bluuebunny/crossref_metadata_2025_split huggingface dataset:
Migrasomes, a new mode of intercellular communication
Authors: Jiang Yuyun , Liu Xi , Ye Jixian , Ma Yongbin , Mao Jiahui , Feng Dingqi , Wang Xuefeng 
Published: May 2023

AbstractMigrasomes are newly discovered extracellular vesicles (EVs) that are formed in migrating cells and mediate intercellular communication. However, their size, biological generation, cargo packaging, transport, and effects on recipient cells by migrasomes are different from those of other EVs. In addition to mediating organ morphogenesis during zebrafish gastrulation, discarding damaged mitochondria, and lateral transport of mRNA and proteins, growing evidence has demonstrated that migrasomes mediate a variety of pathological processes. In this review, we summarize the discovery, mechanisms of formation, isolation, identification, and mediation of cellular communication in migrasomes. We discuss migrasome-mediated disease processes, such as osteoclast differentiation, proliferative vitreoretinopathy, tumor cell metastasis by PD-L1 transport, immune cell chemotaxis to the site of infection by chemokines, angiogenesis promotion via angiogenic factors by immune cells, and leukemic cells chemotaxis to the site of mesenchymal stromal cells. Moreover, as new EVs, we propose the potential of migrasomes for disease diagnosis and treatment.
Potential of CRISPR/Cas system as emerging tools in the detection of viral hepatitis infection
Authors: Bahrulolum Howra , Tarrahimofrad Hossein , Rouzbahani Fatemeh Nouri , Nooraei Saghi , Sameh Mehdi Mousavi , Hajizade Abbas , Ahmadian Gholamreza 
Published: May 2023

AbstractViral hepatitis, the most common cause of inflammatory liver disease, affects hundreds of millions of people worldwide. It is most commonly associated with one of the five nominal hepatitis viruses (hepatitis A–E viruses). HBV and HCV can cause acute infections and lifelong, persistent chronic infections, while HAV and HEV cause self-limiting acute infections. HAV and HEV are predominantly transmitted through the fecal-oral route, while diseases transmitted by the other forms are blood-borne diseases. Despite the success in the treatment of viral hepatitis and the development of HAV and HBV vaccines, there is still no accurate diagnosis at the genetic level for these diseases. Timely diagnosis of viral hepatitis is a prerequisite for efficient therapeutic intervention. Due to the specificity and sensitivity of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated sequences (Cas) technology, it has the potential to meet critical needs in the field of diagnosis of viral diseases and can be used in versatile point-of-care (POC) diagnostic applications to detect viruses with both DNA and RNA genomes. In this review, we discuss recent advances in CRISPR–Cas diagnostics tools and assess their potential and prospects in rapid and effective strategies for the diagnosis and control of viral hepatitis infection.
An investigation of the internal morphology of asbestos ferruginous bodies: constraining their role in the onset of malignant mesothelioma
Authors: Avramescu Maya-Liliana , Potiszil Christian , Kunihiro Tak , Okabe Kazunori , Nakamura Eizo 
Published: May 2023

Abstract
Background
Asbestos is a fibrous mineral that was widely used in the past. However, asbestos inhalation is associated with an aggressive type of cancer known as malignant mesothelioma (MM). After inhalation, an iron-rich coat forms around the asbestos fibres, together the coat and fibre are termed an “asbestos ferruginous body” (AFB). AFBs are the main features associated with asbestos-induced MM. Whilst several studies have investigated the external morphology of AFBs, none have characterised the internal morphology. Here, cross-sections of multiple AFBs from two smokers and two non-smokers are compared to investigate the effects of smoking on the onset and growth of AFBs. Morphological and chemical observations of AFBs were undertaken by transmission electron microscopy, energy dispersive x-ray spectroscopy and selected area diffraction.

