bluuebunny/crossref_metadata_2025 huggingface dataset:
A Preliminary Inquiry Into the Potential Mechanism of Huang-Lian-Jie-Du Decoction in Treating Rheumatoid Arthritis via Network Pharmacology and Molecular Docking
Authors: Li Chenlu , Pan Jingjing , Xu Chang , Jin Zhenlin , Chen Xupeng
Published: January 2022

Huang-Lian-Jie-Du decoction (HLJDD) has been widely applied to treat inflammation-associated diseases for thousands of years in China. However, the concrete molecular mechanism of HLJDD in the treatment of rheumatoid arthritis (RA) remains unclear. In this work, network pharmacology and molecular docking were applied to preliminarily analyze the potential active ingredients, drug targets, and related pathways of HLJDD on treating RA. A total of 102 active compounds with corresponding 189 targets were identified from HLJDD, and 41 common targets were further identified by intersecting with RA-related targets. Functional enrichment analysis was performed to screen the biological pathways associated with RA. Ten hub targets were further identified through constructing the protein–protein interaction (PPI) network of common targets, which were mainly enriched in the interleukin-17 (IL-17) signaling pathway, tumor necrosis factor (TNF) signaling pathway, and Toll-like receptor signaling pathway. Furthermore, a complex botanical drugs-ingredients-hub-targets-disease network was successfully constructed. The molecular docking results exhibited that these vital ingredients of HLJDD had a stable binding to the hub targets. Among these ingredients, quercetin (MOL000098) was the most common molecule with stable binding to all the targets, and PTGS2 was considered the most important target with multiple regulations by the most active ingredients. In vitro, we successfully validated the inhibitory role of quercetin in the cellular proliferation of human RA fibroblast-like synoviocyte cell line (MH7A cells). These findings indicated that the potential mechanisms of HLJDD for RA treatment might be attributed to inhibiting the immune-inflammatory response, reducing the release of chemokines, and alleviating the destruction of extracellular matrix (ECM) in the synovial compartment.
CEP250 is Required for Maintaining Centrosome Cohesion in the Germline and Fertility in Male Mice
Authors: Floriot Sandrine , Bellutti Laura , Castille Johan , Moison Pauline , Messiaen Sébastien , Passet Bruno , Boulanger Laurent , Boukadiri Abdelhak , Tourpin Sophie , Beauvallet Christian , Vilotte Marthe , Riviere Julie , Péchoux Christine , Bertaud Maud , Vilotte Jean-Luc , Livera Gabriel
Published: January 2022

Male gametogenesis involves both mitotic divisions to amplify germ cell progenitors that gradually differentiate and meiotic divisions. Centrosomal regulation is essential for both types of divisions, with centrioles remaining tightly paired during the interphase. Here, we generated and characterized the phenotype of mutant mice devoid of Cep250/C-Nap1, a gene encoding for a docking protein for fibers linking centrioles, and characterized their phenotype. The Cep250-/- mice presented with no major defects, apart from male infertility due to a reduction in the spermatogonial pool and the meiotic blockade. Spermatogonial stem cells expressing Zbtb16 were not affected, whereas the differentiating spermatogonia were vastly lost. These cells displayed abnormal γH2AX-staining, accompanied by an increase in the apoptotic rate. The few germ cells that survived at this stage, entered the meiotic prophase I and were arrested at a pachytene-like stage, likely due to synapsis defects and the unrepaired DNA double-strand breaks. In these cells, centrosomes split up precociously, with γ-tubulin foci being separated whereas these were closely associated in wild-type cells. Interestingly, this lack of cohesion was also observed in wild-type female meiocytes, likely explaining the normal fertility of Cep250-/- female mice. Taken together, this study proposes a specific requirement of centrosome cohesion in the male germline, with a crucial role of CEP250 in both differentiating spermatogonia and meiotic spermatocytes.
p53-Induced LINC00893 Regulates RBFOX2 Stability to Suppress Gastric Cancer Progression
Authors: Ou Xinde , Zhou Xingyu , Li Jin , Ye Jinning , Liu Haohan , Fang Deliang , Cai Qinbo , Cai Shirong , He Yulong , Xu Jianbo
Published: January 2022

Long noncoding RNAs (lncRNAs) have been reported to regulate diverse tumorigenic processes. However, little is known about long intergenic non-protein coding RNA 00893 (LINC00893) and its role in gastric cancer (GC). Herein we investigated its biological functions and molecular mechanism in GC. LINC00893 was decreased in GC tissues but significantly elevated in AGS cells after treatment with Nutlin-3. In GC patients, it was found that low expression of LINC00893 was correlated with tumor growth, metastasis and poor survival. Functionally, overexpression of LINC00893 suppressed the proliferation, migration and invasion of GC cells. Mechanistically, LINC00893 regulated the expression of epithelial-mesenchymal transition (EMT)-related proteins by binding to RNA binding fox-1 homolog 2 (RBFOX2) and promoting its ubiquitin-mediated degradation, thus suppressing the EMT and related functions of GC. In addition, the transcription factor p53 can regulate the expression of LINC00893 in an indirect way. Taken together, these results suggested that LINC00893 regulated by p53 repressed GC proliferation, migration and invasion by functioning as a binding site for RBFOX2 to regulate its stability and the expression of EMT-related proteins. LINC00893 acts as a tumor-inhibiting lncRNA that is induced by p53 in GC and regulates EMT by binding to RBFOX2, thus providing a novel experimental basis for the clinical treatment of GC.
RNAi Screen of RING/U-Box Domain Ubiquitin Ligases Identifies Critical Regulators of Tissue Regeneration in Planarians
Authors: Allen John M. , Balagtas Madison , Barajas Elizabeth , Cano Macip Carolina , Alvarez Zepeda Sarai , Iberkleid Ionit , Duncan Elizabeth M. , Zayas Ricardo M.
Published: January 2022

