing challenges when establishing disease association studies in ethnic groups that inhabit the region and reducing the capacity to translate genetic research into clinical practice. This study was conceived to address a gap of knowledge, aiming to characterize CEHs in the United Arab Emirates (UAE) population through segregation analysis of high-resolution, pedigree-phased, MHC haplotypes derived from 41 families. Twenty per cent (20.5%) of the total haplotype pool derived from this study cohort were identified as putative CEHs in the UAE population. These consisted of CEHs that have been previously detected in other ethnic groups, including the South Asian CEH 8.2 [HLA- C*07:02-B*08:01-DRB1*03:01-DQA1*05:01-DQB1*02:01 (H.F. 0.094)] and the common East Asian CEH 58.1 [HLA- C*03:02-B*58:01-DRB1*03:01- DQA1*05:01-DQB1*02:01 (H.F. 0.024)]. Additionally, three novel CEHs were identified in the current cohort, including HLA- C*15:02-B*40:06-DRB1*16:02-DQB1*05:02 (H.F. 0.035), HLA- C*16:02-B*51:01-DRB1*16:01-DQA1*01:02-DQB1*05:02 (H.F. 0.029), and HLA- C*03:02-B*58:01-DRB1*16:01-DQA1*01:02-DQB1*05:02 (H.F. 0.024). Overall, the results indicate a substantial gene flow with neighbouring ethnic groups in the contemporary UAE population including South Asian, East Asian, African, and European populations. Importantly, alleles and haplotypes that have been previously associated with autoimmune diseases (e.g., Type 1 Diabetes) were also present. In this regard, this study emphasizes that an appreciation for ethnic differences can provide insights into subpopulation-specific disease-related polymorphisms, which has remained a difficult endeavour.
An internet of radiation sensor system (IoRSS) to detect radioactive sources out of regulatory control
Authors: Tran-Quang Vinh , Dao-Viet Hung
Published: May 2022

A radioactive source that is not under regulatory control, either because it has never been under regulatory control or because it has been abandoned, lost, misplaced, stolen, or otherwise transferred without proper authorization, is considered an orphan source. Orphan sources are usually gathered as scrap metal because of their heavy metallic containers. Melting an orphan source with scrap metal produces contaminated recycled metal and waste; the consequences will be extremely serious for humans and the environment, affecting the economy and social stability. In this paper, we propose and develop an Internet of Radiation Sensor System (IoRSS) to detect radioactive sources out of regulatory control in scrap metal recycling and production facilities. It is a complete IoT system consisting of a network of wirelessly connected radiometric devices that optimizes the detection, localization, and identification of radioactive sources by integrating data from multiple portable radiation detectors. The proposed IoRSS system creates a robust and flexible network architecture along with advanced data fusion algorithms that combine information from many detectors. The IoRSS system provides advanced search and monitoring capabilities in a large coverage area and in difficult operational environments.
Real-time realizable mobile imaging photoplethysmography
Authors: Lee Hooseok , Ko Hoon , Chung Heewon , Nam Yunyoung , Hong Sangjin , Lee Jinseok
Published: May 2022

Photoplethysmography imaging (PPGI) sensors have attracted a significant amount of attention as they enable the remote monitoring of heart rates (HRs) and thus do not require any additional devices to be worn on fingers or wrists. In this study, we mounted PPGI sensors on a robot for active and autonomous HR (R-AAH) estimation. We proposed an algorithm that provides accurate HR estimation, which can be performed in real time using vision and robot manipulation algorithms. By simplifying the extraction of facial skin images using saturation (S) values in the HSV color space, and selecting pixels based on the most frequent S value within the face image, we achieved a reliable HR assessment. The results of the proposed algorithm using the R-AAH method were evaluated by rigorous comparison with the results of existing algorithms on the UBFC-RPPG dataset (n = 42). The proposed algorithm yielded an average absolute error (AAE) of 0.71 beats per minute (bpm). The developed algorithm is simple, with a processing time of less than 1 s (275 ms for an 8-s window). The algorithm was further validated on our own dataset (BAMI-RPPG dataset [n = 14]) with an AAE of 0.82 bpm.
Complex function solution for deformation and failure mechanism of inclined coal seam roadway
Authors: Xiong Xianyu , Dai Jun , Xinnian Chen , Ouyang Yibo
Published: May 2022

The stressed environment of the inclined coal seam roadway is complex and changeable, and the damage degree of surrounding rock increases, threatening the safe mining of coal mines. In order to take targeted support measures to control the stability of roadway surrounding rock, it is very important to study the stress and deformation characteristics of roadway surrounding rock in inclined coal seam. Therefore, this paper analyzes the deformation and failure law of inclined coal seam roadway according to the theory of complex variable function. It optimizes the solution process and accuracy of the mapping function coefficient and deduces the analytical solution of surrounding rock stress and deformation inclined coal seam roadway. The deformation and failure mechanism of surrounding rock in inclined coal seam roadway is revealed theoretically, and further use numerical simulation and physical simulation tests for supplementary analysis and verification. The results show that the stress and deformation of roadway surrounding rock in inclined coal seam show obvious asymmetric distribution characteristics. The stress and deformation of roadway surrounding rock on the right side are greater than on the left side. The two sides of the roadway, the right side of the roof and the roof angle of the right side, are the key positions of roadway stress concentration and deformation. According to the variation law of stress and deformation distribution of roadway surrounding rock, roadway cyclic deformation and failure theory is put forward. The numerical simulation and physical simulation tests show that the deformation and failure law of roadway is consistent with the theoretical analysis results, and there are differences in numerical values. The cyclic deformation and failure mechanism of roadway in inclined coal seam is verified, which can provide theoretical guidance for roadway support design.
Dental imaging using an ultra-high resolution photon-counting CT system
Authors: Ruetters Maurice , Sen Sinan , Gehrig Holger , Bruckner Thomas , Kim Ti-Sun , Lux Christopher J. , Schlemmer Heinz-Peter , Heinze Sarah , Maier Joscha , Kachelrieß Marc , Sawall Stefan
Published: May 2022

