bluuebunny/crossref_metadata_2025_split huggingface dataset:
CircRBM33 downregulation inhibits hypoxia-induced glycolysis and promotes apoptosis of breast cancer cells via a microRNA-542-3p/HIF-1α axis
Authors: Jiang Yiming , Zhang Meiqi , Yu Danlu , Hou Guoxin , Wu Jingyi , Li Fuming 
Published: March 2022

AbstractMany circRNAs are involved in the carcinogenesis of breast cancer (BCa) through the transcription of microRNAs (miRNAs) and mRNAs. This study investigated circRBM33 regulation of the miR-542-3p/hypoxia-inducible factor-1α (HIF-1α) axis in BCa. BCa clinical tissue samples were collected to test differential expressions of circRBM33, miR-542-3p, and HIF-1α. MCF-7 cells were subjected to normoxia or hypoxia and transfected with plasmids that regulated CircRBM33, miR-542-3p, and HIF-1α expression levels. Glycolysis was evaluated by measuring glucose consumption, lactic acid production, and protein expression of hexokinase 2, glucose transporter type 1 and lactic dehydrogenase A. Cell proliferation and apoptosis were also assessed, and the interactions between genes were explored. CircRBM33 and HIF-1α were upregulated, while miR-542-3p was downregulated in BCa tissue samples and cell lines. Hypoxia induced circRBM33 expression in BCa cells, which negatively regulated miR-542-3p expression. CircRBM33 knockdown or miR-542-3p rescue reduced glycolysis and proliferation and promoted apoptosis of BCa cells. MiR-542-3p inhibition rescued circRBM33 knockdown-mediated glycolysis, proliferation and apoptosis of BCa cells. MiR-542-3p targeted HIF-1α, and the overexpression of HIF-1α reversed the effect of miR-542-3p upregulation on glycolysis, proliferation, and apoptosis of BCa cells. Collectively, downregulating circRBM33 suppresses miR-542-3p-targeted HIF-1α expression, resulting in the inhibition of glycolysis and proliferation and the promotion of BCa cells’ apoptosis.
Integrative transcriptomic, evolutionary, and causal inference framework for region-level analysis: Application to COVID-19
Authors: Zhou Dan , Gamazon Eric R. 
Published: March 2022

AbstractWe developed an integrative transcriptomic, evolutionary, and causal inference framework for a deep region-level analysis, which integrates several published approaches and a new summary-statistics-based methodology. To illustrate the framework, we applied it to understanding the host genetics of COVID-19 severity. We identified putative causal genes, including SLC6A20, CXCR6, CCR9, and CCR5 in the locus on 3p21.31, quantifying their effect on mediating expression and on severe COVID-19. We confirmed that individuals who carry the introgressed archaic segment in the locus have a substantially higher risk of developing the severe disease phenotype, estimating its contribution to expression-mediated heritability using a new summary-statistics-based approach we developed here. Through a large-scale phenome-wide scan for the genes in the locus, several potential complications, including inflammatory, immunity, olfactory, and gustatory traits, were identified. Notably, the introgressed segment showed a much higher concentration of expression-mediated causal effect on severity (0.9–11.5 times) than the entire locus, explaining, on average, 15.7% of the causal effect. The region-level framework (implemented in publicly available software, SEGMENT-SCAN) has important implications for the elucidation of molecular mechanisms of disease and the rational design of potentially novel therapeutics.
Small molecule additives in multilayer polymer-clay thin films for improved heat shielding of steel
Authors: Long Carolyn T. , Grunlan Jaime C. 
Published: March 2022

AbstractIn an effort to improve the heat shielding ability of multilayer polymer-clay films, the influence of various small molecule additives was studied. Tris(hydroxymethyl)aminomethane (THAM), pentaerythritol (PER), and ammonium pentaborate (PB) are each utilized in flame retardant applications for the benefits they provide in reducing the propagation of fire. In the present study, these additives combined with polyethylenimine (PEI) and vermiculite (VMT) clay and the resulting growth of the coatings and the thermal resistivity were measured. THAM and PB salts contribute most to the overall growth of the layer-by-layer assembled films, generating an increase in film thickness of 50% or more, while PER has a greater impact on heat shielding. A 14-bilayer (THAM + PER + PEI)/VMT coating (~25 µm thick) on steel can achieve a temperature differential of over 125 °C due to a layering effect that occurs within the architecture of the macroscopic insulation bubble and disordered char. This improved thermal resistivity across a relatively thin film generates a heat shield that can be applied in novel applications such as a single-use protective barrier for aerospace components.
Influence of fuel combustion on the corrosion behavior of pipeline steels in fire flooding technology
Authors: Meng Bo , Wang Jinlong , Yang Lanlan , Zhu Lijuan , Chen Minghui , Zhu Shenglong , Wang Fuhui 
Published: March 2022

