bluuebunny/crossref_metadata_2025_split huggingface dataset:
Designed Rubredoxin miniature in a fully artificial electron chain triggered by visible light
Authors: Chino Marco , Di Costanzo Luigi Franklin , Leone Linda , La Gatta Salvatore , Famulari Antonino , Chiesa Mario , Lombardi Angela , Pavone Vincenzo 
Published: April 2023

AbstractDesigning metal sites into de novo proteins has significantly improved, recently. However, identifying the minimal coordination spheres, able to encompass the necessary information for metal binding and activity, still represents a great challenge, today. Here, we test our understanding with a benchmark, nevertheless difficult, case. We assemble into a miniature 28-residue protein, the quintessential elements required to fold properly around a FeCys4 redox center, and to function efficiently in electron-transfer. This study addresses a challenge in de novo protein design, as it reports the crystal structure of a designed tetra-thiolate metal-binding protein in sub-Å agreement with the intended design. This allows us to well correlate structure to spectroscopic and electrochemical properties. Given its high reduction potential compared to natural and designed FeCys4-containing proteins, we exploit it as terminal electron acceptor of a fully artificial chain triggered by visible light.
Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin
Authors: Wydorski Pawel M. , Osipiuk Jerzy , Lanham Benjamin T. , Tesar Christine , Endres Michael , Engle Elizabeth , Jedrzejczak Robert , Mullapudi Vishruth , Michalska Karolina , Fidelis Krzysztof , Fushman David , Joachimiak Andrzej , Joachimiak Lukasz A. 
Published: April 2023

AbstractThe Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub2) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub2 combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub2 are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub2 modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.
Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies
Authors: Ruffolo Jeffrey A. , Chu Lee-Shin , Mahajan Sai Pooja , Gray Jeffrey J. 
Published: April 2023

AbstractAntibodies have the capacity to bind a diverse set of antigens, and they have become critical therapeutics and diagnostic molecules. The binding of antibodies is facilitated by a set of six hypervariable loops that are diversified through genetic recombination and mutation. Even with recent advances, accurate structural prediction of these loops remains a challenge. Here, we present IgFold, a fast deep learning method for antibody structure prediction. IgFold consists of a pre-trained language model trained on 558 million natural antibody sequences followed by graph networks that directly predict backbone atom coordinates. IgFold predicts structures of similar or better quality than alternative methods (including AlphaFold) in significantly less time (under 25 s). Accurate structure prediction on this timescale makes possible avenues of investigation that were previously infeasible. As a demonstration of IgFold’s capabilities, we predicted structures for 1.4 million paired antibody sequences, providing structural insights to 500-fold more antibodies than have experimentally determined structures.
Protein stabilization of ITF2 by NF-κB prevents colitis-associated cancer development
Authors: Lee Mingyu , Kim Yi-Sook , Lim Suha , Shin Seung-Hyun , Kim Iljin , Kim Jiyoung , Choi Min , Kim Jung Ho , Koh Seong-Joon , Park Jong-Wan , Shin Hyun-Woo 
Published: April 2023

AbstractChronic colonic inflammation is a feature of cancer and is strongly associated with tumorigenesis, but its underlying molecular mechanisms remain poorly understood. Inflammatory conditions increased ITF2 and p65 expression both ex vivo and in vivo, and ITF2 and p65 showed positive correlations. p65 overexpression stabilized ITF2 protein levels by interfering with the binding of Parkin to ITF2. More specifically, the C-terminus of p65 binds to the N-terminus of ITF2 and inhibits ubiquitination, thereby promoting ITF2 stabilization. Parkin acts as a E3 ubiquitin ligase for ITF2 ubiquitination. Intestinal epithelial-specific deletion of ITF2 facilitated nuclear translocation of p65 and thus increased colitis-associated cancer tumorigenesis, which was mediated by Azoxymethane/Dextran sulfate sodium or dextran sulfate sodium. Upregulated ITF2 expression was lost in carcinoma tissues of colitis-associated cancer patients, whereas p65 expression much more increased in both dysplastic and carcinoma regions. Therefore, these findings indicate a critical role for ITF2 in the repression of colitis-associated cancer progression and ITF2 would be an attractive target against inflammatory diseases including colitis-associated cancer.
3D printing of unsupported multi-scale and large-span ceramic via near-infrared assisted direct ink writing
Authors: Zhao Yongqin , Zhu Junzhe , He Wangyan , Liu Yu , Sang Xinxin , Liu Ren 
Published: April 2023

