bluuebunny/crossref_metadata_2025 huggingface dataset:
Virulence regulation of Zn2+ uptake system znuABC on mesophilic Aeromonas salmonicida SRW-OG1
Authors: Wang Jiajia , Xiu Lijun , Qiao Ying , Zhang Youyu
Published: March 2023

Psychrophilic Aeromonas salmonicida could not grow above 25°C and therefore thought unable to infect mammals and humans. In our previous study, a mesophilic A. salmonicida SRW-OG1 was isolated from Epinephelus coioides with furunculosis. Through the analysis of preliminary RNA-seq, it was found that the Zn2+ uptake related genes znuA, znuB and znuC might be involved in the virulence regulation of A. salmonicida SRW-OG1. Therefore, the purpose of this study was to explore the effect of znuABC silencing on the virulence regulation of A. salmonicida SRW-OG1. The results showed that the growth of the znuA-RNAi, znuB-RNAi, and znuC-RNAi strains was severely restricted under the Fe2+ starvation, but surprisingly there was no significant difference under the Zn2+ restriction. In the absence of Zn2+ and Fe2+, the expression level of znuABC was significantly increased. The motility, biofilm formation, adhesion and hemolysis of the znuA-RNAi, znuB-RNAi, and znuC-RNAi strains were significantly reduced. We also detected the expression of znuABC under different growth periods, temperatures, pH, as well as Cu2+ and Pb2+ stresses. The results showed that znuABC was significantly up-regulated in the logarithmic phase and the decline phase of A. salmonicida. Interestingly, the trend of expression levels of the znuABC at 18, 28, and 37°C was reversed to another Zn2+ uptake related gene zupT. Taken together, these indicated that the znuABC was necessary for A. salmonicida SRW-OG1 pathogenicity and environmental adaptability, and was cross regulated by iron starvation, but it was not irreplaceable for A. salmonicida SRW-OG1 Zn2+ uptake in the host.
The Reasons Behind Banking Crises and their Real Economy Impact : Achievements of the 2022 Nobel Laureates in Economics
Authors: Világi Balázs
Published: March 2023

In 2022, the Nobel Prize in economics was awarded jointly to Ben S. Bernanke, Douglas W. Diamond and Philip H. Dybvig, for their research on the financial system that shed light on the reasons for, and the consequences of, bank panics. Diamond and Dybvig showed that the banking system provides socially useful services through maturity transformation and delegated monitoring, and they also pointed out that maturity transformation made the banking system fundamentally vulnerable, which, if left unregulated, may experience bank panics. Bernanke demonstrated the macroeconomic significance of the banking system and analysed the negative macroeconomic impact of bank panics. Their research helped lay the foundations of a regulatory environment that fosters the efficient functioning of the financial system without bank panics.
Household Loan Repayment Difficulties after the Payment Moratorium : Hungarian Experience from the Covid-19 Pandemic
Authors: Aczél Ákos , El-Meouch Nedim Márton , Lakos Gergely , Spéder Balázs
Published: March 2023

We examine the relationship between the widespread, long-lasting debt forbearance on household loans introduced in Hungary at the outbreak of the coronavirus pandemic and subsequent loan repayment difficulties. We estimate linear probability and logit models at the contract level. Although our method is not suitable for identifying causal effects, participation in the moratorium proves to be a strong predictor of subsequent defaults. This is true even if we take into account the wide range of relevant factors observed at the end of the general moratorium period (October 2021). Our main results show that contracts which left the general moratorium at the end of the moratorium and, within this, those that took full advantage of the programme, were on average 3.2 and 4.2 percentage points more likely to become non-performing in September 2022 than those that never participated in the moratorium. This relationship can explain almost half of the differences in default rates between the respective groups.
Comparative Transcriptome of Isonuclear Alloplasmic Strain Revealed the Important Role of Mitochondrial Genome in Regulating Flammulina filiformis
Authors: Liu Jingyu , Li Tianle , Song Linhao , Kong Jinchao , Niu Qichen , Wang Yiting , Wu Chenjian , Deng Bing , Wang Hongkai , Gai Yunpeng
Published: March 2023

The golden–needle mushroom Flammulina filiformis is one of the most precious cultivated edible fungi in the world. Despite recent progress in the study of F. filiformis, there is still a gap in the regulation of the mitochondrial genome during browning, which poses a serious threat to the golden–needle mushroom industry. Comparative transcriptome analysis of two isonuclear alloplasmic strains showed that changes in the mitochondrial genome lead to different gene expression and key biological pathways at different stages in the two isonuclear alloplasmic strains. Furthermore, transcriptome analysis revealed that the mitochondrial genome has a significant role in the regulation of a multitude of critical metabolic pathways relating to the browning of F. filiformis fruiting bodies. Functional enrichment analysis showed that the differentially expressed genes were mainly involved in many vital processes of mitochondria, mitochondrial membrane, and multiple amino acid metabolisms of F. filiformis. Taken together, the current study highlights the crucial role of the mitochondrial genome in the growth of F. filiformis and could be beneficial to genetic breeding of elite varieties of edible fungi.
Soil-Water Effects of Good Agricultural and Environmental Conditions Should Be Weighed in Conjunction with Carbon Farming
Authors: Poláková Jana , Janků Jaroslava , Holec Josef , Soukup Josef
Published: March 2023