AbstractTo study the oxidation behavior of a commonly used pipeline materials of 37Mn5 steel in the process of fire flooding technology, a simulation device of organic fuel combustion was designed and used for comparative study between air and kerosene atmosphere. The products generated after kerosene combustion greatly affected the growth of iron oxides at 600 and 700 °C. In air, the oxide scale shows a defective morphology with bulge and spallation. While in the kerosene atmosphere, carbon particles after incomplete combustion can exist on the surface and inside the oxide scale, which would inhibit the reduction of oxides by carbon in substrate and the decarburization of 37Mn5 steel.
The demography of COVID-19 deaths database, a gateway to well-documented international data
Authors: Caporali Arianna , Garcia Jenny , Couppié Étienne , Poniakina Svitlana , Barbieri Magali , Bonnet Florian , Camarda Carlo Giovanni , Cambois Emmanuelle , Hourani Iris , Korotkova Daria , Meslé France , Penina Olga , Robine Jean-Marie , Sauerberg Markus , Torres Catalina 
Published: March 2022

AbstractNational authorities publish COVID-19 death counts, which are extensively re-circulated and compared; but data are generally poorly sourced and documented. Academics and stakeholders need tools to assess data quality and to track data-related discrepancies for comparability over time or across countries. “The Demography of COVID-19 Deaths” database aims at bridging this gap. It provides COVID-19 death counts along with associated documentation, which includes the exact data sources and points out issues of quality and coverage of the data. The database — launched in April 2020 and continuously updated — contains daily cumulative death counts attributable to COVID-19 broken down by sex and age, place and date of occurrence of the death. Data and metadata undergo quality control checks prior to online release. As of mid-December 2021, it covers 21 countries in Europe and beyond. It is open access at a bilingual (English and French) website with content intended for expert users and non-specialists (https://dc-covid.site.ined.fr/en/; figshare: https://doi.org/10.6084/m9.figshare.c.5807027). Data and metadata are available for each country separately and pooled over all countries.
Finding the closed-form solutions of dissipative oscillatory systems
Authors: Irum Saba , Naeem Imran 
Published: March 2022

AbstractThis paper shows how to use the approximate Hamiltonian approach for the non-conservative system not capable of possessing Hamiltonian. Using the approximate Hamiltonian method for a non-conservative system is not possible in general. We propose a way to obtain the closed-form solutions for such systems. We use the approximate dual Hamiltonian method to construct the first integrals and closed-form solutions of the Van der Pol equation. First the solutions of the initial value VdP equation is obtained using approximate dual Hamiltonian method. Then a good agreement is observed in the comparison between the numerical results and the results through approximate dual Hamiltonian method. Finally, we use the approximate dual Hamiltonian method to find the dual Hamiltonian and first integrals of the forced Van der Pol oscillator and Liénard system. These significant results can be applied to any Van der Pol equation.
Data-driven discovery of Green’s functions with human-understandable deep learning
Authors: Boullé Nicolas , Earls Christopher J. , Townsend Alex 
Published: March 2022

AbstractThere is an opportunity for deep learning to revolutionize science and technology by revealing its findings in a human interpretable manner. To do this, we develop a novel data-driven approach for creating a human–machine partnership to accelerate scientific discovery. By collecting physical system responses under excitations drawn from a Gaussian process, we train rational neural networks to learn Green’s functions of hidden linear partial differential equations. These functions reveal human-understandable properties and features, such as linear conservation laws and symmetries, along with shock and singularity locations, boundary effects, and dominant modes. We illustrate the technique on several examples and capture a range of physics, including advection–diffusion, viscous shocks, and Stokes flow in a lid-driven cavity.
Rumen and lower gut microbiomes relationship with feed efficiency and production traits throughout the lactation of Holstein dairy cows
Authors: Monteiro Hugo F. , Zhou Ziyao , Gomes Marilia S. , Peixoto Phillip M. G. , Bonsaglia Erika C. R. , Canisso Igor F. , Weimer Bart C. , Lima Fabio S. 
Published: March 2022

