bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatics-based prediction of conformational epitopes for Enterovirus A71 and Coxsackievirus A16
Authors: Wang Liping , Zhu Miao , Fang Yulu , Rong Hao , Gao Liuying , Liao Qi , Zhang Lina , Dong Changzheng 
Published: March 2021

AbstractEnterovirus A71 (EV-A71), Coxsackievirus A16 (CV-A16) and CV-A10 are the major causative agents of hand, foot and mouth disease (HFMD). The conformational epitopes play a vital role in monitoring the antigenic evolution, predicting dominant strains and preparing vaccines. In this study, we employed a Bioinformatics-based algorithm to predict the conformational epitopes of EV-A71 and CV-A16 and compared with that of CV-A10. Prediction results revealed that the distribution patterns of conformational epitopes of EV-A71 and CV-A16 were similar to that of CV-A10 and their epitopes likewise consisted of three sites: site 1 (on the “north rim” of the canyon around the fivefold vertex), site 2 (on the “puff”) and site 3 (one part was in the “knob” and the other was near the threefold vertex). The reported epitopes highly overlapped with our predicted epitopes indicating the predicted results were reliable. These data suggested that three-site distribution pattern may be the basic distribution role of epitopes on the enteroviruses capsids. Our prediction results of EV-A71 and CV-A16 can provide essential information for monitoring the antigenic evolution of enterovirus.
Systemic deletion of Atp7b modifies the hepatocytes’ response to copper overload in the mouse models of Wilson disease
Authors: Muchenditsi Abigael , Talbot C. Conover , Gottlieb Aline , Yang Haojun , Kang Byunghak , Boronina Tatiana , Cole Robert , Wang Li , Dev Som , Hamilton James P. , Lutsenko Svetlana 
Published: March 2021

AbstractWilson disease (WD) is caused by inactivation of the copper transporter Atp7b and copper overload in tissues. Mice with Atp7b deleted either globally (systemic inactivation) or only in hepatocyte recapitulate various aspects of human disease. However, their phenotypes vary, and neither the common response to copper overload nor factors contributing to variability are well defined. Using metabolic, histologic, and proteome analyses in three Atp7b-deficient mouse strains, we show that global inactivation of Atp7b enhances and specifically modifies the hepatocyte response to Cu overload. The loss of Atp7b only in hepatocytes dysregulates lipid and nucleic acid metabolisms and increases the abundance of respiratory chain components and redox balancing enzymes. In global knockouts, independently of their background, the metabolism of lipid, nucleic acid, and amino acids is inhibited, respiratory chain components are down-regulated, inflammatory response and regulation of chromosomal replication are enhanced. Decrease in glucokinase and lathosterol oxidase and elevation of mucin-13 and S100A10 are observed in all Atp7b mutant strains and reflect the extent of liver injury. The magnitude of proteomic changes in Atp7b−/− animals inversely correlates with the metallothioneins levels rather than liver Cu content. These findings facilitate identification of WD-specific metabolic and proteomic changes for diagnostic and treatment.
ABA signalling and metabolism are not essential for dark-induced stomatal closure but affect response speed
Authors: Pridgeon Ashley J. , Hetherington Alistair M. 
Published: March 2021

AbstractStomata are microscopic pores that open and close, acting to balance CO2 uptake with water loss. Stomata close in response to various signals including the drought hormone abscisic acid (ABA), microbe-associated-molecular-patterns, high CO2 levels, and darkness. The signalling pathways underlying ABA-induced stomatal closure are well known, however, the mechanism for dark-induced stomatal closure is less clear. ABA signalling has been suggested to play a role in dark-induced stomatal closure, but it is unclear how this occurs. Here we investigate the role of ABA in promoting dark-induced stomatal closure. Tracking stomatal movements on the surface of leaf discs we find, although steady state stomatal apertures are affected by mutations in ABA signalling and metabolism genes, all mutants investigated close in response to darkness. However, we observed a delayed response to darkness for certain ABA signalling and metabolism mutants. Investigating this further in the quadruple ABA receptor mutant (pyr1pyl1pyl2pyl4), compared with wild-type, we found reduced stomatal conductance kinetics. Although our results suggest a non-essential role for ABA in dark-induced stomatal closure, we show that ABA modulates the speed of the dark-induced closure response. These results highlight the role of ABA signalling and metabolic pathways as potential targets for enhancing stomatal movement kinetics.
Hyperparameter optimisation and validation of registration algorithms for measuring regional ventricular deformation using retrospective gated computed tomography images
Authors: Razeghi Orod , Heinrich Mattias , Fastl Thomas E. , Corrado Cesare , Karim Rashed , De Vecchi Adelaide , Banks Tom , Donnelly Patrick , Behar Jonathan M. , Gould Justin , Rajani Ronak , Rinaldi Christopher A. , Niederer Steven 
Published: March 2021

