bluuebunny/crossref_metadata_2025_split huggingface dataset:
SIRT6 mediates MRTF-A deacetylation in vascular endothelial cells to antagonize oxLDL-induced ICAM-1 transcription
Authors: Huang Shan , Shao Tinghui , Liu Hong , Wang Qianyun , Li Tianfa , Zhao Qianwen 
Published: March 2022

AbstractOxidized low-density lipoprotein (oxLDL), a known risk factor for atherosclerosis, activates the transcription of adhesion molecules (ICAM-1) in endothelial cells. We previously showed that myocardin-related transcription factor A (MRTF-A) mediates oxLDL-induced ICAM-1 transcription. Here we confirm that ICAM-1 transactivation paralleled dynamic alterations in MRTF-A acetylation. Since treatment with the antioxidant NAC dampened MRTF-A acetylation, MRTF-A acetylation appeared to be sensitive to cellular redox status. Of interest, silencing of SIRT6, a lysine deacetylase, restored MRTF-A acetylation despite the addition of NAC. SIRT6 directly interacted with MRTF-A to modulate MRTF-A acetylation. Deacetylation of MRTF-A by SIRT6 led to its nuclear expulsion thus dampening MRTF-A occupancy on the ICAM-1 promoter. Moreover, SIRT6 expression was downregulated with oxLDL stimulation likely owing to promoter hypermethylation in endothelial cells. DNA methyltransferase 1 (DNMT1) was recruited to the SIRT6 promoter and mediated SIRT6 repression. The ability of DNMT1 to repress SIRT6 promoter partly was dependent on ROS-sensitive serine 154 phosphorylation. In conclusion, our data unveil a novel DNMT1-SIRT6 axis that contributes to the regulation of MRTF-A acetylation and ICAM-1 transactivation in endothelial cells.
Long noncoding RNA LINC00518 contributes to proliferation and metastasis in lung adenocarcinoma via the miR-335-3p/CTHRC1 Axis
Authors: Shen Ruoyi , Cai Xin , Shen Dan , Zhang Ruochen , Zhang Weijie , Zhang Yang , Li Yue , Wang Anqi , Zeng Yuanyuan , Zhu Jianjie , Liu Zeyi , Huang Jian-an 
Published: March 2022

AbstractLong intergenic nonprotein coding RNA 518 (LINC00518) is recognized to impart cancer proliferation and metastasis in lung adenocarcinoma (LUAD). However, the study about the relationship between LINC00518 and LUAD is shallow so far. In our work, LINC00518 was predicted to be a negative regulator in LUAD based on the TCGA database. It was further verified that the cell proliferation, colony formation, migration, and invasion of LUAD could be obviously inhibited by the knockdown of LINC00518. Moreover, miR-335-3p/CTHRC1 axis was intensively possible to be a critical regulator in the effect of LINC00518 on LUAD via visual ceRNA network. Importantly the progress of LUAD was relevant to the active CTHRC1 which was realized by the target of LINC00518 to miR-335-3p. Furthermore, the knockdown of LINC00518 exhibited a synergistic effect with VS6063, an inhibitor of FAK protein, in the suppression of LUAD indicating that miR-335-3p/CTHRC1 axis was potentially exploitable as a targeted intervention to integrin β3/FAK signal pathway in LUAD. All the collective results demonstrated that LINC00518 could be a promising biomarker of the prognosis of LUAD and possibly a therapeutic target via miR-335-3p/CTHRC1 axis.
Unravelling a new many-body large-hole polaron in a transition metal oxide that promotes high photocatalytic activity
Authors: Chi Xiao , Mandal Lily , Liu Cuibo , Fauzi Angga Dito , Chaudhuri Anindita , Whitcher Thomas J. , Jani Hariom Kirit , Chen Zhongxin , Xi Shibo , Diao Caozheng , Naradipa Muhammad Avicenna , Yu Xiaojiang , Yang Ping , Castro-Neto Antonio Helio , Breese Mark B. H. , Loh Kian Ping , Venkatesan Thirumalai Venky , Rusydi Andrivo 
Published: March 2022

