bluuebunny/crossref_metadata_2025 huggingface dataset:
Ensemble deep learning models for protein secondary structure prediction using bidirectional temporal convolution and bidirectional long short-term memory
Authors: Yuan Lu , Ma Yuming , Liu Yihui
Published: February 2023

Protein secondary structure prediction (PSSP) is a challenging task in computational biology. However, existing models with deep architectures are not sufficient and comprehensive for deep long-range feature extraction of long sequences. This paper proposes a novel deep learning model to improve Protein secondary structure prediction. In the model, our proposed bidirectional temporal convolutional network (BTCN) can extract the bidirectional deep local dependencies in protein sequences segmented by the sliding window technique, the bidirectional long short-term memory (BLSTM) network can extract the global interactions between residues, and our proposed multi-scale bidirectional temporal convolutional network (MSBTCN) can further capture the bidirectional multi-scale long-range features of residues while preserving the hidden layer information more comprehensively. In particular, we also propose that fusing the features of 3-state and 8-state Protein secondary structure prediction can further improve the prediction accuracy. Moreover, we also propose and compare multiple novel deep models by combining bidirectional long short-term memory with temporal convolutional network (TCN), reverse temporal convolutional network (RTCN), multi-scale temporal convolutional network (multi-scale bidirectional temporal convolutional network), bidirectional temporal convolutional network and multi-scale bidirectional temporal convolutional network, respectively. Furthermore, we demonstrate that the reverse prediction of secondary structure outperforms the forward prediction, suggesting that amino acids at later positions have a greater impact on secondary structure recognition. Experimental results on benchmark datasets including CASP10, CASP11, CASP12, CASP13, CASP14, and CB513 show that our methods achieve better prediction performance compared to five state-of-the-art methods.
Current and future outlook of loaded components in hydrogel composites for the treatment of chronic diabetic ulcers
Authors: Cui Jiaming , Zhang Siqi , Cheng Songmiao , Shen Hai
Published: February 2023

Due to recalcitrant microangiopathy and chronic infection, traditional treatments do not easily produce satisfactory results for chronic diabetic ulcers. In recent years, due to the advantages of high biocompatibility and modifiability, an increasing number of hydrogel materials have been applied to the treatment of chronic wounds in diabetic patients. Research on composite hydrogels has received increasing attention since loading different components can greatly increase the ability of composite hydrogels to treat chronic diabetic wounds. This review summarizes and details a variety of newly loaded components currently used in hydrogel composites for the treatment of chronic diabetic ulcers, such as polymer/polysaccharides/organic chemicals, stem cells/exosomes/progenitor cells, chelating agents/metal ions, plant extracts, proteins (cytokines/peptides/enzymes) and nucleoside products, and medicines/drugs, to help researchers understand the characteristics of these components in the treatment of diabetic chronic wounds. This review also discusses a number of components that have not yet been applied but have the potential to be loaded into hydrogels, all of which play roles in the biomedical field and may become important loading components in the future. This review provides a “loading component shelf” for researchers of composite hydrogels and a theoretical basis for the future construction of “all-in-one” hydrogels.
Design of a novel bioink suitable for the 3D printing of lymphoid cells
Authors: Ribezzi Davide , Pinos Riccardo , Bonetti Lorenzo , Cellani Marco , Barbaglio Federica , Scielzo Cristina , Farè Silvia
Published: February 2023

Introduction: For decades, in vitro 2D cell culture techniques have been employed in research, but they fail to recapitulate the complexity of natural tissues. 3D bioprinting could potentially overcome this drawback due to the possibility to control the spatial disposition of living cells and the geometry of the 3D scaffold.

Materials and methods: This study reports the design and characterization of a novel bioink for extrusion bioprinting, analyzing different blend formulations composed of alginate, gelatin, and methylcellulose, suitable as cell-laden bioink for lymphoid cells, in particular those isolated from patients with Chronic Lymphocytic Leukemia (CLL). The rheological properties as a function of temperature and the printability of the formulations were investigated to define the optimal printing parameters. In vitro stability of the printed scaffolds was investigated under culture conditions and compression tests were performed on printed and bioprinted scaffolds to compare their mechanical properties with those of fresh lymphoid tissue. Finally, MEC1, a CLL cell line, was bioprinted to investigate cell viability, cell density, and cell capability to be released from the scaffold over time.