Regenerative processes depend on the interpretation of signals to coordinate cell behaviors. The role of ubiquitin-mediated signaling is known to be important in many cellular and biological contexts, but its role in regeneration is not well understood. To investigate how ubiquitylation impacts tissue regeneration in vivo, we are studying planarians that are capable of regenerating after nearly any injury using a population of stem cells. Here we used RNAi to screen RING/U-box E3 ubiquitin ligases that are highly expressed in planarian stem cells and stem cell progeny. RNAi screening identified nine genes with functions in regeneration, including the spliceosomal factor prpf19 and histone modifier rnf2; based on their known roles in developmental processes, we further investigated these two genes. We found that prpf19 was required for animal survival but not for stem cell maintenance, suggesting a role in promoting cell differentiation. Because RNF2 is the catalytic subunit of the Polycomb Repressive Complex 1 (PRC1), we also examined other putative members of this complex (CBX and PHC). We observed a striking phenotype of regional tissue misspecification in cbx and phc RNAi planarians. To identify genes regulated by PRC1, we performed RNA-seq after knocking down rnf2 or phc. Although these proteins are predicted to function in the same complex, we found that the set of genes differentially expressed in rnf2 versus phc RNAi were largely non-overlapping. Using in situ hybridization, we showed that rnf2 regulates gene expression levels within a tissue type, whereas phc is necessary for the spatial restriction of gene expression, findings consistent with their respective in vivo phenotypes. This work not only uncovered roles for RING/U-box E3 ligases in stem cell regulation and regeneration, but also identified differential gene targets for two putative PRC1 factors required for maintaining cell-type-specific gene expression in planarians.
Nature-Derived and Synthetic Additives to poly(ɛ-Caprolactone) Nanofibrous Systems for Biomedicine; an Updated Overview
Authors: Homaeigohar Shahin , Boccaccini Aldo R.
Published: January 2022

As a low cost, biocompatible, and bioresorbable synthetic polymer, poly (ɛ-caprolactone) (PCL) is widely used for different biomedical applications including drug delivery, wound dressing, and tissue engineering. An extensive range of in vitro and in vivo tests has proven the favourable applicability of PCL in biomedicine, bringing about the FDA approval for a plethora of PCL made medical or drug delivery systems. This popular polymer, widely researched since the 1970s, can be readily processed through various techniques such as 3D printing and electrospinning to create biomimetic and customized medical products. However, low mechanical strength, insufficient number of cellular recognition sites, poor bioactivity, and hydrophobicity are main shortcomings of PCL limiting its broader use for biomedical applications. To maintain and benefit from the high potential of PCL, yet addressing its physicochemical and biological challenges, blending with nature-derived (bio)polymers and incorporation of nanofillers have been extensively investigated. Here, we discuss novel additives that have been meant for enhancement of PCL nanofiber properties and thus for further extension of the PCL nanofiber application domain. The most recent researches (since 2017) have been covered and an updated overview about hybrid PCL nanofibers is presented with focus on those including nature-derived additives, e.g., polysaccharides and proteins, and synthetic additives, e.g., inorganic and carbon nanomaterials.
Evidence of Fire Use by Homo erectus pekinensis: An XRD Study of Archaeological Bones From Zhoukoudian Locality 1, China
Authors: Huang Chao , Li Jingshu , Gao Xing
Published: January 2022

Zhoukoudian Locality 1 is well known both for the discovery of Homo erectus fossils and for the presence of early evidence of controlled use of fire by hominins; However, the nature of the latter had been seriously questioned since mid-1980s. To obtain substantial evidence of fire use by hominins, we combine macroscopic observations and XRD analysis on 23 fossil bones from new excavations in Layers 4 and 5. The crystalline index shows that at least 15 fossil bones were heated above 600°C, and this is partly consistent with macroscopic observations. The high intensity burning of bones may indicate strong evidence of hominin-controlled use of fire at Layer 4. Future work should focus on archaeological materials from lower layers to improve our understanding of the nature of colored bones and gain more solid evidence of fire use by early humans at Zhoukoudian.
Investigating the Role of Earthquakes on the Stability of Dangerous Rock Masses and Rockfall Dynamics
Authors: Zheng Lu , Wu Yihan , Zhu Zhiyuan , Ren Kaihui , Wei Qi , Wu Wei , Zhang Hong
Published: January 2022

In recent years, earthquake rockfalls have occurred frequently all over the world, resulting in heavy casualties and property losses. Unfortunately, research on rockfall dynamics upon earthquake events is still rare due to limited field and experimental data, and restricted to numerical simulations of only two dimensions. In order to primarily reveal the role of earthquakes on rockfall, this study focused on the stability of rock blocks on an inclined slope, and following rockfall dynamics by three-dimensional discontinuous deformation analysis (3-D DDA). First, earthquake input methods were discussed and implemented for the triangulated regular network (TRN) in 3-D DDA. The effectiveness was verified by comparison with analytical solution results of a single block on the inclined slope under seismic loads. Further, by discussing the variations of the boundary chart of failure modes, it indicated that the block was more prone to slide even with a large friction angle, became instability under seismic conditions. Moreover, a regular dodecahedron rock block was released on a stochastic roughness slope with two platforms through parallel realizations. The indices of the movement characteristics of the block, such as runout distance, lateral displacement range, and resting position, were investigated. The results showed that the maximum runout distance was not sensitive to seismic load, but the lateral displacement range was significantly sensitive to seismic load and increased appreciably. Through the 3D-DDA numerical simulations, both rock stability and rockfall behaviors under earthquake conditions could be better understood. Furthermore, it will be helpful to by analyzing trajectories and kinetic energies predict earthquake rockfall disasters and design reasonable protective countermeasures under earthquake scenarios.
Numerical Simulation Study of the Upper Aquifer Impact on the Coalbed Methane Production
Authors: Ping Yue , Simin Qu , Yafei Zhang , Jiawei Tu , Wei Ning , Jing Duan
Published: January 2022

