bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biological evaluations of decellularized extracellular matrix collagen microparticles prepared based on plant enzymes and aqueous two-phase method
Authors: Liu YaWen , Huang Ching-Cheng , Wang YuanYuan , Xu Jun , Wang GuoDing , Bai XinPeng 
Published: March 2021

Abstract
For patients with extensive full-thickness burns who do not have sufficient autologous split-thickness skin for skin grafts, the application of biological skin substitutes may be considered. The aim of this study was to find an optimal new type method for the production of a biovital skin substitute based on acellular dermal matrix (ADM) and preclinical evaluations. In this work, 25 methods of ADM production were assessed. The proposed methods are based on the use of the following enzymes: papain, Carica papaya lipase (CPL), and purification using a polymer/salt aqueous two-phase system. The obtained ADM samples were characterized via scanning electron microscopy (SEM), porosity measurement and water vapor transmission test. Results showed that the collagen bundles of ADM microparticles were intact and orderly. Through differential scanning calorimetry (DSC), thermo gravimetric analysis (TGA) and biocompatibility tests, the results indicated that the proportion of papain and CPL was the same and 5 h processing time are the optimum conditions for ADM preparation and the material showed good biocompatibility. Our results suggested that the potential of developing this kind of decellularization process to manufacture ADM scaffolds for clinical application.
Antioxidant biocompatible composite collagen dressing for diabetic wound healing in rat model
Authors: Qian Bei , Li Jialun , Guo Ke , Guo Nengqiang , Zhong Aimei , Yang Jie , Wang Jiecong , Xiao Peng , Sun Jiaming , Xiong Lingyun 
Published: March 2021

Abstract
Associated with persistent oxidative stress, altered inflammatory responses, poor angiogenesis and epithelization, wound healing in diabetic patients is impaired. N-acetylcysteine (NAC) is reported to resist excess reactive oxygen species (ROS) production, prompt angiogenesis and maturation of the epidermis. Studies have revealed that graphene oxide (GO) can regulate cellular behavior and form cross-links with naturally biodegradable polymers such as collagen (COL) to construct composite scaffolds. Here, we reported a COL-based implantable scaffold containing a mixture of GO capable of the sustained delivery of NAC to evaluate the wound healing in diabetic rats. The morphological, physical characteristics, biocompatibility and NAC release profile of the GO-COL-NAC (GCN) scaffold were evaluated in vitro. Wound healing studies were performed on a 20 mm dorsal full-skin defect of streptozotocin (STZ)-induced diabetic rats. The injured skin tissue was removed at the 18th day post-surgery for histological analysis and determination of glutathione peroxidase (GPx), catalase (CAT) and superoxide dismutase (SOD) activity. In diabetic rats, we confirmed that the GCN scaffold presented a beneficial effect in enhancing the wound healing process. Additionally, due to the sustained release of NAC, the scaffold may potentially induce the antioxidant defense system, upregulating the expression levels of the antioxidant enzymes in the wound tissue. The findings revealed that the antioxidant biocompatible composite collagen dressing could not only deliver NAC in situ for ROS inhibition but also promote the wound healing process. This scaffold with valuable therapy potential might enrich the approaches for surgeon in diabetic wound treatment in the future.
Tuning filament composition and microstructure of 3D-printed bioceramic scaffolds facilitate bone defect regeneration and repair
Authors: Chen Yi , Huang Jiaping , Liu Jiamei , Wei Yingming , Yang Xianyan , Lei Lihong , Chen Lili , Wu Yanmin , Gou Zhongru 
Published: March 2021