Results and discussion: Results showed that, for the selected blends, good shape fidelity and printing accuracy were achieved with a limitation on the number of printed layers. Scaffolds withstood culture conditions showing stability for up to 3 weeks and their mechanical properties were similar to those of lymphoid tissues already reported in the literature. High cell viability after 21 days was observed for both MEC1 and primary peripheral mononuclear cells, confirming the possibility to use the selected formulation to successfully bioprint lymphoid cells by possibly mimicking their native lymphoid microenvironment.
Identification and characterization of a novel molecular classification incorporating oxidative stress and metabolism-related genes for stomach adenocarcinoma in the framework of predictive, preventive, and personalized medicine
Authors: Dong Ying , Yuan Qihang , Ren Jie , Li Hanshuo , Guo Hui , Guan Hewen , Jiang Xueyan , Qi Bing , Li Rongkuan
Published: February 2023

Background

Stomach adenocarcinoma (STAD) is one of the primary contributors to deaths that are due to cancer globally. At the moment, STAD does not have any universally acknowledged biological markers, and its predictive, preventive, and personalized medicine (PPPM) remains sufficient. Oxidative stress can promote cancer by increasing mutagenicity, genomic instability, cell survival, proliferation, and stress resistance pathways. As a direct and indirect result of oncogenic mutations, cancer depends on cellular metabolic reprogramming. However, their roles in STAD remain unclear.

Method

743 STAD samples from GEO and TCGA platforms were selected. Oxidative stress and metabolism-related genes (OMRGs) were acquired from the GeneCard Database. A pan-cancer analysis of 22 OMRGs was first performed. We categorized STAD samples by OMRG mRNA levels. Additionally, we explored the link between oxidative metabolism scores and prognosis, immune checkpoints, immune cell infiltration, and sensitivity to targeted drugs. A series of bioinformatics technologies were employed to further construct the OMRG-based prognostic model and clinical-associated nomogram.

Results

We identified 22 OMRGs that could evaluate the prognoses of patients with STAD. Pan-cancer analysis concluded and highlighted the crucial part of OMRGs in the appearance and development of STAD. Subsequently, 743 STAD samples were categorized into three clusters with the enrichment scores being C2 (upregulated) > C3 (normal) > C1 (downregulated). Patients in C2 had the lowest OS rate, while C1 had the opposite. Oxidative metabolic score significantly correlates with immune cells and immune checkpoints. Drug sensitivity results reveal that a more tailored treatment can be designed based on OMRG. The OMRG-based molecular signature and clinical nomogram have good accuracy for predicting the adverse events of patients with STAD. Both transcriptional and translational levels of ANXA5, APOD, and SLC25A15 exhibited significantly higher in STAD samples.

Conclusion

The OMRG clusters and risk model accurately predicted prognosis and personalized medicine. Based on this model, high-risk patients might be identified in the early stage so that they can receive specialized care and preventative measures, and choose targeted drug beneficiaries to deliver individualized medical services. Our results showed oxidative metabolism in STAD and led to a new route for improving PPPM for STAD.
Promising management strategies to improve crop sustainability and to amend soil salinity
Authors: Mishra Ajay Kumar , Das Rajeswari , George Kerry Rout , Biswal Bisworanjita , Sinha Trisha , Sharma Sheetal , Arora Pooja , Kumar Mukesh
Published: February 2023

