bluuebunny/crossref_metadata_2025_split huggingface dataset:
How Does CO2 Adsorption Alter Coal Wettability? Implications for CO2 Geo‐Sequestration
Authors: Sun X. , Yao Y. , Liu D. , Elsworth D. 
Published: April 2022

AbstractSuccessful sequestration of CO2 into coalbeds relies on sufficient capacity and rates of uptake. Storage volumes are controlled by CO2 adsorption which in turn is affected in a complex manner by the evolving wettability of the sorption surface. However, mechanisms and interrelations between CO2 adsorption and coal wettability remain poorly constrained – especially under recreated in situ reservoir conditions where measurements are difficult. We circumvent this difficulty by combining direct measurements of adsorbed water and inferred wettability through Nuclear Magnetic Resonance spectroscopy with mechanisms recovered from molecular dynamic (MD) simulations. The MD simulations confirm that CO2 gas molecules adsorb to the coal pore surface, partially displace the adsorbed water, and transform the coal surface into a heterogeneous surface comprising solid interspersed with gas pockets. We then use the Cassie‐Baxter equation as a basis to characterize the wettability of this heterogeneous H2O‐solid‐CO2 surface to clarify the relationship between CO2 adsorption and coal wettability – using measurements of adsorbed H2O, alone. This enables the first direct evaluation of coal wettability at in situ pressures of CO2. Constrained observations suggest that water wettability weakens significantly with increasing CO2 pressure. Under low CO2 pressure, changes in wettability are contributed directly by CO2 adsorption and increases in CO2 density ‐ when CO2 adsorption reaches saturation at high gas pressure, then changes are determined primarily by changes in CO2 density. We document a robust method and results for the accurate prediction of CO2 storage capacity in coalbeds and concomitant enhanced methane recovery.
Modeling Performance of SCALE‐AMPS: Simulations of Arctic Mixed‐Phase Clouds Observed During SHEBA
Authors: Ong Chia Rui , Koike Makoto , Hashino Tempei , Miura Hiroaki 
Published: April 2022

AbstractThe Advanced Microphysics Prediction System (AMPS), which adopts a two‐moment hybrid‐bin habit‐predicting scheme, was previously developed to study cloud microphysical processes that depend on ice habit; however, only one particular atmospheric model, the University of Wisconsin‐Nonhydrostatic Modeling System, has been used to test the AMPS. In this study, AMPS is implemented into the Scalable Computing for Advanced Library and Environment (SCALE) large‐eddy simulation model. The AMPS Eulerian advection scheme for non‐mass characteristic variables of ice particles, such as axis lengths, is refined to minimize numerical artifacts. The resulting SCALE‐AMPS model successfully reproduces features of mixed‐phase clouds observed during the Surface Heat Budget of the Arctic campaign, including liquid water path (LWP), ice particle size distributions, and ice habits, when ice particle number concentrations (Nice) are reproduced. Sensitivity studies show that increases in Nice result in reductions of LWP that are generally consistent with previous results. Interestingly, LWP reductions lead to changes in ice habits through increases in cloud temperature due to weaker cloud top radiative cooling. Furthermore, aspect ratios of precipitating particles also change following LWP reductions, because in Bigg's immersion freezing scheme, adopted in this study, the aspect ratios depend on the initial size of the ice particles and freezing rates depend on both temperature and droplet size. Because habits of ice particles affect their growth rates, fall speeds, and collision rates, the results obtained in this study reveal possible feedback processes of Arctic mixed‐phase clouds operating through ice habits.
Material-specific high-resolution table-top extreme ultraviolet microscopy
Authors: Eschen Wilhelm , Loetgering Lars , Schuster Vittoria , Klas Robert , Kirsche Alexander , Berthold Lutz , Steinert Michael , Pertsch Thomas , Gross Herbert , Krause Michael , Limpert Jens , Rothhardt Jan 
Published: April 2022