Abstract
It is still a challenge to optimize the component distribution and microporous structures in scaffolds for tailoring biodegradation (ion releasing) and enhancing bone defect repair within an expected time stage. Herein, the core–shell-typed nonstoichiometric wollastonite (4% and 10% Mg-doping calcium silicate; CSiMg4, CSiMg10) macroporous scaffolds with microporous shells (adding ∼10 μm PS microspheres into shell-layer slurry) were fabricated via 3D printing. The initial mechanical properties and bio-dissolution (ion releasing) in vitro, and osteogenic capacity in vivo of the bioceramic scaffolds were evaluated systematically. It was shown that endowing high-density micropores in the sparingly dissolvable CSiMg10 or dissolvable CSiMg4 shell layer inevitably led to nearly 30% reduction of compressive strength, but such micropores could readily tune the ion release behaviour of the scaffolds (CSiMg4@CSiMg10 vs. CSiMg4@CSiMg10-p; CSiMg10@CSiMg4 vs. CSiMg10@CSiMg4-p). Based on the in rabbit femoral bone defect repair model, the 3D μCT reconstruction and histological observation demonstrated that the CSiMg4@CSiMg10-p scaffolds displayed markedly higher osteogenic capability than the other scaffolds after 12 weeks of implantation. It demonstrated that core–shell bioceramic 3D printing technique can be developed to fabricate single-phase or biphasic bioactive ceramic scaffolds with accurately tailored filament biodegradation for promoting bone defect regeneration and repair in some specific pathological conditions.
Autologous haematopoietic stem cell transplantation restores the suppressive capacity of regulatory B cells in systemic sclerosis patients
Authors: Lima-Júnior João R , Arruda Lucas C M , Gonçalves Maynara S , Dias Juliana B E , Moraes Daniela A , Covas Dimas T , Simões Belinda P , Oliveira Maria Carolina , Malmegrim Kelen C R 
Published: March 2021

Abstract

Objectives
The rationale of autologous haematopoietic stem cell transplantation (AHSCT) for autoimmune diseases is that high-dose immunosuppression eradicates autoreactive T and B cells and the infused autologous haematopoietic stem cells promote reconstitution of a naïve and self-tolerant immune system. The aim of this study was to evaluate the reconstitution of different B cell subsets, both quantitatively and functionally, in SSc patients treated with AHSCT.

Methods
Peripheral blood was harvested from 22 SSc patients before transplantation and at 30, 60, 120, 180 and 360 days post-AHSCT. Immunophenotyping of B cell subsets, B cell cytokine production, signalling pathways and suppressive capacity of regulatory B cells (Bregs) were assessed by flow cytometry.

Results
Naïve B cell frequencies increased from 60 to 360 days post-AHSCT compared with pre-transplantation. Conversely, memory B cell frequencies decreased during the same period. Plasma cell frequencies transiently decreased at 60 days post-AHSCT. IL-10-producing Bregs CD19+CD24hiCD38hi and CD19+CD24hiCD27+ frequencies increased at 180 days. Moreover, the phosphorylation of extracellular signal-regulated kinase 1/2 and p38 mitogen-activated protein kinase increased in B cells reconstituted post-AHSCT. Notably, CD19+CD24hiCD38hi Bregs recovered their ability to suppress production of Th1 cytokines by CD4+ T cells at 360 days post-AHSCT. Finally, IL-6 and TGF-β1-producing B cells decreased following AHSCT.

Conclusion
Taken together, these results suggest improvements in immunoregulatory and anti-fibrotic mechanisms after AHSCT for SSc, which may contribute to re-establishment of self-tolerance and clinical remission.
Adaptation and withdrawal of feeding dried Aspergillus oryzae fermentation product to dairy cattle and goats on in vitro NDF digestibility of selected forage sources
Authors: Hymes-Fecht Ursula C , Casper David P 
Published: March 2021