AbstractFermentation of dietary nutrients in ruminants' gastrointestinal (GI) tract is an essential mechanism utilized to meet daily energy requirements. Especially in lactating dairy cows, the GI microbiome plays a pivotal role in the breakdown of indigestible plant polysaccharides and supply most AAs, fatty acids, and gluconeogenic precursors for milk synthesis. Although the contribution of the rumen microbiome to production efficiency in dairy cows has been widely researched over the years, variations throughout the lactation and the lower gut microbiome contribution to these traits remain poorly characterized. Therefore, we investigated throughout lactation the relationship between the rumen and lower gut microbiomes with production efficiency traits in Holstein cows. We found that the microbiome from both locations has temporal stability throughout lactation, yet factors such as feed intake levels played a significant role in shaping microbiome diversity. The composition of the rumen microbiome was dependent on feed intake. In contrast, the lower gut microbiome was less dependent on feed intake and associated with a potentially enhanced ability to digest dietary nutrients. Therefore, milk production traits may be more correlated with microorganisms present in the lower gut than previously expected. The current study's findings advance our understanding of the temporal relationship of the rumen and lower gut microbiomes by enabling a broader overview of the gut microbiome and production efficiency towards more sustainable livestock production.
Evidence for association of Vibrio echinoideorum with tissue necrosis on test of the green sea urchin Strongylocentrotus droebachiensis
Authors: Hira Jonathan , Stensvåg Klara 
Published: March 2022

Abstract“Sea urchin lesion syndrome” is known as sea urchin disease with the progressive development of necrotic epidermal tissue and loss of external organs, including appendages on the outer body surface. Recently, a novel strain, Vibrio echinoideorum has been isolated from the lesion of green sea urchin (Strongylocentrotus droebachiensis), an economically important mariculture species in Norway. V. echinoideorum has not been reported elsewhere in association with green sea urchin lesion syndrome. Therefore, in this study, an immersion based bacterial challenge experiment was performed to expose sea urchins (wounded and non-wounded) to V. echinoideorum, thereby mimicking a nearly natural host–pathogen interaction under controlled conditions. This infection experiment demonstrated that only the injured sea urchins developed the lesion to a significant degree when exposed to V. echinoideorum. Pure cultures of the employed bacterial strain were recovered from the infected animals and its identity was confirmed by the MALDI-TOF MS spectra profiling. Additionally, the hemolytic phenotype of V. echinoideorum substantiated its virulence potential towards the host, and this was also supported by the cytolytic effect on red spherule cells of sea urchin. Furthermore, the genome sequence of V. echinoideorum was assumed to encode potential virulence genes and were subjected to in silico comparison with the established virulence factors of Vibrio vulnificus and Vibrio tasmaniensis. This comparative virulence profile provided novel insights about virulence genes and their putative functions related to chemotaxis, adherence, invasion, evasion of the host immune system, and damage of host tissue and cells. Thus, it supports the pathogenicity of V. echinoideorum. In conclusion, the interaction of V. echinoideorum with injured sea urchin facilitates the development of lesion syndrome and therefore, revealing its potentiality as an opportunistic pathogen.
Time crystal dynamics in a weakly modulated stochastic time delayed system
Authors: Tiana-Alsina Jordi , Masoller Cristina 
Published: March 2022