AbstractMicroscopy with extreme ultraviolet (EUV) radiation holds promise for high-resolution imaging with excellent material contrast, due to the short wavelength and numerous element-specific absorption edges available in this spectral range. At the same time, EUV radiation has significantly larger penetration depths than electrons. It thus enables a nano-scale view into complex three-dimensional structures that are important for material science, semiconductor metrology, and next-generation nano-devices. Here, we present high-resolution and material-specific microscopy at 13.5 nm wavelength. We combine a highly stable, high photon-flux, table-top EUV source with an interferometrically stabilized ptychography setup. By utilizing structured EUV illumination, we overcome the limitations of conventional EUV focusing optics and demonstrate high-resolution microscopy at a half-pitch lateral resolution of 16 nm. Moreover, we propose mixed-state orthogonal probe relaxation ptychography, enabling robust phase-contrast imaging over wide fields of view and long acquisition times. In this way, the complex transmission of an integrated circuit is precisely reconstructed, allowing for the classification of the material composition of mesoscopic semiconductor systems.
Neuron-specific enolase promotes stem cell-like characteristics of small-cell lung cancer by downregulating NBL1 and activating the BMP2/Smad/ID1 pathway
Authors: Lu Lin , Zha Zhiqiang , Zhang Peiling , Wang Peipei , Liu Xia , Fang Xisheng , Weng Chengyin , Li Baoxiu , Mao Haibo , Wang Lina , Guan Mingmei , Wu Yong , Xu Zhixiang , Liu Zhongqiu , Liu Guolong 
Published: April 2022

AbstractLittle is known about the biological functions of neuron-specific enolase (NSE) as a specific biomarker for small-cell lung cancer (SCLC). Herein, we elucidate the effect and mechanism of NSE on SCLC stem cell-like characteristics. Upregulated NSE expression was observed in spheroid cells. The gain-of-function and loss-of-function approaches demonstrated that modulation of NSE positively regulated cell proliferation, drug resistance, spherical clone formation, tumor growth, and stem cell-like characteristics of SCLC cells. Mechanistic studies revealed that NSE might downregulate the expression of neuroblastoma suppressor of tumorigenicity 1 (NBL1) by interacting with NBL1, thereby attenuating the competitive inhibitory effect of NBL1 on BMP2 and enhancing the interaction between BMP2 and BMPR1A; this, in turn, may activate the BMP2/Smad/ID1 pathway and promote SCLC stem cell-like characteristics. Moreover, overexpression of NBL1or knockdown of BMP2 rescued the NSE-induced stem cell-like characteristics. In clinical specimens, NSE expression was positively associated with ALDH1A1 expression and negatively correlated with NBL1 expression. High NSE and ALDH1A1 expressions and low NBL1 expression were correlated with poor prognosis in patients with SCLC. In summary, our study demonstrated that NSE promoted stem cell-like characteristics of SCLC via NBL1 and the activation of the BMP2/Smad/ID1 pathway.
ICAM-1 promotes cancer progression by regulating SRC activity as an adapter protein in colorectal cancer
Authors: Lim Eun-Ji , Kang Jae-Hyeok , Kim Yeon-Ju , Kim Seungmo , Lee Su-Jae 
Published: April 2022

AbstractColorectal cancer (CRC) has a 5-year survival rate of <10%, as it can metastasize to the lungs and liver. Anticancer drugs and targeted therapies used to treat metastatic colorectal cancer have insufficient therapeutic efficacy and are associated with complications. Therefore, research to develop new targeted therapeutics is necessary. Here, we present a novel discovery that intracellular adhesion molecule-1 (ICAM-1) is a potential therapeutic target to enhance therapeutic effectiveness for CRC. ICAM-1 is an important regulator of cell–cell interactions and recent studies have shown that it promotes malignancy in several carcinomas. However, little is known about its effect on CRC. Therefore, we conducted a study to define the mechanism by which ICAM-1 acts. ICAM-1 is phosphorylated by tyrosine-protein kinase Met (c-MET), and phosphorylated ICAM-1 can interact with SRC to increase SRC activity. Consequently, ICAM-1 may further accelerate SRC signaling, promoting the malignant potential of cancer. In addition, treatment with antibodies targeting ICAM-1 showed excellent therapeutic effects in reducing metastasis and angiogenesis. These findings suggest for the first time that ICAM-1 is an important adapter protein capable of mediating the c-MET-SRC signaling axis. Therefore, ICAM-1 can be used as a novel therapeutic target and a metastatic marker for CRC.
Molecular basis of antibiotic self-resistance in a bee larvae pathogen
Authors: Dang Tam , Loll Bernhard , Müller Sebastian , Skobalj Ranko , Ebeling Julia , Bulatov Timur , Gensel Sebastian , Göbel Josefine , Wahl Markus C. , Genersch Elke , Mainz Andi , Süssmuth Roderich D. 
Published: April 2022