AbstractIn the three-dimensional printing process of ceramic with low-angle structures, additional supporting structures are usually employed to avoid collapse of overhanging parts. However, the extra supporting structures not only affect printing efficiency, but the problems caused by their removal are also a matter of concern. Herein, we present a ceramic printing method, which can realize printing of unsupported multi-scale and large-span ceramics through the combination of direct ink writing and near-infrared induced up-conversion particles-assisted photopolymerization. This printing technology enables in-situ curing of multi-scale filaments with diameters ranging from 410 µm to 3.50 mm, and ceramic structures of torsion spring, three-dimensional bending and cantilever beam were successfully constructed through unsupported printing. This method will bring more innovation to the unsupported 3D manufacturing of complex shape ceramics.
Solvent-derived defects suppress adsorption in MOF-74
Authors: Fu Yao , Yao Yifeng , Forse Alexander C. , Li Jianhua , Mochizuki Kenji , Long Jeffrey R. , Reimer Jeffrey A. , De Paëpe Gaël , Kong Xueqian 
Published: April 2023

AbstractDefects in metal-organic frameworks (MOFs) have great impact on their nano-scale structure and physiochemical properties. However, isolated defects are easily concealed when the frameworks are interrogated by typical characterization methods. In this work, we unveil the presence of solvent-derived formate defects in MOF-74, an important class of MOFs with open metal sites. With multi-dimensional solid-state nuclear magnetic resonance (NMR) investigations, we uncover the ligand substitution role of formate and its chemical origin from decomposed N,N-dimethylformamide (DMF) solvent. The placement and coordination structure of formate defects are determined by 13C NMR and density functional theory (DFT) calculations. The extra metal-oxygen bonds with formates partially eliminate open metal sites and lead to a quantitative decrease of N2 and CO2 adsorption with respect to the defect concentration. In-situ NMR analysis and molecular simulations of CO2 dynamics elaborate the adsorption mechanisms in defective MOF-74. Our study establishes comprehensive strategies to search, elucidate and manipulate defects in MOFs.
Colonization with ubiquitous protist Blastocystis ST1 ameliorates DSS-induced colitis and promotes beneficial microbiota and immune outcomes
Authors: Deng Lei , Wojciech Lukasz , Png Chin Wen , Kioh Yan Qin Dorinda , Ng Geok Choo , Chan Eric Chun Yong , Zhang Yongliang , Gascoigne Nicholas R. J. , Tan Kevin Shyong Wei 
Published: April 2023

AbstractBlastocystisis a species complex that exhibits extensive genetic diversity, evidenced by its classification into several genetically distinct subtypes (ST). Although several studies have shown the relationships between a specific subtype and gut microbiota, there is no study to show the effect of the ubiquitousBlastocystisST1 on the gut microbiota and host health. Here, we show thatBlastocystisST1 colonization increased the proportion of beneficial bacteriaAlloprevotellaandAkkermansia, and induced Th2 and Treg cell responses in normal healthy mice. ST1-colonized mice showed decreases in the severity of DSS-induced colitis when compared to non-colonized mice. Furthermore, mice transplanted with ST1-altered gut microbiota were refractory to dextran sulfate sodium (DSS)-induced colitis via induction of Treg cells and elevated short-chain fat acid (SCFA) production. Our results suggest that colonization withBlastocystisST1, one of the most common subtypes in humans, exerts beneficial effects on host health through modulating the gut microbiota and adaptive immune responses.
Immunization with a Trypanosoma cruzi cyclophilin-19 deletion mutant protects against acute Chagas disease in mice
Authors: Jha Bijay Kumar , Varikuti Sanjay , Verma Chaitenya , Shivahare Rahul , Bishop Nicholas , Dos Santos Gregory P. , McDonald Jacquelyn , Sur Aakash , Myler Peter J. , Schenkman Sergio , Satoskar Abhay R. , McGwire Bradford S. 
Published: April 2023