AbstractTime crystal oscillations in interacting, periodically driven many-particle systems are highly regular oscillations that persist for long periods of time, are robust to perturbations, and whose frequency differs from the frequency of the driving signal. Making use of underlying similarities of spatially-extended systems and time-delayed systems (TDSs), we present an experimental demonstration of time-crystal-like behavior in a stochastic, weakly modulated TDS. We consider a semiconductor laser near threshold with delayed feedback, whose output intensity shows abrupt spikes at irregular times. When the laser current is driven with a small-amplitude periodic signal we show that the interaction of delayed feedback and modulation can generate long-range regularity in the timing of the spikes, which lock to the modulation and, despite the presence of noise, remain in phase over thousands of modulation cycles. With pulsed modulation we find harmonic and subharmonic locking, while with sinusoidal modulation, we find only subharmonic locking, which is a characteristic feature of time-crystal behavior.
Theophylline-encapsulated Nile Tilapia fish scale-based collagen nanoparticles effectively target the lungs of male Sprague–Dawley rats
Authors: Anwar Mohammed Moustapha , Shalaby Manal Aly , Saeed Hesham , Mostafa Haitham Mohammed , Hamouda Dalia Galal , Nounou Howaida 
Published: March 2022

AbstractNile Tilapia fish scale collagen has high biodegradability, excellent biocompatibility, and low antigenicity. We assessed both the encapsulation efficiency of theophylline into Nile Tilapia fish scale-based collagen nanoparticles and their stability as a pulmonary drug delivery system in male Sprague–Dawley rats. The present study has demonstrated the successful encapsulation of theophylline into the synthesised nanoparticles as shown by spectrophotometric analysis, light microscope, scanning electron microscope, transmission electron microscope, and dynamic light scattering. The antibacterial activity of the nanoparticles improves with increasing their concentrations. Intratracheal treatment of rats using theophylline-encapsulated nanoparticles reduced the levels of creatinine, alanine transaminase, and aspartate transaminase, compared to the control group. Nevertheless, nanoparticles combined with theophylline exhibited no effects on cholesterol and triglycerides levels. Histopathological examination revealed typical uniform and diffuse thickening of the alveolar walls with capillary oedema in treated rats. We concluded that the synthesised collagen nanoparticles appropriately target the lungs of male Sprague–Dawley rats when delivered via a nebuliser, showing good tolerability to lung cells. However, dose ratio of collagen nanoparticles to theophylline needs further evaluation. The nanoprecipitation method may be optimised to involve poorly water-soluble inhaled drugs, and avoid the drawbacks of traditional drug delivery.
Non-invasive tests for liver fibrosis assessment in patients with chronic liver diseases: a prospective study
Authors: Thanapirom Kessarin , Suksawatamnuay Sirinporn , Tanpowpong Natthaporn , Chaopathomkul Bundit , Sriphoosanaphan Supachaya , Thaimai Panarat , Srisoonthorn Nunthiya , Treeprasertsuk Sombat , Komolmit Piyawat 
Published: March 2022

AbstractThere is an urgent need of non-invasive tests (NITs) for monitoring treatment response and disease progression in chronic liver disease. Liver stiffness (LS) evaluated by transient elastography (TE), shear wave elastography (SWE), and magnetic resonance elastography (MRE) and serum markers e.g. APRI and FIB-4 scores were assessed at baseline and the 1-year follow-up. In all, 89 chronic hepatitis C virus (HCV) patients with sustained virological response and 93 non-alcoholic fatty liver disease (NAFLD) patients were included. There was a significantly strong correlation among imaging techniques. Using MRE as the reference standard, the area under the receiver operating characteristics curves for TE, SWE, APRI, and FIB-4 in detecting stage1–4 fibrosis were 0.88–0.95, 0.87–0.96, 0.83–0.89, and 0.79–0.92, respectively. In chronic HCV patients, the values of TE, SWE, MRE, APRI and FIB-4 significantly decreased from baseline to the 1-year follow-up. Liver steatosis did not significantly change over time. In NAFLD, compared to obese patients, non-obese patients had less LS and steatosis at baseline, and these values did not show significant changes at the 1-year follow-up. Our study suggests that the current NITs have a good correlation and accuracy in monitoring the treatment outcomes in patients with chronic liver diseases.
Unsupervised machine learning for identifying important visual features through bag-of-words using histopathology data from chronic kidney disease
Authors: Lee Joonsang , Warner Elisa , Shaikhouni Salma , Bitzer Markus , Kretzler Matthias , Gipson Debbie , Pennathur Subramaniam , Bellovich Keith , Bhat Zeenat , Gadegbeku Crystal , Massengill Susan , Perumal Kalyani , Saha Jharna , Yang Yingbao , Luo Jinghui , Zhang Xin , Mariani Laura , Hodgin Jeffrey B. , Rao Arvind ,   the C-PROBE Study
Published: March 2022

