bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal whole blood dilution protocol for preprocessing samples prior to circulating tumor cell capture by size‐based isolation
Authors: Fu Tianhao , Li Sheng , Wei Liang , Huang Shaoyi , Xue Yan , Cui Kai 
Published: June 2022

AbstractBackgroundThis study compared whole blood dilution versus density gradient centrifugation for pre‐processing blood samples prior to circulating tumor cell (CTC) capture on the efficiency of CTC separation by size‐based isolation.Materials and methodsWhole blood from a healthy volunteer spiked with SKBR3 cells was used to optimize the whole blood dilution protocol for sample volume, dilution ratio, and paraformaldehyde (PFA) concentration. Whole blood from healthy volunteers spiked with SKBR3, A549, or PC3 cells, and whole blood from patients with advanced gastric, esophageal, or liver cancer, was used to compare pre‐processing by the optimal whole blood dilution protocol with density‐gradient centrifugation. All statistical evaluations were performed using Student t test of the Statistical Package for Social Sciences (SPSS version 17.0).ResultsIn blood samples from healthy volunteers, spiked SKBR3 cell recovery rates were highest in 5 ml of whole blood, diluted with 2.5 ml buffer, and fixed with 0.2% PFA, and spiked SKBR3, A549, and PC3 cell recovery rates from 5 ml whole blood were significantly greater when using the optimized whole blood dilution protocol (87.67% ± 1.76%, 79.50% ± 0.50% and 71.83% ± 1.04%, respectively) compared to density‐gradient centrifugation (46.83 ± 1.76%, 37.00 ± 1.50% and 41.00 ± 1.50%, respectively).
Generation of MiRNA sponge constructs targeting multiple MiRNAs
Authors: Jie Junjin , Liu Danni , Wang Yifan , Wu Qiong , Wu Tingting , Fang Rong 
Published: June 2022

AbstractBackgroundMicroRNAs(miRNAs) are key regulators of gene expression in plants, animals and some viruses. Hence, alteration of miRNA levels in cells or tissues is common for miRNA studies. Loss‐of‐function of miRNA can be achieved using antisense oligonucleotides, sponges and gene knockout models.MethodsHere, we showed an efficient, rational and economical way to construct multi‐targeted miRNA sponges with desired copies. Four copies of miRNA sponge are used as “building‐blocks”.ResultsThese building‐blocks, which can target same miRNA or different miRNAs, are linked together through ligation. Each time of ligation can double the number of sponge copies.ConclusionsIn this way, we constructed lentivirus vectors harboring sponges targeting miR‐21, miR‐31 and miR‐155 and the combination of two miRNA sponges can inhibit cancer cell growth significantly.
Circulating microRNAs (miR‐16, miR‐22, miR‐122) expression and early diagnosis of hepatocellular carcinoma
Authors: Fang Yujia , Yan Dong , Wang Lixin , Zhang Jie , He Qingfang 
Published: June 2022

AbstractPurposeCirculating microRNA (miRNA) has been reported to have diagnostic value in multiple tumors. To identify serum miRNAs for early diagnosis of hepatocellular carcinoma (HCC), we analyzed the differential miRNA expression between HCC patients and controls.MethodsReal‐time reverse transcription polymerase chain reaction (RT‐PCR) was carried out to detect serum miR‐16, miR‐22, and miR‐122 expression in 100 HCC patients and 100 controls (including hepatitis B, liver cirrhosis, liver metastases, hepatic hemangioma, health group, and each of them had 20 subjects). The miRNA expression results were combined with alpha‐fetoprotein (AFP) to evaluate the diagnostic efficacy in HCC through receiver operating characteristic (ROC) curve. And the target genes were predicted through bioinformatics methods.ResultsCompared with controls, the expression of miR‐16 and miR‐122 significantly increased in early‐stage HCC patients, while no significant changes were detected in miR‐22. The ROC curve analysis demonstrated that miR‐16 and miR‐122 had a high diagnostic efficacy (AUC 0.798 and 0.759), and it was improved when combined with AFP (AUC 0.862). When compared with each of the five groups in the controls, the results showed that miR‐16 of HCC was significantly higher than liver cirrhosis (AUC 0.936), liver metastases, and health; miR‐122 was significantly higher than liver metastases, hepatitis B, and health. Moreover, 175 and 101 potential target genes were regulated by miR‐16 and miR‐122, respectively. And most of the target genes were enriched in the PI3K, MAPK, FoxO signaling pathways, and pathways in cancer.ConclusionOur findings illustrate that both circulating miR‐16 and miR‐122 can provide value for early diagnosis of HCC and they are potential biomarkers for the early‐stage HCC.
Population Pharmacokinetics of Hydroxychloroquine Sulfate in Healthcare Workers, Given for Prophylaxis Against Coronavirus Disease 2019 (COVID‐19) in India
Authors: Raj Jeffrey Pradeep , Gogtay Nithya Jaideep , Pandey Avaneesh , Kakkar Ashish Kumar , Shafiq Nusrat , Mekala Padmaja , Pingali Usharani , Raju Arun Prasath , Mallayasamy Surulivelrajan , Kshirsagar Nilima Arun 
Published: June 2022

