bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influenza vaccination and the risk of COVID-19 infection and severe illness in older adults in the United States
Authors: Huang Kelly , Lin Shu-Wen , Sheng Wang-Huei , Wang Chi-Chuan 
Published: May 2021

AbstractThe coronavirus disease of 2019 (COVID-19) has caused a global pandemic and led to nearly three million deaths globally. As of April 2021, there are still many countries that do not have COVID-19 vaccines. Before the COVID-19 vaccines were developed, some evidence suggested that an influenza vaccine may stimulate nonspecific immune responses that reduce the risk of COVID-19 infection or the severity of COVID-19 illness after infection. This study evaluated the association between influenza vaccination and the risk of COVID-19 infection. We conducted a retrospective cross-sectional study with data from July 1, 2019, to June 30, 2020 with the Claims data from Symphony Health database. The study population was adults age 65 years old or older who received influenza vaccination between September 1 and December 31 of 2019. The main outcomes and measures were odds of COVID-19 infection and severe COVID-19 illness after January 15, 2020. We found the adjusted odds ratio (aOR) of COVID-19 infection risk between the influenza-vaccination group and no-influenza-vaccination group was 0.76 (95% confidence interval (CI), 0.75–0.77). Among COVID-19 patients, the aOR of developing severe COVID-19 illness was 0.72 (95% CI, 0.68–0.76) between the influenza-vaccination group and the no-influenza-vaccination group. When the influenza-vaccination group and the other-vaccination group were compared, the aOR of COVID-19 infection was 0.95 (95% CI, 0.93–0.97), and the aOR of developing a severe COVID-19 illness was 0.95 (95% CI, 0.80–1.13). The influenza vaccine may marginally protect people from COVID-19 infection.
Improving the longevity of optically-read quantum dot physical unclonable functions
Authors: Longmate Kieran D. , Abdelazim Nema M. , Ball Elliott M. , Majaniemi Joonas , Young Robert J. 
Published: May 2021

AbstractQuantum dot physically unclonable functions (QD-PUFs) provide a promising solution to the issue of counterfeiting. When quantum dots are deposited on a surface to create a token, they form a unique pattern that is unlikely to ever be reproduced in another token that is manufactured using the same process. It would also be an extreme engineering challenge to deterministically place quantum dots to create a forgery of a specific device. The degradation of the optical response of quantum dots over time, however, places a limitation on their practical usefulness. Here we report methods to minimise the degradation of photoluminescence (PL) from InP/ZnS quantum dots suspended in a polymer and demonstrate reliable authentication using a fingerprinting technique to extract a signature from PL, even after significant degradation has occurred. Using these techniques, it was found that the addition of a polylauryl methacrylate (PLMA) copolymer improved the longevity of devices. The best performing example of this was the Polystyrene-PLMA based material. From this, it is projected that 1000 bits of information could be extracted and read after a period of years, therefore providing a compelling solution to the issue of counterfeiting.
A novel method for dendrochronology of large historical wooden objects using line trajectory X-ray tomography
Authors: Bossema Francien G. , Domínguez-Delmás Marta , Palenstijn Willem Jan , Kostenko Alexander , Dorscheid Jan , Coban Sophia Bethany , Hermens Erma , Batenburg K. Joost 
Published: May 2021

AbstractDendrochronology is an essential tool to determine the date and provenance of wood from historical art objects. As standard methods to access the tree rings are invasive, X-ray computed tomography (CT) has been proposed for non-invasive dendrochronological investigation. While traditional CT can provide clear images of the inner structure of wooden objects, it requires their full rotation, imposing strong limitations on the size of the object. These limitations have previously encouraged investigations into alternative acquisition trajectories, including trajectories with only linear movement. In this paper, we use such a line-trajectory (LT) X-ray tomography technique to retrieve tree-ring patterns from large wooden objects. We demonstrate that by moving a wooden artifact sideways between the static X-ray source and the detector during acquisition, sharp reconstruction images of the tree rings can be produced. We validate this technique using computer simulations and two wooden test planks, and demonstrate it on a large iconic chest from the Rijksmuseum collection (Amsterdam, The Netherlands). The LT scanning method can be easily implemented in standard X-ray imaging units available at museum research facilities. Therefore, this scanning technique represents a major step towards the standard implementation of non-invasive dendrochronology on large wooden cultural heritage objects.
Genetic variant of TTLL11 gene and subsequent ciliary defects are associated with idiopathic scoliosis in a 5-generation UK family
Authors: Mathieu Hélène , Patten Shunmoogum A. , Aragon-Martin Jose Antonio , Ocaka Louise , Simpson Michael , Child Anne , Moldovan Florina 
Published: May 2021