Soil-water practice is essential for farm sustainability, thereby establishing the reference level for agricultural policy of the European Union (EU). This paper focuses on the critical gap in the knowledge surrounding comparison of soil-water effects of Good Agricultural and Environmental Conditions (GAEC) and carbon farming. We aim to interrogate the tasks assigned to soil-water standards during the 2005–2020 timeframe and identify soil-water effects under selected soil-water GAEC topics. The farm-level and landscape-scale effects were weighed for each standard. The investigation included an extensive meta-review of documents that featured scientific work on sustainable practice. In each GAEC document, soil-water sustainability was weighed vis-a-vis carbon farming. Our main finding was that the identification of soil-water effects within GAEC was addressed both at farm-enterprise level (E) and landscape scale (L). This identification was very similar among the sampled Member States (Czech Republic, Hungary, Poland, and Slovakia). A small differentiation was detected in how exact the guidance under each standard was in each of these Member States, and hence how the prioritization was scored, ranging from 1, most influential, to 5, least influential. The scores that prevailed were 2.5–5 on the part of the scoring instrument. Carbon farming is a welcome addition to the corpus of good farming practice and is complementary to GAEC.
GeoDanceHive: An Operational Hive for Honeybees Dances Recording
Authors: Galopin Sylvain , Touya Guillaume , Aupinel Pierrick , Richard Freddie-Jeanne
Published: March 2023

Honeybees are known for their ability to communicate about resources in their environment. They inform the other foragers by performing specific dance sequences according to the spatial characteristics of the resource. The purpose of our study is to provide a new tool for honeybees dances recording, usable in the field, in a practical and fully automated way, without condemning the harvest of honey. We designed and equipped an outdoor prototype of a production hive, later called “GeoDanceHive”, allowing the continuous recording of honeybees’ behavior such as dances and their analysis. The GeoDanceHive is divided into two sections, one for the colony and the other serving as a recording studio. The time record of dances can be set up from minutes to several months. To validate the encoding and sampling quality, we used an artificial feeder and visual decoding to generate maps with the vector endpoints deduced from the dance information. The use of the GeoDanceHive is designed for a wide range of users, who can meet different objectives, such as researchers or professional beekeepers. Thus, our hive is a powerful tool for honeybees studies in the field and could highly contribute to facilitating new research approaches and a better understanding landscape ecology of key pollinators.
RNA-Seq Study on the Longissimus thoracis Muscle of Italian Large White Pigs Fed Extruded Linseed with or without Antioxidants and Polyphenols
Authors: Vegni Jacopo , Sun Ying , Seemann Stefan E. , Zappaterra Martina , Davoli Roberta , Dall’Olio Stefania , Gorodkin Jan , Zambonelli Paolo
Published: March 2023

The addition of n-3 polyunsaturated fatty acids (n-3 PUFAs) to the swine diet increases their content in muscle cells, and the additional supplementation of antioxidants promotes their oxidative stability. However, to date, the functionality of these components within muscle tissue is not well understood. Using a published RNA-seq dataset and a selective workflow, the study aimed to find the differences in gene expression and investigate how differentially expressed genes (DEGs) were implicated in the cellular composition and metabolism of muscle tissue of 48 Italian Large White pigs under different dietary conditions. A functional enrichment analysis of DEGs, using Cytoscape, revealed that the diet enriched with extruded linseed and supplemented with vitamin E and selenium promoted a more rapid and massive immune system response because the overall function of muscle tissue was improved, while those enriched with extruded linseed and supplemented with grape skin and oregano extracts promoted the presence and oxidative stability of n-3 PUFAs, increasing the anti-inflammatory potential of the muscular tissue.
Genetic Parameters for a Weighted Analysis of Survivability in Dairy Cattle
Authors: Černá Michaela , Zavadilová Ludmila , Vostrý Luboš , Bauer Jiří , Šplíchal Jiří , Vařeka Jan , Fulínová Daniela , Brzáková Michaela
Published: March 2023

The genetic parameters for the survival of Holstein cows, analysed in nine consecutive time periods during the first three calving intervals, were estimated. The earlier the animals are culled, the more they are informationally underestimated. This undervaluing can be remedied by using a weighted analysis that balances the amount of information. If the method of estimating breeding values changes, the genetic parameters will also change. The Holstein cattle dataset from 2005 to 2017 used in this study included 1,813,636 survival records from 298,290 cows. The pedigree with three generations of ancestors included 660,476 individuals. Linear repeatability models estimated genetic parameters for overall and functional survivability. Due to weights, heritability increased from 0.013 to 0.057. Repeatability with weights was 0.505. The standard deviations of breeding values were 1.75 and 2.18 without weights and 6.04 and 6.20 with weights. Including weights in the calculation increased the additive variance proportion and the breeding values’ reliabilities. We conclude that the main contribution of the weighted method we have presented is to compensate for the lack of records in culled individuals with a positive impact on the reliability of the breeding value.
Abundance of Amino Acid Transporters and mTOR Pathway Components in the Gastrointestinal Tract of Lactating Holstein Cows
Authors: Jiang Qianming , Sherlock Danielle N. , Guyader Jessie , Loor Juan J.
Published: March 2023