AbstractHealthcare workers (HCWs) and frontline workers were recommended hydroxychloroquine (HCQ) 400 mg twice a day on day 1, followed by 400 mg once weekly for the next 7 weeks, as prophylaxis against COVID‐19. There was limited information on the population pharmacokinetics (popPK) of HCQ in an Indian setting when administered for prophylaxis against COVID‐19, and hence this study was proposed. It was a multicentric prospective study conducted at 3 sites in India wherein HCWs who were already on HCQ prophylaxis, who were about to start prophylaxis or who had stopped the prophylaxis for any reason were enrolled. Each participant gave 2 to 6 blood samples at different time points and whole‐blood HCQ concentrations were assayed using liquid chromatography with tandem mass spectrometry (LC MS/MS). popPK analysis was performed using PUMAS 1.1.0. A total of N = 338 blood samples from N = 121 participants were included in the popPK analysis. A 2‐compartment structural model with linear elimination was able to explain the observed data. Body weight was found to be a significant covariate influencing drug clearance. The final model was assessed using goodness‐of‐fit plots, a visual predictive check and a bootstrap, all of which confirmed that the model was appropriate. Simulations based on the current regimen showed that trough values were below the half‐maximal effective concentration (EC50) of 0.7 μmol against COVID‐19. A new weight‐based dosage regimen was proposed to maintain the trough concentration above the EC50 threshold.
Emerging roles of circRNAs in mice kidney with aging
Authors: Gao Fanfan , Li Jie , Liang Shanshan , Wei Limin , He Xin , Liu Sixiu , Cheng Xin , Shi Kehui , Jiang Hongli , Chen Lei 
Published: June 2022

AbstractCircular RNA (circRNA) is a novel type of noncoding RNA expressed in different tissues and species. Up to now, little is known of the function and expression of circRNAs in kidney aging. In this research, we used RNA sequencing to identify 11,929 circRNAs in kidney from 3‐, 12‐, and 24‐month‐old mice, of which 12 circRNAs were validated by qPCR. Based on the validated circRNAs and their predicted miRNA‐mRNA target pairs, a circRNA‐miRNA‐mRNA interactions network was conducted. Bioinformatics analysis for all the mRNAs in the ceRNA network showed that the most enriched gene ontology (GO) term and one of the most enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were associated with endoplasmic reticulum (ER). The network also identified circNpas2, which was decreased significantly in mice kidney during aging, as a hub gene. Subsequently, we found that the cell cycle was arrested in G1 phase and the expression of P53 and P16 increased significantly in the circNpas2‐knockdown cells. Moreover, knockdown of circNpas2 inhibited expression of ER‐related proteins, HSPA5 and ERO1L. Taken together, our findings contribute to a better understanding of the role played by circRNA during kidney aging and provide potential therapeutic targets for the prevention of kidney aging.Research Highlights
This study is the first to systematically analyze the dysregulated circRNAs and ceRNA network during renal aging.
The dysregulated circRNAs during renal aging are most enriched in ER stress‐related pathway.
CircNpas2 regulates senescence in TCMK‐1.
Endothelial extracellular vesicles promote tumour growth by tumour‐associated macrophage reprogramming
Authors: Njock Makon‐Sébastien , O'Grady Tina , Nivelles Olivier , Lion Michelle , Jacques Sophie , Cambier Maureen , Herkenne Stephanie , Muller Florian , Christian Aurélie , Remacle Claire , Guiot Julien , Rahmouni Souad , Dequiedt Franck , Struman Ingrid 
Published: June 2022