AbstractRecent dose reduction techniques have made retrospective computed tomography (CT) scans more applicable and extracting myocardial function from cardiac computed tomography (CCT) images feasible. However, hyperparameters of generic image intensity-based registration techniques, which are used for tracking motion, have not been systematically optimised for this modality. There is limited work on their validation for measuring regional strains from retrospective gated CCT images and open-source software for motion analysis is not widely available. We calculated strain using our open-source platform by applying an image registration warping field to a triangulated mesh of the left ventricular endocardium. We optimised hyperparameters of two registration methods to track the wall motion. Both methods required a single semi-automated segmentation of the left ventricle cavity at end-diastolic phase. The motion was characterised by the circumferential and longitudinal strains, as well as local area change throughout the cardiac cycle from a dataset of 24 patients. The derived motion was validated against manually annotated anatomical landmarks and the calculation of strains were verified using idealised problems. Optimising hyperparameters of registration methods allowed tracking of anatomical measurements with a mean error of 6.63% across frames, landmarks, and patients, comparable to an intra-observer error of 7.98%. Both registration methods differentiated between normal and dyssynchronous contraction patterns based on circumferential strain ($$p_1=0.0065$$

p
1

=
0.0065

, $$p_2=0.0011$$

p
2

=
0.0011

). To test whether a typical 10 temporal frames sampling of retrospective gated CCT datasets affects measuring cardiac mechanics, we compared motion tracking results from 10 and 20 frames datasets and found a maximum error of $$8.51\pm 0.8\%$$

8.51
±
0.8
%

. Our findings show that intensity-based registration techniques with optimal hyperparameters are able to accurately measure regional strains from CCT in a very short amount of time. Furthermore, sufficient sensitivity can be achieved to identify heart failure patients and left ventricle mechanics can be quantified with 10 reconstructed temporal frames. Our open-source platform will support increased use of CCT for quantifying cardiac mechanics.
Synthesis of silver nanostructure on gold nanoparticle using near field assisted second harmonic generation
Authors: Yatsui Takashi , Brandenburg Felix , Leuschel Benjamin , Soppera Olivier 
Published: March 2021

AbstractBy using gold (Au) nanoparticles (NPs) as an optical near-field source under far-field illumination in combination with a silver (Ag) ion solution containing a photoinitiator, we coated Ag on Au NPs using a near-field (NF)-assisted process. We evaluated the change in the size of the NPs using transmission electron microscopy. Evaluation of the synthesized Ag volume over illumination power confirmed the squared power dependence of the NP volume with illumination using 808 nm light, i.e., a wavelength longer than the absorption edge wavelength of the photoinitiator molecules. The rate of volume increase was much lower than the plasmonic field enhancement effect. Therefore, the squared power dependency of the volume increase using a wavelength longer than the absorption edge wavelength originated from NF-assisted second-harmonic generation and the resulting excitation.
Global multi-method analysis of interaction parameters for reversibly self-associating macromolecules at high concentrations
Authors: Parupudi Arun , Chaturvedi Sumit K. , Adão Regina , Harkness Robert W. , Dragulin-Otto Sonia , Kay Lewis E. , Esfandiary Reza , Zhao Huaying , Schuck Peter 
Published: March 2021