Clinical photon-counting CT (PCCT) offers a spatial resolution of about 200 µm and might allow for acquisitions close to conventional dental CBCTs. In this study, the capabilities of this new system in comparison to dental CBCTs shall be evaluated. All 8 apical osteolysis identified in CBCT were identified by both readers in all three PCCT scan protocols. Mean visibility scores showed statistical significant differences for root canals(p = 0.0001), periodontal space(p = 0.0090), cortical(p = 0.0003) and spongious bone(p = 0.0293) in favor of high and medium dose PCCT acquisitions. Overall, both devices showed excellent image quality of all structures assessed. Interrater-agreement showed high values for all protocols in all structures. Bland–Altman plots revealed a high concordance of both modalities with the reference measurements. In vitro, ultra-high resolution PCCT can reliably identify different diagnostic entities and structures relevant for dental diagnostics similar to conventional dental CBCT with similar radiation dose. Acquisitions of five cadaveric heads were performed in an experimental CT-system containing an ultra-high resolution PC detector (0.25 mm pixel size in isocenter) as well as in a dental CBCT scanner. Acquisitions were performed using dose levels of 8.5 mGy, 38.0 mGy and 66.5 mGy (CTDI16cm) in case of PCCT and of 8.94 mGy (CTDI16cm) in case of CBCT. The quality of delineation of hard tissues, root-canals, periodontal-space as well as apical osteolysis was assessed by two readers. Mean visibility scores and interrater-agreement (overall agreement (%)) were calculated. Vertical bone loss (bl) and thickness (bt) of the buccal bone lamina of 15 lower incisors were measured and compared to reference measurements by ore microscopy and clinical probing.
New cyanobacterial genus Argonema is hiding in soil crusts around the world
Authors: Skoupý Svatopluk , Stanojković Aleksandar , Pavlíková Markéta , Poulíčková Aloisie , Dvořák Petr
Published: May 2022

Cyanobacteria are crucial primary producers in soil and soil crusts. However, their biodiversity in these habitats remains poorly understood, especially in the tropical and polar regions. We employed whole genome sequencing, morphology, and ecology to describe a novel cyanobacterial genus Argonema isolated from Antarctica. Extreme environments are renowned for their relatively high number of endemic species, but whether cyanobacteria are endemic or not is open to much current debate. To determine if a cyanobacterial lineage is endemic is a time consuming, elaborate, and expensive global sampling effort. Thus, we propose an approach that will help to overcome the limits of the sampling effort and better understand the global distribution of cyanobacterial clades. We employed a Sequencing Read Archive, which provides a rich source of data from thousands of environmental samples. We developed a framework for a characterization of the global distribution of any microbial species using Sequencing Read Archive. Using this approach, we found that Argonema is actually cosmopolitan in arid regions. It provides further evidence that endemic microbial taxa are likely to be much rarer than expected.
Altered epithelial barrier functions in the colon of patients with spina bifida
Authors: Brochard Charlène , Bouguen Guillaume , Olivier Raphael , Durand Tony , Henno Sébastien , Peyronnet Benoît , Pagenault Mael , Lefèvre Chloé , Boudry Gaëlle , Croyal Mikael , Fautrel Alain , Esvan Maxime , Ropert Alain , Dariel Anne , Siproudhis Laurent , Neunlist Michel
Published: May 2022

Our objectives were to better characterize the colorectal function of patients with Spina Bifida (SB). Patients with SB and healthy volunteers (HVs) completed prospectively a standardized questionnaire, clinical evaluation, rectal barostat, colonoscopy with biopsies and faecal collection. The data from 36 adults with SB (age: 38.8 [34.1–47.2]) were compared with those of 16 HVs (age: 39.0 [31.0–46.5]). Compared to HVs, rectal compliance was lower in patients with SB (p = 0.01), whereas rectal tone was higher (p = 0.0015). Ex vivo paracellular permeability was increased in patients with SB (p = 0.0008) and inversely correlated with rectal compliance (r = − 0.563, p = 0.002). The expression of key tight junction proteins and inflammatory markers was comparable between SB and HVs, except for an increase in Claudin-1 immunoreactivity (p = 0.04) in SB compared to HVs. TGFβ1 and GDNF mRNAs were expressed at higher levels in patients with SB (p = 0.02 and p = 0.008). The levels of acetate, propionate and butyrate in faecal samples were reduced (p = 0.04, p = 0.01, and p = 0.02, respectively). Our findings provide evidence that anorectal and epithelial functions are altered in patients with SB. The alterations in these key functions might represent new therapeutic targets, in particular using microbiota-derived approaches.

Clinical Trials: NCT02440984 and NCT03054415.