bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deformation constraints of graphene oxide nanochannels under reverse osmosis
Authors: Guan Kecheng , Guo Yanan , Li Zhan , Jia Yuandong , Shen Qin , Nakagawa Keizo , Yoshioka Tomohisa , Liu Gongping , Jin Wanqin , Matsuyama Hideto 
Published: February 2023

AbstractNanochannels in laminated graphene oxide nanosheets featuring confined mass transport have attracted interest in multiple research fields. The use of nanochannels for reverse osmosis is a prospect for developing next-generation synthetic water-treatment membranes. The robustness of nanochannels under high-pressure conditions is vital for effectively separating water and ions with sub-nanometer precision. Although several strategies have been developed to address this issue, the inconsistent response of nanochannels to external conditions used in membrane processes has rarely been investigated. In this study, we develop a robust interlayer channel by balancing the associated chemistry and confinement stability to exclude salt solutes. We build a series of membrane nanochannels with similar physical dimensions but different channel functionalities and reveal their divergent deformation behaviors under different conditions. The deformation constraint effectively endows the nanochannel with rapid deformation recovery and excellent ion exclusion performance under variable pressure conditions. This study can help understand the deformation behavior of two-dimensional nanochannels in pressure-driven membrane processes and develop strategies for the corresponding deformation constraints regarding the pore wall and interior.
Evaluating native-like structures of RNA-protein complexes through the deep learning method
Authors: Zeng Chengwei , Jian Yiren , Vosoughi Soroush , Zeng Chen , Zhao Yunjie 
Published: February 2023

AbstractRNA-protein complexes underlie numerous cellular processes, including basic translation and gene regulation. The high-resolution structure determination of the RNA-protein complexes is essential for elucidating their functions. Therefore, computational methods capable of identifying the native-like RNA-protein structures are needed. To address this challenge, we thus develop DRPScore, a deep-learning-based approach for identifying native-like RNA-protein structures. DRPScore is tested on representative sets of RNA-protein complexes with various degrees of binding-induced conformation change ranging from fully rigid docking (bound-bound) to fully flexible docking (unbound-unbound). Out of the top 20 predictions, DRPScore selects native-like structures with a success rate of 91.67% on the testing set of bound RNA-protein complexes and 56.14% on the unbound complexes. DRPScore consistently outperforms existing methods with a roughly 10.53–15.79% improvement, even for the most difficult unbound cases. Furthermore, DRPScore significantly improves the accuracy of the native interface interaction predictions. DRPScore should be broadly useful for modeling and designing RNA-protein complexes.
Renewable formate from sunlight, biomass and carbon dioxide in a photoelectrochemical cell
Authors: Pan Yuyang , Zhang Huiyan , Zhang Bowen , Gong Feng , Feng Jianyong , Huang Huiting , Vanka Srinivas , Fan Ronglei , Cao Qi , Shen Mingrong , Li Zhaosheng , Zou Zhigang , Xiao Rui , Chu Sheng 
Published: February 2023

AbstractThe sustainable production of chemicals and fuels from abundant solar energy and renewable carbon sources provides a promising route to reduce climate-changing CO2emissions and our dependence on fossil resources. Here, we demonstrate solar-powered formate production from readily available biomass wastes and CO2feedstocks via photoelectrochemistry. Non-precious NiOOH/α-Fe2O3and Bi/GaN/Si wafer were used as photoanode and photocathode, respectively. Concurrent photoanodic biomass oxidation and photocathodic CO2reduction towards formate with high Faradaic efficiencies over 85% were achieved at both photoelectrodes. The integrated biomass-CO2photoelectrolysis system reduces the cell voltage by 32% due to the thermodynamically favorable biomass oxidation over conventional water oxidation. Moreover, we show solar-driven formate production with a record-high yield of 23.3 μmol cm−2h−1as well as high robustness using the hybrid photoelectrode system. The present work opens opportunities for sustainable chemical and fuel production using abundant and renewable resources on earth—sunlight, biomass and CO2.
Epidermal injury-induced derepression of key regulator ATML1 in newly exposed cells elicits epidermis regeneration
Authors: Iida Hiroyuki , Mähönen Ari Pekka , Jürgens Gerd , Takada Shinobu 
Published: February 2023