AbstractIdiopathic scoliosis (IS) is a complex 3D deformation of the spine with a strong genetic component, most commonly found in adolescent girls. Adolescent idiopathic scoliosis (AIS) affects around 3% of the general population. In a 5-generation UK family, linkage analysis identified the locus 9q31.2-q34.2 as a candidate region for AIS; however, the causative gene remained unidentified. Here, using exome sequencing we identified a rare insertion c.1569_1570insTT in the tubulin tyrosine ligase like gene, member 11 (TTLL11) within that locus, as the IS causative gene in this British family. Two other TTLL11 mutations were also identified in two additional AIS cases in the same cohort. Analyses of primary cells of individuals carrying the c.1569_1570insTT (NM_194252) mutation reveal a defect at the primary cilia level, which is less present, smaller and less polyglutamylated compared to control. Further, in a zebrafish, the knock down of ttll11, and the mutated ttll11 confirmed its role in spine development and ciliary function in the fish retina. These findings provide evidence that mutations in TTLL11, a ciliary gene, contribute to the pathogenesis of IS.
Extracellular DNA of slow growers of mycobacteria and its contribution to biofilm formation and drug tolerance
Authors: Ilinov Aleksandr , Nishiyama Akihito , Namba Hiroki , Fukushima Yukari , Takihara Hayato , Nakajima Chie , Savitskaya Anna , Gebretsadik Gebremichal , Hakamata Mariko , Ozeki Yuriko , Tateishi Yoshitaka , Okuda Shujiro , Suzuki Yasuhiko , Vinnik Yuri S. , Matsumoto Sohkichi 
Published: May 2021

AbstractDNA is basically an intracellular molecule that stores genetic information and carries instructions for growth and reproduction in all cellular organisms. However, in some bacteria, DNA has additional roles outside the cells as extracellular DNA (eDNA), which is an essential component of biofilm formation and hence antibiotic tolerance. Mycobacteria include life-threating human pathogens, most of which are slow growers. However, little is known about the nature of pathogenic mycobacteria’s eDNA. Here we found that eDNA is present in slow-growing mycobacterial pathogens, such as Mycobacterium tuberculosis, M. intracellulare, and M. avium at exponential growth phase. In contrast, eDNA is little in all tested rapid-growing mycobacteria. The physiological impact of disrupted eDNA on slow-growing mycobacteria include reduced pellicle formation, floating biofilm, and enhanced susceptibility to isoniazid and amikacin. Isolation and sequencing of eDNA revealed that it is identical to the genomic DNA in M. tuberculosis and M. intracellulare. In contrast, accumulation of phage DNA in eDNA of M. avium, suggests that the DNA released differs among mycobacterial species. Our data show important functions of eDNA necessary for biofilm formation and drug tolerance in slow-growing mycobacteria.
Flow of long chain hydrocarbons through carbon nanotubes (CNTs)
Authors: Asai Pranay , Panja Palash , Velasco Raul , Deo Milind 
Published: May 2021

AbstractThe pressure-driven flow of long-chain hydrocarbons in nanosized pores is important in energy, environmental, biological, and pharmaceutical applications. This paper examines the flow of hexane, heptane, and decane in carbon nanotubes (CNTs) of pore diameters 1–8 nm using molecular dynamic simulations. Enhancement of water flow in CNTs in comparison to rates predicted by continuum models has been well established in the literature. Our work was intended to observe if molecular dynamic simulations of hydrocarbon flow in CNTs produced similar enhancements. We used the OPLS-AA force field to simulate the hydrocarbons and the CNTs. Our simulations predicted the bulk densities of the hydrocarbons to be within 3% of the literature values. Molecular sizes and shapes of the hydrocarbon molecules compared to the pore size create interesting density patterns for smaller sized CNTs. We observed moderate flow enhancements for all the hydrocarbons (1–100) flowing through small-sized CNTs. For very small CNTs the larger hydrocarbons were forced to flow in a cork-screw fashion. As a result of this flow orientation, the larger molecules flowed as effectively (similar enhancements) as the smaller hydrocarbons.
Real-time multi-task diffractive deep neural networks via hardware-software co-design
Authors: Li Yingjie , Chen Ruiyang , Sensale-Rodriguez Berardi , Gao Weilu , Yu Cunxi 
Published: May 2021