Results
The AFBs of all patients were composed of concentric layers of 2-line or 6-line ferrihydrite, with small spherical features being observed on the outside of the AFBs and within the cross-sections. The spherical components are of a similar size to Fe-rich inclusions found within macrophages from mice injected with asbestos fibres in a previous study. As such, the spherical components composing the AFBs may result from the deposition of Fe-rich inclusions during frustrated phagocytosis. The AFBs were also variable in terms of their Fe, P and Ca abundances, with some layers recording higher Fe concentrations (dense layers), whilst others lower Fe concentrations (porous layers). Furthermore, smokers were found to have smaller and overall denser AFBs than non-smokers.

Conclusions
The AFBs of smokers and non-smokers show differences in their morphology, indicating they grew in lung environments that experienced disparate conditions. Both the asbestos fibres of smokers and non-smokers were likely subjected to frustrated phagocytosis and accreted mucopolysaccharides, resulting in Fe accumulation and AFB formation. However, smokers’ AFBs experienced a more uniform Fe-supply within the lung environment compared to non-smokers, likely due to Fe complexation from cigarette smoke, yielding denser, smaller and more Fe-rich AFBs. Moreover, the lack of any non-ferrihydrite Fe phases in the AFBs may indicate that the ferritin shell was intact, and that ROS may not be the main driver for the onset of MM.
Analysis of 665 thyroid nodules using both EU-TIRADS and ACR TI-RADS classification systems
Authors: Borges Ana Paula , Antunes Célia , Caseiro-Alves Filipe , Donato Paulo 
Published: May 2023

Abstract
Background
Ultrasound-based classification systems allow stratification of thyroid nodules to recommend fine-needle aspiration (FNA) based on their malignancy risk. However, these have discrepancies that may have an impact in thyroid cancer detection. We aimed to compare European Thyroid Association (EU-TIRADS) and American College of Radiology (ACR TI-RADS), in terms of FNA indication and diagnostic performance.

Methods
Retrospective study of 665 thyroid nodules from 598 patients who underwent ultrasound and fine-needle aspiration at a tertiary-care institution between January 1st of 2016 and July 31st of 2019. Based on their sonographic features they were classified according to the EU-TIRADS and ACR TI-RADS classification and then their cytological results were obtained. Differences in FNA indications according to these two classifications were analysed. In patients who underwent surgical removal of the nodules, the final pathological diagnosis was obtained.

Results
A statistically significant association was found between EU-TIRADS and ACR TI-RADS classification systems (p < 0.001). ACR TI-RADS allowed greatest reduction in FNA performed (32% vs 24.5%). A different risk category was obtained in 174 (26.1%) nodules, mostly higher with EU-TIRADS. The indication to FNA changed in 54 (8.1%) nodules (49 only indicated following EU-TIRADS recommendations), of which 4 had Bethesda IV and 5 had Bethesda III cytology. The FNA indication in a higher number of nodules using EU-TIRADS was due to difference in the dimensional threshold for FNA on low-risk nodules; to the fact that hypoechogenicity in a mixed nodule ascribes it moderate risk, while using ACR TI-RADS it would only be considered of low risk, and to the use of isolated sonographic features, namely marked hypoechogenicity, microcalcifications and irregular margins, to automatically categorize a nodules as high risk in EU-TIRADS, while ACR TI-RADS requires a group of potentially suspicious features to consider a nodule of high risk. The analysis of pathology proven nodules revealed equally good sensitivity of both systems in the detection of malignancy, but weak specificity, slightly greater with ACR TI-RADS (27.1% vs 18.6%).

Conclusions
The EU-TIRADS and ACR TI-RADS are both suitable to assess thyroid nodules and through risk stratification avoid unnecessary FNA. FNA was less performed using ACR TI-RADS, which was slightly more efficiency in excluding malignancy.
Effects of airway pressure release ventilation on lung physiology assessed by electrical impedance tomography in patients with early moderate-to-severe ARDS
Authors: Li Ruiting , Wu Yongran , Zhang Hongling , Wang Azhen , Zhao Xin , Yuan Shiying , Yang Le , Zou Xiaojing , Shang You , Zhao Zhanqi 
Published: May 2023

Abstract
Objective
The aim of this study was to investigate the physiological impact of airway pressure release ventilation (APRV) on patients with early moderate-to-severe acute respiratory distress syndrome (ARDS) by electrical impedance tomography (EIT).