The coalbed methane (CBM) resources in the Qinshui Basin are abundant with exceptional production potential. Coalbed methane wells usually need to be hydraulically fractured to build economical production. However, the exploration and production experiences have shown that the penetration distances of hydraulic fractures in the vertical direction of coal seams are uncertain, which may lead to fracture communication of the layers above and beneath aquifer layers, resulting in divergent production dynamics among coalbed methane producers. It has been observed that some of the CBM wells in Block M produced significantly more water than other wells in the surrounding area. It is suspected that the hydraulic fracturing among these producers may have communicated to the sandstone aquifers. To address the above challenge, this study investigated the geological characteristics of the aforementioned aquifer and coalbed layers, established a three-dimensional geological model, applied numerical simulation to quantify the influence of the aquifer on the production of the CBM wells, and developed a method to improve the history matching of CBM production simulation with the influence of the aquifer considered. This method has significantly improved the accuracy of the history matching performance and the reliability of the remaining gas study. The results from this study laid the foundation for the subsequent development strategy optimization.
An Investigation of the Kinetic Modeling and Ignition Delay Time of Methanol—Syngas Fuel
Authors: Chen Yexin , Jiang Yankun , Wen Xin , Liu Huimeng
Published: January 2022

The recycling of exhaust heat in internal combustion engines to dissociate the methanol, followed by its blending with methanol to produce engine fuel, is promising for improving the efficiency of engines, and reducing emissions. The kinetic model MEOHSYNGAS1.0 for the methanol–syngas fuel is proposed by reducing the detailed chemical kinetic model (Mech15.34). Shock tube experiments are conducted to measure the ignition delay time of methanol blended with dissociated methanol gas at different dissociated methanol ratios (0, 30, 50, and 100%). The model is validated by the experimental data of the present work and with data from the literature. The effects of the equivalence ratio, pressure, and dissociated methanol ratio on the ignition delay time are investigated through reaction path analysis and sensitivity analysis. When the dissociated methanol ratio does not surpass 50%, the ignition delay time increases with the increase in the dissociated methanol ratio, which is more obvious in the low temperature range, and but decreases with the increase in temperature.
Actively Participating in University-Sponsored Ecological Research Increases High School Students’ Knowledge of and Attitudes About Science
Authors: Rollwagen-Bollens Gretchen , Holmlund Tamara , Wait Jude
Published: January 2022

The Next Generation Science Standards call for students to “investigate the natural world through the processes of scientific inquiry.” Yet, it is rare for secondary students in the U.S. to engage in authentic scientific investigations of natural phenomena. The Columbia River Estuary Science Education and Outreach (CRESCENDO) Project was a 2-year (2016–2018) university-high school partnership between scientists and science education researchers from Washington State University (WSU) and science teachers and students from five public high schools located adjacent to the Columbia River Estuary (CRE). The teachers and students collaborated with WSU scientists on a rigorous ecological study of the CRE, which provided an opportunity to study how engaging students in authentic scientific research would impact their ecological knowledge and their attitudes toward environmental stewardship. Our study methods included online attitude surveys and knowledge assessments for all participating students, classroom observations, and semi-structured small group interviews with 3–5 students from each school at the end of each year of the project. We found that many students made significant gains in their ecological knowledge and understanding of scientific inquiry practices, demonstrating deeper understanding of the connections between local land use and water quality in the CRE, as well how nutrient concentrations vary seasonally and along the axis of the estuary. Students also showed enthusiasm for taking part in a “real” scientific research project, collaborating with university scientists, contributing “their” data to an investigative effort that extended beyond their own school, and the opportunity to get outdoors during science class. We identified five “key elements” of the CRESCENDO project that contributed to its success, and which would allow our model of a consistent, long-term (months) and immersive research experience for high school students to be transferrable to university-school partnerships across a range of size, location, research mission, and resource availability. Finally, this project also provided more evidence in support of place-based approaches for student learning, and the importance of immersing students in their environments where they can study the natural world by asking relevant questions and generating novel data about the science topics that matter to them.
Barriers to Therapeutic Use of Hydroxyurea for Sickle Cell Disease in Nigeria: A Cross-Sectional Survey
Authors: Okocha Emmanuel Chide , Gyamfi Joyce , Ryan Nessa , Babalola Oluwatoyin , Etuk Eno-Abasi , Chianumba Reuben , Nwegbu Maxwell , Isa Hezekiah , Madu Anazoeze Jude , Adegoke Samuel , Nnebe-Agumandu Uche , Brown Biobele , Peprah Emmanuel , Nnodu Obiageli E.
Published: January 2022

Background: Sickle cell disease, the inherited blood disorder characterized by anemia, severe pain and other vaso-occlusive complications, acute chest syndrome, disproportionate hospitalization, and early mortality, has significant financial, social, and psychosocial impacts and drains individuals, families, and health systems globally. Hydroxyurea could improve the health of the 300,000 individuals born each year with sickle cell disease in sub-Saharan Africa; however, challenges to adoption and adherence persist. This study assessed the barriers to therapeutic use of hydroxyurea for sickle cell disease within the Nigerian healthcare system, specifically from the level of the patient, provider, and health system.

