bluuebunny/crossref_metadata_2025_split huggingface dataset:
EGFR core fucosylation, induced by hepatitis C virus, promotes TRIM40-mediated-RIG-I ubiquitination and suppresses interferon-I antiviral defenses
Authors: Pan Qiu , Xie Yan , Zhang Ying , Guo Xinqi , Wang Jing , Liu Min , Zhang Xiao-Lian 
Published: January 2024

AbstractAberrant N-glycosylation has been implicated in viral diseases. Alpha-(1,6)-fucosyltransferase (FUT8) is the sole enzyme responsible for core fucosylation of N-glycans during glycoprotein biosynthesis. Here we find that multiple viral envelope proteins, including Hepatitis C Virus (HCV)-E2, Vesicular stomatitis virus (VSV)-G, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-Spike and human immunodeficiency virus (HIV)-gp120, enhance FUT8 expression and core fucosylation. HCV-E2 manipulates host transcription factor SNAIL to induce FUT8 expression through EGFR-AKT-SNAIL activation. The aberrant increased-FUT8 expression promotes TRIM40-mediated RIG-I K48-ubiquitination and suppresses the antiviral interferon (IFN)-I response through core fucosylated-EGFR-JAK1-STAT3-RIG-I signaling. FUT8 inhibitor 2FF, N-glycosylation site-specific mutation (Q352AT) of EGFR, and tissue-targeted Fut8 silencing significantly increase antiviral IFN-I responses and suppress RNA viral replication, suggesting that core fucosylation mediated by FUT8 is critical for antiviral innate immunity. These findings reveal an immune evasion mechanism in which virus-induced FUT8 suppresses endogenous RIG-I-mediated antiviral defenses by enhancing core fucosylated EGFR-mediated activation.
Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages
Authors: Barcia-Cruz Rubén , Goudenège David , Moura de Sousa Jorge A. , Piel Damien , Marbouty Martial , Rocha Eduardo P. C. , Le Roux Frédérique 
Published: January 2024

AbstractPhage satellites are bacterial genetic elements that co-opt phage machinery for their own dissemination. Here we identify a family of satellites, named Phage-Inducible Chromosomal Minimalist Islands (PICMIs), that are broadly distributed in marine bacteria of the family Vibrionaceae. A typical PICMI is characterized by reduced gene content, does not encode genes for capsid remodelling, and packages its DNA as a concatemer. PICMIs integrate in the bacterial host genome next to the fis regulator, and encode three core proteins necessary for excision and replication. PICMIs are dependent on virulent phage particles to spread to other bacteria, and protect their hosts from other competitive phages without interfering with their helper phage. Thus, our work broadens our understanding of phage satellites and narrows down the minimal number of functions necessary to hijack a tailed phage.
False vacuum decay via bubble formation in ferromagnetic superfluids
Authors: Zenesini A. , Berti A. , Cominotti R. , Rogora C. , Moss I. G. , Billam T. P. , Carusotto I. , Lamporesi G. , Recati A. , Ferrari G. 
Published: January 2024

AbstractMetastability stems from the finite lifetime of a state when a lower-energy configuration is available but only by tunnelling through an energy barrier. It is observed in many natural situations, including in chemical processes and in electron field ionization. In classical many-body systems, metastability naturally emerges in the presence of a first-order phase transition. A prototypical example is a supercooled vapour. The extension to quantum field theory and quantum many-body systems has attracted significant interest in the context of statistical physics, protein folding and cosmology, for which thermal and quantum fluctuations are expected to trigger the transition from the metastable state (false vacuum) to the ground state (true vacuum) through the probabilistic nucleation of spatially localized bubbles. However, the long-standing theoretical progress in estimating the relaxation rate of the metastable field through bubble nucleation has not been validated experimentally. Here we experimentally observe bubble nucleation in isolated and coherently coupled atomic superfluids, and we support our observations with numerical simulations. The agreement between our observations and an analytic formula based on instanton theory confirms our physical understanding of the decay process and promotes coherently coupled atomic superfluids as an ideal platform to investigate out-of-equilibrium quantum field phenomena.
Deciphering cell states and genealogies of human haematopoiesis
Authors: Weng Chen , Yu Fulong , Yang Dian , Poeschla Michael , Liggett L. Alexander , Jones Matthew G. , Qiu Xiaojie , Wahlster Lara , Caulier Alexis , Hussmann Jeffrey A. , Schnell Alexandra , Yost Kathryn E. , Koblan Luke W. , Martin-Rufino Jorge D. , Min Joseph , Hammond Alessandro , Ssozi Daniel , Bueno Raphael , Mallidi Hari , Kreso Antonia , Escabi Javier , Rideout William M. , Jacks Tyler , Hormoz Sahand , van Galen Peter , Weissman Jonathan S. , Sankaran Vijay G. 
Published: January 2024