AbstractPlant cell fate determination depends on the relative positions of the cells in developing organisms. The shoot epidermis, the outermost cell layer of the above-ground organs in land plants, protects plants from environmental stresses. How the shoot epidermis is formed only from the outermost cells has remained unknown. Here we show that when inner leaf mesophyll cells are exposed to the surface, these cells show up-regulation of ATML1, a master regulator for epidermal cell identity in Arabidopsis thaliana. Epidermal cell types such as stomatal guard cells regenerate from young inner-lineage tissues that have a potential to accumulate ATML1 protein after epidermal injury. Surgical analyses indicate that application of pressure to the exposed site was sufficient to inhibit ATML1 derepression in the outermost mesophyll cells, suggesting this process requires pressure release. Furthermore, pharmacological analyses suggest that ATML1 derepression in the outermost mesophyll cells require cortical microtubule formation, MAPK signaling and proteasome activity. Our results suggest that surface-positional cues involving mechanical signaling are used to restrict ATML1 activity to the outermost cells and facilitate epidermal differentiation.
Evolution of enzyme functionality in the flavin-containing monooxygenases
Authors: Bailleul Gautier , Yang Guang , Nicoll Callum R. , Mattevi Andrea , Fraaije Marco W. , Mascotti Maria Laura 
Published: February 2023

AbstractAmong the molecular mechanisms of adaptation in biology, enzyme functional diversification is indispensable. By allowing organisms to expand their catalytic repertoires and adopt fundamentally different chemistries, animals can harness or eliminate new-found substances and xenobiotics that they are exposed to in new environments. Here, we explore the flavin-containing monooxygenases (FMOs) that are essential for xenobiotic detoxification. Employing a paleobiochemistry approach in combination with enzymology techniques we disclose the set of historical substitutions responsible for the family’s functional diversification in tetrapods. Remarkably, a few amino acid replacements differentiate an ancestral multi-tasking FMO into a more specialized monooxygenase by modulating the oxygenating flavin intermediate. Our findings substantiate an ongoing premise that enzymatic function hinges on a subset of residues that is not limited to the active site core.
Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants
Authors: Yu Haisheng , Liu Banghui , Zhang Yudi , Gao Xijie , Wang Qian , Xiang Haitao , Peng Xiaofang , Xie Caixia , Wang Yaping , Hu Peiyu , Shi Jingrong , Shi Quan , Zheng Pingqian , Feng Chengqian , Tang Guofang , Liu Xiaopan , Guo Liliangzi , Lin Xiumei , Li Jiaojiao , Liu Chuanyu , Huang Yaling , Yang Naibo , Chen Qiuluan , Li Zimu , Su Mengzhen , Yan Qihong , Pei Rongjuan , Chen Xinwen , Liu Longqi , Hu Fengyu , Liang Dan , Ke Bixia , Ke Changwen , Li Feng , He Jun , Wang Meiniang , Chen Ling , Xiong Xiaoli , Tang Xiaoping 
Published: February 2023

AbstractSARS-CoV-2 Omicron variants feature highly mutated spike proteins with extraordinary abilities in evading antibodies isolated earlier in the pandemic. Investigation of memory B cells from patients primarily with breakthrough infections with the Delta variant enables isolation of a number of neutralizing antibodies cross-reactive to heterologous variants of concern (VOCs) including Omicron variants (BA.1-BA.4). Structural studies identify altered complementarity determining region (CDR) amino acids and highly unusual heavy chain CDR2 insertions respectively in two representative cross-neutralizing antibodies—YB9-258 and YB13-292. These features are putatively introduced by somatic hypermutation and they are heavily involved in epitope recognition to broaden neutralization breadth. Previously, insertions/deletions were rarely reported for antiviral antibodies except for those induced by HIV-1 chronic infections. These data provide molecular mechanisms for cross-neutralization of heterologous SARS-CoV-2 variants by antibodies isolated from Delta variant infected patients with implications for future vaccination strategy.
Molecular imaging of liver inflammation using an anti-VCAM-1 nanobody
Authors: Nachit Maxime , Montemagno Christopher , Clerc Romain , Ahmadi Mitra , Briand François , Bacot Sandrine , Devoogdt Nick , Serdjebi Cindy , Ghezzi Catherine , Sulpice Thierry , Broisat Alexis , Leclercq Isabelle A. , Perret Pascale 
Published: February 2023

