bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA editing, RNA modifications, and transcriptional units in Listeria monocytogenes
Authors: Duru Ilhan Cem , Ylinen Anne , Grigore-Gurgu Leontina , Riedel Christian U. , Paulin Lars , Auvinen Petri 
Published: April 2022

Abstract
Background: The Gram-positive foodborne pathogen Listeria monocytogenes can resist several stress conditions, and therefore, food processing facilities employ methods with high energy demand, such as high pressure processing (HPP), to eliminate L. monocytogenes. Detection of novel genomic and transcriptomic functions may enable food processing methods to better target pathogens. In this study, we aimed to reveal organization of the transcriptional units of barotolerant L. monocytogenes strain RO15 using novel sequencing methods such as Cappable-seq and direct RNA sequencing. The identified transcriptional units allowed prediction of transcription terminator, promoter, and operon structures. Moreover, RNA modification of the whole transcriptome by direct RNA-seq in L. monocytogenes strain RO15 and ScottA revealed post-transcriptional mechanisms in L. monocytogenes. RNA editing was investigated in both strain RO15 and ScottA to elucidate functions of RNA editing during HPP.Results: We observed 1641 transcription start sites (TSSs) in L. monocytogenes strain RO15 based on Cappable-seq. Comparison of HPP-treated and control samples indicated that some prophage genes might alter their TSSs used under different conditions. Short Illumina RNA-seq reads indicate that RNA editing (A to I) occurs in L. monocytogenes on several genes. Some of the target genes, such as hpf, RNA editing happened only after HPP, indicating that RNA editing might be an important mechanism in L. monocytogenes when recovering óf the HPP injury. TACG was the most common motif of RNA editing in both strains (RO15 and ScottA). We observed that RNA editing sites cannot be identified by long Nanopore direct RNA-seq reads with the current methodologies. The whole transcriptome RNA modification analysis showed that thousands of bases were modified in both strains. Motif analysis of the RNA modification sites detected via direct RNA sequencing indicated that a GATGA-like motif is used in L. monocytogenes during RNA modification. Lastly, we were able to construct the whole transcriptome annotation using the long reads, which revealed operon structures in both L. monocytogenes RO15 and ScottA.Conclusion: Here, we employed two novel sequencing methods, Cappable-seq and direct RNA sequencing, for L. monocytogenes. The results enhanced our understanding of transcriptional units of L. monocytogenes. We revealed that RNA editing is used in L. monocytogenes during HPP recovery, which brings a new perspective to developing novel methods to eliminate L. monocytogenes during food processes. Whole transcriptome RNA modification analysis was performed for the first time in bacteria, potentially providing a new basis for studying novel post-transcriptional functionalities in bacteria.
Expression and clinical significance of VEGF and markers of EMT in gastric cancer
Authors: Zhang Yue , Wang Yanyan , Zhao Menglin , Mi Jiaqi , Li Xinwei , Li Huiyuan , Tang Mingyue , Geng Zhijun , Zuo Lugen , Song Xue , Wang Zishu , Wang Qiang , Su Fang 
Published: April 2022

Abstract
To explore the association of the levels of vascular endothelial growth factor (VEGF) and markers of epithelial − mesenchymal transition (EMT) in gastric cancer with histopathological features and long-term prognosis. Immunohistochemistry was used to quantitatively assess the expression of VEGF in gastric cancer tissues and adjacent tissues and to detect the expression level of EMT markers in gastric cancer tissues. Here we show that VEGF and EMT markers expression were significantly correlated with depth of tumor invasion and gastric cancer stage (P < 0.05), degree of differentiation and lymph node metastasis (P < 0.001). We found that the rate of VEGF positivity in gastric cancer tissues was 52.05%, which was significantly higher than that in adjacent cancer tissues (16.84%). In gastric cancer, the association between VEGF and E-cadherin was negative (r=-0.188, P < 0.05), whereas VEGF and N-cadherin were positively correlated (r = 0.214, P < 0.05). Furthermore, Kaplan-Meier analysis and a Cox regression model were used to analyze the effect of VEGF and EMT marker expression on the survival of the patients. We found that the overall survival of gastric cancer patients was correlated with VEGF (P < 0.001), N-cadherin (P < 0.001), E-cadherin (P = 0.002) expression and parts of histopathological features. VEGF and EMT markers exist side by side and play a part together in the development of gastric cancer, which provides new ideas for evaluating the prognosis of gastric cancer and researching targeted drugs.
Colostomy delays cell loss in the brain and improves juvenile survival in a neonatal rat model of Hirschsprung’s disease
Authors: Xie Dan , Du Yitong , Wang Yutao , Croaker Geoffrey David Hain , Wei Zheng Zachory , Song Zan-Min 
Published: April 2022