Abstract
Nutritional fermentation aids [dried Aspergillus oryzae fermentation product (AO)] are used in livestock production to increase nutrient digestion and production efficiency. The objective was to determine AO impact on neutral detergent fiber (NDF) degradation of selected forage sources (FS). A series of in vitro fermentation experiments were conducted using rumen fluid (RF) from rumen fistulated dairy heifers or dairy goats evaluating AO at 0.0, 0.3, or 0.6 g/L inclusion rates. In experiment I, the optimum AO concentration using alfalfa hay (AH), Bermuda grass (BG) hay, and peanut skins (PS) was determined via 48-h in vitro neutral detergent fiber digestion (IVNDFd). In experiment II, 0.0 g/L and 0.3 g/L AO were used to determine in vitro dry matter digestion (IVDMD), in vitro organic matter digestion (IVOMD), IVNDFd, and NDF digestion kinetics. In experiment III, in vivo AO ruminal adaptation (AD) and withdrawal (WD) times were determined for both dairy heifers and goats on IVDMD, IVOMD, IVNDFd, and NDF digestion kinetics. In experiment I, IVNDFd was similar using RF from dairy heifers or goats with IVNDFd being increased 10%, 28%, and 23% for AH, BG, and PS, respectively, at 0.3 g/L of AO compared with 0.0 g/L AO, while adding 0.6 g/L AO reduced IVNDFd among all FS. In experiment II, IVNDFd was greater when adding 0.0 g/L AO compared with 0.3 g/L AO using dairy goat RF (26.7% and 37.6%, respectively) among all FS. The mean retention time and 50% digestion times were greater, while digestion rate was lower for PS compared to AH and BG. In vitro dry matter (DM) and organic matter (OM) digestibilities were greater with AO for AH and BG compared to PS but varied with RF donor source. In experiment III, in vitro DM digestibility increased then decreased with adaptation time, while AO withdrawal increased digestion of DM, OM, and NDF. The NDF digestion kinetics were similar across all FS (AH, BG, and PS), which resulted in no clear determination of AO adaptation and withdrawal times needed for AO efficacy. The optimal AO inclusion rate was determined to be 0.3 g/L for improving in vitro NDF digestion, but subsequent experiments could not confirm that inclusion rate. Inclusion rates greater than 0.3 g/L depressed NDF degradation, which should be avoided due to depression of NDF digestion. Sourcing ruminal fluid from dairy heifers or goats for conducting in vitro fermentations resulted in similar DM, OM, and NDF digestion and NDF degradation kinetics.
MicroRNA‐191‐5p ameliorates amyloid‐β1‐40–mediated retinal pigment epithelium cell injury by suppressing the NLRP3 inflammasome pathway
Authors: Chen Jieqiong , Sun Junran , Hu Yifan , Wan Xiaoling , Wang Yuwei , Gao Min , Liang Jian , Liu Te , Sun Xiaodong 
Published: March 2021

AbstractAmyloid β (Aβ) is a crucial component of drusen, the hallmark of the early stage of age‐related macular degeneration (AMD), and can cause retinal pigment epithelium (RPE) cell damage through activation of the inflammatory response. MicroRNAs play a critical role in inflammation. However, the mechanism underlying the effect of microRNAs on the NLRP3 inflammasome induced by Aβ remains poorly understood. In the present study, we demonstrated that Aβ1‐40‐mediated RPE damage by inducing a decrease in endogenous miR‐191‐5p expression. This led to the upregulation of its target gene, C/EBPβ. C/EBPβ acts as a transcription factor for NLRP3, promotes its transcription, and upregulates the downstream inflammatory factors Caspase‐1 and IL‐1β. Correspondingly, overexpression of miR‐191‐5p alleviated RPE cell injury by suppressing inflammation. The present study elucidates a novel transcriptional regulatory mechanism of the NLRP3 inflammasome. Our findings suggest an anti‐inflammatory effect of miR‐191‐5p in Aβ1‐40‐induced RPE impairment, shedding light on novel preventive or therapeutic approaches for AMD‐associated RPE impairment.
ATM inhibitor KU‐55933 induces apoptosis and inhibits motility by blocking GLUT1‐mediated glucose uptake in aggressive cancer cells with sustained activation of Akt
Authors: Harris Benjamin R. E. , Zhang Ye , Tao Jianxin , Shen Renhui , Zhao Xiaoqian , Cleary Margot P. , Wang Tong , Yang Da‐Qing 
Published: March 2021

AbstractEnhanced glucose uptake is coupled with elevated aerobic glycolysis (the Warburg effect) in cancer cells and is closely correlated with increased tumor aggressiveness and poor prognosis. We previously discovered that ATM, a protein kinase deficient in Ataxia‐telangiectasia (A‐T) disease, is an insulin‐responsive protein that participates in insulin‐mediated glucose uptake in muscle cells by stimulating glucose transporter 4 (GLUT4) translocation. However, the role of ATM in glucose uptake and tumorigenesis of cancer cells is unclear. In the present study, we found that aggressive breast and prostate cancer cell lines with overactivated Akt activity exhibit enhanced glucose uptake and GLUT1 translocation upon insulin treatment, and KU‐55933, a specific inhibitor of ATM, inhibits insulin‐mediated glucose uptake by blocking translocation of GLUT1 to the cell surface. KU‐55933 also inhibits aerobic glycolysis and ATP production in these cells. Moreover, KU‐55933 induces apoptosis and inhibits motility of cancer cells by inhibiting glucose uptake. Our results showed that while high concentration of glucose and insulin promote the expression of a mesenchymal biomarker (vimentin) in these cancer cells, KU‐55933 strongly inhibits its expression as well as epithelial to mesenchymal transition. The roles of ATM in stimulating glucose uptake, glycolysis, motility, and proliferation of cancer cells were demonstrated by knocking‐down ATM in these cells. KU‐55933 treatment also inhibits tumor growth and metastasis in vivo in mouse mammary tumors through inhibition of GLUT1 translocation and vimentin expression. These results suggest that ATM acts as a promoter of tumorigenesis in cancer cells with overactivated Akt, and KU‐55933 induces apoptosis and inhibits motility by blocking GLUT1‐mediated glucose uptake and glycolysis in these cancer cells, which may lead to the use of KU‐55933 and its analogs as new preventive or therapeutic agents against cancer.
Hypoxia‐inducible factor‐dependent induction of myeloid‐derived netrin‐1 attenuates natural killer cell infiltration during endotoxin‐induced lung injury
Authors: Berg Nathaniel K. , Li Jiwen , Kim Boyun , Mills Tingting , Pei Guangsheng , Zhao Zhongming , Li Xiangyun , Zhang Xu , Ruan Wei , Eltzschig Holger K. , Yuan Xiaoyi 
Published: March 2021