AbstractDeep neural networks (DNNs) have substantial computational requirements, which greatly limit their performance in resource-constrained environments. Recently, there are increasing efforts on optical neural networks and optical computing based DNNs hardware, which bring significant advantages for deep learning systems in terms of their power efficiency, parallelism and computational speed. Among them, free-space diffractive deep neural networks (D2NNs) based on the light diffraction, feature millions of neurons in each layer interconnected with neurons in neighboring layers. However, due to the challenge of implementing reconfigurability, deploying different DNNs algorithms requires re-building and duplicating the physical diffractive systems, which significantly degrades the hardware efficiency in practical application scenarios. Thus, this work proposes a novel hardware-software co-design method that enables first-of-its-like real-time multi-task learning in D22NNs that automatically recognizes which task is being deployed in real-time. Our experimental results demonstrate significant improvements in versatility, hardware efficiency, and also demonstrate and quantify the robustness of proposed multi-task D2NN architecture under wide noise ranges of all system components. In addition, we propose a domain-specific regularization algorithm for training the proposed multi-task architecture, which can be used to flexibly adjust the desired performance for each task.
Transcriptional analysis of the response of C. elegans to ethanol exposure
Authors: Sterken Mark G. , van Wijk Marijke H. , Quamme Elizabeth C. , Riksen Joost A. G. , Carnell Lucinda , Mathies Laura D. , Davies Andrew G. , Kammenga Jan E. , Bettinger Jill C. 
Published: May 2021

AbstractEthanol-induced transcriptional changes underlie important physiological responses to ethanol that are likely to contribute to the addictive properties of the drug. We examined the transcriptional responses ofCaenorhabditis elegansacross a timecourse of ethanol exposure, between 30 min and 8 h, to determine what genes and genetic pathways are regulated in response to ethanol in this model. We found that short exposures to ethanol (up to 2 h) induced expression of metabolic enzymes involved in metabolizing ethanol and retinol, while longer exposure (8 h) had much more profound effects on the transcriptome. Several genes that are known to be involved in the physiological response to ethanol, including direct ethanol targets, were regulated at 8 h of exposure. This longer exposure to ethanol also resulted in the regulation of genes involved in cilia function, which is consistent with an important role for the effects of ethanol on cilia in the deleterious effects of chronic ethanol consumption in humans. Finally, we found that food deprivation for an 8-h period induced gene expression changes that were somewhat ameliorated by the presence of ethanol, supporting previous observations that worms can use ethanol as a calorie source.
Whole brain functional recordings at cellular resolution in zebrafish larvae with 3D scanning multiphoton microscopy
Authors: Bruzzone Matteo , Chiarello Enrico , Albanesi Marco , Miletto Petrazzini Maria Elena , Megighian Aram , Lodovichi Claudia , dal Maschio Marco 
Published: May 2021

AbstractOptical recordings of neuronal activity at cellular resolution represent an invaluable tool to investigate brain mechanisms. Zebrafish larvae is one of the few model organisms where, using fluorescence-based reporters of the cell activity, it is possible to optically reconstruct the neuronal dynamics across the whole brain. Typically, leveraging the reduced light scattering, methods like lightsheet, structured illumination, and light-field microscopy use spatially extended excitation profiles to detect in parallel activity signals from multiple cells. Here, we present an alternative design for whole brain imaging based on sequential 3D point-scanning excitation. Our approach relies on a multiphoton microscope integrating an electrically tunable lens. We first apply our approach, adopting the GCaMP6s activity reporter, to detect functional responses from retinal ganglion cells (RGC) arborization fields at different depths within the zebrafish larva midbrain. Then, in larvae expressing a nuclear localized GCaMP6s, we recorded whole brain activity with cellular resolution. Adopting a semi-automatic cell segmentation, this allowed reconstructing the activity from up to 52,000 individual neurons across the brain. In conclusion, this design can easily retrofit existing imaging systems and represents a compact, versatile and reliable tool to investigate neuronal activity across the larva brain at high resolution.
Novel human neutralizing mAbs specific for Spike-RBD of SARS-CoV-2
Authors: Passariello Margherita , Gentile Chiara , Ferrucci Veronica , Sasso Emanuele , Vetrei Cinzia , Fusco Giovanna , Viscardi Maurizio , Brandi Sergio , Cerino Pellegrino , Zambrano Nicola , Zollo Massimo , De Lorenzo Claudia 
Published: May 2021