AbstractThe human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived haematopoietic stem cells (HSCs)1. Perturbations to this process underlie diverse diseases, but the clonal contributions to human haematopoiesis and how this changes with age remain incompletely understood. Although recent insights have emerged from barcoding studies in model systems2–5, simultaneous detection of cell states and phylogenies from natural barcodes in humans remains challenging. Here we introduce an improved, single-cell lineage-tracing system based on deep detection of naturally occurring mitochondrial DNA mutations with simultaneous readout of transcriptional states and chromatin accessibility. We use this system to define the clonal architecture of HSCs and map the physiological state and output of clones. We uncover functional heterogeneity in HSC clones, which is stable over months and manifests as both differences in total HSC output and biases towards the production of different mature cell types. We also find that the diversity of HSC clones decreases markedly with age, leading to an oligoclonal structure with multiple distinct clonal expansions. Our study thus provides a clonally resolved and cell-state-aware atlas of human haematopoiesis at single-cell resolution, showing an unappreciated functional diversity of human HSC clones and, more broadly, paving the way for refined studies of clonal dynamics across a range of tissues in human health and disease.
Effects of eccentric loading on performance of concrete columns reinforced with glass fiber-reinforced polymer bars
Authors: Shakouri Mahmoudabadi Nasim , Bahrami Alireza , Saghir Saba , Ahmad Afaq , Iqbal Muhammad , Elchalakani Mohamed , Özkılıç Yasin Onuralp 
Published: January 2024

AbstractGlass fiber-reinforced polymer (GFRP) reinforcements are superior to traditional steel bars in concrete structures, particularly in vertical elements like columns, and offer significant advantages over conventional steel bars when subjected to axial and eccentric loadings. However, there is limited experimental and numerical research on the behavior of GFRP-reinforced concrete (RC) columns under eccentric loading having different spacing of stirrups. In this study, six specimens were cast under three different values of eccentricities (25 mm, 50 mm, and 75 mm) with two groups of stirrups spacing (50 mm and 100 mm). The experimental results showed that by increasing the eccentricity value, there was a reduction in the load-carrying capacity of the specimens. The finite element ABAQUS software was used for the numerical investigation of this study. The results from the finite element analysis (FEA) were close to the experimental results and within the acceptable range. The maximum difference between the experimental and FEA results was 3.61% for the axial load and 12.06% for the deformation.
Expression levels and clinical significance of ferroptosis-related genes in patients with myocardial infarction
Authors: Huang Lei , Wang Xiaoyang , Hu Bin , Rong Shuling 
Published: January 2024

AbstractMyocardial infarction (MI) is the most serious type of cardiovascular disease and the leading cause of cardiac death.Ferroptosis is one of the newly discovered programmed cell death modes in MI, but its mechanism of action in MI has not been clarified.In this study, we analyzed the expression changes of ferroptosis-related genes in MI and explored the potential mechanisms of ferroptosis-related functions in myocardial infarction. Public data sets GSE19339, GSE97320 and GSE141512 were retrieved from the Gene Expression Omnibus (GEO) Datasets public database. After data preprocessing, differentially expressed genes were screened, and differentially expressed ferroptosis-related genes associated with myocardial infarction were obtained. The biological function and signaling pathway enrichment analysis were performed to establish the PPI interaction network specific to heart tissue, and the differential diagnosis significance of differentially expressed ferroptosis-related genes associated with myocardial infarction was analyzed by ROC curve and decision tree model.A total of 317 genes showed significant changes in expression levels in patients with myocardial infarction, including 205 down-regulated genes and 112 up-regulated genes.Gene Ontology (GO) enrichment analysis and functional classification of Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways showed that these genes were mainly involved in signaling pathways or biological functions related to inflammation and apoptosis.Five differentially expressed ferroptosis-related genes (SLC2A3, EPAS1, HMOX1, ATM, FANCD2) were obtained, all of which played key biological functions in cardiac tissue function. SLC2A3, EPAS1, HMOX1, ATM and FANCD2 genes all had good diagnostic value for myocardial infarction (P < 0.05). The increase of SLC2A3, EPAS1 and HMOX1 are risk factors for myocardial infarction, while ATM and FANCD2 are protective factors.Decision tree analysis showed that SLC2A3, HMOX1, ATM, FANCD2 gene had higher net yield in diagnosing myocardial infarction. In summary, the mechanism of ferroptosis is involved in the occurrence and progression of myocardial infarction. In this study, five differentially expressed ferroptosis-related genes associated with myocardial infarction were retrieved, which may be good biomarkers of ferroptosis after MI.These findings also suggest that the differential expression of ferroptosis-related genes associated with myocardial infarction has significant diagnostic significance for myocardial infarction.
Impacts of sugarcane industrial effluent as an alternate source of irrigation on growth, chlorophyll contents and antioxidants of different canola varieties
Authors: Ullah Hafeez , Elahi Nosheen Noor , Imtiaz Muhammad , Shah Muhammad Nadeem , Asiri Mohammed , Alshahrani Mohammad Y. 
Published: January 2024