AbstractA many-body large polaron, which is important for both fundamental physics and technological applications, has been predicted to occur in bismuth vanadate (BiVO4). Herein, using a combination of high-resolution spectroscopic ellipsometry, X-ray absorption spectroscopy at the V L3,2- and O K-edges, and high-resolution X-ray diffraction supported by theoretical calculations, we reveal a new many-body large-hole polaron in W-doped BiVO4 films and the interplay of the large-hole polaron and indirect bandgap when determining the photocatalytic activity. With various W doping concentrations and temperatures, anomalous spectral weight transfers in the complex dielectric function are observed, revealing electronic correlations, particularly the on-site Coulomb interactions of O p (Upp) and V d (Udd), and screening in BiVO4. Due to the distortion of BiO8 dodecahedra and Udd, Bi 6 s is lifted to the top of the valance band, which results in the formation of an indirect bandgap and a large-hole polaron. The large-hole polaron is found to form as a localized midgap state, consisting of O p hybridized with the V d and Bi sp orbitals, and this is important when determining the high photocatalytic activity of BiVO4. Our results show the importance of the interplay among the charge, orbital, and lattice degrees of freedom in forming the many-body large-hole polaron, which improves the conductivity and results in a transition metal oxide with high photocatalytic activity.
NSC-derived extracellular matrix-modified GelMA hydrogel fibrous scaffolds for spinal cord injury repair
Authors: Chen Zheng , Wang Lin , Chen Chichi , Sun Jie , Luo Junchao , Cui Wenguo , Zhu Can , Zhou Xiaozhong , Liu Xingzhi , Yang Huilin , Shi Qin 
Published: March 2022

AbstractCell-derived extracellular matrix (ECM) has been applied in spinal cord injury (SCI) regeneration because of its various biological functions. However, insufficient mechanical properties limit its wide application. Herein, we developed GelMA/ECM hydrogel fibrous scaffolds (GelMA/ECM scaffolds) that can recruit and enhance the differentiation of neural stem cells (NSCs) by electrospinning and decellularization techniques. Moreover, the GelMA/ECM scaffolds had good mechanical properties and reinforced cell adhesion and proliferation. Compared to GelMA hydrogel fibrous scaffolds (GelMA scaffolds), GelMA/ECM scaffolds promoted more NSCs toward neurons by markedly enhancing the expression of MAP-2 and Tuj-1 and decreasing GFAP expression. In addition, the GelMA/ECM scaffolds significantly reduced the proportion of M1-phenotype macrophages, which is favorable for SCI repair. In vivo, the GelMA/ECM scaffolds recruited NSCs at the injured site, promoted neuron regeneration, and reduced the formation of glial scars and the inflammatory response, which further led to a significant improvement in the functional recovery of SCI. Therefore, this scaffold shows potential in regenerative medicine, mainly in SCI.
Change and variability in Antarctic coastal exposure, 1979–2020
Authors: Reid P. A. , Massom R. A. 
Published: March 2022

AbstractIncreased exposure of Antarctica’s coastal environment to open ocean and waves due to loss of a protective sea-ice “buffer” has important ramifications for ice-shelf stability, coastal erosion, important ice-ocean-atmosphere interactions and shallow benthic ecosystems. Here, we introduce a climate and environmental metric based on the ongoing long-term satellite sea-ice concentration record, namely Coastal Exposure Length. This is a daily measure of change and variability in the length and incidence of Antarctic coastline lacking any protective sea-ice buffer offshore. For 1979–2020, ~50% of Antarctica’s ~17,850-km coastline had no sea ice offshore each summer, with minimal exposure in winter. Regional summer/maximum contributions vary from 45% (Amundsen-Bellingshausen seas) to 58% (Indian Ocean and Ross Sea), with circumpolar annual exposure ranging from 38% (2019) to 63% (1993). The annual maximum length of Antarctic coastal exposure decreased by ~30 km (~0.32%) per year for 1979–2020, composed of distinct regional and seasonal contributions.
White matter integrity in mice requires continuous myelin synthesis at the inner tongue
Authors: Meschkat Martin , Steyer Anna M. , Weil Marie-Theres , Kusch Kathrin , Jahn Olaf , Piepkorn Lars , Agüi-Gonzalez Paola , Phan Nhu Thi Ngoc , Ruhwedel Torben , Sadowski Boguslawa , Rizzoli Silvio O. , Werner Hauke B. , Ehrenreich Hannelore , Nave Klaus-Armin , Möbius Wiebke 
Published: March 2022

