bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlations between miR-223/mTOR/S6K pathway and RA activity and antibody levels
Authors: Jiang Zhen , Liu Juan , Bai Wen-hua 
Published: April 2023

Abstract
Objective: To investigate the expression levels of miR-223 and mTOR/S6K pathways in synovial tissues of rheumatoid arthritis (RA) and their correlation with disease activity and antibody levels.
Methods: 17 hospitalized patients with moderate to severe disease RA were selected. During the same period, 9 patients hospitalized for knee osteoarthritis (OA) operation were involved. The synovial tissue of the knees was obtained under the guidance of ultrasound in RA group and obtained by orthopedic surgeons in OA group. The expression levels of mTOR, S6K, RPS6 mRNAs and miR-223 level in the synovial tissue were detected by QRT-PCR. The differences of miR-223 level and the mRNA levels of mTOR, S6K and RPS6 between the two groups were analyzed. The correlations between the level of miR-223 and the mRNA levels of mTOR, S6K and RPS6 were analyzed and the correlations between miR-223 level, the levels of mTOR, S6K, RPS6 mRNA and anti-CCP antibody and disease activity indicators were also analyzed in RA group.
Results: The miR-223 level in RA group was significantly increased compared with OA group (P<0.05), and the mRNA levels of S6K and RPS6 in RA group were significantly decreased compared with OA group (P<0.05). The miR-223 level in RA group was negatively correlated with the mRNA levels of S6K and RPS6 (P<0.05), but there was no significant correlation between miR-223 level and the level of mTOR mRNA (P>0.05). The levels of miR-223 and mTOR mRNA in RA group were negatively correlated with the serum anti-CCP antibody level (P<0.05), and the level of RPS6 mRNA was positively correlated with the anti-CCP antibody level (P<0.05). The miR-223 level in RA group was positively correlated with the serum CRP level (P<0.05). RPS6 mRNA level was negatively correlated with CRP level (P<0.05).
Conclusion: Abnormal miR-223/mTOR/S6K pathway exists in the synovial tissue of RA knee joints, which is correlated with the levels of anti-CCP antibody and CRP, indicating the direction for further research on the pathogenesis of RA.
Pulmonary parenchymal segmentation based on CT images of lungs in a highland population
Authors: Zhang Lijun , Dong Jianmin , Ye Kai , Wang Yinghan 
Published: April 2023

Abstract
In response to the more complex characterization of lung CT image data in the highland population, the problem of left and right lung adhesions, gross contours and blurred borders that are very likely to arise during lung parenchymal segmentation, we propose a new network structure based on U-Net for lung parenchyma segmentation in highland population. First, we introduce residual block, which replaced ordinary convolution with residual convolution in the encoding stage to improve the speed of network convergence and accuracy; Then, the Augmented Attention Module (AAM) is introduced in the skip connection part to enhance the feature of the lung parenchyma contour information; Finally, considering the processing efficiency of the network, we reduce the depth of the network model to 4 layers. After that, we verify the effectiveness of our method on the public dataset LUNA16, and the segmentation results show that the selected evaluation indicators are improved to varying degrees. This shows that our proposed method has a good effect on the segmentation of lung parenchyma. Finally, applying our method to lung CT image segmentation in a highland population gives some advantages over other existing methods.
Development and validation of a nomogram for predicting metabolic-associated fatty liver disease in the Chinese physical examination population
Authors: Zhou Bingqian , Gong Ni , Huang Xinjuan , Zhu Jingchi , Qin Chunxiang , He Qingnan 
Published: April 2023

Abstract
Aim We aim to develop and validate a nomogram including readily available clinical and laboratory indicators to predict the risk of MAFLD in the Chinese physical examination population.Methods The annual physical examination data of Chinese adults from 2016 to 2020 were retrospectively analyzed. We extracted the clinical data of 138 664 subjects and randomized participants to the development and validation groups (7:3). Significant predictors associated with MAFLD were identified by using univariate and random forest, and the nomogram was constructed to predict the risk of MAFLD based on a Lasso-Logistic model. Receiver operating characteristic curve analysis, calibration curves, and decision curve analysis were used to verify the discrimination, calibration, and clinical practicability of the nomogram, respectively.Results Ten variables were selected to establish the nomogram for predicting MAFLD risk: sex, age, waist circumference, uric acid, BMI, WHR, SBP, FPG, TG, and ALT. The nomogram built on the non-overfitting multivariable model showed good prediction of discrimination (AUC 0.914, 95% CI: 0.911–0.917), calibration, and clinical utility.Conclusions This nomogram can be used as a quick screening tool to assess MAFLD risk and identify individuals at high risk of MAFLD, thus contributing to the improved management of MAFLD.
Optimal placement of ureteral access sheath in retrograde intrarenal surgery
Authors: Chen Yujun , Cheng Xiaofeng , Yang Heng , Deng Wen , Chen Luyao , Zhou Xiaocheng , Wang Gongxian 
Published: April 2023