Abstract
Hirschsprung’s disease (HSCR) is a congenital malformation characterized by the absence of enteric ganglia in the distal intestine and gut obstruction. Our previous study indicates the brain pathology during the disease progression. A subpopulation of HSCR patients is also associated with anomalies of the central nervous system. Little is known about the cellular changes in the brains of HSCR patients due to the lack of human tissues. In the investigation, we studied a rat model of HSCR, known as spotting lethal (sl/sl) ETB-/- rats, which carries a spontaneous deletion in endothelin receptor B (human gene name: EDNRB) and manifests a similar phenotype as humans with HSCR. Homozygous mutant sl/sl rats were rescued from premature death by colostomy and they survived to juvenile age. By measuring the body weight, the body growth was not revealed to be significantly different between ETB-/- and wildtype ETB+/+ or heterozygous (+/sl) ETB+/- groups that all underwent the same colostomy. Cell loss was investigated in several brain regions by using terminal deoxynucleotidyltransferase-mediated dUTP nick end-labeling assay (TUNEL) in ETB+/+, ETB-/-, and ETB+/- rats. Number of TUNEL positive cells in the cerebellum and the hippocamps of ETB-/- rats was still increased compared with that in the ETB+/+ and ETB+/- rats. TUNEL positive cells were observed in the molecular layer and granular cell layers of the cerebellum. In contrast, no significant difference in the density of TUNEL positive cells was revealed in the cerebral cortex. These results suggest that either endothelin receptor B sl mutation or colostomy has predominant lasting effects on the cell survival/loss in the cerebellum and hippocampus of adult ETB-/- rats. Our findings provide the information on cellular changes in the brains of patients with HSCR due to congenital EDNRB mutation as well as clinically relevant interventions.
Heterologous expression and functional characterization of Drosophila suzukii OR69a transcript variants unveiled response to kairomones and to a candidate pheromone
Authors: Cattaneo Alberto Maria , Witzgall Peter , Kwadha Charles A. , Becher Paul G. , III William B. Walker 
Published: April 2022

Abstract
Background
Drosophila suzukii is among the main pests of berries, and to which control, primarily through application of insecticides is challenging and urges alternative strategies. Methods based on targeting chemical sensing and interfering with the behavior of this pest insect are promising, and are facilitated by the isolation and functional characterization of chemosensory receptors aimed to identify behaviorally active ligands. In our previous investigations, we functionally characterized subunits of the OR69a locus of Drosophila melanogaster as being capable to bind both pheromones and kairomones. OR69a is well conserved within the genus Drosophila, and represents a candidate target for a broad behavioral interference based on chemosensory communication towards the design of novel control strategies.
Results
By means of heterologous expression in empty ab3A neurons of D. melanogaster together with Single Sensillum Recording (SSR), we screened three OR69a-subunits we have identified in D. suzukii (DsuzOR69aA, DsuzOR69aB, DsuzOR69aC) with a panel of 48 ligands. We deorphanized these subunits to several compounds, including two possible kairomones (3-octanol and R-carvone) and (Z)-4-nonenal, a possible fly-emitted volatile compound, although with different pharmacological qualities. By coupling Gas Chromatography to Single Sensillum Recording (GC-SSR), we demonstrated these three ligands enhance ab3A-spiking at nanogram aliquots in a complementary fashion among the different OR69a variants, and we identified another possible kairomone, methyl salicylate, as the most active and specific ligand for the sole subunit DsuzOR69aB. In testing headspaces collected from D. suzukii female and from the fly-associated yeast Hanseniaspora uvarum by GC-SSR we did not observe activation from female headspaces but activation from headspaces collected from yeast. In situ hybridization analysis conducted on D. suzukii antennae suggested unique expression of OR69a-subunits into specific neurons as well as their possible co-expression within the same neurons.
Conclusions
The OR69a-subunits of D. suzukii constitute cation channels, which binding suggests kairomone specificity, even if effects may coexist for binding the possible fly-emitted volatile compound (Z)-4-nonenal in a complementary fashion. Among the possible kairomones, methyl salicylate is the most active ligand and it demonstrated to be specific to the sole DsuzOR69aB subunit, inspiring future investigation to validate potentials of this compound for D. suzukii pest control strategies.
The Transmembrane and Cytosolic Domains of Equine Herpesvirus Type 1 Glycoprotein D Determine Golgi Retention by Regulating Vesicle Formation
Authors: Wang Shimin , Ren Xin-Rong , Duan Qi-Ying , Chen Lin-Hui 
Published: April 2022