AbstractWeak macromolecular interactions assume a dominant role in the behavior of highly concentrated solutions, and are at the center of a variety of fields ranging from colloidal chemistry to cell biology, neurodegenerative diseases, and manufacturing of protein drugs. They are frequently measured in different biophysical techniques in the form of second virial coefficients, and nonideality coefficients of sedimentation and diffusion, which may be related mechanistically to macromolecular distance distributions in solution and interparticle potentials. A problem arises for proteins where reversible self-association often complicates the concentration-dependent behavior, such that grossly inconsistent coefficients are measured in experiments based on different techniques, confounding quantitative conclusions. Here we present a global multi-method analysis that synergistically bridges gaps in resolution and sensitivity of orthogonal techniques. We demonstrate the method with a panel of monoclonal antibodies exhibiting different degrees of self-association. We show how their concentration-dependent behavior, examined by static and dynamic light scattering and sedimentation velocity, can be jointly described in a self-consistent framework that separates nonideality coefficients from self-association properties, and thereby extends the quantitative interpretation of nonideality coefficients to probe dynamics in highly concentrated protein solutions.
Precision medicine and machine learning towards the prediction of the outcome of potential celiac disease
Authors: Piccialli Francesco , Calabrò Francesco , Crisci Danilo , Cuomo Salvatore , Prezioso Edoardo , Mandile Roberta , Troncone Riccardo , Greco Luigi , Auricchio Renata 
Published: March 2021

AbstractPotential Celiac Patients (PCD) bear the Celiac Disease (CD) genetic predisposition, a significant production of antihuman transglutaminase antibodies, but no morphological changes in the small bowel mucosa. A minority of patients (17%) showed clinical symptoms and need a gluten free diet at time of diagnosis, while the majority progress over several years (up to a decade) without any clinical problem neither a progression of the small intestine mucosal damage even when they continued to assume gluten in their diet. Recently we developed a traditional multivariate approach to predict the natural history, on the base of the information at enrolment (time 0) by a discriminant analysis model. Still, the traditional multivariate model requires stringent assumptions that may not be answered in the clinical setting. Starting from a follow-up dataset available for PCD, we propose the application of Machine Learning (ML) methodologies to extend the analysis on available clinical data and to detect most influent features predicting the outcome. These features, collected at time of diagnosis, should be capable to classify patients who will develop duodenal atrophy from those who will remain potential. Four ML methods were adopted to select features predictive of the outcome; the feature selection procedure was indeed capable to reduce the number of overall features from 85 to 19. ML methodologies (Random Forests, Extremely Randomized Trees, and Boosted Trees, Logistic Regression) were adopted, obtaining high values of accuracy: all report an accuracy above 75%. The specificity score was always more than 75% also, with two of the considered methods over 98%, while the best performance of sensitivity was 60%. The best model, optimized Boosted Trees, was able to classify PCD starting from the selected 19 features with an accuracy of 0.80, sensitivity of 0.58 and specificity of 0.84. Finally, with this work, we are able to categorize PCD patients that can more likely develop overt CD using ML. ML techniques appear to be an innovative approach to predict the outcome of PCD, since they provide a step forward in the direction of precision medicine aimed to customize healthcare, medical therapies, decisions, and practices tailoring the clinical management of PCD children.
Comparison of MiSeq, MinION, and hybrid genome sequencing for analysis of Campylobacter jejuni
Authors: Neal-McKinney Jason M. , Liu Kun C. , Lock Christopher M. , Wu Wen-Hsin , Hu Jinxin 
Published: March 2021