Abstract
Purpose: To explore the optimal location of ureteral access sheath (UAS) in retrograde intrarenal lithotripsy (RIRS).
Materials and methods: RIRS model was built by AutoCAD 2011 software, and imported COMSOL 5.6 software to computer simulation. An RIRS model was constructed in vitro to analyze the distribution pattern of stone fragments, and compare the weight of stone fragments carried out by the irrigation fluid when the UAS is in different positions.
Results: Computer simulation showed that the highest flow of irrigation fluid was in the channel of flexible ureteroscopy (f-URS) and in the lumen of UAS. From the f-URS to the renal collection system and then to the UAS, the velocity of irrigation fluid changes gradually from high-flow to low-flow and then to high-flow. When the f-URS and the UAS are at the same level, the irrigation fluid is always at a state of high flow during the process from f-URS to UAS. When the f-URS and the UAS are at the same level, it can increase the local intrarenal pressure (IRP) at the front of f-URS. The stone fragments are mainly sediment in the low-flow region of irrigation fluid. More stone fragments could follow the irrigation fluid out of the body when the tip of f-URS and the tip of UAS are at the same level (P＜0.001).
Conclusions: The UAS should be brought closer to the stone in RIRS. And more stone fragments can be taken out of the body by the effect of irrigation fluid.
Agreement between the Multi-Beat Analysis algorithm for cardiac output estimation and 2D echocardiography in the ICU
Authors: Saseedharan Sanjith , Thingna Aalia , Pawar Komal , Kadam Vaijayant 
Published: April 2023

Abstract
Background Cardiac output (CO) and stroke volume (SV) monitoring are cornerstones of hemodynamic management in patients at risk of shock. The multi-beat analysis (MBA) method provides continuous estimates of CO and SV by analysis of a patient’s arterial blood pressure waveform. In this study we assessed the agreement of CO and SV between 2D echocardiography (CO-ECHO and SV-ECHO) and the multi-beat analysis (MBA) method via the Argos monitor (CO-MON and SV-MON).Methods Fifty patients with a wide range of diagnoses were prospectively enrolled in the ICU in this observational, method comparison study. One set of paired, simultaneous measurements was recorded for each patient.Results for the 50 included data points in the study the mean difference between CO-ECHO and CO-MON was − 0.05 ± 0.58 L/min with limits of agreement from − 1.18 to + 1.08 L/min and a percentage error of 21.5%. The mean difference between SV-ECHO and SV-MON was − 0.9 ± 6.6 mL with limits of agreement from − 13.9 to + 12.0 mL and a percentage error of 22.8%.Conclusion Accuracy of the MBA method was clinically acceptable as compared to 2D echocardiography.
Non-Local EPR Correlations using Quaternion Spin
Authors: Sanctuary Bryan 
Published: April 2023

Abstract
A statistical simulation is presented which reproduces the correlation obtained from EPR coincidence experiments without non-local connectivity. We suggest that spin carries two complementary properties. In addition to the spin polarization, we identify spin coherence. This spin attribute is anti-symmetric and generates the helicity. In addition this spin has structure formed from two orthogonal magnetic moments. From these, a resonance spin results from their coupling in free flight. Upon encountering a filter, the resonance spin 1 decouples back into two independent spins of ½, with one aligning with the filter and the other randomizing.
The process of decoupling the resonance spin is responsible for the quantum correlation which results in the observe violation of Bell's Inequalities. The polarized states give a CHSH value of 2 while the resonance spin give a CHSH value of 1. Coherence can only be formulated by the existence of a bivector which gives a spin the same geometric structure as a photon.
Although this work is not about Bell's theorem, we note that there are no hidden variables (HV). The only local variable is the angle that orients a spin on the Bloch sphere, first identified in the 1920's. The new features introduced are changing the spin symmetry from SU(2) to the quaternion group, Q8, and the introduction of a bivector into spin which leads to an element of reality which is anti-Hermitian. The calculations use standard spin algebra, and properties of quaternions.
March 28, 2023
Precise isolation of high-quality RNA from leaves and storage roots of cassava (Manihot esculenta) for gene expression studies.
Authors: Reuben-Kalu Jane Ijeoma , Eswaran Kokiladevi , Muthurajan Raveendran , Doraiswamy Uma , Venkatasamy Balasubramani , Shanmugam Kavitha P. 
Published: April 2023