AbstractHuman infection with the protozoan parasite Trypanosoma cruzi causes Chagas disease for which there are no prophylactic vaccines. Cyclophilin 19 is a secreted cis-trans peptidyl isomerase expressed in all life stages of Trypanosoma cruzi. This protein in the insect stage leads to the inactivation of insect anti-parasitic peptides and parasite transformation whereas in the intracellular amastigotes it participates in generating ROS promoting the growth of parasites. We have generated a parasite mutant with depleted expression of Cyp19 by removal of 2 of 3 genes encoding this protein using double allelic homologous recombination. The mutant parasite line failed to replicate when inoculated into host cells in vitro or in mice indicating that Cyp19 is critical for infectivity. The mutant parasite line also fails to replicate in or cause clinical disease in immuno-deficient mice further validating their lack of virulence. Repeated inoculation of mutant parasites into immuno-competent mice elicits parasite-specific trypanolytic antibodies and a Th-1 biased immune response and challenge of mutant immunized mice with virulent wild-type parasites is 100% effective at preventing death from acute disease. These results suggest that parasite Cyp19 may be candidate for small molecule drug targeting and that the mutant parasite line may warrant further immunization studies for prevention of Chagas disease.
A comprehensive review on LDH-based catalysts to activate persulfates for the degradation of organic pollutants
Authors: Abd El-Monaem Eman M. , Elshishini Hala M. , Bakr Sara S. , El-Aqapa Hisham G. , Hosny Mohamed , Andaluri Gangadhar , El-Subruiti Gehan M. , Omer Ahmed M. , Eltaweil Abdelazeem S. 
Published: April 2023

AbstractDegradation of organic contaminants into less toxic substances is the best option to remove these compounds rather than using conventional techniques. The sulfate radical-based-advanced oxidation process is an effective strategy that degrades organic contaminants by activating peroxymonosulfate (PMS). Such a strategy generates singlet oxygen (1O2), hydroxyl ($$^ \bullet \!{{{\mathrm{OH}}}}$$∙OH), and sulfate ($${{{\mathrm{SO}}}}_4^{ \bullet\! - }$$SO4∙−) radicals.$${{{\mathrm{SO}}}}_4^{ \bullet \!- }$$SO4∙−is distinguished by its high oxidation selectivity and activity toward the degradation of organic contaminates compared to other radicals. Various catalysts are employed in PMS activation including layered doubled hydroxides (LDHs), which are characterized by their facile synthesis and high catalytic activity. This review article is the first attempt to compile the recent progress in the degradation of common organic pollutants including aromatic compounds, pharmaceutical residues, and dyes via the PMS activation using LDH-based catalysts. The degradation pathways, reaction parameters’ influence, stability of LDHs, and comparisons between different LDH-based catalysts are investigated in this work.
Complete Global Total Electron Content Map Dataset based on a Video Imputation Algorithm VISTA
Authors: Sun Hu , Chen Yang , Zou Shasha , Ren Jiaen , Chang Yurui , Wang Zihan , Coster Anthea 
Published: April 2023

AbstractIonospheric total electron content (TEC) derived from multi-frequency Global Navigation Satellite System (GNSS) signals and the relevant products have become one of the most utilized parameters in the space weather and ionospheric research community. However, there are a couple of challenges in using the global TEC map data including large data gaps over oceans and the potential of losing meso-scale ionospheric structures when applying traditional reconstruction and smoothing algorithms. In this paper, we describe and release a global TEC map database, constructed and completed based on the Madrigal TEC database with a novel video imputation algorithm called VISTA (Video Imputation with SoftImpute, Temporal smoothing and Auxiliary data). The complete TEC maps reveal important large-scale TEC structures and preserve the observed meso-scale structures. Basic ideas and the pipeline of the video imputation algorithm are introduced briefly, followed by discussions on the computational costs and fine tuning of the adopted algorithm. Discussions on potential usages of the complete TEC database are given, together with a concrete example of applying this database.
Blast loads and variability on cylindrical shells under different charge orientations
Authors: Yin Fei , Zhi Xudong , Fan Feng , Wei Wuchen , Zheng Dianshuang 
Published: April 2023