AbstractPathologists use visual classification to assess patient kidney biopsy samples when diagnosing the underlying cause of kidney disease. However, the assessment is qualitative, or semi-quantitative at best, and reproducibility is challenging. To discover previously unknown features which predict patient outcomes and overcome substantial interobserver variability, we developed an unsupervised bag-of-words model. Our study applied to the C-PROBE cohort of patients with chronic kidney disease (CKD). 107,471 histopathology images were obtained from 161 biopsy cores and identified important morphological features in biopsy tissue that are highly predictive of the presence of CKD both at the time of biopsy and in one year. To evaluate the performance of our model, we estimated the AUC and its 95% confidence interval. We show that this method is reliable and reproducible and can achieve 0.93 AUC at predicting glomerular filtration rate at the time of biopsy as well as predicting a loss of function at one year. Additionally, with this method, we ranked the identified morphological features according to their importance as diagnostic markers for chronic kidney disease. In this study, we have demonstrated the feasibility of using an unsupervised machine learning method without human input in order to predict the level of kidney function in CKD. The results from our study indicate that the visual dictionary, or visual image pattern, obtained from unsupervised machine learning can predict outcomes using machine-derived values that correspond to both known and unknown clinically relevant features.
Characteristic functional cores revealed by hyperbolic disc embedding and k-core percolation on resting-state fMRI
Authors: Whi Wonseok , Huh Youngmin , Ha Seunggyun , Lee Hyekyoung , Kang Hyejin , Lee Dong Soo 
Published: March 2022

AbstractHyperbolic disc embedding and k-core percolation reveal the hierarchical structure of functional connectivity on resting-state fMRI (rsfMRI). Using 180 normal adults’ rsfMRI data from the human connectome project database, we visualized inter-voxel relations by embedding voxels on the hyperbolic space using the $${\mathbb{S}}^{1} /{\mathbb{H}}^{2}$$

S

1

/

H

2

model. We also conducted k-core percolation on 30 participants to investigate core voxels for each individual. It recursively peels the layer off, and this procedure leaves voxels embedded in the center of the hyperbolic disc. We used independent components to classify core voxels, and it revealed stereotypes of individuals such as visual network dominant, default mode network dominant, and distributed patterns. Characteristic core structures of resting-state brain connectivity of normal subjects disclosed the distributed or asymmetric contribution of voxels to the kmax-core, which suggests the hierarchical dominance of certain IC subnetworks characteristic of subgroups of individuals at rest.
Interferon-γ signal drives differentiation of T-bethi atypical memory B cells into plasma cells following Plasmodium vivax infection
Authors: Kochayoo Piyawan , Thawornpan Pongsakorn , Wangriatisak Kittikorn , Changrob Siriruk , Leepiyasakulchai Chaniya , Khowawisetsut Ladawan , Adams John H. , Chootong Patchanee 
Published: March 2022

AbstractFor development of a long-lasting protective malaria vaccine, it is crucial to understand whether Plasmodium-induced memory B cells (MBCs) or plasma cells develop and stably contribute to protective immunity, or on the contrary the parasite suppresses antibody responses by inducing MBC dysfunction. The expansion of T-bethi atypical MBCs is described in chronic Plasmodium falciparum-exposed individuals. However, it remains unclear whether accumulation of T-bethi atypical MBCs is indicative of a protective role or rather an impaired function of the immune system in malaria. Here, the phenotypic and functional features of T-bethi atypical MBCs were studied in P. vivax patients living in an area of low malaria transmission. During P. vivax infection, the patients produced a twofold higher frequency of T-bethi atypical MBCs compared to malaria non-exposed individuals. This distinct atypical MBC subset had a switched IgG phenotype with overexpression of activation markers and FcRL5, and decreased Syk phosphorylation upon BCR stimulation. Post-infection, expansion of T-bethi IgG+ atypical MBCs was maintained for at least 3 months. Further studies of the contribution of T-bethi atypical MBC function to humoral immunity showed that synergizing IFN-γ with TLR7/8 and IL-21 signals was required for their differentiation into plasma cells and antibody secretion.