Data from non-ruminants indicate that amino acid (AA) transport into cells can regulate mTOR pathway activity and protein synthesis. Whether mTOR is expressed in the ruminant gastrointestinal tract (GIT) and how it may be related to AA transporters and the AA concentrations in the tissue is unknown. Ruminal papillae and the epithelia of the duodenum, jejunum, and ileum collected at slaughter from eight clinically healthy Holstein in mid-lactation were used. Metabolites and RNA were extracted from tissue for liquid chromatography–mass spectrometry and RT-qPCR analysis. The glycine and asparagine concentrations in the rumen were greater than those in the intestine (p < 0.05), but the concentrations of other AAs were greater in the small intestine than those in the rumen. Among the 20 AAs identified, the concentrations of glutamate, alanine, and glycine were the greatest. The mRNA abundances of AKT1 and MTOR were greater in the small intestine than those in the rumen (p < 0.05). Similarly, the SLC1A1, SLC6A6, SLC7A8, SLC38A1, SLC38A7, and SLC43A2 mRNA abundances were greater (p < 0.05) in the small intestine than those in the rumen. The mRNA abundances of SLC1A5, SLC3A2, and SLC7A5 were greater in the rumen than those in the small intestine (p < 0.05). Overall, the present study provides fundamental data on the relationship between mTOR pathway components and the transport of AAs in different sections of the gastrointestinal tract.
The Antioxidant Properties of Lavandula multifida Extract Contribute to Its Beneficial Effects in High-Fat Diet-Induced Obesity in Mice
Authors: Molina-Tijeras Jose Alberto , Ruiz-Malagón Antonio Jesús , Hidalgo-García Laura , Diez-Echave Patricia , Rodríguez-Sojo María Jesús , Cádiz-Gurrea María de la Luz , Segura-Carretero Antonio , del Palacio José Pérez , González-Tejero María Reyes , Rodríguez-Cabezas María Elena , Gálvez Julio , Rodríguez-Nogales Alba , Vezza Teresa , Algieri Francesca
Published: March 2023

Obesity is a worldwide public health problem whose prevalence rate has increased steadily over the last few years. Therefore, it is urgent to improve the management of obesity and its comorbidities, and plant-based treatments are receiving increasing attention worldwide. In this regard, the present study aimed to investigate a well-characterized extract of Lavandula multifida (LME) in an experimental model of obesity in mice and explore the underlying mechanisms. Interestingly, the daily administration of LME reduced weight gain as well as improved insulin sensitivity and glucose tolerance. Additionally, LME ameliorated the inflammatory state in both liver and adipose tissue by decreasing the expression of various proinflammatory mediators (Il-6, Tnf-α, Il-1β, Jnk-1, Pparα, Pparγ, and Ampk) and prevented increased gut permeability by regulating the expression of mucins (Muc-1, Muc-2, and Muc-3) and proteins implicated in epithelial barrier integrity maintenance (Ocln, Tjp1, and Tff-3). In addition, LME showed the ability to reduce oxidative stress by inhibiting nitrite production on macrophages and lipid peroxidation. These results suggest that LME may represent a promising complementary approach for the management of obesity and its comorbidities.
Secure and Efficient Federated Gradient Boosting Decision Trees
Authors: Zhao Xue , Li Xiaohui , Sun Shuang , Jia Xu
Published: March 2023

In recent years, federated GBDTs have gradually replaced traditional GBDTs, and become the focus of academic research. They are used to solve the task of structured data mining. Aiming at the problems of information leakage, insufficient model accuracy and high communication cost in the existing schemes of horizontal federated GBDTs, this paper proposes an algorithm of gradient boosting decision trees based on horizontal federated learning, that is, secure and efficient FL for GBDTs (SeFB). The algorithm uses locality sensitive hashing (LSH) to build a tree by collecting similar information of instances without exposing the original data of participants. In the stage of updating the tree, the algorithm aggregates the local gradients of all data participants and calculates the global leaf weights, so as to improve the accuracy of the model and reduce the communication cost. Finally, the experimental analysis shows that the algorithm can protect the privacy of the original data, and the communication cost is low. At the same time, the performance of the unbalanced binary data set is evaluated. The results show that SeFB algorithm compared with the existing schemes of horizontal federated GBDTs, the accuracy is improved by 2.53% on average.
CNN-Based Crosswalk Pedestrian Situation Recognition System Using Mask-R-CNN and CDA
Authors: Lee Sac , Hwang Jaemin , Kim Junbeom , Han Jinho
Published: March 2023