AbstractMyelin, the electrically insulating sheath on axons, undergoes dynamic changes over time. However, it is composed of proteins with long lifetimes. This raises the question how such a stable structure is renewed. Here, we study the integrity of myelinated tracts after experimentally preventing the formation of new myelin in the CNS of adult mice, using an inducible Mbp null allele. Oligodendrocytes survive recombination, continue to express myelin genes, but they fail to maintain compacted myelin sheaths. Using 3D electron microscopy and mass spectrometry imaging we visualize myelin-like membranes failing to incorporate adaxonally, most prominently at juxta-paranodes. Myelinoid body formation indicates degradation of existing myelin at the abaxonal side and the inner tongue of the sheath. Thinning of compact myelin and shortening of internodes result in the loss of about 50% of myelin and axonal pathology within 20 weeks post recombination. In summary, our data suggest that functional axon-myelin units require the continuous incorporation of new myelin membranes.
Associations between alcohol consumption and gray and white matter volumes in the UK Biobank
Authors: Daviet Remi , Aydogan Gökhan , Jagannathan Kanchana , Spilka Nathaniel , Koellinger Philipp D. , Kranzler Henry R. , Nave Gideon , Wetherill Reagan R. 
Published: March 2022

AbstractHeavy alcohol consumption has been associated with brain atrophy, neuronal loss, and poorer white matter fiber integrity. However, there is conflicting evidence on whether light-to-moderate alcohol consumption shows similar negative associations with brain structure. To address this, we examine the associations between alcohol intake and brain structure using multimodal imaging data from 36,678 generally healthy middle-aged and older adults from the UK Biobank, controlling for numerous potential confounds. Consistent with prior literature, we find negative associations between alcohol intake and brain macrostructure and microstructure. Specifically, alcohol intake is negatively associated with global brain volume measures, regional gray matter volumes, and white matter microstructure. Here, we show that the negative associations between alcohol intake and brain macrostructure and microstructure are already apparent in individuals consuming an average of only one to two daily alcohol units, and become stronger as alcohol intake increases.
Demonstration of non-destructive and isotope-sensitive material analysis using a short-pulsed laser-driven epi-thermal neutron source
Authors: Zimmer Marc , Scheuren Stefan , Kleinschmidt Annika , Mitura Nikodem , Tebartz Alexandra , Schaumann Gabriel , Abel Torsten , Ebert Tina , Hesse Markus , Zähter Şêro , Vogel Sven C. , Merle Oliver , Ahlers Rolf-Jürgen , Duarte Pinto Serge , Peschke Maximilian , Kröll Thorsten , Bagnoud Vincent , Rödel Christian , Roth Markus 
Published: March 2022

AbstractNeutrons are a valuable tool for non-destructive material investigation as their interaction cross sections with matter are isotope sensitive and can be used complementary to x-rays. So far, most neutron applications have been limited to large-scale facilities such as nuclear research reactors, spallation sources, and accelerator-driven neutron sources. Here we show the design and optimization of a laser-driven neutron source in the epi-thermal and thermal energy range, which is used for non-invasive material analysis. Neutron resonance spectroscopy, neutron radiography, and neutron resonance imaging with moderated neutrons are demonstrated for investigating samples in terms of isotope composition and thickness. The experimental results encourage applications in non-destructive and isotope-sensitive material analysis and pave the way for compact laser-driven neutron sources with high application potential.
A programmable qudit-based quantum processor
Authors: Chi Yulin , Huang Jieshan , Zhang Zhanchuan , Mao Jun , Zhou Zinan , Chen Xiaojiong , Zhai Chonghao , Bao Jueming , Dai Tianxiang , Yuan Huihong , Zhang Ming , Dai Daoxin , Tang Bo , Yang Yan , Li Zhihua , Ding Yunhong , Oxenløwe Leif K. , Thompson Mark G. , O’Brien Jeremy L. , Li Yan , Gong Qihuang , Wang Jianwei 
Published: March 2022

AbstractControlling and programming quantum devices to process quantum information by the unit of quantum dit, i.e., qudit, provides the possibilities for noise-resilient quantum communications, delicate quantum molecular simulations, and efficient quantum computations, showing great potential to enhance the capabilities of qubit-based quantum technologies. Here, we report a programmable qudit-based quantum processor in silicon-photonic integrated circuits and demonstrate its enhancement of quantum computational parallelism. The processor monolithically integrates all the key functionalities and capabilities of initialisation, manipulation, and measurement of the two quantum quart (ququart) states and multi-value quantum-controlled logic gates with high-level fidelities. By reprogramming the configuration of the processor, we implemented the most basic quantum Fourier transform algorithms, all in quaternary, to benchmark the enhancement of quantum parallelism using qudits, which include generalised Deutsch-Jozsa and Bernstein-Vazirani algorithms, quaternary phase estimation and fast factorization algorithms. The monolithic integration and high programmability have allowed the implementations of more than one million high-fidelity preparations, operations and projections of qudit states in the processor. Our work shows an integrated photonic quantum technology for qudit-based quantum computing with enhanced capacity, accuracy, and efficiency, which could lead to the acceleration of building a large-scale quantum computer.
Ubiquitin and a charged loop regulate the ubiquitin E3 ligase activity of Ark2C
Authors: Paluda Andrej , Middleton Adam J. , Rossig Claudia , Mace Peter D. , Day Catherine L. 
Published: March 2022