Abstract
The isolation of RNA from leaves and storage roots of cassava (Manihot esculenta) is a challenging one, due to the presence of large amounts of polyphenolic compounds, polysaccharides, and tuber proteins. RNA with high quality and intact integrity is vital for gene expression studies. We hereby report a precise, reproducible, and less cumbersome technique for isolating high-quality RNA from leaves and storage roots of cassava with minimal contamination from polyphenols, polysaccharides, and other secondary metabolites, using affordable reagents. This protocol functions without guanidinium salts in the extraction buffer. The presence of guanidinium salts usually leads to the formation of agglomerates during the extraction of RNA from plant tissues with high starch contents. RNA was isolated from leaves and storage roots of 10 different casava genotypes which yielded between 1576.1 to 2861.9 µg/ml for RNA isolated from the leaf tissues and 2761.2 to 3873.5 µg/ml for RNA isolated from the storage roots. The A260:A280 ratios of the total RNA were more than 2.0 for both leaf and storage root samples, indicating minimal contamination from polysaccharides and polyphenols. The RNA samples recorded intact integrity, as demonstrated by clear 28 S and 18 S rRNA bands observed on agarose gel electrophoresis. The RIN values ranged between 7.2 to 8.0. Also, the RNA samples were successfully used for transcriptome sequencing. The present method which yielded high-quality and transcriptionally competent RNA samples is suitable for use in gene expression studies and downstream applications in molecular breeding of cassava and related root/tuber crops.
Effect of glucocorticoids on the development of COVID-19-associated pulmonary aspergillosis: a meta-analysis of 21 studies and 5174 patients
Authors: Hashim Zia , Nath Alok , Khan Ajmal , Gupta Mansi , Kumar Anup , Chatterjee Riksoam , Dhiman Radha Krishan , Hoenigl Martin , Tripathy Naresh Kumar 
Published: April 2023

Abstract
Objective:
COVID-19-associated pulmonary aspergillosis (CAPA) remains a high mortality mycotic infection throughout the pandemic, and glucocorticoids (GCs) may be its root cause. We aimed to evaluate the effect of systemic GC treatment on the development of CAPA.
Methods: We systematically searched the PubMed, Google Scholar, Scopus, and Embase databases to collect eligible studies published until December 31, 2022. The pooled outcome of CAPA development was calculated as the log odds ratio (LOR) with 95% confidence intervals (CI) using a random effect model.
Results: A total of 21 studies with 5174 patients were included. Of these, 20 studies with 4675 patients consisting of 2565 treated with GC but without other immunomodulators (GC group) and 2110 treated without GC and other immunomodulators (controls) were analyzed. The pooled LOR of CAPA development was higher for the GC group than for the control group (0.54; 95% CI: 0.22, 0.86; p<0.01). In the subgroups, the pooled LOR was higher for high-dose GC (0.90; 95% CI: 0.17, 1.62: p=0.01) and dexamethasone (0.71; 95% CI: 0.35, 1.07; p<0.01)-treated patients, but there was no significant difference for low-dose GC (0.41; 95% CI: -0.07, 0.89; p=0.09)- and non-dexamethasone GC (0.21; 95% CI: -0.36, 0.79; p=0.47)-treated patients versus controls.
Conclusion: GC treatment increased the risk of CAPA development, and the risk was associated with the use of high-dose GC or dexamethasone therapy.
Multi-laboratory evaluation of staphylococcal enterotoxin detection by the RIDASCREEN® SE A, B, C, D, E ELISA kit
Authors: McCallum Kristina , Phillips Robert 
Published: April 2023