Researchers are studying CNN (convolutional neural networks) in various ways for image classification. Sometimes, they must classify two or more objects in an image into different situations according to their location. We developed a new learning method that colored objects from images and extracted them to distinguish the relationship between objects with different colors. We can apply this method in certain situations, such as pedestrians in a crosswalk. This paper presents a method for learning pedestrian situations on CNN using Mask R-CNN (Region-based CNN) and CDA (Crosswalk Detection Algorithm). With this method, we classified the location of the pedestrians into two situations: safety and danger. We organized the process of preprocessing and learning images into three stages. In Stage 1, we used Mask R-CNN to detect pedestrians. In Stage 2, we detected crosswalks with the CDA and placed colors on detected objects. In Stage 3, we combined crosswalks and pedestrian objects into one image and then, learned the image to CNN. We trained ResNet50 and Xception using images in the proposed method and evaluated the accuracy of the results. When tested experimentally, ResNet50 exhibited 96.7% accuracy and Xception showed 98.7% accuracy. We then created an image that simplified the situation with two colored boxes of crosswalks and pedestrians. We confirmed that the learned CNN with the images of colored boxes could classify the same test images applied in the previous experiment with 96% accuracy by ResNet50. This result indicates that the proposed system is suitable for classifying pedestrian safety and dangerous situations by accurately dividing the positions of the two objects.
Experimental and Numerical Investigation of the Mesoscale Size Effect in Notched Woven Composites
Authors: Ferrarese Andrea , Boursier Niutta Carlo , Ciampaglia Alberto , Ciardiello Raffaele , Paolino Davide S. , Belingardi Giovanni
Published: March 2023

The uniaxial strength of 2 × 2 twill carbon fiber-epoxy composite with circular open holes is governed by the stress concentration induced by the notch, as well as by the variation of the material response with the stress localization. In this study, these concurrent phenomena were studied using an experimental-numerical approach, considering the effect of the composite heterogeneity. An innovative simplified mesoscale model using shell elements to replicate the woven pattern was developed. The material properties of the model were identified with a data-driven optimization scheme that minimizes the difference between the experimental full-field strain, measured with Digital Image Correlation, and the one predicted by the model itself. The elastic properties identified for the material at tow level are analogous to that of a unidirectional composite, with longitudinal and transverse moduli of around 102 GPa and 15 GPa, respectively. The calibrated model was used to analyze the stress concentration and localization induced by circular notches with increasing diameter. A size effect describing the increase in the carbon fiber tow strength following the increase in stress localization was observed. The mesoscale material strength was found to increase by about 2.5 times in the presence of the notch, from 2131 to 3922 MPa in fiber direction, partially balancing the stress intensification effect of the hole that leads to an approximately three-fold stress increase in the material.
Investigation of Failure Causes of Oil Pump Based on Operating Conditions
Authors: Lee Jong-Jik , Kim Yongjin , Lee Taehyun , Kim Myung-Sung , Kim Jeong-Hyeon , Tak Hyun-Jin , Park Jong-Won , Oh Dongho
Published: March 2023

Pumps, as core pieces of equipment in ships, are installed in the engine room to supply refined oil to the engine. Pump failure causes critical problems for ship operations. Therefore, failure-monitoring-based diagnosis technology is an essential requirement in the shipbuilding industry. For this purpose, a database containing information about the failure states depending on the main cause of the failure cases of the pump needs to be developed. In the present study, failure causes of pumps based on actual accident records were quantitatively analyzed. Then, failure modes for the bearing, coupling, sealing, and screw, which are the core parts of the oil pump, were determined. Test infrastructures for the oil pump were developed to obtain normal and abnormal data considering diverse operating conditions. Based on the vibration data from the accelerometer installed on the test infrastructures, the frequency of failure was analyzed through Fast Fourier Transform (FFT). In addition, more precise results were obtained by performing Short-Time Fourier Transform (STFT) for the FFT results that indicated severe failure. Finally, over 200 data entries were accumulated on the core parts of the oil pump, considering normal as well as abnormal operating conditions. The database constructed in this study is expected to help in investigating failure diagnosis and prediction of algorithm models for ship management.
Research Progress in the Flight Characteristics of Flyers Driven by Different Technologies
Authors: Zhang Guodong , Zhao Yulong , Fan Chunhui
Published: March 2023

Flyers driven by various technologies have been widely used as effective shock loading techniques in the ignition of energetic materials, space debris impact modeling, equation of state measurement, etc. However, their flying characteristics have the greatest influence on application reliability. The flying velocity, as well as the flyer’s planarity and integrity, are crucial characteristics. Therefore, mainstream flyer-driving technologies are examined in this study, and research progress in investigation approaches on flyer velocity and morphology are reviewed. Furthermore, for each flyer-driving technique, the affecting factors of flyer velocity and morphology are summarized. Current research deficiencies are highlighted, and future research directions are discussed, including the parallel coupling of various driving principles, quantitative characterizations of the flyer’s planarity and integrity, and the physical model matching the flying process.
Development of a Simple Protocol for Zymogram-Based Isolation and Characterization of Gingipains from Porphyromonas gingivalis: The Causative Agent of Periodontitis
Authors: Wei Eng Sze , Kavitha Ramasamy , Sa’ad Mohammad Auwal , Lalitha Pattabhiraman , Fuloria Neeraj Kumar , Ravichandran Manickam , Fuloria Shivkanya
Published: March 2023