Abstract
Accumulating evidence suggests that envelope proteins play an important role in viral secondary envelopment; however, the molecular mechanisms involved are poorly understood. To clarify these mechanisms, we studied the localization of equine herpesvirus type 1 (EHV-1) envelope proteins and found that glycoprotein D of EHV-1 (gDEHV−1) was mostly retained in the Golgi complex, unlike that of HSV-1 and PRV. We used a gene truncation and replacement strategy to investigate the determinant sequence responsible for the Golgi retention phenotype and found that Golgi retention signals exhibit multi-domain features. The extracellular domain of gDEHV−1 (ECDEHV−1) is an endoplasmic reticulum (ER)-resident domain. The transmembrane domain and cytoplasmic tail (TM-CT) of gDEHV−1 was found to help the protein reside in the Golgi complex. Once each of the dual domains was deleted or replaced, the mutant gD remained in the ER. (TM-CT)EHV−1 preferentially binds to the endomembrane and induces a large number of vesicles that may originate from the Golgi complex or ER-Golgi intermediate compartment. Membrane fusion was hardly observed between the cell membrane and the induced vesicles. These findings provide further insight into the molecular mechanism underlying the Golgi retention of gDEHV−1, enhancing our understanding of viral secondary envelopment.
Three-year outcomes between early and delayed invasive strategies in older adults with non-ST-segment elevation myocardial infarction receiving new- generation drug-eluting stents
Authors: Kim Yong Hoon , Her Ae-Young , Rha Seung-Woon , Choi Cheol Ung , choi Byoung Geol , Kim Ji Bak , Park Soohyung , Kang Dong Oh , Park Ji Young , Park Sang-Ho , Jeong Myung Ho 
Published: April 2022

Abstract
We evaluated the 3-year clinical outcomes following early invasive (EI) and delayed invasive (DI) strategies in older adults with non-ST-segment elevation myocardial infarction (NSTEMI) undergoing successful new-generation drug-eluting stents (DESs) implantation to reflect current real-world practice. Overall, 4513 patients with NSTEMI were recruited from Korea Acute Myocardial Infarction Registry-National Institute of Health. They were divided into two groups according to their ages: group A (age ≥65 years, n = 2,253) and group B (age <65 years, n = 2,260). These two groups of patients were further divided into two subgroups: group EI (A1 or B1) and DI (A2 or B2). The primary clinical outcome was the occurrence of major adverse cardiac and cerebrovascular events (MACCEs), defined by all-cause death, recurrent MI (re-MI), and any repeat coronary revascularization. The secondary clinical outcome was stent thrombosis (ST). In both, group A and B, after multivariable-adjusted and propensity score-adjusted analyses, the primary and secondary clinical outcomes were not significantly different between the EI and DI groups. Even after the analysis was confined to those having complex lesions, these major clinical outcomes were similar between these two groups. The EI and DI strategies in older adults with NSTEMI receiving new-generation DES showed comparable results.Clinical Trial Registration: URL: http://cris.nih.go.kr/cris/en/; Unique identifier: KCT0000863.
Efficient electrocatalytic reduction of CO2 to ethane over nitrogen-doped Fe2O3
Authors: Chen Peng , Zhang Pei , Kang Xinchen , Zheng Lirong , Mo Guang , Wu Ruizhi , Tai Jing , Han Buxing 
Published: April 2022