AbstractTumour‐derived extracellular vesicles (EVs) participate in tumour progression by deregulating various physiological processes including angiogenesis and inflammation. Here we report that EVs released by endothelial cells in a mammary tumour environment participate in the recruitment of macrophages within the tumour, leading to an immunomodulatory phenotype permissive for tumour growth. Using RNA‐Seq approaches, we identified several microRNAs (miRNAs) found in endothelial EVs sharing common targets involved in the regulation of the immune system. To further study the impact of these miRNAs in a mouse tumour model, we focused on three miRNAs that are conserved between humans and mouse, that is, miR‐142‐5p, miR‐183‐5p and miR‐222‐3p. These miRNAs are released from endothelial cells in a tumour microenvironment and are transferred via EVs to macrophages. In mouse mammary tumour models, treatment with EVs enriched in these miRNAs leads to a polarization of macrophages toward an M2‐like phenotype, which in turn promotes tumour growth.
Nausea and vomiting caused by candida esophagitis in an elderly frail patient
Authors: Kiba Takayoshi , Kotoh Naoki , Namba Yoichiro , Nose Soichiro , Tsuboi Masahiro 
Published: June 2022

AbstractAn elderly frail lady with features of malnutrition was investigated by endoscopy because of nausea and vomiting. Candida esophagitis was found, and there was symptomatic and endoscopic resolution after treatment with amphotericin B.
In silico characterization of fructosyl peptide oxidase properties from Eupenicillium terrenum
Authors: Rahmatabadi Seyyed Soheil , Mobini Keivan , Askari Soudabeh , Najafian Javad , Karami Keyvan , Soleymani Bijan , Mostafaie Ali 
Published: June 2022

AbstractFructosyl peptide oxidase (FPOX) enzyme from Eupenicillium terrenum has a high potential to be applied as a diagnostic enzyme. The aim of the present study is the characterization of FPOX from E. terrenum using different bioinformatics tools. The computational prediction of the RNA and protein secondary structures of FPOX, solubility profile in Escherichia coli, stability, domains, and functional properties were performed. In the FPOX protein, six motifs were detected. The d‐amino acid oxidase motif was found as the most important motif that is a FAD‐dependent oxidoreductase. The cysteines including 97, 154, 234, 280, and 360 showed a lower score than −10 that have a low possibility for participitation in the formation of the SS bond. The 56.52% of FPOX amino acids are nonpolar. Random coils are dominant in the FPOX sequence, followed by alpha‐helix and extended strand. The fpox gene is capable of generating a stable RNA secondary structure (−423.90 kcal/mol) in E. coli. FPOX has a large number of hydrophobic amino acids. FPOX showed a low solubility in E. coli which has several aggregation‐prone sites in its 3‐D structure. According to the scores, the best mutation candidate for increasing solubility was the conversion of methionine 302 to arginine. The melting temperature of FPOX based on its amino acid sequence was 55°C to 65°C. The amounts of thermodynamic parameters for the FPOX enzyme were −137.4 kcal/mol, −3.59 kcal/(mol K), and −6.8 kcal/mol for standard folding enthalpy, heat capacity, and folding free energy, respectively. In conclusion, the in silico study of proteins can provide a valuable method for better understanding the protein properties and functions for use in our purposes.
Pretreatment Multiparametric MRI‐Based Radiomics Analysis for the Diagnosis of Breast Phyllodes Tumors
Authors: Ma Xiaowen , Gong Jing , Hu Feixiang , Tang Wei , Gu Yajia , Peng Weijun 
Published: June 2022