Methods
In this single-center prospective physiological study, adult patients with early moderate-to-severe ARDS mechanically ventilated with APRV were assessed by EIT shortly after APRV (T0), and 6 h (T1), 12 h (T2), and 24 h (T3) after APRV initiation. Regional ventilation and perfusion distribution, dead space (%), shunt (%), and ventilation/perfusion matching (%) based on EIT measurement at different time points were compared. Additionally, clinical variables related to respiratory and hemodynamic condition were analyzed.

Results
Twelve patients were included in the study. After APRV, lung ventilation and perfusion were significantly redistributed to dorsal region. One indicator of ventilation distribution heterogeneity is the global inhomogeneity index, which decreased gradually [0.61 (0.55–0.62) to 0.50 (0.42–0.53), p < 0.001]. The other is the center of ventilation, which gradually shifted towards the dorsal region (43.31 ± 5.07 to 46.84 ± 4.96%, p = 0.048). The dorsal ventilation/perfusion matching increased significantly from T0 to T3 (25.72 ± 9.01 to 29.80 ± 7.19%, p = 0.007). Better dorsal ventilation (%) was significantly correlated with higher PaO2/FiO2 (r = 0.624, p = 0.001) and lower PaCO2 (r = -0.408, p = 0.048).

Conclusions
APRV optimizes the distribution of ventilation and perfusion, reducing lung heterogeneity, which potentially reduces the risk of ventilator-induced lung injury.
Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize
Authors: Hartwig Thomas , Banf Michael , Prietsch Gisele Passaia , Zhu Jia-Ying , Mora-Ramírez Isabel , Schippers Jos H. M. , Snodgrass Samantha J. , Seetharam Arun S. , Huettel Bruno , Kolkman Judith M. , Yang Jinliang , Engelhorn Julia , Wang Zhi-Yong 
Published: May 2023

Abstract
Background
Genetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic diversity. Brassinosteroid is a growth hormone that has major effects on plant phenotypes. Genetic variation in brassinosteroid-responsive cis-elements likely contributes to trait variation. Pinpointing such regulatory variations and quantitative genomic analysis of the variation in TF-target binding, however, remains challenging. How variation in transcriptional targets of signaling pathways such as the brassinosteroid pathway contributes to phenotypic variation is an important question to be investigated with innovative approaches.

Results
Here, we use a hybrid allele-specific chromatin binding sequencing (HASCh-seq) approach and identify variations in target binding of the brassinosteroid-responsive TF ZmBZR1 in maize. HASCh-seq in the B73xMo17 F1s identifies thousands of target genes of ZmBZR1. Allele-specific ZmBZR1 binding (ASB) has been observed for 18.3% of target genes and is enriched in promoter and enhancer regions. About a quarter of the ASB sites correlate with sequence variation in BZR1-binding motifs and another quarter correlate with haplotype-specific DNA methylation, suggesting that both genetic and epigenetic variations contribute to the high level of variation in ZmBZR1 occupancy. Comparison with GWAS data shows linkage of hundreds of ASB loci to important yield and disease-related traits.

Conclusion
Our study provides a robust method for analyzing genome-wide variations of TF occupancy and identifies genetic and epigenetic variations of the brassinosteroid response transcription network in maize.
General improvements versus interruptive or non-interruptive alerts in the blood order set: study protocol for a randomized control trial to improve packed red blood cell utilization
Authors: Mistry Neelam , Richardson Vanessa , Carey Evan , Porter Samuel , Pincus Sharon , Novins-Montague Sylvie , Elmer Megan , Lin Chen-Tan , Ho P. Michael , Anstett Tyler 
Published: May 2023

Abstract
Background
Blood transfusions can serve as a life-saving treatment, but inappropriate blood product transfusions can result in patient harm and excess costs for health systems. Despite published evidence supporting restricted packed red blood cell (pRBC) usage, many providers transfuse outside of guidelines. Here, we report a novel prospective, randomized control trial to increase guideline-concordant pRBC transfusions comparing three variations of clinical decision support (CDS) in the electronic health record (EHR).