By affecting 10% of the world’s total arable land, soil salinity has become a potential threat to feeding the exploding population. As per the current scenario, among 1,125 million hectares of salt-affected land, nearly 76 million hectares are seriously affected due to human-induced salinization. Due to soil salinization, crop productivity is being hampered. In order to enhance productivity, there is an urgent need to shift from traditional methods to advanced 3E (efficient, economic, and environmentally sound) technology for soil salinity reclamation and management to achieve better soil health and sustainable crop production. The detailed mechanism of salt interference with various pathways involved in plant growth and development needs to be understood. This article critically reviews the mechanism of harmful salt interference with nutrient dynamics in soil and various physiological pathways involved in crop growth to apply various soil-oriented (crop residue management, biochar application, and agroforestry system) and plant-oriented [plant growth-promoting microbes (PGPMs), plant growth regulators, and nanotechnology] promising reclamation and rehabilitation approaches to mitigate its hazardous effect on soil salinity. The monitoring and assessment of salt-affected soils through remote sensing (RS) and geographical information systems (GISs) are pivotal in the management and framing of long-term policies to confront alarming threats to crop productivity and sustainability. This study provides an insight into recent developments in soil salinity management and proposes futuristic solutions that could ameliorate soil salinity to attain crop sustainability under adverse environmental conditions.
Responses of crop production and soil health to chemical nitrogen fertilization in a maize-wheat rotation system
Authors: Deng Meihua , Ma Hua , Sadeghpour Amir , Yang Guiling , Hu Yan , Yang Dong
Published: February 2023

Chemical nitrogen (N) fertilizer is generally applied at high rates to maximize crop yields and also many non-grain farmlands are being converted into grain production to ensure grain production safety in China now. To test the effects of chemical N on crop production and soil health, a 3-year trial with urea and controlled-release fertilizer was conducted in a maize (Zea mays L.)-wheat (Triticum aestivum L.) system shifted from vegetable farmland by evaluating the effects of N fertilization on crop yields, typical soil properties, and soil bacterial community using 16S rRNA gene sequencing. The maximum crop yield and aboveground N uptake efficiency was achieved at 150 kg N ha-1 for wheat and 200 kg N ha-1 for maize. After three cropping seasons, the soil N properties were notably altered. For each kg of N applied, soil pH decreased at a rate of 0.0004–0.0012 pH units. The soil total N (TN) and total carbon (TC) content reached a higher stability at certain cumulative N application rates. However, the C/N ratio linearly decreased as N rate increased. Consequently, N application significantly decreased soil bacterial diversity owing to the decrease of α-diversity indexes of Shannon and Pielou_e. At the phylum level, chemical N application significantly depleted members of Acidobacteria, Chloroflexi and Nitrospirae, but the growth of Actinobacteria, Gemmatimonadetes, Firmicutes and Patescibacteria were improved. Compared with urea, the controlled-release fertilizer did not significantly change crop yields, soil bacterial diversity, soil TN and TC content. Overall, our results indicated that chemical N promoted crop yields at optimum application rates, but excessive N application could result in a decline in soil health, specifically accelerated soil acidification, a decrease in soil bacterial diversity, and soil C and N imbalance.
Research on the upgrading of China’s regional industrial structure based on the perspective of green finance
Authors: Kong Haojia , Xu Yun , Zhang Ruizhe , Tang Decai , Boamah Valentina , Wu Guangliang , Zhou Biao
Published: February 2023

Under the initiative of sustainable development, green financial mechanisms have become an important object to study environmental protection and reduce energy consumption and environmental pollution. This paper explores the mechanism of green finance’s effect on China’s industrial structure through panel regression and mediating effect models using panel data from 30 Chinese provinces and cities from 2009 to 2019. The findings show that 1) the level of green finance is high in both eastern and central regions, but the industrial structure in the eastern region is the most balanced and reasonable. From the results, the consistency between the industrial structure and the level of green finance development is stronger in eastern China. 2) The study of the mechanism of green finance’s role through the intermediary effect model shows that there is an overall mechanism of green finance influencing the upgrading of industrial structure through the financial sector in China, but it is manifested as partial intermediation, and the direct role of green finance on the industrial structure is more obvious. 3) In the analysis of regional heterogeneity, the intermediary role of the financial industry does not exist in the eastern and western regions, while the central region shows a masking effect. In response to these results and to promote the transformation and upgrading of industrial structure, the recommendation of this paper is to focus on the important role of financial institutions in developing green finance to adjust industrial structure, especially in the central region, where both green finance and industrial structure are at an intermediate level. Each region should adjust its industrial structure according to the time and place and promote upgrading the industrial structure.
Integrated analysis reveals common DNA methylation patterns of alcohol-associated cancers: A pan-cancer analysis
Authors: Liu Xingyu , Chen Jiarui , Li Jiali , Zeng Zihang , Jiang Xueping , Gao Yanping , Huang Zhengrong , Wu Qiuji , Gong Yan , Xie Conghua
Published: February 2023