AbstractPaenibacillus larvae, the causative agent of the devastating honey-bee disease American Foulbrood, produces the cationic polyketide-peptide hybrid paenilamicin that displays antibacterial and antifungal activity. Its biosynthetic gene cluster contains a gene coding for theN-acetyltransferase PamZ. We show that PamZ acts as self-resistance factor inPaenibacillus larvaeby deactivation of paenilamicin. Using tandem mass spectrometry, nuclear magnetic resonance spectroscopy and synthetic diastereomers, we identified the N-terminal amino group of the agmatinamic acid as theN-acetylation site. These findings highlight the pharmacophore region of paenilamicin, which we very recently identified as a ribosome inhibitor. Here, we further determined the crystal structure of PamZ:acetyl-CoA complex at 1.34 Å resolution. An unusual tandem-domain architecture provides a well-defined substrate-binding groove decorated with negatively-charged residues to specifically attract the cationic paenilamicin. Our results will help to understand the mode of action of paenilamicin and its role in pathogenicity ofPaenibacillus larvaeto fight American Foulbrood.
CFTR mRNAs with nonsense codons are degraded by the SMG6-mediated endonucleolytic decay pathway
Authors: Sanderlin Edward J. , Keenan Melissa M. , Mense Martin , Revenko Alexey S. , Monia Brett P. , Guo Shuling , Huang Lulu 
Published: April 2022

AbstractApproximately 10% of cystic fibrosis patients harbor nonsense mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene which can generate nonsense codons in the CFTR mRNA and subsequently activate the nonsense-mediated decay (NMD) pathway resulting in rapid mRNA degradation. However, it is not known which NMD branches govern the decay of CFTR mRNAs containing nonsense codons. Here we utilize antisense oligonucleotides targeting NMD factors to evaluate the regulation of nonsense codon-containing CFTR mRNAs by the NMD pathway. We observe that CFTR mRNAs with nonsense codons G542X, R1162X, and W1282X, but not Y122X, require UPF2 and UPF3 for NMD. Furthermore, we demonstrate that all evaluated CFTR mRNAs harboring nonsense codons are degraded by the SMG6-mediated endonucleolytic pathway rather than the SMG5-SMG7-mediated exonucleolytic pathway. Finally, we show that upregulation of all evaluated CFTR mRNAs with nonsense codons by NMD pathway inhibition improves outcomes of translational readthrough therapy.
Photoinduced ynamide structural reshuffling and functionalization
Authors: Mutra Mohana Reddy , Wang Jeh‐Jeng 
Published: April 2022

AbstractThe radical chemistry of ynamides has recently drawn the attention of synthetic organic chemists to the construction of various N-heterocyclic compounds. Nevertheless, the ynamide-radical chemistry remains a long-standing challenge for chemists due to its high reactivity, undesirable byproducts, severe inherent regio- and chemoselective problems. Importantly, the ynamide C(sp)-N bond fission remains an unsolved challenge. In this paper, we observe Photoinduced radical trigger regio- and chemoselective ynamide bond fission, structural reshuffling and functionalization of 2-alkynyl-ynamides to prepare synthetically inaccessible/challenging chalcogen-substituted indole derivatives with excellent step/atom economy. The key breakthroughs of this work includes, ynamide bond cleavage, divergent radical precursors, broad scope, easy to handle, larger-scale reactions, generation of multiple bonds (N-C(sp2), C(sp2)-C(sp2), C(sp2)-SO2R/C-SR, and C-I/C-Se/C-H) in a few minutes without photocatalysts, metals, oxidants, additives. Control experiments and 13C-labeling experiments supporting the conclusion that sulfone radicals contribute to ynamide structural reshuffling processes via a radical pathway.
In crystallo observation of three metal ion promoted DNA polymerase misincorporation
Authors: Chang Caleb , Lee Luo Christie , Gao Yang 
Published: April 2022

AbstractError-free replication of DNA is essential for life. Despite the proofreading capability of several polymerases, intrinsic polymerase fidelity is in general much higher than what base-pairing energies can provide. Although researchers have investigated this long-standing question with kinetics, structural determination, and computational simulations, the structural factors that dictate polymerase fidelity are not fully resolved. Time-resolved crystallography has elucidated correct nucleotide incorporation and established a three-metal-ion-dependent catalytic mechanism for polymerases. Using X-ray time-resolved crystallography, we visualize the complete DNA misincorporation process catalyzed by DNA polymerase η. The resulting molecular snapshots suggest primer 3´-OH alignment mediated by A-site metal ion binding is the key step in substrate discrimination. Moreover, we observe that C-site metal ion binding preceded the nucleotidyl transfer reaction and demonstrate that the C-site metal ion is strictly required for misincorporation. Our results highlight the essential but separate roles of the three metal ions in DNA synthesis.
Comprehensive profiling of 1015 patients’ exomes reveals genomic-clinical associations in colorectal cancer
Authors: Zhao Qi , Wang Feng , Chen Yan-Xing , Chen Shifu , Yao Yi-Chen , Zeng Zhao-Lei , Jiang Teng-Jia , Wang Ying-Nan , Wu Chen-Yi , Jing Ying , Huang You-Sheng , Zhang Jing , Wang Zi-Xian , He Ming-Ming , Pu Heng-Ying , Mai Zong-Jiong , Wu Qi-Nian , Long Renwen , Zhang Xiaoni , Huang Tanxiao , Xu Mingyan , Qiu Miao-Zheng , Luo Hui-Yan , Li Yu-Hong , Zhang Dong-Shen , Jia Wei-Hua , Chen Gong , Ding Pei-Rong , Li Li-Ren , Lu Zheng-Hai , Pan Zhi-Zhong , Xu Rui-Hua 
Published: April 2022