AbstractTo date, a biopsy is mandatory to evaluate parenchymal inflammation in the liver. Here, we evaluated whether molecular imaging of vascular cell adhesion molecule-1 (VCAM-1) could be used as an alternative non-invasive tool to detect liver inflammation in the setting of chronic liver disease. To do so, we radiolabeled anti-VCAM-1 nanobody (99mTc-cAbVCAM1-5) and used single-photon emission computed tomography (SPECT) to quantify liver uptake in preclinical models of non-alcoholic fatty liver disease (NAFLD) with various degree of liver inflammation: wild-type mice fed a normal or high-fat diet (HFD), FOZ fed a HFD and C57BL6/J fed a choline-deficient or -supplemented HFD. 99mTc-cAbVCAM1-5 uptake strongly correlates with liver histological inflammatory score and with molecular inflammatory markers. The diagnostic power to detect any degree of liver inflammation is excellent (AUROC 0.85–0.99). These data build the rationale to investigate 99mTc-cAbVCAM1-5 imaging to detect liver inflammation in patients with NAFLD, a largely unmet medical need.
Versatile domain mapping of scanning electron nanobeam diffraction datasets utilising variational autoencoders
Authors: Bridger A. , David W. I. F. , Wood T. J. , Danaie M. , Butler K. T. 
Published: February 2023

AbstractCharacterisation of structure across the nanometre scale is key to bridging the gap between the local atomic environment and macro-scale and can be achieved by means of scanning electron nanobeam diffraction (SEND). As a technique, SEND allows for a broad range of samples, due to being relatively tolerant of specimen thickness with low electron dosage. This, coupled with the capacity for automation of data collection over wide areas, allows for statistically representative probing of the microstructure. This paper outlines a versatile, data-driven approach for producing domain maps, and a statistical approach for assessing their applicability. The workflow utilises a Variational AutoEncoder to identify the sources of variance in the diffraction signal, and this, in combination with clustering techniques, is used to produce domain maps. This approach is agnostic to domain crystallinity, requires no prior knowledge of crystal structure, and does not require simulation of a library of expected diffraction patterns.
All-hazards dataset mined from the US National Incident Management System 1999–2020
Authors: St. Denis Lise A. , Short Karen C. , McConnell Kathryn , Cook Maxwell C. , Mietkiewicz Nathan P. , Buckland Mollie , Balch Jennifer K. 
Published: February 2023

AbstractThis paper describes a dataset mined from the public archive (1999–2020) of the US National Incident Management System Incident Status Summary (ICS-209) forms (a total of 187,160 reports for 35,170 incidents, including 34,478 wildland fires). This system captures detailed daily/regular information on incident development and response, including social and economic impacts. Most (98.4%) reports are wildland fire-related, with other incident types including hurricane, hazardous materials, flood, tornado, search and rescue, civil unrest, and winter storms. The archive, although publicly available, has been difficult to use for research due to multiple record formats, inconsistent data entry, and no clean pathway from individual reports to high-level incident analysis. Here, we describe the open-source, reproducible methods used to produce a science-grade version of the data, including formal connections made to other published wildland fire data products. Among other applications, this integrated and spatially augmented dataset enables exploration of the daily progression of the most costly, damaging, and deadly environmental-hazard events in recent US history.
The spontaneous emergence of rhythmic coordination in turn taking
Authors: Zamm Anna , Debener Stefan , Sebanz Natalie 
Published: February 2023

AbstractTurn-taking is a feature of many social interactions such as group music-making, where partners must alternate turns with high precision and accuracy. In two studies of musical rhythm coordination, we investigated how joint action partners learn to coordinate the timing of turn-taking. Musically inexperienced individuals learned to tap at the rate of a pacing cue individually or jointly (in turn with a partner), where each tap produced the next tone in a melodic sequence. In Study 1, partners alternated turns every tap, whereas in Study 2 partners alternated turns every two taps. Findings revealed that partners did not achieve the same level of performance accuracy or precision of inter-tap intervals (ITIs) when producing tapping sequences jointly relative to individually, despite showing learning (increased ITI accuracy and precision across the experiment) in both tasks. Strikingly, partners imposed rhythmic patterns onto jointly produced sequences that captured the temporal structure of turns. Together, learning to produce novel temporal sequences in turn with a partner appears to be more challenging than learning to produce the same sequences alone. Critically, partners may impose rhythmic structures onto turn-taking sequences as a strategy for facilitating coordination.
Diagnosing malignant distal bile duct obstruction using artificial intelligence based on clinical biomarkers
Authors: Sugimoto Yuichi , Kurita Yusuke , Kuwahara Takamichi , Satou Motokazu , Meguro Koki , Hosono Kunihiro , Kubota Kensuke , Hara Kazuo , Nakajima Atsushi 
Published: February 2023