Gingipains (RgpA, RgpB, and Kgp) are major virulence factors of the periodontitis-causing bacterium Porphyromonas gingivalis. Isolation of gingipains from the crude protein sample of P. gingivalis is critical for studying the underlying invasion mechanism that contributes to periodontitis, Alzheimer’s disease, and cardiovascular disease (CVD). Chromatographic processes and molecular cloning are two standard techniques often used for gingipains isolation, which are time-consuming and costly. In this study, considerably easier methods based on passive-mediated diffusion gel elution and gelatin zymogram were used to isolate and characterize gingipains. Importantly, proteins eluted from Native-PAGE showed enzymatic activity for both Rgp and Kgp. In gelatin zymography, the proteins with a molecular size of ~50 kDa and above 245 kDa were suggested as arginine-specific gingipains. The passive diffusion-mediated gel elution method is a simpler technique to isolate gingipains from crude protein samples of P. gingivalis. By using covalent and highly specific gingipain inhibitors, gelatin zymography enabled an individual characterization of gingipain activity and inhibition. Finally, this protocol can be easily extended by adding the isoelectric focusing to further improve the protein separation and characterization.
Electrochemical Modelling of Na-MCl2 Battery Cells Based on an Expanded Approximation Method
Authors: Büttner Nils , Purr Foelke , Sangrós Giménez Clara , Richter Maria , Nousch Laura , Zellmer Sabrina , Michaelis Alexander
Published: March 2023

Battery models are mathematical systems that aim to simulate real battery cell sufficiently accurately. Finding a comprise between complexity, computational effort and accuracy is thereby key. In particular, modelling sodium–nickel–chloride/iron-chloride cells (Na-NiCl2/FeCl2), as a promising alternative for stationary energy storage, bears some challenges. The literature shows a few interesting approaches, but in most of them the second active material (NiCl2 or FeCl2) or the entire discharging/charging cycle is not considered. In this work, an electrochemical and thermal model of Na-NiCl2/FeCl2 battery cells is presented. Based on an equivalent circuit approach combined with electrochemical calculations, the hybrid model provides information on the performance of the cell for charging and discharging with a constant current. By dividing the cathode space into segments, internal material and charge flows are predicted, allowing important insights into the internal cell processes. Besides a low calculation effort, the model also allows a flexible adaption of cathode composition and cell design, which makes it a promising tool for the development of single battery cells as well as battery modules and battery systems.
Preparation of Electrospun Membranes and Their Use as Separators in Lithium Batteries
Authors: Di Carli Mariasole , Aurora Annalisa , Rinaldi Antonio , Fiaschini Noemi , Prosini Pier Paolo
Published: March 2023

In this work, electrospun nanofiber membranes are investigated as separators for lithium batteries. Membrane consisting of polyacrylonitrile-polycaprolactone mixtures were produced following a combinatorial approach inspired by design of experiments to identify the relationships between process parameters and microstructural properties. The microstructure of the non-woven fibrous mats was characterized by scanning electron microscopy to measure thickness and fiber distribution. Temperature and relative humidity during membrane deposition were also tracked to include them in the statistical analysis and highlight their influence on the properties of the resulting membranes. The functional evaluation of the membranes was conducted by electrochemical impedance spectroscopy, after soaking the membrane in the electrolyte, to measure ion transport properties. All the separators showed specific conductivities higher than 1.5 × 10−3 S. The electrochemical performance was also evaluated when the membranes were used as actual separators in coin-cells assembled in-house, stacking the electrolyte-soaked membranes between a lithium anode and a LiFePO4-based cathode. Among all, the PAN/PCL 50:50 showed excellent cycling stability, with a high initial capacity of 150 mAhg−1 and a coulombic efficiency of 99.6%.
Minimizing the Anticodon-Recognized Loop of Methanococcus jannaschii Tyrosyl-tRNA Synthetase to Improve the Efficiency of Incorporating Noncanonical Amino Acids
Authors: Hu Zhiyang , Liang Jinming , Su Taogeng , Zhang Di , Li Hao , Gao Xiangdong , Yao Wenbin , Song Xiaoda
Published: March 2023

In the field of genetic code expansion (GCE), improvements in the efficiency of noncanonical amino acid (ncAA) incorporation have received continuous attention. By analyzing the reported gene sequences of giant virus species, we noticed some sequence differences at the tRNA binding interface. On the basis of the structural and activity differences between Methanococcus jannaschii Tyrosyl-tRNA Synthetase (MjTyrRS) and mimivirus Tyrosyl-tRNA Synthetase (MVTyrRS), we found that the size of the anticodon-recognized loop of MjTyrRS influences its suppression activity regarding triplet and specific quadruplet codons. Therefore, three MjTyrRS mutants with loop minimization were designed. The suppression of wild-type MjTyrRS loop-minimized mutants increased by 1.8–4.3-fold, and the MjTyrRS variants enhanced the activity of the incorporation of ncAAs by 15–150% through loop minimization. In addition, for specific quadruplet codons, the loop minimization of MjTyrRS also improves the suppression efficiency. These results suggest that loop minimization of MjTyrRS may provide a general strategy for the efficient synthesis of ncAAs-containing proteins.
scTransSort: Transformers for Intelligent Annotation of Cell Types by Gene Embeddings
Authors: Jiao Linfang , Wang Gan , Dai Huanhuan , Li Xue , Wang Shuang , Song Tao
Published: March 2023