Methods: We used purposive sampling to recruit participants from 13 regions in Nigeria. A cross-sectional survey was administered to physicians (n = 70), nurses or counselors (n = 17), and patients or their caregivers (n = 33) at 13 health centers. Findings were mapped onto the appropriate Consolidated Framework for Implementation Research (CFIR) domains.

Results: This study was able to identify factors that mapped onto the inner setting, outer setting, and characteristics of individuals domains of CFIR. The majority of physicians (74.3%) prescribe hydroxyurea, and half stated hydroxyurea is the standard of care. Among clinicians, barriers included limited knowledge of the drug, as well as low self-efficacy to prescribe among physicians and to counsel among nurses; perceived side effects; perceived patient preference for traditional medicine; cost for patient and expense of accompanying laboratory monitoring; and limited availability of the drug and equipment for laboratory monitoring. Among patients and caregivers, barriers included lack of knowledge; perceived side effects; cost; religious beliefs of disease causation; and lack of pediatric formulation.

Conclusions: Findings suggest that patient, provider, and health systems-level interventions are needed to improve hydroxyurea uptake among providers and adherence among patients with sickle cell disease in Nigeria. Interventions such as patient education, provider training, and policy change could address the disproportionate burden of sickle cell disease in sub-Saharan Africa and thus improve health equity.
Contribution of Rare and Low-Frequency Variants to Multiple Sclerosis Susceptibility in the Italian Continental Population
Authors: Clarelli Ferdinando , Barizzone Nadia , Mangano Eleonora , Zuccalà Miriam , Basagni Chiara , Anand Santosh , Sorosina Melissa , Mascia Elisabetta , Santoro Silvia ,   PROGEMUS,   PROGRESSO, Guerini Franca Rosa , Virgilio Eleonora , Gallo Antonio , Pizzino Alessandro , Comi Cristoforo , Martinelli Vittorio , Comi Giancarlo , De Bellis Gianluca , Leone Maurizio , Filippi Massimo , Esposito Federica , Bordoni Roberta , Martinelli Boneschi Filippo , D'Alfonso Sandra
Published: January 2022

Genome-wide association studies identified over 200 risk loci for multiple sclerosis (MS) focusing on common variants, which account for about 50% of disease heritability. The goal of this study was to investigate whether low-frequency and rare functional variants, located in MS-established associated loci, may contribute to disease risk in a relatively homogeneous population, testing their cumulative effect (burden) with gene-wise tests. We sequenced 98 genes in 588 Italian patients with MS and 408 matched healthy controls (HCs). Variants were selected using different filtering criteria based on allelic frequency and in silico functional impacts. Genes showing a significant burden (n = 17) were sequenced in an independent cohort of 504 MS and 504 HC. The highest signal in both cohorts was observed for the disruptive variants (stop-gain, stop-loss, or splicing variants) located in EFCAB13, a gene coding for a protein of an unknown function (p < 10–4). Among these variants, the minor allele of a stop-gain variant showed a significantly higher frequency in MS versus HC in both sequenced cohorts (p = 0.0093 and p = 0.025), confirmed by a meta-analysis on a third independent cohort of 1298 MS and 1430 HC (p = 0.001) assayed with an SNP array. Real-time PCR on 14 heterozygous individuals for this variant did not evidence the presence of the stop-gain allele, suggesting a transcript degradation by non-sense mediated decay, supported by the evidence that the carriers of the stop-gain variant had a lower expression of this gene (p = 0.0184). In conclusion, we identified a novel low-frequency functional variant associated with MS susceptibility, suggesting the possible role of rare/low-frequency variants in MS as reported for other complex diseases.
A Chromosome-Level Genome Assembly of Yellowtail Kingfish (Seriola lalandi)
Authors: Li Shuo , Liu Kaiqiang , Cui Aijun , Hao Xiancai , Wang Bin , Wang Hong-Yan , Jiang Yan , Wang Qian , Feng Bo , Xu Yongjiang , Shao Changwei , Liu Xuezhou
Published: January 2022

Yellowtail kingfish (Seriola lalandi) is a pelagic marine piscivore with a circumglobal distribution. It is particularly suitable for open ocean aquaculture owing to its large body size, fast swimming, rapid growth, and high economic value. A high-precision genome is of great significance for future genetic breeding research and large-scale aquaculture in the open ocean. PacBio, Illumina, and Hi-C data were combined to assemble chromosome-level reference genome with the size of 648.34 Mb (contig N50: 28.52 Mb). 175 contigs was anchored onto 24 chromosomes with lengths ranging from 12.28 to 34.59 Mb, and 99.79% of the whole genome sequence was covered. The BUSCOs of genome and gene were 94.20 and 95.70%, respectively. Gene families associated with adaptive behaviors, such as olfactory receptors and HSP70 gene families, expanded in the genome of S. lalandi. An analysis of selection pressure revealed 652 fast-evolving genes, among which mkxb, popdc2, dlx6, and ifitm5 may be related to rapid growth traits. The data generated in this study provide a valuable resource for understanding the genetic basis of S. lalandi traits.
The Expression of Inflammasomes NLRP1 and NLRP3, Toll-Like Receptors, and Vitamin D Receptor in Synovial Fibroblasts From Patients With Different Types of Knee Arthritis
Authors: Sakalyte Regina , Denkovskij Jaroslav , Bernotiene Eiva , Stropuviene Sigita , Mikulenaite Silvija Ona , Kvederas Giedrius , Porvaneckas Narunas , Tutkus Vytautas , Venalis Algirdas , Butrimiene Irena
Published: January 2022