AbstractDiagnosing distal bile duct obstruction remains challenging. This study aimed to examine the diagnostic ability of artificial intelligence (AI) based on clinical biomarkers in diagnosing malignant distal bile duct obstruction. A total of 206 patients with distal bile duct obstruction were included in this study. Clinical laboratory parameters were collected from the patients and evaluated using AI. All clinical parameters were input into the AI algorithm, and the AI value for malignant distal bile duct obstruction was calculated. The benign and malignant diagnostic capabilities of AI and other factors (alkaline phosphatase [ALP], intrahepatic bile duct [IHBD] diameters, and total bile duct [CBD] diameters) were compared. Benign and malignant bile duct obstruction were diagnosed in 142 and 64 patients, respectively. The median AI value of malignant distal bile duct obstruction was significantly greater than that of benign distal bile duct obstruction (0.991 vs. 0.002, p < 0.001). The area under the receiver operating characteristic curve of AI, ALP, IHBD diameter, and CBD diameter were 0.908, 0.795, 0.794, and 0.775, respectively. AI showed a sensitivity, specificity, and accuracy of 83.1%, 87.2%, and 85.9%. AI-based on clinical biomarkers could serve as an auxiliary for diagnosing malignant bile duct obstruction.
A fragment of type VI collagen alpha-6 chain is elevated in serum from patients with atopic dermatitis, psoriasis, hidradenitis suppurativa, systemic lupus erythematosus and melanoma
Authors: Holm Nielsen Signe , Port Helena , Møller Hausgaard Cecilie , Holm Jesper Grønlund , Thyssen Jacob P. , Groen Solveig Skovlund , Karsdal Morten , Nielsen Valdemar Wendelboe , Egeberg Alexander , Bay-Jensen Anne-Christine , Thomsen Simon Francis 
Published: February 2023

AbstractExtracellular matrix (ECM) remodeling of the skin is a continuous process necessary for maintaining tissue homeostasis. Type VI collagen (COL6) is characterized as a beaded filament, located in the dermal ECM, where COL6-α6-chain has been demonstrated upregulated in atopic dermatitis. The aim of this study was to develop and validate a competitive ELISA, targeting the N-terminal of COL6-α6-chain, named C6A6, and evaluate its associations with the dermatological condition’s atopic dermatitis, psoriasis, hidradenitis suppurativa, systemic lupus erythematosus, systemic sclerosis, urticaria, vitiligo, and cutaneous malignant melanoma in comparison, to healthy controls. A monoclonal antibody was raised and employed in an ELISA assay. The assay was developed, technically validated, and evaluated in two independent patient cohorts. Cohort 1 showed C6A6 was significantly elevated in patients with atopic dermatitis (p < 0.0001), psoriasis (p < 0.0001), hidradenitis suppurativa (p = 0.0095), systemic lupus erythematosus (p = 0.0032) and melanoma (p < 0.0001) compared to healthy donors. Cohort 2 confirmed C6A6 being upregulated in atopic dermatitis compared to healthy controls (p < 0.0001), but also associated with disease severity (SCORAD, p = 0.046) and lowered in patients receiving calcineurin inhibitors (p = 0.014). These findings are hypothesis generating, and the utility of the C6A6 biomarker for disease severity and treatment response needs to be validated in larger cohorts and longitudinal studies.
Synthesis of a magnetic polystyrene-supported Cu(II)-containing heterocyclic complex as a magnetically separable and reusable catalyst for the preparation of N-sulfonyl-N-aryl tetrazoles
Authors: Nasrollahzadeh Mahmoud , Motahharifar Narjes , Pakzad Khatereh , Khorsandi Zahra , Baran Talat , Wang Jinghan , Kruppke Benjamin , Khonakdar Hossein Ali 
Published: February 2023