BackgroundPreoperative pathological grading assessment is important for patients with breast phyllodes tumors (PTs).PurposeTo develop and validate a clinical–radiomics model based on multiparametric MRI and clinical information for the pretreatment differential diagnosis of PTs.Study TypeRetrospective.PopulationA total of 216 patients with PTs, 133 in the training cohort (55 benign PTs [BPTs] and 78 borderline/malignant PTs [BMPTs]) and 83 in the validation cohort (28 BPTs and 55 BMPTs).Field Strength/Sequence1.5 T and 3 T; T2‐weighted imaging (T2WI), precontrast T1‐weighted imaging (T1WI) and dynamic contrast‐enhanced T1‐weighted imaging (DCE‐T1WI).AssessmentA total of 3138 radiomics features were computed to decode the imaging phenotypes of PTs. To build the classification models, the following workflow was followed: minimum–maximum scaling normalization method, recursive feature elimination based on ridge regression (Ridge‐RFE), synthetic minority oversampling technique, and support vector machine classifier. We established several models based on the statistically significant features (Ridge‐RFE selected) of each sequence to distinguish BPTs from BMPTs, including precontrast T1WI model, DCE‐T1WI phase 1 model, T1WI feature fusion model, T2WI model, T1WI + T2WI model, clinical feature model, conventional MRI characteristics model, and combined clinical–radiomics model.Statistical TestsUnivariate analysis was utilized to compare variables between the BPT and BMPT groups. The receiver operating characteristic curve (ROC) analysis was used to evaluate the diagnostic performance of these models.ResultsIn the training cohort, the clinical–radiomics model had excellent diagnostic efficiency, with an area under ROC (AUC) of 0.91 ± 0.02 (95% CI: 0.87–0.94). In the validation cohort, the AUCs were 0.79 ± 0.05 (95% CI: 0.70–0.87) for the combined model and 0.77 ± 0.05 (95% CI: 0.67–0.85) for the radiomics model.Data ConclusionCompared with conventional MRI characteristics, radiomics features extracted from multiparametric MRI are helpful for improving the accuracy of differentiating the pathological grades of PTs preoperatively. The model based on radiomics and clinical information is expected to become a potential noninvasive tool for the assessment of PTs grades.Evidence Level4Technical EfficacyStage 2
Transchromosomic bovines‐derived broadly neutralizing antibodies as potent biotherapeutics to counter important emerging viral pathogens with a special focus on SARS‐CoV‐2, MERS‐CoV, Ebola, Zika, HIV‐1, and influenza A virus
Authors: Saied AbdulRahman A. , Nascimento Manuela Sales Lima , do Nascimento Rangel Adriano Henrique , Skowron Krzysztof , Grudlewska‐Buda Katarzyna , Dhama Kuldeep , Shah Jaffer , Abdeen Ahmed , El‐Mayet Fouad S. , Ahmed Hassan , Metwally Asmaa A. 
Published: June 2022

AbstractHistorically, passive immunotherapy is an approved approach for protecting and treating humans against various diseases when other alternative therapeutic options are unavailable. Human polyclonal antibodies (hpAbs) can be made from convalescent human donor serum, although it is considered limited due to pandemics and the urgent requirement. Additionally, polyclonal antibodies (pAbs) could be generated from animals, but they may cause severe immunoreactivity and, once "humanized," may have lower neutralization efficiency. Transchromosomic bovines (TcBs) have been developed to address these concerns by creating robust neutralizing hpAbs, which are useful in preventing and/or curing human infections in response to hyperimmunization with vaccines holding adjuvants and/or immune stimulators over an extensive period. Unlike other animal‐derived pAbs, potent hpAbs could be promptly produced from TcB in large amounts to assist against an outbreak scenario. Some of these highly efficacious TcB‐derived antibodies have already neutralized and blocked diseases in clinical studies. Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has numerous variants classified into variants of concern (VOCs), variants of interest (VOIs), and variants under monitoring. Although these variants possess different mutations, such as N501Y, E484K, K417N, K417T, L452R, T478K, and P681R, SAB‐185 has shown broad neutralizing activity against VOCs, such as Alpha, Beta, Gamma, Delta, and Omicron variants, and VOIs, such as Epsilon, Iota, Kappa, and Lambda variants. This article highlights recent developments in the field of bovine‐derived biotherapeutics, which are seen as a practical platform for developing safe and effective antivirals with broad activity, particularly considering emerging viral infections such as SARS‐CoV‐2, Ebola, Middle East respiratory syndrome coronavirus, Zika, human immunodeficiency virus type 1, and influenza A virus. Antibodies in the bovine serum or colostrum, which have been proved to be more protective than their human counterparts, are also reviewed.
Development of an efficient iterative genome editing method in Bacillus subtilis using the CRISPR‐AsCpf1 system
Authors: Zhao Xingcong , Chen Xi , Xue Yanbing , Wang Xuedong 
Published: June 2022