Activated rheumatoid arthritis (RA) synovial fibroblasts (SFs) are among the most important cells promoting RA pathogenesis. They are considered active contributors to the initiation, progression, and perpetuation of the disease; therefore, early detection of RASF activation could advance contemporary diagnosis and adequate treatment of undifferentiated early inflammatory arthritis (EA). In this study, we investigated the expression of nucleotide-binding, oligomerization domain (NOD)-like receptor family, pyrin domain containing (NLRP)1, NLRP3 inflammasomes, Toll-like receptor (TLR)1, TLR2, TLR4, vitamin D receptor (VDR), and secretion of matrix metalloproteinases (MMPs) in SFs isolated from patients with RA, osteoarthritis (OA), EA, and control individuals (CN) after knee surgical intervention. C-reactive protein, general blood test, anticyclic citrullinated peptide (anti-CCP), rheumatoid factor (RF), and vitamin D (vitD) in patients’ sera were performed. Cells were stimulated or not with 100 ng/ml tumor necrosis factor alpha (TNF-α) or/and 1 nM or/and 0.01 nM vitamin D3 for 72 h. The expression levels of NLRP1, NLRP3, TLR1, TLR2, TLR4, and VDR in all examined SFs were analyzed by quantitative real-time PCR (RT-qPCR). Additionally, the secretion of IL-1β by SFs and MMPs were determined by ELISA and Luminex technology. The expression of NLRP3 was correlated with the levels of CRP, RF, and anti-CCP, suggesting its implication in SF inflammatory activation. In the TNF-α-stimulated SFs, a significantly lower expression of NLRP3 and TLR4 was observed in the RA group, compared with the other tested forms of arthritis. Moreover, upregulation of NLRP3 expression by TNF-α alone or in combination with vitD3 was observed, further indicating involvement of NLRP3 in the inflammatory responses of SFs. Secretion of IL-1β was not detected in any sample, while TNF-α upregulated the levels of secreted MMP-1, MMP-7, MMP-8, MMP-12, and MMP-13 in all patient groups. Attenuating effects of vitD on the expression of NLRP3, TLR1, and TLR4 suggest potential protective effects of vitD on the inflammatory responses in SFs. However, longer studies may be needed to confirm or fully rule out the potential implication of vitD in SF activation in inflammatory arthritis. Both VDR and NLRP3 in the TNF-α-stimulated SFs negatively correlated with the age of patients, suggesting potential age-related changes in the local inflammatory responses.
Immunodominant and Neutralizing Linear B-Cell Epitopes Spanning the Spike and Membrane Proteins of Porcine Epidemic Diarrhea Virus
Authors: Polyiam Kanokporn , Ruengjitchatchawalya Marasri , Mekvichitsaeng Phenjun , Kaeoket Kampon , Hoonsuwan Tawatchai , Joiphaeng Pichai , Roshorm Yaowaluck Maprang
Published: January 2022

Porcine epidemic diarrhea virus (PEDV) is the causative agent of PED, an enteric disease that causes high mortality rates in piglets. PEDV is an alphacoronavirus that has high genetic diversity. Insights into neutralizing B-cell epitopes of all genetically diverse PEDV strains are of importance, particularly for designing a vaccine that can provide broad protection against PEDV. In this work, we aimed to explore the landscape of linear B-cell epitopes on the spike (S) and membrane (M) proteins of global PEDV strains. All amino acid sequences of the PEDV S and M proteins were retrieved from the NCBI database and grouped. Immunoinformatics-based methods were next developed and used to identify putative linear B-cell epitopes from 14 and 5 consensus sequences generated from distinct groups of the S and M proteins, respectively. ELISA testing predicted peptides with PEDV-positive sera revealed nine novel immunodominant epitopes on the S protein. Importantly, seven of these novel immunodominant epitopes and other subdominant epitopes were demonstrated to be neutralizing epitopes by neutralization–inhibition assay. Our findings unveil important roles of the PEDV S2 subunit in both immune stimulation and virus neutralization. Additionally, our study shows the first time that the M protein is also the target of PEDV neutralization with seven neutralizing epitopes identified. Conservancy profiles of the epitopes are also provided. In this study, we offer immunoinformatics-based methods for linear B-cell epitope identification and a more complete profile of linear B-cell epitopes across the PEDV S and M proteins, which may contribute to the development of a greater next-generation PEDV vaccine as well as peptide-based immunoassays.
Short Chain Fatty Acids Taken at Time of Thrombectomy in Acute Ischemic Stroke Patients Are Independent of Stroke Severity But Associated With Inflammatory Markers and Worse Symptoms at Discharge
Authors: Henry Nicholas , Frank Jacqueline , McLouth Christopher , Trout Amanda L. , Morris Andrew , Chen Jianzhong , Stowe Ann M. , Fraser Justin F. , Pennypacker Keith
Published: January 2022

Introduction

Short chain fatty acids (SCFA) are gut microbiota-derived metabolites that contribute to the gut-brain axis and may impact stroke outcomes following gut dysbiosis. We evaluated plasma SCFA concentrations against stroke severity parameters and identified SCFA-associated protein networks.