The RIDASCREEN® SE A, B, C, D, E kit was evaluated for use as a secondary test for the detection of staphylococcal enterotoxins in meat matrices Seven state agriculture and public health laboratories participated in the study. The study demonstrated that the kit is able to detect each of the five serotypes in hot dogs, breaded chicken nuggets, bologna, and ready-to-eat barbeque meat. Staphylococcal enterotoxins were detected at a minimum of 1.0 ng/g in all matrices and at levels as low as 0.375 ng/g in some matrices. While cross-reaction between some serotypes is seen, false negative and false positive results were minimally observed. When used along with the BioMerieux VIDAS® SET2 automated immunoassay test, this kit provides a secondary assay to use as confirmation for the presence of staphylococcal enterotoxins in a meat sample.https://doi.org/10.21423/jrs-v07p001
Core and Supplementary Studies to Assess the Safety of Genetically Modified (GM) Plants Used for Food and Feed
Authors: Brune Phil , Chakravarthy Suma , Graser Gerson , Mathesius Carey A. , McClain Scott , S. Petrick Jay , Sauve-Ciencewicki Alaina , Schafer Barry , Silvanovich Andre , Brink Kent , Burgin Kristina , Bushey Dean , L. Cheever Matthew , Edrington Thomas , Fu Huihua , Habex Veerle , Herman Rod A. , Islamovic Emir , Lipscomb Elizabeth A. , Motyka Shawn , Privalle Laura , Ranjan Rakesh , Roper Jason , Song Ping , Tilton Gregory , Zhang John , Waters Stephen , Ramos Adela , Hendrickson Culler Angela , Hunst Penny , Gast Rachel , Mahadeo Debbie , Goodwin Laurie 
Published: April 2023

Genetically modified (GM) plants used for food and feed have an established history of safe use over more than 25 years of their commercialization. Developers and regulatory authorities have accumulated extensive experience in evaluating their safety over time. The studies required for the safety assessment of GM plants used for food and feed should now be re-defined to leverage this experience and increased scientific knowledge. This paper, a companion paper for Waters et al. also published in this issue, presents a systematic approach for the safety assessment of newly expressed proteins (NEPs) in GM plants by evaluating the two components of risk: hazard and exposure. Although the paper focuses on NEPs, the principles presented could also apply to other expression products that do not result in a NEP. A set of core studies is recommended, along with supplementary studies, if needed, to evaluate whether the GM plant poses risk. Core studies include molecular and protein characterization and hazard identification encompassing toxicity and allergenicity. In the absence of hazard, core studies are sufficient to conclude that GM plants are as safe as their conventional counterparts. Depending on the GM trait and intended use, supplementary studies should be performed to characterize hazard and exposure when a hazard is identified. Problem formulation should be used to identify hypothesis-driven supplementary studies. Acute toxicity studies, compositional assessment, and dietary exposure assessment are recommended to be hypothesis-driven supplementary studies. Further discussion on the current food and feed safety assessment landscape for GM plants and the use of problem formulation as a tool for identifying supplementary studies can be found in the companion paper [62].
doi: 10.21423/jrs-v09i1brune
Stacked Trait Products Are As Safe As Non-Genetically Modified (GM) Products Developed By Conventional Breeding Practices
Authors: Goodwin Laurie , Hunst Penny , Burzio Luis , Rowe Laura , Money Stephanie , Chakravarthy Suma 
Published: April 2023

International safety assessments and independent publications conclude that stacking genetically modified (GM) traits (events) through conventional breeding poses no greater risk to food or feed safety than stacking multiple non-GM traits by conventional breeding. Stacked trait products are not substantially different from their conventional comparator or their GM parent plants. Additional safety assessment of a stacked trait product produced by conventional breeding should not be required unless there is a plausible and testable hypothesis for interaction of the traits. However, the different approaches employed for the regulation of stacked trait products between countries results in asynchronous approvals, increasing the potential for trade flow disruptions, and adds to the regulatory burden for product developers. Considering their proven safety and benefit over the past 20+ years, regulatory authorities in some countries do not regulate stacked trait products, while others have simplified the approval process based on experience and sound science, reducing or eliminating the need for additional regulatory oversight. Countries that choose to regulate stacked trait products should consider integrating the more than 20 years of safety assessment experience, history of safe use, and global regulatory experience, in their approach to reduce redundancy, simplify regulations, and minimize the likelihood for trade disruption.
doi: 10.21423/jrs-v09i1goodwin
Regulatory Assessment of Off-Target Changes and Spurious DNA Insertions in Gene-Edited Organisms for Agri-Food Use
Authors: Lema Martin 
Published: April 2023