Background: The role of alcohol in carcinogenesis has received increasing attention in recent years. Evidence shows its impacts on various aspects, including epigenetics alteration. The DNA methylation patterns underlying alcohol-associated cancers are not fully understood.

Methods: We investigated the aberrant DNA methylation patterns in four alcohol-associated cancers based on the Illumina HumanMethylation450 BeadChip. Pearson coefficient correlations were identified between differential methylated CpG probes and annotated genes. Transcriptional factor motifs were enriched and clustered using MEME Suite, and a regulatory network was constructed.

Results: In each cancer, differential methylated probes (DMPs) were identified, and 172 hypermethylated and 21 hypomethylated pan-cancer DMPs (PDMPs) were examined further. Annotated genes significantly regulated by PDMPs were investigated and enriched in transcriptional misregulation in cancers. The CpG island chr19:58220189–58220517 was hypermethylated in all four cancers and silenced in the transcription factor ZNF154. Various biological effects were exerted by 33 hypermethylated and seven hypomethylated transcriptional factor motifs grouped into five clusters. Eleven pan-cancer DMPs were identified to be associated with clinical outcomes in the four alcohol-associated cancers, which might provide a potential point of view for clinical outcome prediction.

Conclusion: This study provides an integrated insight into DNA methylation patterns in alcohol-associated cancers and reveals the corresponding features, influences, and potential mechanisms.
Development and validation of a pyroptosis-related genes signature for risk stratification in gliomas
Authors: Sun Penggang , Wang Xinyu , Zhong Junzhe , Yu Daohan , Xuan Hanwen , Xu Tianye , Song Dan , Yang Changxiao , Wang Pandeng , Liu Yuxiang , Meng Xiangqi , Cai Jinquan
Published: February 2023

Background: Glioma is a highly heterogeneous disease, causing the prognostic prediction a challenge. Pyroptosis, a programmed cell death mediated by gasdermin (GSDM), is characterized by cell swelling and the release of inflammatory factors. Pyroptosis occurs in several types of tumor cells, including gliomas. However, the value of pyroptosis-related genes (PRGs) in the prognosis of glioma remains to be further clarified.

Methods: In this study, mRNA expression profiles and clinical data of glioma patients were acquired from TCGA and CGGA databases, and one hundred and eighteen PRGs were obtained from the Molecular Signatures Database and GeneCards. Then, consensus clustering analysis was performed to cluster glioma patients. The least absolute shrinkage and selection operator (LASSO) Cox regression model was used to establish a polygenic signature. Functional verification of the pyroptosis-related gene GSDMD was achieved by gene knockdown and western blotting. Moreover, the immune infiltration status between two different risk groups were analyzed through the “gsva” R package.

Results: Our results demonstrated that the majority of PRGs (82.2%) were differentially expressed between lower-grade gliomas (LGG) and glioblastoma (GBM) in the TCGA cohort. In univariate Cox regression analysis, eighty-three PRGs were shown to be associated with overall survival (OS). A five-gene signature was constructed to divide patients into two risk groups. Compared with patients in the low-risk group, patients in the high-risk group had obviously shorter OS (p < 0.001). Also, we found that the high-risk group showed a higher infiltrating score of immune cells and immune-related functions. Risk score was an independent predictor of OS (HR > 1, p < 0.001). Furthermore, knockdown of GSDMD decreased the expression of IL-1β and cleaved caspase-1.