Methods

The Blood and Clot Thrombectomy Registry and Collaboration (BACTRAC), a continuously enrolling tissue bank, was used to obtain stroke samples. Arterial blood distal and proximal to the thrombus was obtained from Acute Ischemic Stroke (AIS) Patients (n=53) during thrombectomy. Patient demographics, stroke presentation and outcome parameters were reported. The SCFAs were isolated from proximal plasma via chemical derivatization UHPLC coupled tandem mass spectrometry using electrospray ionization and multiple reaction monitoring. Proteomic levels for 184 cardioembolic and inflammatory proteins was quantified from systemic and intracranial plasma by Olink. Arterial blood from cerebrovascular patients undergoing elective neurointerventional procedures was used as controls.

Results

Acetate positively correlated with time from last known normal (LKN) and was significantly lower in stroke patients compared to control. Isobutyrate, Butyrate and 2-Methylbutyrate negatively correlated with %ΔNIHSS. Isobutyrate and 2-Methylbutyrate positively correlated with NIHSS discharge. SCFA concentrations were not associated with NIHSS admission, infarct volume, or edema volume. Multiple SCFAs positively associated with systemic and pro-inflammatory cytokines, most notably IL-6, TNF-α, VCAM1, IL-17, and MCP-1.

Conclusions

Plasma SCFA concentrations taken at time of stroke are not associated with stroke severity at presentation. However, higher levels of SCFAs at the time of stroke are associated with increased markers of inflammation, less recovery from admission to discharge, and worse symptom burden at discharge.
Enhanced Immune Responses by Virus-Mimetic Polymeric Nanostructures Against Infectious Diseases
Authors: Li Xinpei , Liu Shengqiu , Yin Panchao , Chen Kun
Published: January 2022

Intermittent outbreaks of global pandemic disease have spurred new sensors and medicines development for the prevention of disease spread. This perspective specifically covers recent advances, challenges, and future directions in virus-mimetic polymeric nanostructures and their application in biological medicines with a special emphasis on subunit vaccine development. With tailorable compositions and properties, polymers facilitate the ingenious design of various polymeric nanostructures. As one type of polymeric nanostructures, virus-mimetic polymeric nanostructures have been developed as an attractive platform for enhanced immune responses, since they combine the merits of polymer nanocores with the biomimetic characteristic of virus which displays multivalent epitopes on their surfaces. This perspective also provides an applicative approach to rationally design virus-mimetic polymeric platforms based on nanostructures that are self-assembled by using polymers as templates and the antigens and metal oxide clusters loaded on their surface to mimic viruses in size and surface antigenicity. Sub-200 nm virus-mimetic polymeric nanostructures are in a relatively lower level of endotoxins and can promote the antigens to elicit potent humoral and cellular immune responses against pathogenic bacteria. The promising development of virus-mimetic polymeric nanostructures will continue to protect human health from common pathogens and emerging infectious threats.
Metabolic and Immune Markers for Precise Monitoring of COVID-19 Severity and Treatment
Authors: Rendeiro André F. , Vorkas Charles Kyriakos , Krumsiek Jan , Singh Harjot K. , Kapadia Shashi N. , Cappelli Luca Vincenzo , Cacciapuoti Maria Teresa , Inghirami Giorgio , Elemento Olivier , Salvatore Mirella
Published: January 2022

Deep understanding of the SARS-CoV-2 effects on host molecular pathways is paramount for the discovery of early biomarkers of outcome of coronavirus disease 2019 (COVID-19) and the identification of novel therapeutic targets. In that light, we generated metabolomic data from COVID-19 patient blood using high-throughput targeted nuclear magnetic resonance (NMR) spectroscopy and high-dimensional flow cytometry. We find considerable changes in serum metabolome composition of COVID-19 patients associated with disease severity, and response to tocilizumab treatment. We built a clinically annotated, biologically-interpretable space for precise time-resolved disease monitoring and characterize the temporal dynamics of metabolomic change along the clinical course of COVID-19 patients and in response to therapy. Finally, we leverage joint immuno-metabolic measurements to provide a novel approach for patient stratification and early prediction of severe disease. Our results show that high-dimensional metabolomic and joint immune-metabolic readouts provide rich information content for elucidation of the host’s response to infection and empower discovery of novel metabolic-driven therapies, as well as precise and efficient clinical action.
The Immune Response to SARS-CoV-2 Vaccination: Insights Learned From Adult Patients With Common Variable Immune Deficiency
Authors: Quinti Isabella , Locatelli Franco , Carsetti Rita
Published: January 2022

CVID patients have an increased susceptibility to vaccine-preventable infections. The question on the potential benefits of immunization of CVID patients against SARS-CoV-2 offered the possibility to analyze the defective mechanisms of immune responses to a novel antigen. In CVID, as in immunocompetent subjects, the role of B and T cells is different between infected and vaccinated individuals. Upon vaccination, variable anti-Spike IgG responses have been found in different CVID cohorts. Immunization with two doses of mRNA vaccine did not generate Spike-specific classical memory B cells (MBCs) but atypical memory B cells (ATM) with low binding capacity to Spike protein. Spike-specific T-cells responses were also induced in CVID patients with a variable frequency, differently from specific T cells produced after multiple exposures to viral antigens following influenza virus immunization and infection. The immune response elicited by SARS-CoV-2 infection was enhanced by subsequent immunization underlying the need to immunize convalescent COVID-19 CVID patients after recovery. In particular, immunization after SARS-Cov-2 infection generated Spike-specific classical memory B cells (MBCs) with low binding capacity to Spike protein and Spike-specific antibodies in a high percentage of CVID patients. The search for a strategy to elicit an adequate immune response post-vaccination in CVID patients is necessary. Since reinfection with SARS-CoV-2 has been documented, at present SARS-CoV-2 positive CVID patients might benefit from new preventing strategy based on administration of anti-SARS-CoV-2 monoclonal antibodies.
A Novel Humanized Anti-Interleukin-6 Antibody HZ0408b With Anti-Rheumatoid Arthritis Therapeutic Potential
Authors: Liu Xiaolei , Li Li , Wang Qian , Jiang Fengchao , Zhang Pei , Guo Fei , Liu Hongjun , Huang Jian
Published: January 2022