Abstract
Non-copper catalysts are seldom reported to generate C2+ products, and the efficient over these catalysts were low. In this work, we reported an iron-based catalyst centered in nitrogen doped γ-Fe2O3 (xFe2O3-N), which yielded C2H6 as major product in H-cell. At –2.0 V vs Ag/Ag+, the Faradaic efficiency (FE) for ethane reaches 42% with current densities of 32 mA cm−2. This is the first report about selective CO2 reduction to ethane (C2H6) over iron-based catalyst. Results showed that catalyst possessing FeO1.5-nNn sites enriched with oxygen vacancies was beneficial for the stabilization of *COOH intermediate. The exposure of two adjacent surfaces of Fe atoms was conducive to lower the energy barrier for C−C coupling over FeO1.5-nNn sites, facilitating the generation of C2H6. This work provides a strategy for design of novel iron-based catalyst with tunable local coordination and electronic structures for converting CO2 into C2 products in CO2RR.
Developing Novel Feeds for Cattle from Food Waste and Crop Residue Biomass to Strengthen the Regenerative Capacity of Agri-Food Systems
Authors: Dou Zhengxia , Toth John D. , Pitta Dipti W. , Bender Joseph S. Joseph S. , Hennessy Meagan L. , Vecchiarelli Bonnie , Indugu Nagaraju , Chen Ting , Li Yunyun , Sherman Rachel , Deutsch Jonathan , Hu Bo , Shurson Gerald C. , Parsons Brianna , Baker Linda D. 
Published: April 2022

Abstract
Modern agri-food systems generate large amounts of crop-based biomass that are unfit for direct human consumption but potentially eligible for upcycling via livestock feeding for production of meats, milk, and eggs. This study aims to develop novel feeds for cattle from some of those biomass materials through the natural microbial-driven processes of ensiling. Fruit and vegetables resembling supermarket discards were ensiled alone or co-ensiled with corn crop residues, mushroom wastes, etc. via laboratory experiments. Longitudinal sample analyses showed that (co-)ensiling was successful, with pH and fermentation acids falling within desirable ranges (pH < 4.5, the acids 5–13% DM with lactic acid dominating). The (co-)ensiled products had key nutritional parameters comparable to those of good quality forages commonly used on dairy farms. Additionally, in vitro incubation results indicated that the ensiled products could substitute certain conventional feeds while maintaining diet digestibility. Our findings provide a proof of principle for generating quality novel feeds for cattle from food discards and under-utilized crop residues. Future scale-up studies and animal feeding trials to demonstrate the utility of this approach can help societies begin re-purposing and more effectively utilizing otherwise-untapped feedstock resources, strengthening the regenerative capacity of agri-food systems towards a more sustainable food future.
Abnormal functional connectivity of the intrinsic networks in adolescent bipolar I versus bipolar II disorder
Authors: Xiao Qian , Zhang Gui , Zhong Yuan 
Published: April 2022

Abstract
Background: The symptoms of pediatric bipolar disorder (PBD)-I and PBD-II differ, but accurate identification at an early stage is difficult and may prevent effective treatment of this disorder. Therefore, it is urgent to elucidate a biological marker based on objective imaging indicators to help distinguish the two. Therefore, this research aims to compare the functional connectivity between PBD-I patient and PBD-II patient in different brain networks. Methods: Our study enrolled 31 PBD-I and 23 PBD-II patients from 12 to 17 years of age. They were analyzed by resting state-functional connectivity through Independent component analysis（ICA）. Results: We found differences between PBD-I and PBD-II in functional connectivity of the default network, frontoparietal network, salience network and limbic system. In addition, the clinical features, cognitive functions are associated with the functional connectivity of the intrinsic networks in PBD-I and PBD-II separately. Conclusion: This research is the first to find differences in functional connectivity between PBD-I and PBD-II, suggesting that abnormality of the functional connectivity within large networks may be biomarkers that help differentiate PBD-I from PBD-II in the future.
Study on Speed Transfer Characteristics of Double-deck ball bearing Based on Generalized Four-terminal Parameter Method
Authors: Zhang Xinming , Hu Jing , Zhang Bangcheng 
Published: April 2022