AbstractThe sugarcane industry often utilizes effluent for irrigation purposes; however, its intricate composition and elevated metal contaminants pose a potential risk of soil and crop contamination. Consequently, it is imperative to employ effective strategies to ensure the safe utilization of this resource for crop cultivation. One such strategy involves the dilution of sugarcane industry effluent. Dilution is a practical approach to mitigate its toxicity, minimizing its adverse impact on soil and crop health. That’s why the current study explored the best dilution of sugarcane industrial effluent (SW) for cultivating canola varieties. A total of 15 canola varieties were cultivated 0%, 20%, 40%, 60%, 80%, and 100% SW. Results showed that 60% SW Faisalabad Canola and Punjab Canola improved germination, shoot length, root length, shoot fresh and dry weight, root fresh and dry weight, and chlorophyll contents compared to other treatments and control. AARI Canola and CON-III showed poor growth and chlorophyll contents under 60%SW. Dunkled and Oscar cultivars showed moderate improvement in growth and chlorophyll contents under 60SW. The 60% SW can be recommended for maximum growth benefits in canola cultivars, specifically Faisalabad Canola and Punjab Canola. At 20SW, the root dry weight of Faisalabad Canola increased by 2.7%, while Punjab Canola increased by 3.4%. Canola showed the highest increase in POD activity compared to the control, with a 55.45% increase, followed by Sandal Canola, with a 43.26% increase. However, additional field-level experiments are needed to determine the best cultivars suitable for optimal growth under 80SW and 60SW irrigation conditions.
Hypothyroidism and hyperthyroidism related to gynecologic cancers: a nationwide population-based cohort study
Authors: Leung John Hang , Wang Shyh-Yau , Leung Henry W. C. , Yu Teng-Shun , Chan Agnes L. F. 
Published: January 2024

AbstractThe purpose of this study was to assess the risks of hyperthyroidism and hypothyroidism related to gynecological cancers. Population-based retrospective cohort study. We conducted a cohort study using the Taiwan National Health Insurance Research Database to explore hyperthyroidism and hypothyroidism associated with site-specific gynecologic cancers in women from January 1, 2000 to December 31, 2018. The examined gynecologic cancers included endometrial (EC), uterine corpus cancer (UC), and ovarian cancer (OC). The incidence and hazard ratios were quantified using Cox proportional hazards models. The incidence of developing gynecological (Gyn) cancers in the hyperthyroid and hypothyroid women was 0.29 and 0.44 per 1000 person-years, which was 0.86 fold lower and 1.13 fold higher than that in the comparison cohort (p < 0.001). Compared with patients aged 20–40 years, patients in older age groups had a lower and higher risk of developing Gyn cancers (for hyperthyroid, 40–65 years: adjusted hazard ratio (aHR) = 0.82; > 65 years: aHR = 0.94; for hypothyroid, adjusted hazard ratio (aHR) = 1.26; > 65 years: aHR = 1.38). Compared with the non-hypothyroid women and non-hyperthyroid women beyond 6 years of follow-up, hypothyroid and hyperthyroid women showed decreased risk of Gyn cancers. Medication treatment for hyperthyroid and hypothyroid disease did not showed significant association in subgroup analyses (aHR = 0.99 and 0.80, respectively). Our results show that women with hyperthyroidism have a significantly reduced risk of gynecological cancers, whereas women with hypothyroidism have a slightly increased risk of gynecological cancers suggesting an association between thyroid function level and risk of gynecological cancers.
The effect of dopaminergic treatment on whole body kinematics explored through network theory
Authors: Romano Antonella , Liparoti Marianna , Minino Roberta , Polverino Arianna , Cipriano Lorenzo , Carotenuto Anna , Tafuri Domenico , Sorrentino Giuseppe , Sorrentino Pierpaolo , Troisi Lopez Emahnuel 
Published: January 2024