Interleukin-6 (IL-6), a pleiotropic cytokine that regulates immune responses and inflammatory reactions, plays a pivotal role in the development of rheumatoid arthritis (RA). Blockade of IL-6 signaling with the monoclonal antibody (mAb) represents an important advancement in RA treatment. Although two IL-6 receptor antibodies are already available in the clinic, there is no mAb specifically targeting the human IL-6 to block IL-6 signaling for RA treatment. In this study, we have developed a novel humanized anti-IL-6 mAb HZ-0408b with potent binding and neutralizing activity to human IL-6. We demonstrated that HZ-0408b has a high species specificity and low cross-reactivity. Moreover, HZ-0408b showed a more potent inhibitory effect on IL-6 signaling than Siltuximab, an FDA-approved anti-IL-6 chimeric mAb. HZ-0408b is comparable to Olokizumab, a humanized mAb against IL-6 that is already in phase III studies. We observed that HZ-0408b is well tolerated at doses that can achieve therapeutic serum levels in cynomolgus monkey. Most importantly, we proved that HZ-0408b treatment significantly ameliorated joint swelling after the onset of arthritis and dramatically reduced plasma C-reactive protein (CRP) levels in a monkey collagen-induced arthritis (CIA) model. Collectively, our findings using non-human primates indicate that humanized anti-IL-6 mAb HZ-0408b has excellent safety and efficacy profiles for RA therapy.
Recent Advances in the Role of Arid5a in Immune Diseases and Cancer
Authors: Nyati Kishan Kumar , Kishimoto Tadamitsu
Published: January 2022

AT-rich interactive domain 5a (Arid5a) is a nucleic acid binding protein. In this review, we highlight recent advances in the association of Arid5a with inflammation and human diseases. Arid5a is known as a protein that performs dual functions. In in vitro and in vivo studies, it was found that an inflammation-dependent increase in Arid5a expression mediates both transcriptional and post-transcriptional regulatory effects that are implicated in immune regulation and cellular homeostasis. A series of publications demonstrated that inhibiting Arid5a augmented several processes, such as preventing septic shock, experimental autoimmune encephalomyelitis, acute lung injury, invasion and metastasis, immune evasion, epithelial-to-mesenchymal transition, and the M1-like tumor-associated macrophage (TAM) to M2-like TAM transition. In addition, Arid5a controls adipogenesis and obesity in mice to maintain metabolic homeostasis. Taken together, recent progress indicates that Arid5a exhibits multifaceted, both beneficial and detrimental, roles in health and disease and suggest the relevance of Arid5a as a potential therapeutic target.
Physicochemical Characteristics of Aedes Mosquito Breeding Habitats in Suburban and Urban Areas of Kinshasa, Democratic Republic of the Congo
Authors: Mbanzulu Kennedy Makola , Mboera Leonard E. G. , Wumba Roger , Engbu Danoff , Bojabwa Michael Mondjo , Zanga Josué , Mitashi Patrick Mulopo , Misinzo Gerald , Kimera Sharadhuli Iddi
Published: January 2022

Background

The knowledge of key elements of the ecosystem affecting mosquito distribution and their population dynamics is essential for designing mosquito-borne disease interventions. The present study characterized the physicochemical properties ofAedesmosquito breeding habitats in Democratic Republic of the Congo.

Methods

A cross-sectional survey was carried out in Kinshasa, from February to April 2021. The physicochemical characteristics of the natural and artificial aquatic habitats ofAedeswere measured using a multiparametric device.

Results

Out of 438 breeding habitats inspected, 273 (62.3%) contained mosquito larvae. TheAedesmosquitoes identified in 76.19% of positive breeding sites wereAedes albopictus(67.30%) andAedes aegypti(37.98%). The median values of dissolved oxygen (DO) (1.0), turbidity (19.15), and salinity (0.115) in water breeding sites ofAedeswere respectively 0.8, 55.0, and 0.29 inCulexbreeding sites (p< 0.05). The physicochemical characteristics of the breeding habitat forAe. aegyptiandAe. albopictuswere almost identical. In urban areas, the median temperature was 29.82 while it was 29.60 in suburban areas (p< 0.05). Significantly, the salinity was higher in bamboo and metal containers while DO was higher in tins. After analysis using simple linear regression, total dissolved solids (r = 0.23;p= 0.000), conductivity (r = 0.23), salinity (r = 0.23), and temperature (r = 0.13) were associated with larval density (p< 0.05). In the final model (r = 0.30,p= 0.01), salinity (r = 0.23) and DO (r = 0.138) adjusted to temperature, pH, and turbidity were associated positively to larvae density.