AbstractBacillus subtilis is a useful chassis in the fields of synthetic biology and metabolic engineering for chemical production. Here, we constructed CRISPR‐AsCpf1‐based expression plasmids with the temperature‐sensitive replicon for iterative genome editing in B. subtilis. This method allowed gene insertion and large genomic deletion with an editing efficiency of up 80%–100% and rapid plasmid curing to facilitate the iterative genome editing in B. subtilis 168. Using the customized CRISPR‐AsCpf1 system, we successfully and efficiently implemented the related gene editing in B. subtilis 168 for hyaluronic acid (HA) biosynthesis, HA synthase gene (hasA) insertion, UDP‐glucose‐dehydrogenase gene (tuaD) insertion, and eps gene cluster (epsA‐O) deletion. The heterologous production of HA was realized by the engineered strain with a yield of 1.39 g/L. These results support the finding that the CRISPR‐AsCpf1 system is highly efficient in bacteria genome editing and provide valuable guidance and essential references for genome engineering in B. subtilis using the CRISPR‐AsCpf1 system.
Efficient searching for NICE public health guidelines: Would using fewer sources still find the evidence?
Authors: Levay Paul , Heath Andrea , Tuvey Daniel 
Published: June 2022

AbstractSystematic searches are integral to identifying the evidence that is used in National Institute for Health and Care Excellence (NICE) public health guidelines (PHGs). This study analyses the sources, including bibliographic databases and other techniques, required for PHGs. The aims were to analyse the sources used to identify the publications included in NICE PHGs; and to assess whether fewer sources could have been searched to retrieve these publications. Data showing how the included publications had been identified was collated using search summary tables. Three scenarios were created to test various combinations of sources to determine whether fewer sources could have been used. The sample included 29 evidence reviews, compiled using 13 searches, to support 10 PHG topics. Across the PHGs, 23 databases and six other techniques retrieved included publications. A mean reduction in total results of 6.5% could have been made if the minimum set of sources plus Cochrane Library, Embase, and MEDLINE were searched. On average, Cochrane Library, Embase, and MEDLINE contributed 76.8% of the included publications, with other databases adding 11% and other techniques 12.2%. None of the searches had a minimum set that was comprised entirely of databases. There was not a core set of sources for PHGs. A range of databases and techniques, covering a multi‐disciplinary evidence base, was required to identify all included publications. It would be possible to reduce the number of sources searched and make some gains in productivity. It is important to create a tailored set of sources to do an efficient search.
Temporal Sequence of Laryngeal Vestibule Closure and Reopening is Associated With Airway Protection
Authors: Shu Kechen , Perera Subashan , Mahoney Amanda S. , Mao Shitong , Coyle James L. , Sejdić Ervin 
Published: June 2022

BackgroundUpper esophageal sphincter opening (UESO), and laryngeal vestibule closure (LVC) are two essential kinematic events whose timings are crucial for adequate bolus clearance and airway protection during swallowing. Their temporal characteristics can be quantified through time‐consuming analysis of videofluoroscopic swallow studies (VFSS).ObjectivesWe sought to establish a model to predict the odds of penetration or aspiration during swallowing based on 15 temporal factors of UES and laryngeal vestibule kinematics.MethodsManual temporal measurements and ratings of penetration and aspiration were conducted on a videofluoroscopic dataset of 408 swallows from 99 patients. A generalized estimating equation model was deployed to analyze association between individual factors and the risk of penetration or aspiration.ResultsThe results indicated that the latencies of laryngeal vestibular events and the time lapse between UESO onset and LVC were highly related to penetration or aspiration. The predictive model incorporating patient demographics and bolus presentation showed that delayed LVC by 0.1 s or delayed LVO by 1% of the swallow duration (average 0.018 s) was associated with a 17.19% and 2.68% increase in odds of airway invasion, respectively.ConclusionThis predictive model provides insight into kinematic factors that underscore the interaction between the intricate timing of laryngeal kinematics and airway protection. Recent investigation in automatic noninvasive or videofluoroscopic detection of laryngeal kinematics would provide clinicians access to objective measurements not commonly quantified in VFSS. Consequently, the temporal and sequential understanding of these kinematics may interpret such measurements to an estimation of the risk of aspiration or penetration which would give rise to rapid computer‐assisted dysphagia diagnosis.Level of Evidence2 Laryngoscope, 133:521–527, 2023