AbstractThree-dimensional motion analysis represents a quantitative approach to assess spatio-temporal and kinematic changes in health and disease. However, these parameters provide only segmental information, discarding minor changes of complex whole body kinematics characterizing physiological and/or pathological conditions. We aimed to assess how levodopa intake affects the whole body, analyzing the kinematic interactions during gait in Parkinson’s disease (PD) through network theory which assess the relationships between elements of a system. To this end, we analysed gait data of 23 people with PD applying network theory to the acceleration kinematic data of 21 markers placed on participants’ body landmarks. We obtained a matrix of kinematic interactions (i.e., the kinectome) for each participant, before and after the levodopa intake, we performed a topological analysis to evaluate the large-scale interactions among body elements, and a multilinear regression analysis to verify whether the kinectome’s topology could predict the clinical variations induced by levodopa. We found that, following levodopa intake, patients with PD showed less trunk and head synchronization (p-head = 0.048;p-7th cervical vertebrae = 0.032;p-10th thoracic vertebrae = 0.006) and an improved upper-lower limbs synchronization (elbows right,p = 0.002; left,p = 0.005), (wrists right,p = 0.003; left,p = 0.002; knees right,p = 0.003; left,p = 0.039) proportional to the UPDRS-III scores. These results may be attributable to the reduction of rigidity, following pharmacological treatment.
Deep learning based CETSA feature prediction cross multiple cell lines with latent space representation
Authors: Zhao Shenghao , Yang Xulei , Zeng Zeng , Qian Peisheng , Zhao Ziyuan , Dai Lingyun , Prabhu Nayana , Nordlund Pär , Tam Wai Leong 
Published: January 2024

AbstractMass spectrometry-coupled cellular thermal shift assay (MS-CETSA), a biophysical principle-based technique that measures the thermal stability of proteins at the proteome level inside the cell, has contributed significantly to the understanding of drug mechanisms of action and the dissection of protein interaction dynamics in different cellular states. One of the barriers to the wide applications of MS-CETSA is that MS-CETSA experiments must be performed on the specific cell lines of interest, which is typically time-consuming and costly in terms of labeling reagents and mass spectrometry time. In this study, we aim to predict CETSA features in various cell lines by introducing a computational framework called CycleDNN based on deep neural network technology. For a given set of n cell lines, CycleDNN comprises n auto-encoders. Each auto-encoder includes an encoder to convert CETSA features from one cell line into latent features in a latent space $$\mathbb {Z}$$
Z
. It also features a decoder that transforms the latent features back into CETSA features for another cell line. In such a way, the proposed CycleDNN creates a cyclic prediction of CETSA features across different cell lines. The prediction loss, cycle-consistency loss, and latent space regularization loss are used to guide the model training. Experimental results on a public CETSA dataset demonstrate the effectiveness of our proposed approach. Furthermore, we confirm the validity of the predicted MS-CETSA data from our proposed CycleDNN through validation in protein–protein interaction prediction.
Species-specific SNP arrays for non-invasive genetic monitoring of a vulnerable bat
Authors: Thavornkanlapachai Rujiporn , Armstrong Kyle N. , Knuckey Chris , Huntley Bart , Hanrahan Nicola , Ottewell Kym 
Published: January 2024