Conclusion

TheAedesbreeding sites and mosquito density were significantly influenced by water salinity, DO, temperature, pH, and turbidity.
Characterization of Heavily Irradiated Dielectrics for Pixel Sensors Coupling Insulator Applications
Authors: Bharthuar S. , Golovleva M. , Bezak M. , Brücken E. , Gädda A. , Härkönen J. , Karadzhinova-Ferrer A. , Kramarenko N. , Kirschenmann S. , Koponen P. , Luukka P. , Mizohata K. , Ott J. , Tuominen E.
Published: January 2022

An increase in the radiation levels during the high-luminosity operation of the Large Hadron Collider calls for the development of silicon-based pixel detectors that are used for particle tracking and vertex reconstruction. Unlike the conventionally used conductively coupled (DC-coupled) detectors that are prone to an increment in leakage currents due to radiation, capacitively coupled (AC-coupled) detectors are anticipated to be in operation in future collider experiments suitable for tracking purposes. The implementation of AC-coupling to micro-scale pixel sensor areas enables one to provide an enhanced isolation of radiation-induced leakage currents. The motivation of this study is the development of new generation capacitively coupled (AC-coupled) pixel sensors with coupling insulators having good dielectric strength and radiation hardness simultaneously. The AC-coupling insulator thin films were aluminum oxide (Al2O3) and hafnium oxide (HfO2) grown by the atomic layer deposition (ALD) method. A comparison study was performed based on the dielectric material used in MOS, MOSFET, and AC-coupled pixel prototypes processed on high resistivity p-type Magnetic Czochralski silicon (MCz-Si) substrates. Post-irradiation studies with 10 MeV protons up to a fluence of 1015 protons/cm2 suggest HfO2 to be a better candidate as it provides higher sensitivity with negative charge accumulation on irradiation. Furthermore, even though the nature of the dielectric does not affect the electric field within the AC-coupled pixel sensor, samples with HfO2 are comparatively less susceptible to undergo an early breakdown due to irradiation. Edge-transient current technique (e-TCT) measurements show a prominent double-junction effect as expected in heavily irradiated p-type detectors, in accordance with the simulation studies.
Pharmacomicrobiomics: Exploiting the Drug-Microbiota Interactions in Antihypertensive Treatment
Authors: Chen Hui-Qing , Gong Jin-Yu , Xing Kai , Liu Mou-Ze , Ren Huan , Luo Jian-Quan
Published: January 2022

Hypertension is a leading risk factor for cardiovascular diseases and can reduce life expectancy. Owing to the widespread use of antihypertensive drugs, patients with hypertension have improved blood pressure control over the past few decades. However, for a considerable part of the population, these drugs still cannot significantly improve their symptoms. In order to explore the reasons behind, pharmacomicrobiomics provide unique insights into the drug treatment of hypertension by investigating the effect of bidirectional interaction between gut microbiota and antihypertensive drugs. This review discusses the relationship between antihypertensive drugs and the gut microbiome, including changes in drug pharmacokinetics and gut microbiota composition. In addition, we highlight how our current knowledge of antihypertensive drug-microbiota interactions to develop gut microbiota-based personalized ways for disease management, including antihypertensive response biomarker, microbial-targeted therapies, probiotics therapy. Ultimately, a better understanding of the impact of pharmacomicrobiomics in the treatment of hypertension will provide important information for guiding rational clinical use and individualized use.
Integrated Array Tomography for 3D Correlative Light and Electron Microscopy
Authors: Lane Ryan , Wolters Anouk H. G. , Giepmans Ben N. G. , Hoogenboom Jacob P.
Published: January 2022

Volume electron microscopy (EM) of biological systems has grown exponentially in recent years due to innovative large-scale imaging approaches. As a standalone imaging method, however, large-scale EM typically has two major limitations: slow rates of acquisition and the difficulty to provide targeted biological information. We developed a 3D image acquisition and reconstruction pipeline that overcomes both of these limitations by using a widefield fluorescence microscope integrated inside of a scanning electron microscope. The workflow consists of acquiring large field of view fluorescence microscopy (FM) images, which guide to regions of interest for successive EM (integrated correlative light and electron microscopy). High precision EM-FM overlay is achieved using cathodoluminescent markers. We conduct a proof-of-concept of our integrated workflow on immunolabelled serial sections of tissues. Acquisitions are limited to regions containing biological targets, expediting total acquisition times and reducing the burden of excess data by tens or hundreds of GBs.
CBCT Verification of SRT for Patients With Brain Metastases
Authors: Papp Judit , Simon Mihály , Csiki Emese , Kovács Árpád
Published: January 2022

Background

The aim of our work is to demonstrate the role of image guidance and volumetric imaging in stereotactic radiotherapy (SRT) of brain metastases.

Methods

Between 2018 and 2020, 106 patients underwent intracranial stereotactic radiotherapy. 10 patients with metastatic brain tumors treated with SRT were randomly selected and included in our study model. Patients were scanned pre- and post-treatment with cone beam CT. Total of 100 verifications of 50 stereotaxic treatments were performed and analyzed.

Results

Population mean X, Y, Z values were -0.13 cm, -0.04 cm, -0.03 cm, respectively, rotation values 0.81°, 0.51°, 0.46°, respectively. Systematic error components for translational displacements pre corrections were as follows: 0.14 cm for X, 0.13 cm for Y and 0.1 cm for Z. Systematic error components of the post-treatment HR 3D CBCTs were as follows: 0.01 cm for X, 0.06 cm for Y and 0.04 cm for Z.

Conclusions

Population mean values close to 0 confirmed that there is no systematic variation in our system and the accuracy of our equipment and tools is reliable. HR 3D CBCT scans performed pre SRTs further refine patient and target volume setting, support medical decision making and eliminate the possibility of gross error.