AbstractThe sequencing, assembly, and analysis of bacterial genomes is central to tracking and characterizing foodborne pathogens. The bulk of bacterial genome sequencing at the US Food and Drug Administration is performed using short-read Illumina MiSeq technology, resulting in highly accurate but fragmented genomic sequences. The MinION sequencer from Oxford Nanopore is an evolving technology that produces long-read sequencing data with low equipment cost. The goal of this study was to compare Campylobacter genome assemblies generated from MiSeq and MinION data independently, as well as hybrid genome assemblies combining both data types. Two reference strains and two field isolates of C. jejuni were sequenced using MiSeq and MinION, and the sequence data were assembled using the software programs SPAdes and Canu, respectively. Hybrid genome assembly was performed using the program Unicycler. Comparison of the C. jejuni 81-176 and RM1221 genome assemblies to the PacBio reference genomes revealed that the SPAdes assemblies had the most accurate nucleotide identity, while the hybrid assemblies were the most contiguous. Assemblies generated only from MinION data using Canu were the least accurate, containing many indels and substitutions that affected downstream analyses. The hybrid sequencing approach was the most useful for detecting plasmids, large genome rearrangements, and repetitive elements such as rRNA and tRNA genes. The full genomes of both C. jejuni field isolates were completed and circularized using hybrid sequencing, and a plasmid was detected in one isolate. Continued development of nanopore sequencing technologies will likely enhance the accuracy of hybrid genome assemblies and enable public health laboratories to routinely generate complete circularized bacterial genome sequences.
Characterization of an active LINE-1 in the naked mole-rat genome
Authors: Yamaguchi Shunichi , Nohara Shizuka , Nishikawa Yuki , Suzuki Yusuke , Kawamura Yoshimi , Miura Kyoko , Tomonaga Keizo , Ueda Keiji , Honda Tomoyuki 
Published: March 2021

AbstractNaked mole-rats (NMRs, Heterocephalus glaber) are the longest-living rodent species. A reason for their long lifespan is pronounced cancer resistance. Therefore, researchers believe that NMRs have unknown secrets of cancer resistance and seek to find them. Here, to reveal the secrets, we noticed a retrotransposon, long interspersed nuclear element 1 (L1). L1s can amplify themselves and are considered endogenous oncogenic mutagens. Since the NMR genome contains fewer L1-derived sequences than other mammalian genomes, we reasoned that the retrotransposition activity of L1s in the NMR genome is lower than those in other mammalian genomes. In this study, we successfully cloned an intact L1 from the NMR genome and named it NMR-L1. An L1 retrotransposition assay using the NMR-L1 reporter revealed that NMR-L1 was active retrotransposon, but its activity was lower than that of human and mouse L1s. Despite lower retrotrasposition activity, NMR-L1 was still capable of inducing cell senescence, a tumor-protective system. NMR-L1 required the 3′ untranslated region (UTR) for retrotransposition, suggesting that NMR-L1 is a stringent-type of L1. We also confirmed the 5′ UTR promoter activity of NMR-L1. Finally, we identified the G-quadruplex structure of the 3′ UTR, which modulated the retrotransposition activity of NMR-L1. Taken together, the data indicate that NMR-L1 retrotranspose less efficiently, which may contribute to the cancer resistance of NMRs.
Band structure engineering of NiS2 monolayer by transition metal doping
Authors: Khalatbari H. , Vishkayi S. Izadi , Oskouian M. , Soleimani H. Rahimpour 
Published: March 2021

AbstractBy using density functional theory calculations, we have studied the effects of V-, Cr-, Mn-, Fe- and Co-doped on the electronic and magnetic properties of the 1T-NiS2 monolayer. The results show that pure 1T-NiS2 monolayer is a non-magnetic semiconductor. Whereas depending on the species of transition metal atom, the substituted 1T-NiS2 monolayer can become a magnetic semiconductor (Mn-doped), half-metal (V- and Fe-doped) and magnetic (Cr-doped) or non-magnetic (Co-doped) metal. The results indicate that the magnetism can be controlled by the doping of 3d transition metal atoms on the monolayer. In this paper, the engineering of the electric and magnetic properties of 1T-NiS2 monolayer is revealed. It is clear that it could have a promising application in new nanoelectronic and spintronic devices.
In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy
Authors: Sikkema Hendrik R. , Poolman Bert 
Published: March 2021