Conclusion: Our study constructed a new PRGs signature, which can be used to predict the prognosis of glioma patients. Targeting pyroptosis might serve as a potential therapeutic strategy for glioma.
Risk of hospitalization and vaccine effectiveness among COVID-19 patients in the UAE during the Delta and Omicron outbreaks
Authors: Albreiki Mohammed , Mousa Mira , Azman Syafiq Kamarul , Vurivi Hema , Alhalwachi Zainab , Alshehhi Fatima , AlShamsi Safiya , Marzouqi Nada Al , Alawadi Tayba , Alrand Hussain , Oulhaj Abderrahim , Fikri Asma , Alsafar Habiba
Published: February 2023

Introduction

A rapid increase in COVID-19 cases due to the spread of the Delta and Omicron variants in vaccinated populations has raised concerns about the hospitalization risk associated with, and the effectiveness of, COVID-19 vaccines.

Method

This case–control study aims to determine the hospitalization risk associated with the inactivated BBIBP-CorV (Sinopharm) and mRNA BNT162b2 (Pfizer–BionTech) vaccines, and their effectiveness reducing the rate of hospital admission between 28 May 2021 and 13 January 2022, during the Delta and Omicron outbreaks. The estimation of vaccine effectiveness of 4,618 samples was based on the number of patients hospitalized at different vaccination statuses, adjusted for confounding variables.

Results

Hospitalization risk increases in patients affected with the Omicron variant if patients are aged ≤ 18 years (OR 6.41, 95% CI 2.90 to 14.17; p < 0.001), and in patients affected with the Delta variant if they are aged > 45 years (OR 3.41, 95% CI 2.21 to 5.50; p < 0.001). Vaccine effectiveness reducing the rate of hospital admission for fully vaccinated participants infected with the Delta and Omicron variants was similar for both the BBIBP-CorV (94%, 95% CI 90% to 97%; 90%, 95% CI 74% to 96%) and BNT162b2 vaccines (95%, 95% CI 61% to 99.3%; 94%, 95% CI 53% to 99%), respectively.

Discussion

The BBIBP-CorV and BNT162b2 vaccines utilized in the UAE vaccination program were highly effective in reducing the rate of COVID-19-related hospitalization during the Delta and Omicron outbreaks, and further effort must be taken to achieve high vaccine coverage rates in children and adolescents in the global context to reduce the hospitalization risk associated with COVID-19 on an international scale.
Systemic inflammatory markers in patients with polyneuropathies
Authors: García-Fernández Patricia , Höfflin Klemens , Rausch Antonia , Strommer Katharina , Neumann Astrid , Cebulla Nadine , Reinhold Ann-Kristin , Rittner Heike , Üçeyler Nurcan , Sommer Claudia
Published: February 2023

Introduction

In patients with peripheral neuropathies (PNP), neuropathic pain is present in 50% of the cases, independent of the etiology. The pathophysiology of pain is poorly understood, and inflammatory processes have been found to be involved in neuro-degeneration, -regeneration and pain. While previous studies have found a local upregulation of inflammatory mediators in patients with PNP, there is a high variability described in the cytokines present systemically in sera and cerebrospinal fluid (CSF). We hypothesized that the development of PNP and neuropathic pain is associated with enhanced systemic inflammation.

Methods

To test our hypothesis, we performed a comprehensive analysis of the protein, lipid and gene expression of different pro- and anti-inflammatory markers in blood and CSF from patients with PNP and controls.

Results

While we found differences between PNP and controls in specific cytokines or lipids, such as CCL2 or oleoylcarnitine, PNP patients and controls did not present major differences in systemic inflammatory markers in general. IL-10 and CCL2 levels were related to measures of axonal damage and neuropathic pain. Lastly, we describe a strong interaction between inflammation and neurodegeneration at the nerve roots in a specific subgroup of PNP patients with blood-CSF barrier dysfunction.

