bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractC1GalT1 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

AbstractThe 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

AbstractLimited 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

AbstractDNA 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

AbstractEcological 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

AbstractA 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

AbstractAngle-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

AbstractTopological 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

AbstractSnowfall 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

AbstractThe 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

AbstractNeuroinflammation 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

AbstractThe 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

AbstractArtificial 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

AbstractEmpty 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

AbstractSince 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

AbstractMagnetic 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.