AbstractSepsis and sepsis‐associated lung inflammation significantly contribute to the morbidity and mortality of critical illness. Here, we examined the hypothesis that neuronal guidance proteins could orchestrate inflammatory events during endotoxin‐induced lung injury. Through a targeted array, we identified netrin‐1 as the top upregulated neuronal guidance protein in macrophages treated with lipopolysaccharide (LPS). Furthermore, we found that netrin‐1 is highly enriched in infiltrating myeloid cells, particularly in macrophages during LPS‐induced lung injury. Transcriptional studies implicate hypoxia‐inducible factor HIF‐1α in the transcriptional induction of netrin‐1 during LPS treatment. Subsequently, the deletion of netrin‐1 in the myeloid compartment (Ntn1loxp/loxp LysM Cre) resulted in exaggerated mortality and lung inflammation. Surprisingly, further studies revealed enhanced natural killer cells (NK cells) infiltration in Ntn1loxp/loxp LysM Cre mice, and neutralization of NK cell chemoattractant chemokine (C‐C motif) ligand 2 (CCL2) reversed the exaggerated lung inflammation. Together, these studies provide functional insight into myeloid cell‐derived netrin‐1 in controlling lung inflammation through the modulation of CCL2‐dependent infiltration of NK cells.
Proteomic/transcriptomic analysis of erythropoiesis
Authors: Brand Marjorie , Ranish Jeffrey A. 
Published: March 2021

Purpose of review
Erythropoiesis is a hierarchical process by which hematopoietic stem cells give rise to red blood cells through gradual cell fate restriction and maturation. Deciphering this process requires the establishment of dynamic gene regulatory networks (GRNs) that predict the response of hematopoietic cells to signals from the environment. Although GRNs have historically been derived from transcriptomic data, recent proteomic studies have revealed a major role for posttranscriptional mechanisms in regulating gene expression during erythropoiesis. These new findings highlight the need to integrate proteomic data into GRNs for a refined understanding of erythropoiesis.

Recent findings
Here, we review recent proteomic studies that have furthered our understanding of erythropoiesis with a focus on quantitative mass spectrometry approaches to measure the abundance of transcription factors and cofactors during differentiation. Furthermore, we highlight challenges that remain in integrating transcriptomic, proteomic, and other omics data into a predictive model of erythropoiesis, and discuss the future prospect of single-cell proteomics.

Summary
Recent proteomic studies have considerably expanded our knowledge of erythropoiesis beyond the traditional transcriptomic-centric perspective. These findings have both opened up new avenues of research to increase our understanding of erythroid differentiation, while at the same time presenting new challenges in integrating multiple layers of information into a comprehensive gene regulatory model.
An Innovative antibody-based Plug-and-Play strategy for SARS-CoV-2
Authors: Shivange Gururaj , Gogoi Debananda , Tushir-Singh Jogender 
Published: March 2021