Single-cell transcriptomics is rapidly advancing our understanding of the composition of complex tissues and biological cells, and single-cell RNA sequencing (scRNA-seq) holds great potential for identifying and characterizing the cell composition of complex tissues. Cell type identification by analyzing scRNA-seq data is mostly limited by time-consuming and irreproducible manual annotation. As scRNA-seq technology scales to thousands of cells per experiment, the exponential increase in the number of cell samples makes manual annotation more difficult. On the other hand, the sparsity of gene transcriptome data remains a major challenge. This paper applied the idea of the transformer to single-cell classification tasks based on scRNA-seq data. We propose scTransSort, a cell-type annotation method pretrained with single-cell transcriptomics data. The scTransSort incorporates a method of representing genes as gene expression embedding blocks to reduce the sparsity of data used for cell type identification and reduce the computational complexity. The feature of scTransSort is that its implementation of intelligent information extraction for unordered data, automatically extracting valid features of cell types without the need for manually labeled features and additional references. In experiments on cells from 35 human and 26 mouse tissues, scTransSort successfully elucidated its high accuracy and high performance for cell type identification, and demonstrated its own high robustness and generalization ability.
LRRK2 Structure-Based Activation Mechanism and Pathogenesis
Authors: Zhang Xiaojuan , Kortholt Arjan
Published: March 2023

Mutations in the multidomain protein Leucine-rich-repeat kinase 2 (LRRK2) have been identified as a genetic risk factor for both sporadic and familial Parkinson’s disease (PD). LRRK2 has two enzymatic domains: a RocCOR tandem with GTPase activity and a kinase domain. In addition, LRRK2 has three N-terminal domains: ARM (Armadillo repeat), ANK (Ankyrin repeat), and LRR (Leucine-rich-repeat), and a C-terminal WD40 domain, all of which are involved in mediating protein–protein interactions (PPIs) and regulation of the LRRK2 catalytic core. The PD-related mutations have been found in nearly all LRRK2 domains, and most of them have increased kinase activity and/or decreased GTPase activity. The complex activation mechanism of LRRK2 includes at least intramolecular regulation, dimerization, and membrane recruitment. In this review, we highlight the recent developments in the structural characterization of LRRK2 and discuss these developments from the perspective of the LRRK2 activation mechanism, the pathological role of the PD mutants, and therapeutic targeting.
Epigenetics Approaches toward Precision Medicine for Idiopathic Pulmonary Fibrosis: Focus on DNA Methylation
Authors: Effendi Wiwin Is , Nagano Tatsuya
Published: March 2023

Genetic information is not transmitted solely by DNA but by the epigenetics process. Epigenetics describes molecular missing link pathways that could bridge the gap between the genetic background and environmental risk factors that contribute to the pathogenesis of pulmonary fibrosis. Specific epigenetic patterns, especially DNA methylation, histone modifications, long non-coding, and microRNA (miRNAs), affect the endophenotypes underlying the development of idiopathic pulmonary fibrosis (IPF). Among all the epigenetic marks, DNA methylation modifications have been the most widely studied in IPF. This review summarizes the current knowledge concerning DNA methylation changes in pulmonary fibrosis and demonstrates a promising novel epigenetics-based precision medicine.
Effects of Taurine on Gut Microbiota Homeostasis: An Evaluation Based on Two Models of Gut Dysbiosis
Authors: Qian Weike , Li Mingyang , Yu Leilei , Tian Fengwei , Zhao Jianxin , Zhai Qixiao
Published: March 2023

Taurine, an abundant free amino acid, plays multiple roles in the body, including bile acid conjugation, osmoregulation, oxidative stress, and inflammation prevention. Although the relationship between taurine and the gut has been briefly described, the effects of taurine on the reconstitution of intestinal flora homeostasis under conditions of gut dysbiosis and underlying mechanisms remain unclear. This study examined the effects of taurine on the intestinal flora and homeostasis of healthy mice and mice with dysbiosis caused by antibiotic treatment and pathogenic bacterial infections. The results showed that taurine supplementation could significantly regulate intestinal microflora, alter fecal bile acid composition, reverse the decrease in Lactobacillus abundance, boost intestinal immunity in response to antibiotic exposure, resist colonization by Citrobacter rodentium, and enhance the diversity of flora during infection. Our results indicate that taurine has the potential to shape the gut microbiota of mice and positively affect the restoration of intestinal homeostasis. Thus, taurine can be utilized as a targeted regulator to re-establish a normal microenvironment and to treat or prevent gut dysbiosis.
Psychomotor Performance after 30 h of Sleep Deprivation Combined with Exercise
Authors: Mikulski Tomasz , Górecka Monika , Bogdan Anna , Młynarczyk Magdalena , Ziemba Andrzej W.
Published: March 2023