AbstractIn this work, a cost-effective, environmentally friendly, and convenient method for synthesizing a novel heterogeneous catalyst via modification of polystyrene using tetrazole-copper magnetic complex [Ps@Tet-Cu(II)@Fe3O4] has been successfully developed. The synthesized complex was analyzed using TEM (transmission electron microscopy), HRTEM (high resolution-transmission electron microscopy), STEM (scanning transmission electron microscopy), FFT (Fast Fourier transform), XRD (X-ray diffraction), FT-IR (Fourier transform-infrared spectroscopy), TG/DTG (Thermogravimetry and differential thermogravimetry), ICP-OES (Inductively coupled plasma-optical emission spectrometry), Vibrating sample magnetometer (VSM), EDS (energy dispersive X-ray spectroscopy), and elemental mapping. N-Sulfonyl-N-aryl tetrazoles were synthesized in high yields from N-sulfonyl-N-aryl cyanamides and sodium azide using Ps@Tet-Cu(II)@Fe3O4 nanocatalyst. The Ps@Tet-Cu(II)@Fe3O4 complex can be recycled and reused easily multiple times using an external magnet without significant loss of catalytic activity.
Antibacterial and antioxidant double-layered nanofibrous mat promotes wound healing in diabetic rats
Authors: Nejaddehbashi Fereshteh , Rafiee Zeinab , Orazizadeh Mahmoud , Bayati Vahid , Hemmati Aliasghar , Hashemitabar Mahmoud , Makvandi Pooyan 
Published: February 2023

AbstractDiabetic wounds are problematic to heal owing to microbial infections as well as decreased proliferation and high concentrations of reactive oxygen species. In this study, a double-layered nanofibrous mat containing grape seed extract (GSE) and silver sulfadiazine (SSD) was fabricated. A synthetic biodegradable polymer, e.g., polycaprolactone (PCL), and a natural material (i.e., collagen) were employed as wound dressing substances. The results showed that GSE possesses antioxidant activity which can be helpful in reducing free radicals. The platform exhibited antibacterial activity against gram-positive and -negative bacteria. The double-layered nanofibrous mat containing GSE and SSD not only was not toxic but also amplified the cell proliferation compared to a pure mat, showing the effect of plant extract. After induction of a round wound, the animals were divided into three groups, namely (1) normal group (receiving + GSE/-GSE nanofiber), (2) diabetic group (receiving + GSE/-GSE nanofiber), and (3) control group (receiving gauze). In vivo evaluation demonstrated no significant differences in the healing process of normal rats. Surprisingly, fully repaired skin was observed on day 14 in the double-layered nanofibrous mat containing GSE in the normal and diabetic groups whereas the wound of diabetic rats treated with pure mat was not completely healed. The macroscopic and microscopic results after 14 days showed the following order in wound repair: Normal/ + GES > Diabetic/ + GSE > Normal/-GES > Diabetic/-GSE > control (with gauze) (p < 0.05). Accordingly, the double-layered nanofibrous mat containing GSE and SSD used in the present study could be considered as a suitable wound dressing in order to shorten healing time and prevent infection during the wound healing process.
Alleviation of arthritis through prevention of neutrophil extracellular traps by an orally available inhibitor of protein arginine deiminase 4
Authors: Gajendran Chandru , Fukui Shoichi , Sadhu Naveen M. , Zainuddin Mohammed , Rajagopal Sridharan , Gosu Ramachandraiah , Gutch Sarah , Fukui Saeko , Sheehy Casey E. , Chu Long , Vishwakarma Santosh , Jeyaraj D. A. , Hallur Gurulingappa , Wagner Denisa D. , Sivanandhan Dhanalakshmi 
Published: February 2023

AbstractProtein arginine deiminases (PAD) 4 is an enzyme that catalyzes citrullination of protein and its role in autoimmune diseases has been established through clinical genetics and gene knock out studies in mice. Further, studies with PAD4 – deficient mice have shown that PAD4 deficiency does not lead to increased infection or immune suppression, which makes PAD4 an attractive therapeutic target for auto-immune and inflammatory diseases. PAD4 has critical enzymatic role of promoting chromatin decondensation and neutrophil extracellular traps (NETs) formation that is associated with a number of immune-mediated pathological conditions. Here, we present a non-covalent PAD4 inhibitor JBI-589 with high PAD4 isoform selectivity and delineated its binding mode at 2.88 Å resolution by X-ray crystallography. We confirmed its effectiveness in inhibiting NET formation in vitro. Additionally, by using two mouse arthritis models for human rheumatoid arthritis (RA), the well-known disease associated with PAD4 clinically, we established its efficacy in vivo. These results suggest that JBI-589 would be beneficial for both PAD4 and NET-associated pathological conditions.