AbstractGenetic tagging from scats is one of the minimally invasive sampling (MIS) monitoring approaches commonly used to guide management decisions and evaluate conservation efforts. Microsatellite markers have traditionally been used but are prone to genotyping errors. Here, we present a novel method for individual identification in the Threatened ghost bat Macroderma gigas using custom-designed Single Nucleotide Polymorphism (SNP) arrays on the MassARRAY system. We identified 611 informative SNPs from DArTseq data from which three SNP panels (44–50 SNPs per panel) were designed. We applied SNP genotyping and molecular sexing to 209 M. gigas scats collected from seven caves in the Pilbara, Western Australia, employing a two-step genotyping protocol and identifying unique genotypes using a custom-made R package, ScatMatch. Following data cleaning, the average amplification rate was 0.90 ± 0.01 and SNP genotyping errors were low (allelic dropout 0.003 ± 0.000) allowing clustering of scats based on one or fewer allelic mismatches. We identified 19 unique bats (9 confirmed/likely males and 10 confirmed/likely females) from a maternity and multiple transitory roosts, with two male bats detected using roosts, 9 km and 47 m apart. The accuracy of our SNP panels enabled a high level of confidence in the identification of individual bats. Targeted SNP genotyping is a valuable tool for monitoring and tracking of non-model species through a minimally invasive sampling approach.
Comparative assessment of phenolic composition profile and biological activities of green extract and conventional extracts of Salvia sclarea
Authors: Quradha Mohammed Mansour , Duru Mehmet Emin , Kucukaydin Selcuk , Tamfu Alfred Ngenge , Iqbal Mudassar , Bibi Hamida , Khan Rasool , Ceylan Ozgur 
Published: January 2024

AbstractIn recent years, there have been an attempt to develop safe and environmental friendly solvents to replace conventional solvents, and use for extraction bioactive compounds from natural sources. A current investigation involved the preparation of green, methanolic, and ultrasonic extracts of S. sclarea, and compared their phenolic profiling using HPLC–DAD, antibacterial, antioxidant, and enzyme inhibition activities. The HPLC–DAD analysis revealed that Rosmarinic acid was the main content in all extracts, with Ellagic acid only present in the green extract. The green extract exhibited superior anti-biofilm activity against S. Aureus and E. Faecalis compared to the other extracts at MIC concentration. Furthermore, the green extract also displayed the highest inhibition of swarming motility in P. Aeruginosa with inhibition range 68.0 ± 2.1 (MIC) to 19.5 ± 0.6 (MIC/4). and better enzyme inhibitory activity against BChE (with IC50 = 131.6 ± 0.98 µg/mL) and AChE (with inhibition 47.00 ± 1.50%) compared to the other extracts; while, the ultrasonic extract showed strong inhibition of violacein production by C. Violaceum with a inhibition range 05.5 ± 0.1 (MIC/32) to 100 ± 0.00 (MIC), followed by the green extract with a inhibition range 15.0 ± 0.5 (MIC/8) to 100 ± 0.00 (MIC), additionally, the ultrasonic and methanoic extracts showed significant activity against urease enzyme with (IC50 = 171.6 ± 0.95 µg/mL and IC5 0 = 187.5 ± 1.32 µg/mL) respectively. Both the green and methanolic extracts showed considerable antioxidant activities, as β-carotene-linoleic acid (IC50 = 5.61 ± 0.47 µg/mL and 5.37 ± 0.27 µg/mL), DPPH· (IC50 = 19.20 ± 0.70 µg/mL and 16.31 ± 0.23 µg/mL), ABTS·+(IC50 = 8.64 ± 0.63 µg/mL and 6.50 ± 0.45 µg/mL) and CUPRAC (A0.5 = 17.22 ± 0.36 µg/mL and 12.28 ± 0.12 µg/mL) respectively, likewise the green extract performing better in metal chelating compared to the other extracts. The green extraction is reported as a cost effective and solvent free method for extracting natural products that produces compounds free of toxic chemicals. This could be the method to be used in the industries as a renewable method.
A novel approach for estimating fertility rates in finite populations using count regression models
Authors: Ahmed Shakeel , Albalawi Olayan , Shabbir Javid 
Published: January 2024

AbstractDemographic health surveys (DHS) contain in-depth information about the demographic characteristics and the factors affecting them. However, fertility rates which are the important indicators of population growth have been estimated by utilizing the design-based approaches. Model-based approach, on the other hand, facilitates efficient predictive estimates for these rates by utilizing the demographic and other family planning related characters. In this article, we first attempt to observe the effect of various socio-demographic and family planing related factors on births counts by fitting different regression models to Pakistan Demographic Health Survey 2017–2018 data under classical as well as Bayesian frameworks. The births occurred during the time periods of 1-year, 3-years and 5-years are taken as the responses and modeled using different non-linear models. The model-based approach is then used for estimation of the fertility measures including age-specific fertility rates, total fertility rate, general fertility rate, and gross reproduction rate for ever-married women in Pakistan. The performance of the model-based estimators is examined using a bootstrapped sampling algorithm. While the age-specific fertility rates are over-estimated for some age groups and under-estimated for others. The model-based fertility estimates are recommended for estimating the demographic indicators at national and sub-national levels when survey data contains incomplete or missing responses.