AbstractThe genetic basis of colorectal cancer (CRC) and its clinical associations remain poorly understood due to limited samples or targeted genes in current studies. Here, we perform ultradeep whole-exome sequencing on 1015 patients with CRC as part of the ChangKang Project. We identify 46 high-confident significantly mutated genes, 8 of which mutate in 14.9% of patients: LYST, DAPK1, CR2, KIF16B, NPIPB15, SYTL2, ZNF91, and KIAA0586. With an unsupervised clustering algorithm, we propose a subtyping strategy that classisfies CRC patients into four genomic subtypes with distinct clinical characteristics, including hypermutated, chromosome instability with high risk, chromosome instability with low risk, and genome stability. Analysis of immunogenicity uncover the association of immunogenicity reduction with genomic subtypes and poor prognosis in CRC. Moreover, we find that mitochondrial DNA copy number is an independent factor for predicting the survival outcome of CRCs. Overall, our results provide CRC-related molecular features for clinical practice and a valuable resource for translational research.
Radical SAM-dependent ether crosslink in daropeptide biosynthesis
Authors: Guo Sijia , Wang Shu , Ma Suze , Deng Zixin , Ding Wei , Zhang Qi 
Published: April 2022

AbstractDarobactin is a ribosomally synthesized and post-translationally modified peptide (RiPP), which possesses potent activity against various Gram-negative bacteria. Darobactin features a highly unique bicyclic scaffold, consisting of an ether crosslink between two Trp residues and a C–C crosslink between a Lys and a Trp. Here we report in vivo and in vitro activity of darobactin synthase DarE. We show DarE is a radical S-adenosylmethionine (rSAM) enzyme and is solely responsible for forming the bicyclic scaffold of darobactin. DarE mainly produced the ether-crosslinked product in vitro, and when the assay was performed in H218O, apparent 18O incorporation was observed into the ether-crosslinked product. These observations suggested an rSAM-dependent process in darobactin biosynthesis, involving a highly unusual oxygen insertion step from a water molecule and subsequent O–H and C–H activations. Genome mining analysis demonstrates the diversity of darobactin-like biosynthetic gene clusters, a subclade of which likely encode monocyclic products with only an ether linkage. We propose the name daropeptide for this growing family of ether-containing RiPPs produced by DarE enzymes.
The critical role of magma degassing in sulphide melt mobility and metal enrichment
Authors: Iacono-Marziano Giada , Le Vaillant Margaux , Godel Belinda M. , Barnes Stephen J. , Arbaret Laurent 
Published: April 2022

AbstractMuch of the world’s supply of battery metals and platinum group elements (PGE) comes from sulphide ore bodies formed in ancient sub-volcanic magma plumbing systems. Research on magmatic sulphide ore genesis mainly focuses on sulphide melt-silicate melt equilibria. However, over the past few years, increasing evidence of the role of volatiles in magmatic sulphide ore systems has come to light. High temperature-high pressure experiments presented here reveal how the association between sulphide melt and a fluid phase may facilitate the coalescence of sulphide droplets and upgrade the metal content of the sulphide melt. We propose that the occurrence of a fluid phase in the magma can favour both accumulation and metal enrichment of a sulphide melt segregated from this magma, independent of the process producing the fluid phase. Here we show how sulphide-fluid associations preserved in the world-class Noril’sk-Talnakh ore deposits, in Polar Siberia, record the processes demonstrated experimentally.
Mitochondrial electron transport chain is necessary for NLRP3 inflammasome activation
Authors: Billingham Leah K. , Stoolman Joshua S. , Vasan Karthik , Rodriguez Arianne E. , Poor Taylor A. , Szibor Marten , Jacobs Howard T. , Reczek Colleen R. , Rashidi Aida , Zhang Peng , Miska Jason , Chandel Navdeep S. 
Published: April 2022