AbstractA large family of E3 ligases that contain both substrate recruitment and RING domains confer specificity within the ubiquitylation cascade. Regulation of RING E3s depends on modulating their ability to stabilise the RING bound E2~ubiquitin conjugate in the activated (or closed) conformation. Here we report the structure of the Ark2C RING bound to both a regulatory ubiquitin molecule and an activated E2~ubiquitin conjugate. The structure shows that the RING domain and non-covalently bound ubiquitin molecule together make contacts that stabilise the activated conformation of the conjugate, revealing why ubiquitin is a key regulator of Ark2C activity. We also identify a charged loop N-terminal to the RING domain that enhances activity by interacting with both the regulatory ubiquitin and ubiquitin conjugated to the E2. In addition, the structure suggests how Lys48-linked ubiquitin chains might be assembled by Ark2C and UbcH5b. Together this study identifies features common to RING E3s, as well elements that are unique to Ark2C and related E3s, which enhance assembly of ubiquitin chains.
Homotypic protection against influenza in a pediatric cohort in Managua, Nicaragua
Authors: Wraith Steph , Balmaseda Angel , Carrillo Fausto Andres Bustos , Kuan Guillermina , Huddleston John , Kubale John , Lopez Roger , Ojeda Sergio , Schiller Amy , Lopez Brenda , Sanchez Nery , Webby Richard , Nelson Martha I. , Harris Eva , Gordon Aubree 
Published: March 2022

AbstractThe period of protection from repeat infection following symptomatic influenza is not well established due to limited availability of longitudinal data. Using data from a pediatric cohort in Managua, Nicaragua, we examine the effects of natural influenza virus infection on subsequent infection with the same influenza virus subtype/lineage across multiple seasons, totaling 2,170 RT-PCR-confirmed symptomatic influenza infections. Logistic regression models assessed whether infection in the prior influenza season protected against homologous reinfection. We sequenced viruses from 2011–2019 identifying dominant clades and measuring antigenic distances between hemagglutinin clades. We observe homotypic protection from repeat infection in children infected with influenza A/H1N1pdm (OR 0.12, CI 0.02–0.88), A/H3N2 (OR 0.41, CI 0.24–0.73), and B/Victoria (OR 0.00, CI 0.00–0.14), but not with B/Yamagata viruses (OR 0.60, CI 0.09–2.10). Overall, protection wanes as time or antigenic distance increases. Individuals infected with one subtype or lineage of influenza virus have significantly lower odds of homologous reinfection for the following one to two years; after two years this protection wanes. This protection is demonstrated across multiple seasons, subtypes, and lineages among children.
Unsupervised machine learning for discovery of promising half-Heusler thermoelectric materials
Authors: Jia Xue , Deng Yanshuai , Bao Xin , Yao Honghao , Li Shan , Li Zhou , Chen Chen , Wang Xinyu , Mao Jun , Cao Feng , Sui Jiehe , Wu Junwei , Wang Cuiping , Zhang Qian , Liu Xingjun 
Published: March 2022

AbstractThermoelectric materials can be potentially applied to waste heat recovery and solid-state cooling because they allow a direct energy conversion between heat and electricity and vice versa. The accelerated materials design based on machine learning has enabled the systematic discovery of promising materials. Herein we proposed a successful strategy to discover and design a series of promising half-Heusler thermoelectric materials through the iterative combination of unsupervised machine learning with the labeled known half-Heusler thermoelectric materials. Subsequently, optimized zT values of ~0.5 at 925 K for p-type Sc0.7Y0.3NiSb0.97Sn0.03 and ~0.3 at 778 K for n-type Sc0.65Y0.3Ti0.05NiSb were experimentally achieved on the same parent ScNiSb.
TiO2 nanotube electrode for organic degradation coupled with flow-electrode capacitive deionization for brackish water desalination
Authors: Lim Jihun , Shin Yong-Uk , Son Aseom , Hong Seok Won , Hong Seungkwan 
Published: March 2022