Sleep deprivation (SD) usually impairs psychomotor performance, but most experiments are usually focused on sedentary conditions. The purpose of this study was to evaluate the influence of 30 h of complete SD combined with prolonged, moderate exercise (SDE) on human psychomotor performance. Eleven endurance-trained men accustomed to overnight exertion were tested twice: in well-slept and non-fatigued conditions (Control) and immediately after 30 h of SDE. They performed a multiple-choice reaction time test (MCRT) at rest and during each workload of the graded exercise test to volitional exhaustion. At rest, the MCRT was shorter after SDE than in the Control (300 ± 13 ms vs. 339 ± 11 ms, respectively, p < 0.05). During graded exercise, there were no significant differences in MCRT between groups, but the fastest reaction was observed at lower workloads after SDE (158 ± 7 W vs. 187 ± 11 W in Control, p < 0.05). The total number of missed reactions tended to be higher after SDE (8.4 ± 0.7 vs. 6.3 ± 0.8 in Control, p = 0.06). In conclusion, SDE is different from SD alone; however, well-trained men, accustomed to overnight exertion can maintain psychomotor abilities independently of the extent of central fatigue. Exercise can be used to enhance psychomotor performance in sleep-deprived subjects in whom special caution is required in order to avoid overload.
Effects on Corticospinal Tract Homology of Faremus Personalized Neuromodulation Relieving Fatigue in Multiple Sclerosis: A Proof-of-Concept Study
Authors: Bertoli Massimo , Tataranni Angela , Porziani Susanna , Pasqualetti Patrizio , Gianni Eugenia , Grifoni Joy , L’Abbate Teresa , Armonaite Karolina , Conti Livio , Cancelli Andrea , Cottone Carlo , Marinozzi Franco , Bini Fabiano , Cecconi Federico , Tecchio Franca
Published: March 2023

Objectives: Fatigue in multiple sclerosis (MS) is a frequent and invalidating symptom, which can be relieved by non-invasive neuromodulation, which presents only negligible side effects. A 5-day transcranial direct-current stimulation, 15 min per day, anodically targeting the somatosensory representation of the whole body against a larger occipital cathode was efficacious against MS fatigue (fatigue relief in multiple sclerosis, Faremus treatment). The present proof-of-concept study tested the working hypothesis that Faremus S1 neuromodulation modifies the homology of the dominant and non-dominant corticospinal (CST) circuit recruitment. Methods: CST homology was assessed via the Fréchet distance between the morphologies of motor potentials (MEPs) evoked by transcranial magnetic stimulation in the homologous left- and right-hand muscles of 10 fatigued MS patients before and after Faremus. Results: In the absence of any change in MEP features either as differences between the two body sides or as an effect of the treatment, Faremus changed in physiological direction the CST’s homology. Faremus effects on homology were more evident than recruitment changes within the dominant and non-dominant sides. Conclusions: The Faremus-related CST changes extend the relevance of the balance between hemispheric homologs to the homology between body sides. With this work, we contribute to the development of new network-sensitive measures that can provide new insights into the mechanisms of neuronal functional patterning underlying relevant symptoms.
EEG Dynamics of Error Processing and Associated Behavioral Adjustments in Preschool Children
Authors: Pietto Marcos Luis , Giovannetti Federico , Segretin María Soledad , Lipina Sebastián Javier , Kamienkowski Juan Esteban
Published: March 2023

Preschool children show neural responses and make behavioral adjustments immediately following an error. However, there is a lack of evidence regarding how neural responses to error predict subsequent behavioral adjustments during childhood. The aim of our study was to explore the neural dynamics of error processing and associated behavioral adjustments in preschool children from unsatisfied basic needs (UBN) homes. Using EEG recordings during a go/no-go task, we examined within-subject associations between the error-related negativity (ERN), frontal theta power, post-error slowing, and post-error accuracy. Post-error accuracy increased linearly with post-error slowing, and there was no association between the neural activity of error processing and post-error accuracy. However, during successful error recovery, the frontal theta power, but not the ERN amplitude, was associated positively with post-error slowing. These findings indicated that preschool children from UBN homes adjusted their behavior following an error in an adaptive form and that the error-related theta activity may be associated with the adaptive forms of post-error behavior. Furthermore, our data support the adaptive theory of post-error slowing and point to some degree of separation between the neural mechanisms represented by the ERN and theta.
Effectiveness of SGA-LAIs on Clinical, Cognitive, and Social Domains in Schizophrenia: Results from a Prospective Naturalistic Study
Authors: de Filippis Renato , Staltari Filippo Antonio , Aloi Matteo , Carbone Elvira Anna , Rania Marianna , Destefano Laura , Steardo Jr. Luca , Segura-Garcia Cristina , De Fazio Pasquale
Published: March 2023

We hypothesized that shifting from oral second-generation antipsychotics (SGA) to their long-acting injectable (LAI) counterpart would be beneficial for the psychopathological, cognitive, social, and general health domains in outpatients suffering from schizophrenia. We aimed to evaluate the prospective usefulness of SGA-LAI treatment by carrying out a head-to-head comparison of two different medications (i.e., aripiprazole monohydrate (Ari-LAI) and paliperidone palmitate 1 and 3 month (PP1M, PP3M)) in a real-world setting, assessing the effectiveness and tolerability of Ari-LAI and PP1M/PP3M over a 15 month follow-up. A total of 69 consecutive individuals affected by schizophrenia were screened for eligibility. Finally, 46 outpatients (29 treated with Ari-LAI, 13 with PP1M, and four with PP3M) were evaluated through clinical, functional, and neuropsychological assessment administrated at baseline and after 3-, 12-, and 15-month follow-up periods. Moreover, periodic general medical evaluations were carried out. We estimated an overall improvement over time on the explored outcomes, without differences with respect to the type of LAI investigated, and with a global 16.4% dropout rate. Our findings suggest that switching from oral SGA to SGA-LAIs represents a valid and effective treatment strategy, with significant improvements on psychopathological, cognitive, social, and clinical variables for patients suffering from schizophrenia, regardless of the type of molecule chosen.
Longitudinal Relation between Family Socio-Economic Status and Problem Behaviors in Chinese Children: The Roles of Sense of Coherence and Maternal Warmth
Authors: Mo Bibo , Fu Rui , Liu Xiaoshi , Xu Gangmin , Liu Junsheng , Li Dan
Published: March 2023