AbstractObtaining (dynamic) structure related information on proteins is key for understanding their function. Methods as single-molecule Förster Resonance Energy Transfer (smFRET) and Electron Paramagnetic Resonance (EPR) that measure distances between labeled residues to obtain dynamic information rely on selection of suitable residue pairs for chemical modification. Selection of pairs of amino acids, that show sufficient distance changes upon activity of the protein, can be a tedious process. Here we present an in silico approach that makes use of two or more structures (or structure models) to filter suitable residue pairs for FRET or EPR from all possible pairs within the protein. We apply the method for the study of the conformational dynamics of the substrate-binding domain of the osmoregulatory ATP-Binding Cassette transporter OpuA. This method speeds up the process of designing mutants, and because of its systematic nature, the chances of missing promising candidates are reduced.
Red meat intake is associated with early onset of rheumatoid arthritis: a cross-sectional study
Authors: Jin Jiayang , Li Jing , Gan Yuzhou , Liu Jiajia , Zhao Xiaozhen , Chen Jiali , Zhang Ruijun , Zhong Yan , Chen Xiaomei , Wu Lijun , Xiang Xiaohong , Zhou Yunshan , He Jing , Guo Jianping , Liu Xu , Li Zhanguo 
Published: March 2021

AbstractAccumulating evidence has implicated dietary factors as important risks for rheumatoid arthritis (RA) development, but analyses of the effects of red meat consumption on RA have yielded diverging results. The aim of this study was to explore the association between red meat and RA in a large-scale, cross-sectional study. From June to December 2016, a total of 733 patients were investigated, from which 707 participants were included in the analysis. These patients were divided into two groups according to their consumption of red meat (< 100 g/day; ≥ 100 g/day). The intake of red meat was assessed via physician-administered questionnaire. Generalized linear models were used to analyze relationships between the red meat intake and RA, adjusting for potential confounders including demographic, clinical, laboratory, and other dietary factors. Compared with low-intake red meat RA patients, high-intake red meat patients had an earlier onset age (p = 0.02) and had higher BMI (p = 0.003). The age at disease onset for the high-intake patients was 6.46 years earlier than for low-intake patients, after adjustment for demographic and other possible confounders (β = − 6.46, 95% CI − 9.77, − 3.15; p = 0.0001). Further, stratified analyses showed that this inverse association of red meat intake with RA onset age was especially evident in smokers and overweight patients (BMI ≥ 24 kg/m2). In conclusion, high-intake red meat is associated with early onset of RA, especially in smokers or overweight patients. The findings indicate that eating less red meat could be a recommendation given to patients at risk for RA development.
Thrombomodulin is upregulated in the kidneys of women with pre-eclampsia
Authors: van Aanhold Cleo C. L. , Bos Manon , Mirabito Colafella Katrina M. , van der Hoorn Marie-Louise P. , Wolterbeek Ron , Bruijn Jan A. , Bloemenkamp Kitty W. M. , van den Meiracker Anton H. , Danser A. H. Jan , Baelde Hans J. 
Published: March 2021

AbstractThe endothelial glycoprotein thrombomodulin regulates coagulation, vascular inflammation and apoptosis. In the kidney, thrombomodulin protects the glomerular filtration barrier by eliciting crosstalk between the glomerular endothelium and podocytes. Several glomerular pathologies are characterized by a loss of glomerular thrombomodulin. In women with pre-eclampsia, serum levels of soluble thrombomodulin are increased, possibly reflecting a loss from the glomerular endothelium. We set out to investigate whether thrombomodulin expression is decreased in the kidneys of women with pre-eclampsia and rats exposed to an angiogenesis inhibitor. Thrombomodulin expression was examined using immunohistochemistry and qPCR in renal autopsy tissues collected from 11 pre-eclamptic women, 22 pregnant controls and 11 hypertensive non-pregnant women. Further, kidneys from rats treated with increasing doses of sunitinib or sunitinib in combination with endothelin receptor antagonists were studied. Glomerular thrombomodulin protein levels were increased in the kidneys of women with pre-eclampsia. In parallel, in rats exposed to sunitinib, glomerular thrombomodulin was upregulated in a dose-dependent manner, and the upregulation of glomerular thrombomodulin preceded the onset of histopathological changes. Selective ETAR blockade, but not dual ETA/BR blockade, normalised the sunitinib-induced increase in thrombomodulin expression and albuminuria. We propose that glomerular thrombomodulin expression increases at an early stage of renal damage induced by antiangiogenic conditions. The upregulation of this nephroprotective protein in glomerular endothelial cells might serve as a mechanism to protect the glomerular filtration barrier in pre-eclampsia.