AbstractThe NLRP3 inflammasome is linked to sterile and pathogen-dependent inflammation, and its dysregulation underlies many chronic diseases. Mitochondria have been implicated as regulators of the NLRP3 inflammasome through several mechanisms including generation of mitochondrial reactive oxygen species (ROS). Here, we report that mitochondrial electron transport chain (ETC) complex I, II, III and V inhibitors all prevent NLRP3 inflammasome activation. Ectopic expression of Saccharomyces cerevisiae NADH dehydrogenase (NDI1) or Ciona intestinalis alternative oxidase, which can complement the functional loss of mitochondrial complex I or III, respectively, without generation of ROS, rescued NLRP3 inflammasome activation in the absence of endogenous mitochondrial complex I or complex III function. Metabolomics revealed phosphocreatine (PCr), which can sustain ATP levels, as a common metabolite that is diminished by mitochondrial ETC inhibitors. PCr depletion decreased ATP levels and NLRP3 inflammasome activation. Thus, the mitochondrial ETC sustains NLRP3 inflammasome activation through PCr-dependent generation of ATP, but via a ROS-independent mechanism.
Genome-wide association study identifies loci and candidate genes for grain micronutrients and quality traits in wheat (Triticum aestivum L.)
Authors: Rathan Nagenahalli Dharmegowda , Krishna Hari , Ellur Ranjith Kumar , Sehgal Deepmala , Govindan Velu , Ahlawat Arvind Kumar , Krishnappa Gopalareddy , Jaiswal Jai Prakash , Singh Jang Bahadur , SV Saiprasad , Ambati Divya , Singh Sumit Kumar , Bajpai Kriti , Mahendru-Singh Anju 
Published: April 2022

AbstractMalnutrition due to micronutrients and protein deficiency is recognized among the major global health issues. Genetic biofortification of wheat is a cost-effective and sustainable strategy to mitigate the global micronutrient and protein malnutrition. Genomic regions governing grain zinc concentration (GZnC), grain iron concentration (GFeC), grain protein content (GPC), test weight (TW), and thousand kernel weight (TKW) were investigated in a set of 184 diverse bread wheat genotypes through genome-wide association study (GWAS). The GWAS panel was genotyped using Breeders' 35 K Axiom Array and phenotyped in three different environments during 2019–2020. A total of 55 marker-trait associations (MTAs) were identified representing all three sub-genomes of wheat. The highest number of MTAs were identified for GPC (23), followed by TKW (15), TW (11), GFeC (4), and GZnC (2). Further, a stable SNP was identified for TKW, and also pleiotropic regions were identified for GPC and TKW. In silico analysis revealed important putative candidate genes underlying the identified genomic regions such as F-box-like domain superfamily, Zinc finger CCCH-type proteins, Serine-threonine/tyrosine-protein kinase, Histone deacetylase domain superfamily, and SANT/Myb domain superfamily proteins, etc. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection.
Maximum reduction of energy losses in multicore MgB2 wires by metastructured soft-ferromagnetic coatings
Authors: Kapolka M. , Ruiz H. S. 
Published: April 2022

AbstractWhen compared with rare-earth coated conductors, magnesium diboride superconducting cables are known to show significant advantages by cost and easy production. However, the inherent difficulty for achieving a significant reduction of their magnetization losses in multifilamentary wires, without degrading the high critical current density that is so characteristic of the monowire, is considered as one of the major drawbacks for their practical use in high power density applications. Being this one of the major markets for superconducting cables, from fundamental principles and computational optimization techniques, in this paper we demonstrate how the embedding of the superconducting filaments into soft-ferromagnetic metastructures can render to their full magnetic decoupling, and therefore, to the maximum reduction of the energy losses that can be achieved without deteriorate the critical current density of the cable. The designed multifilamentary metastructure is made of NbTi coated MgB2 superconducting filaments in a Cu-matrix, serving as a reference for validating our model with actual experimental measurements in monowires and multifilamentary wires. The novelty in our computationally aided multifilamentary wires, is that each one of the filaments is embedded within a thin metastructure made of a soft-ferromagnetic layer and a resistive layer. We have found that for soft-ferromagnetic layers with magnetic permeabilities in the range of $$\mu _{r}=$$

μ
r

=

20–100, nearly a full magnetic decoupling between the superconducting filaments can be achieved, leading to efficiencies higher than $$92\%$$

92
%

, and an overall reduction of the AC-losses (including eddy currents at the Cu-matrix) higher than $$50\%$$

50
%

.