Literature has well-documented the relation of family socio-economic status (SES) to children’s problem behaviors, yet the complex mechanisms underlying the relation are not well understood. Therefore, the primary goal of this one-year longitudinal study was to explore the mediating role of children’s sense of coherence and the moderating role of perceived maternal warmth in the association between family SES and externalizing and internalizing problems in Chinese children. The sample consisted of 913 children (493 boys; Mage = 11.50 years, SD = 1.04) in fourth to sixth grades in an urban area in mainland China. Data were obtained from multiple sources, including child self-reports, parental reports, and teacher ratings. The results indicated that children’s sense of coherence mediated the association between family SES and internalizing problem behaviors, but not externalizing problem behaviors. This mediating role was also moderated by maternal warmth and specifically, family SES was negatively associated with internalizing problem behaviors via the sense of coherence for children who perceived high maternal warmth. Generally, these results highlighted the possible roles of a sense of coherence and maternal warmth in the longitudinal implications of family SES for Chinese children’s internalizing problems.
Nonlinear Settlement Calculation of Composite Foundation Based on Tangent Modulus Method: Two Case Studies
Authors: Li Yonghua , Yao Lei , Chen Gaoxiang , Zhao Weijian , Liu Xiangang
Published: March 2023

The tangent modulus method of undisturbed soil is a new method in settlement calculation, which is mainly applied to hard soil with a strong structure, such as silty clay, completely weathered rock, and granite residual soil with an SPT blow count greater than 8. The tangent modulus is mainly obtained from a field plate load test, which can consider the influence of the soil stress level and reflect the nonlinear characteristics of the foundation settlement. In a multi-layer soil foundation, since the deep plate loading test is difficult, a method was proposed to determine the tangent modulus of deep soil. It is assumed that the ratio of the initial tangent modulus to the deformation modulus is equal to the ratio of the unloading–reloading modulus Eurref to the secant modulus E50ref obtained by triaxial unloading–reloading test. Since there are corresponding empirical formulae for SPT counts and the deformation modulus of different types of soils in many regions, the initial tangent modulus can be derived by the above method. In two cases of a composite foundation, the compression modulus and tangent modulus were used to calculate the settlement of the foundation, which is then compared with the measured results. The results show that the proposed method for determining the tangent modulus of deep soil is feasible in theory, and the calculating accuracy of the tangent modulus is significantly higher than that of the traditional compression modulus.
CBCT-to-CT Translation Using Registration-Based Generative Adversarial Networks in Patients with Head and Neck Cancer
Authors: Suwanraksa Chitchaya , Bridhikitti Jidapa , Liamsuwan Thiansin , Chaichulee Sitthichok
Published: March 2023

Recently, deep learning with generative adversarial networks (GANs) has been applied in multi-domain image-to-image translation. This study aims to improve the image quality of cone-beam computed tomography (CBCT) by generating synthetic CT (sCT) that maintains the patient’s anatomy as in CBCT, while having the image quality of CT. As CBCT and CT are acquired at different time points, it is challenging to obtain paired images with aligned anatomy for supervised training. To address this limitation, the study incorporated a registration network (RegNet) into GAN during training. RegNet can dynamically estimate the correct labels, allowing supervised learning with noisy labels. The study developed and evaluated the approach using imaging data from 146 patients with head and neck cancer. The results showed that GAN trained with RegNet performed better than those trained without RegNet. Specifically, in the UNIT model trained with RegNet, the mean absolute error (MAE) was reduced from 40.46 to 37.21, the root mean-square error (RMSE) was reduced from 119.45 to 108.86, the peak signal-to-noise ratio (PSNR) was increased from 28.67 to 29.55, and the structural similarity index (SSIM) was increased from 0.8630 to 0.8791. The sCT generated from the model had fewer artifacts and retained the anatomical information as in CBCT.
Virtual HDR Boost for Prostate Cancer: Rebooting a Classic Treatment Using Modern Tech
Authors: Wegener Eric , Samuels Justin , Sidhom Mark , Trada Yuvnik , Sridharan Swetha , Dickson Samuel , McLeod Nicholas , Martin Jarad M.
Published: March 2023

Prostate cancer (PC) is the most common malignancy in men. Internal radiotherapy (brachytherapy) has been used to treat PC successfully for over a century. In particular, there is level-one evidence of the benefits of using brachytherapy to escalate the dose of radiotherapy compared with standard external beam radiotherapy approaches. However, the use of PC brachytherapy is declining, despite strong evidence for its improved cancer outcomes. A method using external beam radiotherapy known as virtual high-dose-rate brachytherapy boost (vHDRB) aims to noninvasively mimic a brachytherapy boost radiation dose plan. In this review, we consider the evidence supporting brachytherapy boosts for PC and the continuing evolution of vHDRB approaches, culminating in the current generation of clinical trials, which will help define the role of this emerging modality.