AbstractAmong the therapies against the pandemic SARS-CoV-2 virus, monoclonal Antibodies (mAbs) targeting the Spike glycoprotein represent good candidates to interfere in the Spike/ACE2 interaction, preventing virus cell entry. Since anti-spike mAbs, used individually, might be unable to block the virus entry in the case of resistant mutations, we designed an innovative strategy for the isolation of multiple novel human scFvs specific for the binding domain (RBD) of Spike. By panning a large phage display antibody library on immobilized RBD, we obtained specific binders by eluting with ACE2 in order to identify those scFvs recognizing the epitope of Spike interacting with its receptor. We converted the novel scFvs into full size IgG4, differently from the previously isolated IgG1 mAbs, to avoid unwanted potential side effects of IgG1 potent effector functions on immune system. The novel antibodies specifically bind to RBD in a nanomolar range and interfere in the interaction of Spike with ACE2 receptor, either used as purified protein or when expressed on cells in its native conformation. Furthermore, some of them have neutralizing activity for virus infection in cell cultures by using two different SARS-CoV-2 isolates including the highly contagious VOC 202012/01 variant and could become useful therapeutic tools to fight against the SARS-CoV-2 virus.
EGCG promotes PRKCA expression to alleviate LPS-induced acute lung injury and inflammatory response
Authors: Wang Mian , Zhong Hua , Zhang Xian , Huang Xin , Wang Jing , Li Zihao , Chen Mengshi , Xiao Zhenghui 
Published: May 2021

AbstractAcute lung injury (ALI), which could be induced by multiple factors such as lipopolysaccharide (LPS), refer to clinical symptoms of acute respiratory failure, commonly with high morbidity and mortality. Reportedly, active ingredients from green tea have anti-inflammatory and anticancer properties, including epigallocatechin-3-gallate (EGCG). In the present study, protein kinase C alpha (PRKCA) is involved in EGCG protection against LPS-induced inflammation and ALI. EGCG treatment attenuated LPS-stimulated ALI in mice as manifested as improved lung injury scores, decreased total cell amounts, neutrophil amounts and macrophage amounts, inhibited the activity of MPO, decreased wet-to-dry weight ratio of lung tissues, and inhibited release of inflammatory cytokines TNF-α, IL-1β, and IL-6. PRKCA mRNA and protein expression showed to be dramatically decreased by LPS treatment while reversed by EGCG treatment. Within LPS-stimulated ALI mice, PRKCA silencing further aggravated, while PRKCA overexpression attenuated LPS-stimulated inflammation and ALI through MAPK signaling pathway. PRKCA silencing attenuated EGCG protection. Within LPS-induced RAW 264.7 macrophages, EGCG could induce PRKCA expression. Single EGCG treatment or Lv-PRKCA infection attenuated LPS-induced increases in inflammatory factors; PRKCA silencing could reverse the suppressive effects of EGCG upon LPS-stimulated inflammatory factor release. In conclusion, EGCG pretreatment inhibits LPS-induced ALI in mice. The protective mechanism might be associated with the inhibitory effects of PRKCA on proinflammatory cytokine release via macrophages and MAPK signaling pathway.
Frequency domain measurements of melt pool recoil force using modal analysis
Authors: Cullom Tristan , Lough Cody , Altese Nicholas , Bristow Douglas , Landers Robert , Brown Ben , Hartwig Troy , Barnard Andrew , Blough Jason , Johnson Kevin , Kinzel Edward 
Published: May 2021