Methods
All inpatient providers at University of Colorado Hospital (UCH) who order blood transfusions were randomized in a 1:1:1 fashion to the three arms of the study: (1) general order set improvements, (2) general order set improvements plus non-interruptive in-line help text alert, and (3) general order set improvements plus interruptive alert. Transfusing providers received the same randomized order set changes for 18 months. The primary outcome of this study is the guideline-concordant rate of pRBC transfusions. The primary objective of this study is to compare the group using the new interface (arm 1) versus the two groups using the new interface with interruptive or non-interruptive alerts (arms 2 and 3, combined). The secondary objectives compare guideline-concordant transfusion rates between arm 2 and arm 3 as well as comparing all of arms of the study in aggregate to historical controls. This trial concluded after 12 months on April 5, 2022.

Discussion
CDS tools can increase guideline-concordant behavior. This trial will examine three different CDS tools to determine which type is most effective at increasing guideline-concordant blood transfusions.

Trial registration
Registered on ClinicalTrials.gov 3/20/21, NCT04823273. Approved by University of Colorado Institutional Review Board (19–0918), protocol version 1 4/19/2019, approved 4/30/2019.
Imaging features of the PI-RADS for predicting extraprostatic extension of prostate cancer: systematic review and meta-analysis
Authors: Choi Moon Hyung , Kim Dong Hwan , Lee Young Joon , Rha Sung Eun , Lee Ji Youl 
Published: May 2023

Abstract
Objectives
To systematically determine the diagnostic performance of each MRI feature of the PI-RADS for predicting extraprostatic extension (EPE) in prostate cancer.

Methods
A literature search in the MEDLINE and EMBASE databases was conducted to identify original studies reporting the accuracy of each feature on MRI for the dichotomous diagnosis of EPE. The meta-analytic pooled diagnostic odds ratio (DOR), sensitivity, specificity, and their 95% confidence intervals (CIs) were obtained using a bivariate random-effects model.

Results
After screening 1955 studies, 17 studies with a total of 3062 men were included. All six imaging features, i.e., bulging prostatic contour, irregular or spiculated margin, asymmetry or invasion of neurovascular bundle, obliteration of rectoprostatic angle, tumor-capsule interface > 10 mm, and breach of the capsule with evidence of direct tumor extension, were significantly associated with EPE. Breach of the capsule with direct tumor extension demonstrated the highest pooled DOR (15.6, 95% CI [7.7–31.5]) followed by tumor-capsule interface > 10 mm (10.5 [5.4–20.2]), asymmetry or invasion of neurovascular bundle (7.6 [3.8–15.2]), and obliteration of rectoprostatic angle (6.1 [3.8–9.8]). Irregular or spiculated margin showed the lowest pooled DOR (2.3 [1.3–4.2]). Breach of the capsule with direct tumor extension and tumor-capsule interface > 10 mm showed the highest pooled specificity (98.0% [96.2–99.0]) and sensitivity (86.3% [70.0–94.4]), respectively.

Conclusions
Among the six MRI features of prostate cancer, breach of the capsule with direct tumor extension and tumor-capsule interface > 10 mm were the most predictive of EPE with the highest specificity and sensitivity, respectively.

Graphical abstract
An improved integrative GFP-based vector for genetic engineering of Parageobacillus thermoglucosidasius facilitates the identification of a key sporulation regulator
Authors: Millgaard Marie , Bidart Gonzalo Nahuel , Pogrebnyakov Ivan , Nielsen Alex Toftgaard , Welner Ditte Hededam 
Published: May 2023