AbstractA photoelectrochemical (PEC) oxidation and flow-electrode capacitive deionization (FCDI) dual system was explored for the effective treatment of brackish water. Two anodic electrodes with electrochemically self-doped TiO2 arrays (blue-mesh/ blue-plate TiO2 nanotube arrays (BM-TNA & BP-TNA)) were fabricated by annealing at 600 °C, and applied for the treatment of a water system. Specifically, the BM-TNA confirmed lower electrical resistance and superior performance under multiple light source (UV-A, -B, and -C). Furthermore, the system generated powerful oxidizing reactive oxygen species (ROS), which were assessed via degradation of eight organic pollutants: bisphenol-A, 4-chlorophenol, cimetidine, sulfamethoxazole, benzoic acid, phenol, nitrobenzene, and acetaminophen. Decomposition efficiency was stable throughout a wide range of pH, and durability of the BM-TNA electrode was demonstrated through long-term operation. Concurrently, optimization of the FCDI process via key operational parameters (electrode mass loading, and applied voltage) achieved superior desalination performance, and specific energy consumption (SEC). In particular, increased mass loading enhanced charge transportation through the formation of stable charge-percolation pathways, leading to improved solution conductance. Finally, the feasibility of the dual system (PEC-FCDI) was verified through complete degradation of the organic substrates and successful desalination of the brackish water.
A reference set of clinically relevant adverse drug-drug interactions
Authors: Kontsioti Elpida , Maskell Simon , Dutta Bhaskar , Pirmohamed Munir 
Published: March 2022

AbstractThe accurate and timely detection of adverse drug-drug interactions (DDIs) during the postmarketing phase is an important yet complex task with potentially major clinical implications. The development of data mining methodologies that scan healthcare databases for drug safety signals requires appropriate reference sets for performance evaluation. Methodologies for establishing DDI reference sets are limited in the literature, while there is no publicly available resource simultaneously focusing on clinical relevance of DDIs and individual behaviour of interacting drugs. By automatically extracting and aggregating information from multiple clinical resources, we provide a scalable approach for generating a reference set for DDIs that could support research in postmarketing safety surveillance. CRESCENDDI contains 10,286 positive and 4,544 negative controls, covering 454 drugs and 179 adverse events mapped to RxNorm and MedDRA concepts, respectively. It also includes single drug information for the included drugs (i.e., adverse drug reactions, indications, and negative drug-event associations). We demonstrate usability of the resource by scanning a spontaneous reporting system database for signals of DDIs using traditional signal detection algorithms.
In silico identification of single nucleotide variations at CpG sites regulating CpG island existence and size
Authors: Shyamala Nivas , Kongettira Chaitra Lava , Puranam Kaushik , Kupsal Keerthi , Kummari Ramanjaneyulu , Padala Chiranjeevi , Hanumanth Surekha Rani 
Published: March 2022

AbstractGenetic and epigenetic modifications of genes involved in the key regulatory pathways play a significant role in the pathophysiology and progression of multifactorial diseases. The present study is an attempt to identify single nucleotide variations (SNVs) at CpG sites of promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes influencing CpG island (CGI) existence and size associated with the pathophysiology of Diabetes mellitus, Coronary artery disease and Cancers. Promoter sequences located between −2000 to + 2000 bp were retrieved from the EPDnew database and predicted the CpG island using MethPrimer. Further, SNVs at CpG sites were accessed from NCBI, Ensembl while transcription factor (TF) binding sites were accessed using AliBaba2.1. CGI existence and size were determined for each SNV at CpG site with respect to wild type and variant allele by MethPrimer. A total of 200 SNVs at CpG sites were analyzed from the promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes. Of these, only 17 (8.5%) SNVs were found to influence the loss of CGI while 70 (35%) SNVs were found to reduce the size of CGI. It has also been found that 59% (10) of CGI abolishing SNVs are showing differences in binding of TFs. The findings of the study suggest that the candidate SNVs at CpG sites regulating CGI existence and size might influence the DNA methylation status and expression of genes involved in molecular pathways associated with several diseases. The insights of the present study may pave the way for new experimental studies to undertake challenges in DNA methylation, gene expression and protein assays.