AbstractCylindrical shells are widely used in public buildings and military protection fields, and it has a high risk of terrorist attacks and military attacks, it is of great social benefit to carry out the anti-blast design of cylindrical shells, which needs to consider building shape and the shape of blast waves. In this paper, cylindrical charges in five directions were detonated on the outer ground of the scaled cylindrical shell, blast loads of the cylindrical shell were measured and blast waves were photographed. The variation of blast load is analyzed by combining the test and simulation results, the difference in peak overpressure of the blast waves on the end face between five orientations is nearly twice. The blast loads in the axial direction of cylindrical charges have a secondary peak phenomenon, and the blast loads between the axial direction and radial direction of cylindrical charges change abruptly at a specific angle. The experimental and simulation methods provide a reference for establishing a blast load database of typical buildings.
Assessment of experimental OpenCV tracking algorithms for ultrasound videos
Authors: Levin A. A. , Klimov D. D. , Nechunaev A. A. , Prokhorenko L. S. , Mishchenkov D. S. , Nosova A. G. , Astakhov D. A. , Poduraev Y. V. , Panchenkov D. N. 
Published: April 2023

AbstractThis study aims to compare the tracking algorithms provided by the OpenCV library to use on ultrasound video. Despite the widespread application of this computer vision library, few works describe the attempts to use it to track the movement of liver tumors on ultrasound video. Movements of the neoplasms caused by the patient`s breath interfere with the positioning of the instruments during the process of biopsy and radio-frequency ablation. The main hypothesis of the experiment was that tracking neoplasms and correcting the position of the manipulator in case of using robotic-assisted surgery will allow positioning the instruments more precisely. Another goal of the experiment was to check if it is possible to ensure real-time tracking with at least 25 processed frames per second for standard definition video. OpenCV version 4.5.0 was used with 7 tracking algorithms from the extra modules package. They are: Boosting, CSRT, KCF, MedianFlow, MIL, MOSSE, TLD. More than 5600 frames of standard definition were processed during the experiment. Analysis of the results shows that two algorithms—CSRT and KCF—could solve the problem of tumor tracking. They lead the test with 70% and more of Intersection over Union and more than 85% successful searches. They could also be used in real-time processing with an average processing speed of up to frames per second in CSRT and 100 + frames per second for KCF. Tracking results reach the average deviation between centers of neoplasms to 2 mm and maximum deviation less than 5 mm. This experiment also shows that no frames made CSRT and KCF algorithms fail simultaneously. So, the hypothesis for future work is combining these algorithms to work together, with one of them—CSRT—as support for the KCF tracker on the rarely failed frames.
Construction and analysis of a conjunctive diagnostic model of HNSCC with random forest and artificial neural network
Authors: Luo Yao , Zhou Liu-qing , Yang Fan , Chen Jing-cai , Chen Jian-jun , Wang Yan-jun 
Published: April 2023

AbstractHead and neck squamous cell carcinoma (HNSCC) is a heterogeneous tumor that is highly aggressive and ranks fifth among the most common cancers worldwide. Although, the researches that attempted to construct a diagnostic model were deficient in HNSCC. Currently, the gold standard for diagnosing head and neck tumors is pathology, but this requires a traumatic biopsy. There is still a lack of a noninvasive test for such a high—incidence tumor. In order to screen genetic markers and construct diagnostic model, the methods of random forest (RF) and artificial neural network (ANN) were utilized. The data of HNSCC gene expression was accessed from Gene Expression Omnibus (GEO) database; we selected three datasets totally, and we combined 2 datasets (GSE6631 and GSE55547) for screening differentially expressed genes (DEGs) and chose another dataset (GSE13399) for validation. Firstly, the 6 DEGs (CRISP3, SPINK5, KRT4, MMP1, MAL, SPP1) were screened by RF. Subsequently, ANN was applied to calculate the weights of 6 genes. Besides, we created a diagnostic model and nominated it as neuralHNSCC, and the performance of neuralHNSCC by area under curve (AUC) was verified using another dataset. Our model achieved an AUC of 0.998 in the training cohort, and 0.734 in the validation cohort. Furthermore, we used the Cell-type Identification using Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm to investigate the difference in immune cell infiltration between HNSCC and normal tissues initially. The selected 6 DEGs and the constructed novel diagnostic model of HNSCC would make contributions to the diagnosis.
Tuning electronic and magnetic properties through disorder in V2O5 nanoparticles
Authors: Correal Sergio , Hernández-Gómez Daniel , Esquivel Andrea Steffania , Cardona-Rodríguez Alexander , Reiber Andreas , Hernandez Yenny , González-Hernández Rafael , Ramírez Juan Gabriel 
Published: April 2023