AbstractThe novel and highly pathogenic coronavirus (SARS-CoV-2) remains a public health threat worldwide. SARS-CoV-2 enters human host lung cells via its spike protein binding to angiotensin-converting enzyme 2 (ACE2) in a process critical dependent on host protease-mediated fusion event. Thus, effective targeted therapies blocking the first step of viral fusion and cellular entry remains a critical unmet medical need to overcome disease pathology. Here we engineered and describe an antibody-based novel and targeted plug-and-play strategy, which directly competes with the proteolytic activation function of SAR-CoV-2 spike protein. The described strategy involves the engineering of furin substrate residues in IgG1 Fc-extended flexible region of spike targeting antibody. Our results with spike receptor-binding domain (RBD) targeting CR3022 antibody support blockade of the viral function using proof of concept ACE2 overexpressing cells. Our study reveals analytical, safe, and selective mechanistic insights for SARS-CoV-2 therapeutic design and is broadly applicable to the future coronaviridae family members (including mutant variants) exploiting the host protease system for cellular entry.
Human AdV-20-42-42, a promising novel adenoviral vector for gene therapy and vaccine product development
Authors: Ballmann Mónika Z. , Raus Svjetlana , Engelhart Ruben , Kaján Győző L. , van der Zalm Chantal , Papp Tibor , John Lijo , Khan Selina , Custers Jerome , Bakker Wilfried A.M. , van der Schaar Hilde M. , Arnberg Niklas , Lemckert Angelique A.C. , Havenga Menzo , Baker Andrew H. 
Published: March 2021

ABSTRACTPre-existing immune responses towards adenoviral vector limit the use of a vector based on particular serotypes and its clinical applicability for gene therapy and/or vaccination. Therefore, there is a significant interest to vectorize novel adenoviral types that have low seroprevalence in the human population. Here, we describe the discovery and vectorization of a chimeric human adenovirus, which we call HAdV-20-42-42. Full genome sequencing revealed that this virus is closely related to human serotype 42, except for the penton-base which is derived from serotype 20. The HAdV-20-42-42 vector could be propagated stably to high titers on existing E1-complementing packaging cell lines. Receptor binding studies revealed that the vector utilized both CAR and CD46 as receptors for cell entry. Furthermore, the HAdV-20-42-42 vector was potent in transducing human and murine cardiovascular cells and tissues, irrespective of the presence of blood coagulation factor X. In addition, the vector did not sequester in the liver upon intravenous administration in rodents. Finally, we demonstrate that potent T-cell responses against vector-delivered antigens could be induced upon vaccination. In summary, from the data obtained we conclude that HAdV-20-42-42 provides a valuable addition to the portfolio of adenoviral vectors available to develop safe and efficacious products in the fields of gene therapy and vaccination.IMPORTANCEAdenoviral vectors are currently under investigation for a broad range of therapeutic indications in diverse fields, such as oncology and gene therapy, as well as for vaccination both for human and veterinary use. A wealth of data shows that pre-existing immune responses may limit the use of a vector. Particularly in the current climate of global pandemic, there is a need to expand the toolbox with novel adenoviral vectors for vaccine development. Our data demonstrates that we have successfully vectorized a novel adenovirus serotype with low seroprevalence. The cell transduction data and antigen-specific immune responses inducedin vivodemonstrate that this vector is highly promising for the development of gene therapy and vaccine products.
VCFcontam: A Machine Learning Approach to Estimate Cross-Sample Contamination from Variant Call Data
Authors: McCartney-Melstad Evan , Bi Ke , Han James , Foo Catherine K. 
Published: March 2021

AbstractThe quality of genotyping calls resulting from DNA sequencing is reliant on high quality starting genetic material. One factor that can reduce sample quality and lead to misleading genotyping results is genetic contamination of a sample by another source, such as cells or DNA from another sample of the same or different species. Cross-sample contamination by individuals of the same species is particularly difficult to detect in DNA sequencing data, because the contaminating sequence reads look very similar to those of the intended base sample. We introduce a new method that uses a support vector regression model trained onin silicocontaminated datasets to predict empirical contamination using a collection of variables drawn from VCF files, including the fraction of sites that are heterozygous, the fraction of heterozygous sites with imbalanced allele counts, and parameters describing distributions fit to heterozygous allele fractions in a sample. We use the method described here to train a model that can accurately predict the extent of cross-sample contamination within 1% of the actual fraction, for simulated contaminated samples in the 0-5% contamination range, directly from the VCF file.DefinitionsLesser alleleThe allele in a heterozygous position that received less sequencing read support (which may be either the REF or ALT allele).Lesser allele fraction (LAF)The number of sequencing reads supporting the less frequently observed allele divided by the sum of reads supporting both alleles in the genotype at a given genomic position.