AbstractParageobacillus thermoglucosidasius is a thermophilic Gram-positive bacterium, which is a promising host organism for sustainable bio-based production processes. However, to take full advantage of the potential of P. thermoglucosidasius, more efficient tools for genetic engineering are required. The present study describes an improved shuttle vector, which speeds up recombination-based genomic modification by incorporating a thermostable sfGFP variant into the vector backbone. This additional selection marker allows for easier identification of recombinants, thereby removing the need for several culturing steps. The novel GFP-based shuttle is therefore capable of facilitating faster metabolic engineering of P. thermoglucosidasius through genomic deletion, integration, or exchange. To demonstrate the efficiency of the new system, the GFP-based vector was utilised for deletion of the spo0A gene in P. thermoglucosidasius DSM2542. This gene is known to be a key regulator of sporulation in Bacillus subtilis, and it was therefore hypothesised that the deletion of spo0A in P. thermoglucosiadius would produce an analogous sporulation-inhibited phenotype. Subsequent analyses of cell morphology and culture heat resistance suggests that the P. thermoglucosidasius ∆spo0A strain is sporulation-deficient. This strain may be an excellent starting point for future cell factory engineering of P. thermoglucosidasius, as the formation of endospores is normally not a desired trait in large-scale production.
Infection prevention and control measures for preterm infants discharged into the community: a scoping review protocol
Authors: Carruthers Kathryn , Hannis Dorothy , Robinson Jonathan , Armstrong Alan 
Published: May 2023

Abstract

Background
Infection prevention and control (IPC) is an evidence-based and practical approach to prevention of harm by infection (Infection prevention and control https://www.who.int/health-topics/infection-prevention-and-control#tab=tab_1). IPC recommendations targeted at community-acquired infection aim to prevent illness and subsequent hospital readmission. Cohesive guidance for parents of preterm infants has not been clearly established. The review objectives are to identify and map the global characteristics of IPC measures/recommendations for parents of preterm infants discharged home to the community.

Methods
The scoping review will be conducted using the JBI methodological approach for scoping reviews and reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Scoping Review extension (PRISMA ScR) and the PRISMA extension for reporting literature searches in systematic reviews. Electronic databases will be searched and limited by publication year (2013-present day). Grey literature, reference lists and expert-provided sources will be searched against predetermined criteria. A minimum of two authors will independently screen evidence sources and chart evidence on a predetermined charting form. Sources including IPC measures, or recommendations for parents of preterm infants during discharge planning or in the community/home, will be permitted within inclusion criteria. Limits include human studies only and evidence from 2013-present day. Recommendations aimed at professional implementation will be excluded. A descriptive summary of findings will be presented, with diagrammatic and tabular representation.

Discussion
Collated evidence will guide future research which will subsequently aim to develop policy and enhance clinical approaches.

Systematic review registration
This review has been registered on the Open Science Framework (OSF) 4th May 2021, available at https://osf.io/9yhzk.
Blockchain-based collaborative edge computing: efficiency, incentive and trust
Authors: Gao Qinghang , Xiao Jianmao , Cao Yuanlong , Deng Shuiguang , Ouyang Chuying , Feng Zhiyong 
Published: May 2023

AbstractThe rise of 5G technology has driven the development of edge computing. Computation offloading is the key and challenging point in edge computing, which investigates offloading resource-intensive computing tasks from the user side to the cloud or edge side for processing. More consideration needs to be given to load balancing, user variability, and the heterogeneity of edge facilities in relevant research. In addition, most of the research around edge collaboration also revolves around cloud-side collaboration, which pays relatively little attention to the collaboration process between edge nodes, and the incentive and trust issues of the collaboration process need to be addressed. In this paper, we consider the impact of the user demand variability and the edge facility heterogeneity, then propose a method based on Vickrey-Clarke-Groves (VCG) auction theory to accommodate the edge demand response (EDR) process where the number of users and service facilities do not match. The method makes users’ bidding rules satisfy the Nash equilibrium and weakly dominant strategy, which can improve the load balancing of edge nodes, has positive significance in improving the edge resource utilization and reducing the system energy consumption. In particular, combined with blockchain, we further optimize the incentive and trust mechanism of edge collaboration and consider three scenarios: no collaboration, internal collaboration, and incentive collaboration. We also consider the impact of the user task’s transmission distance on the quality of experience (QoE). In addition, we illustrate the possible forking attack of blockchain in collaborative edge computing and propose a solution. We test the performance of the proposed algorithm on a real-world dataset, and the experimental results verify the algorithm’s effectiveness and the edge collaboration’s necessity.