Abstract
The speed transfer ratio is one of the most important parameters of the double-deck ball bearing. For the calculation of speed ratio, most of the theoretical estimation formulas related to the structure are used, but under some measured working conditions, the speed ratio is not only related to structural parameters. To explore the speed transmission mechanism of double-deck ball bearing, a new method for calculating the speed transmission characteristics of double-deck ball bearing is proposed in this paper. The generalized four-terminal parameter method is applied to the speed analysis of double-deck ball bearing for the first time. The speed transmission analysis model of double-deck ball bearing is established by combining the three theories of quasi statics theory, elastohydrodynamic lubrication theory, and generalized four-terminal parameter theory. A variety of factors are taken into account to solve the research status of rotational speed transfer ratio only considering a single factor. The speed transmission characteristics of the double-deck ball bearing after the system are accelerated to the steady-state are studied, and the correctness of the results is verified by experiments, which provides a new idea for the analysis of the speed transmission characteristics of the double-deck ball bearing, and provides a theoretical basis for the exploration and design of the potential application value of the double-deck ball bearing.
Interpretable classification using occlusion sensitivity on multilayer segmented OCT from patients with Multiple Sclerosis and healthy controls
Authors: Khodabandeh Zahra , Rabbani Hossein , Ashtari Fereshteh , Zimmermann Hanna G. , Motamedi Seyedamirhosein , Brandt Alexander U. , Paul Friedemann , Kafieh Rahele 
Published: April 2022

Abstract
Multiple sclerosis (MS) is one of the most prevalent chronic inflammatory diseases caused by demyelination and axonal damage in the central nervous system. Structural retinal imaging via optical coherence tomography (OCT) shows promise as a biomarker for monitoring of MS. There are successful reports regarding application of Artificial Intelligence (AI) in analysis of cross-sectional OCTs in ophthalmologic diseases. However, the alteration of sub-retinal thicknesses in MS are noticeably subtle compared to other ophthalmologic diseases. Therefore, raw cross-sectional OCTs are replaced with multilayer segmented OCTs for discrimination of MS and heathy controls (HCs). To conform to the principles of trustworthy AI, interpretability is provided by visualizing regional layer contribution to classification performance with proposed occlusion sensitivity approach. The robustness of the classification is also guaranteed by showing the effectiveness of the algorithm while being tested on the new independent (but similar) dataset. The most discriminative features from different topologies of the multilayer segmented OCTs are selected by dimension reduction methods. Support vector machine (SVM), random forest (RF), and artificial neural network (ANN) are used for classification. Patient-wise cross-validation (CV) is utilized to evaluate the performance of the algorithm, where the training and test folds contain records from different subjects. The most discriminative topology is determined to be squares with side of 40 pixels and the most influential sub-retinal layers are ganglion cell and inner plexiform layer (GCIPL) and inner nuclear layer (INL). Linear SVM resulted in 88% Accuracy, 78% precision and 63% recall in discrimination of MS and HCs using macular multilayer segmented OCTs.
Application of GCB-Net based on Defect Detection Algorithm for Steel Plates
Authors: Fan BeiBei , Li Weixin 
Published: April 2022

Abstract
In recent years, deep learning convolutional networks have been gradually applied to metal surface inspection. Steel plate defect detection helps improve the efficiency of steel plate production by locating and classifying surface defects on steel plates. The related methods are challenging to balance the accuracy of localization and classification. There are scenarios in the industrial inspection field where the data set is relatively small, and the distribution of defects is significantly irregular; this paper extends the traditional image detection network by introducing an attention mechanism. At the same time, to meet the requirement of higher real-time performance in industrial inspection, the lightweight Ghost network is introduced to replace the original backbone network CSPDarknet53 in YOLOV4 to improve the detection speed of the network. This paper constructs the high accuracy and low latency defect detection algorithm Ghost-CBAM-YOLOV4 Network (GCB-Net). The GCB-Net model is based on the improved YOLOV4 target detection network. The CBAM module and Ghost lightweight network are introduced to complete the prediction of defect categories without reducing the classification and detection accuracy. The desired experimental results are achieved, which is essential for detecting defects in steel plates and improving product quality.