AbstractRecoil pressure is a critical factor affecting the melt pool dynamics during Laser Powder Bed Fusion (LPBF) processes. Recoil pressure depresses the melt pool. When the recoil pressure is low, thermal conduction and capillary forces may be inadequate to provide proper fusion between layers. However, excessive recoil pressure can produce a keyhole inside the melt pool, which is associated with gas porosity. Direct recoil pressure measurements are challenging because it is localized over an area proportionate to the laser spot size producing a force in the mN range. This paper reports a vibration-based approach to quantify the recoil force exerted on a part in a commercial LPBF machine. The measured recoil force is consistent with estimates from high speed synchrotron imaging of entrained particles, and the results show that the recoil force scales with applied laser power and is inversely related to the laser scan speed. These results facilitate further studies of melt pool dynamics and have the potential to aid process development for new materials.
Genome-wide identification of potential biomarkers in multiple myeloma using meta-analysis of mRNA and miRNA expression data
Authors: Katiyar Amit , Kaur Gurvinder , Rani Lata , Jena Lingaraja , Singh Harpreet , Kumar Lalit , Sharma Atul , Kaur Punit , Gupta Ritu 
Published: May 2021

AbstractMultiple myeloma (MM) is a plasma cell malignancy with diverse clinical phenotypes and molecular heterogeneity not completely understood. Differentially expressed genes (DEGs) and miRNAs (DEMs) in MM may influence disease pathogenesis, clinical presentation / drug sensitivities. But these signatures overlap meagrely plausibly due to complexity of myeloma genome, diversity in primary cells studied, molecular technologies/ analytical tools utilized. This warrants further investigations since DEGs/DEMs can impact clinical outcomes and guide personalized therapy. We have conducted genome-wide meta-analysis of DEGs/DEMs in MM versus Normal Plasma Cells (NPCs) and derived unified putative signatures for MM. 100 DEMs and 1,362 DEGs were found deranged between MM and NPCs. Signatures of 37 DEMs (‘Union 37’) and 154 DEGs (‘Union 154’) were deduced that shared 17 DEMs and 22 DEGs with published prognostic signatures, respectively. Two miRs (miR-16–2-3p, 30d-2-3p) correlated with survival outcomes. PPI analysis identified 5 topmost functionally connected hub genes (UBC, ITGA4, HSP90AB1, VCAM1, VCP). Transcription factor regulatory networks were determined for five seed DEGs with ≥ 4 biomarker applications (CDKN1A, CDKN2A, MMP9, IGF1, MKI67) and three topmost up/ down regulated DEMs (miR-23b, 195, let7b/ miR-20a, 155, 92a). Further studies are warranted to establish and translate prognostic potential of these signatures for MM.
Eye-blink artifact removal from single channel EEG with k-means and SSA
Authors: Maddirala Ajay Kumar , Veluvolu Kalyana C 
Published: May 2021

AbstractIn recent years, the usage of portable electroencephalogram (EEG) devices are becoming popular for both clinical and non-clinical applications. In order to provide more comfort to the subject and measure the EEG signals for several hours, these devices usually consists of fewer EEG channels or even with a single EEG channel. However, electrooculogram (EOG) signal, also known as eye-blink artifact, produced by involuntary movement of eyelids, always contaminate the EEG signals. Very few techniques are available to remove these artifacts from single channel EEG and most of these techniques modify the uncontaminated regions of the EEG signal. In this paper, we developed a new framework that combines unsupervised machine learning algorithm (k-means) and singular spectrum analysis (SSA) technique to remove eye blink artifact without modifying actual EEG signal. The novelty of the work lies in the extraction of the eye-blink artifact based on the time-domain features of the EEG signal and the unsupervised machine learning algorithm. The extracted eye-blink artifact is further processed by the SSA method and finally subtracted from the contaminated single channel EEG signal to obtain the corrected EEG signal. Results with synthetic and real EEG signals demonstrate the superiority of the proposed method over the existing methods. Moreover, the frequency based measures [the power spectrum ratio ($$\Gamma $$Γ) and the mean absolute error (MAE)] also show that the proposed method does not modify the uncontaminated regions of the EEG signal while removing the eye-blink artifact.