Worldwide, an increasing number of regulatory systems have begun to consider applications for the authorization of activities involving gene-edited organisms for agri-food use. Although a handful of countries have made advances in establishing regulatory criteria and gathering practical experience in this regard, there is still a general need for regulatory cooperation concerning capacity building and development of harmonized criteria. Consequently, many biotechnology regulators need to quickly become more acquainted with the numerous technological possibilities enclosed under the concept of "gene editing", and to incorporate criteria for their regulatory assessment. This article contains a simplified introduction to the state of the art in genome editing, described from a regulatory perspective. In particular, two issues of higher practical importance are covered in detail, namely, off-target effects and unintended DNA insertions. The detailed review of current evidence regarding those issues serves as the basis for proposing concrete regulatory criteria to address them.
doi: 10.21423/jrs-v09i1lema
Recommendations for Science-Based Safety Assessment of Genetically Modified (GM) Plants for Food and Feed Uses
Authors: Waters Stephen , Ramos Adela , Hendrickson Culler Angela , Hunst Penny , Zeph Lawrence , Gast Rachel , Mahadeo Debbie , Sottosanto Jordan , Huber Scott , Shan Guomin , Chakravarthy Suma , Goodwin Laurie 
Published: April 2023

Since the commercial introduction of genetically modified (GM) plants in agriculture over two decades ago, technology developers and regulatory authorities have gained significant experience in assessing their safety based on assessing potential impact to humans, animals and the environment. Over 3500 independent regulatory agency reviews have positively concluded on the safety of GM plants for food and feed. Yet, divergent and increased regulatory requirements have led to delayed and asynchronous approvals, and have restricted access to innovative products for farmers and consumers. With accumulated knowledge from safety assessments conducted so far, an enhanced understanding of plant genomes, and a history of safe use, it is time to re-evaluate the current approaches to the regulation of GM plants used for food and feed. A stepwise approach using weight-of-evidence should be sufficient for the safety assessment of newly expressed proteins in GM plants. A set of core studies including molecular characterization, expression and characterization of the newly expressed proteins (or other expression product), and safety assessment of the introduced protein are appropriate to characterize the product and assess safety. Using data from core studies, and employing a “problem formulation” approach, the need for supplementary hypothesis-driven or case-by-case studies can be determined. Employing this approach for the evaluation of GM plants will remove regulatory data requirements that do not provide value to the safety assessment and provide a consistent framework for global regulation.
doi: 10.21423/jrs-v09i1waters
Repercussions of politicized regulation exemplified by compulsory new TC1507-maize 90-day rat feeding study
Authors: Roper Jason , Carlson Anne , Podevin Nancy , Wang Yiwei , Mathesius Carey , Herman Rod 
Published: April 2023

Politicized and prescriptive regulation of genetically modified (GM) crops has unintended adverse effects, including misdirected resources and reduced benefits. In the case of animal testing, this suboptimal use of resources includes the needless sacrifice of animals. Whole-food animal feeding studies are generally of negligible value in the risk assessment of GM crops, a position that was affirmed by the European Food Safety Authority (EFSA). Contrary to EFSA’s 2011 position, in 2013, the European Commission directed that 90-day rat studies be conducted for new GM events. As no EFSA guidance was available for hypothesis-free 90-day rat feeding studies, EFSA interpreted this as a mandate to develop a prescriptive study design. Recently, EFSA has retroactively required 90-day rat studies be completed under new study guidelines for previously approved component single events as part of the approval of breeding stacks. Having been unable to secure a derogation (exemption) from EFSA, a new compulsory 90-day rat study was conducted with TC1507 maize to support a breeding-stack submission. As previously shown, TC1507 maize does not adversely affect rats. This politically driven additional animal testing is risk disproportionate, at odds with European and international standards for animal welfare, and provides no scientific value to the safety assessment for GM breeding stacks.