AbstractWe report on the synthesis and characterization of V2O5 nanoparticles grown using a sol–gel method at different calcination temperatures. We observed a surprising reduction in the optical band gap from 2.20 to 1.18 eV with increasing calcination temperature from 400 to 500 °C. Raman and X-Ray diffraction measurements indicated slight changes in the lattice parameters induced by the growth process. However, density functional theory calculations of the Rietveld-refined and pristine structures revealed that the observed optical gap reduction could not be explained by structural changes alone. By introducing oxygen vacancies to the refined structures, we could reproduce the reduction of the band gap. Our calculations also showed that the inclusion of oxygen vacancies at the vanadyl position creates a spin-polarized interband state that reduces the electronic band gap and promotes a magnetic response due to unpaired electrons. This prediction was confirmed by our magnetometry measurements, which exhibited a ferromagnetic-like behavior. Our findings suggest that oxygen vacancies play a crucial role in band gap reduction and the promotion of a ferromagnetic-like response in an otherwise paramagnetic material. This provides a promising route to engineer novel devices.
The increase in intensity and frequency of surface air temperature extremes throughout the western South Atlantic coast
Authors: Sanches Fábio H. C. , Martins Fernando R. , Conti William R. P. , Christofoletti Ronaldo A. 
Published: April 2023

AbstractThe climate is changing. At this stage, it is important to specify an ‘extreme’ climate and identify patterns that indicate its potential harm worldwide, including the coastal zones. Herein, we considered extremes based on the “Peaks Over Threshold” method from the “Extreme Value Theory”. We looked after geographical patterns of surface air temperature (SAT) extremes (e.g., Tmax, Tmin, daily temperature range (DTR), and inter-daily temperature range) over the last 40 years throughout the Brazilian coast. Overall, we found a trend increase in intensity and frequency, but the duration was barely affected. The latitudinal pattern of extremes and the temperatures considered extremes followed the settled perception that areas in higher latitudes will be more affected by the extent of warming. Additionally, the seasonal pattern of DTR demonstrated to be a good approach to make inferences about air mass changes, but joint analyses on extremes with other atmospheric variables are desirable. Given the potential effects of extreme climates on society and natural systems over the world, our study highlights the urge for action to mitigate the effects of the increase in SAT in coastal zones.
Deep generative model super-resolves spatially correlated multiregional climate data
Authors: Oyama Norihiro , Ishizaki Noriko N. , Koide Satoshi , Yoshida Hiroaki 
Published: April 2023

AbstractSuper-resolving the coarse outputs of global climate simulations, termed downscaling, is crucial in making political and social decisions on systems requiring long-term climate change projections. Existing fast super-resolution techniques, however, have yet to preserve the spatially correlated nature of climatological data, which is particularly important when we address systems with spatial expanse, such as the development of transportation infrastructure. Herein, we show an adversarial network-based machine learning enables us to correctly reconstruct the inter-regional spatial correlations in downscaling with high magnification of up to 50 while maintaining pixel-wise statistical consistency. Direct comparison with the measured meteorological data of temperature and precipitation distributions reveals that integrating climatologically important physical information improves the downscaling performance, which prompts us to call this approach $$\pi$$
π
SRGAN (Physics Informed Super-Resolution Generative Adversarial Network). The proposed method has a potential application to the inter-regionally consistent assessment of the climate change impact. Additionally, we present the outcomes of another variant of the deep generative model-based downscaling approach in which the low-resolution precipitation field is substituted with the pressure field, referred to as $$\psi$$
ψ
SRGAN (Precipitation Source Inaccessible SRGAN). Remarkably, this method demonstrates unexpectedly good downscaling performance for the precipitation field.