Conclusion

In patients with PNP systemic inflammatory, markers in blood or CSF do not differ from controls in general, but specific cytokines or lipids do. Our findings further highlight the importance of CSF analysis in patients with peripheral neuropathies.
Case Report: Nontuberculous mycobacterial infections in children with complete DiGeorge anomaly
Authors: Hicks Elizabeth Daly , Agada Noah O. , Yates Tyler R. , Kelly Matthew S. , Tam Jonathan S. , Ferdman Ronald M. , Dibernardo Louis R. , Madden John F. , Moody M. Anthony , Markert Mary Louise
Published: February 2023

Children with complete DiGeorge anomaly (cDGA) have congenital athymia, resulting in severe T cell immunodeficiency and susceptibility to a broad range of infections. We report the clinical course, immunologic phenotypes, treatment, and outcomes of three cases of disseminated nontuberculous mycobacterial infections (NTM) in patients with cDGA who underwent cultured thymus tissue implantation (CTTI). Two patients were diagnosed with Mycobacterium avium complex (MAC) and one patient with Mycobacterium kansasii. All three patients required protracted therapy with multiple antimycobacterial agents. One patient, who was treated with steroids due to concern for immune reconstitution inflammatory syndrome (IRIS), died due to MAC infection. Two patients have completed therapy and are alive and well. T cell counts and cultured thymus tissue biopsies demonstrated good thymic function and thymopoiesis despite NTM infection. Based on our experience with these three patients, we recommend that providers strongly consider macrolide prophylaxis upon diagnosis of cDGA. We obtain mycobacterial blood cultures when cDGA patients have fevers without a localizing source. In cDGA patients with disseminated NTM, treatment should consist of at least two antimycobacterial medications and be provided in close consultation with an infectious diseases subspecialist. Therapy should be continued until T cell reconstitution is achieved.
Immunomodulatory potential of mesenchymal stem cell-derived extracellular vesicles: Targeting immune cells
Authors: Liu Xi , Wei Qian , Lu Lu , Cui Shengnan , Ma Kui , Zhang Wenhua , Ma Fang , Li Haihong , Fu Xiaobing , Zhang Cuiping
Published: February 2023

Various intractable inflammatory diseases caused by disorders of immune systems have pressed heavily on public health. Innate and adaptive immune cells as well as secreted cytokines and chemokines are commanders to mediate our immune systems. Therefore, restoring normal immunomodulatory responses of immune cells is crucial for the treatment of inflammatory diseases. Mesenchymal stem cell derived extracellular vesicles (MSC-EVs) are nano-sized double-membraned vesicles acting as paracrine effectors of MSCs. MSC-EVs, containing a variety of therapeutic agents, have shown great potential in immune modulation. Herein, we discuss the novel regulatory functions of MSC-EVs from different sources in the activities of innate and adaptive immune cells like macrophages, granulocytes, mast cells, natural killer (NK) cells, dendritic cells (DCs) and lymphocytes. Then, we summarize the latest clinical trials of MSC-EVs in inflammatory diseases. Furthermore, we prospect the research trend of MSC-EVs in the field of immune modulation. Despite the fact that the research on the role of MSC-EVs in regulating immune cells is in infancy, this cell-free therapy based on MSC-EVs still offers a promising solution for the treatment of inflammatory diseases.
Cell morphology as a biological fingerprint of chondrocyte phenotype in control and inflammatory conditions
Authors: Selig Mischa , Azizi Saman , Walz Kathrin , Lauer Jasmin C. , Rolauffs Bernd , Hart Melanie L.
Published: February 2023

Introduction

Little is known how inflammatory processes quantitatively affect chondrocyte morphology and how single cell morphometric data could be used as a biological fingerprint of phenotype.

Methods

We investigated whether trainable high-throughput quantitative single cell morphology profiling combined with population-based gene expression analysis can be used to identify biological fingerprints that are discriminatory of control vs. inflammatory phenotypes. The shape of a large number of chondrocytes isolated from bovine healthy and human osteoarthritic (OA) cartilages was quantified under control and inflammatory (IL-1β) conditions using a trainable image analysis technique measuring a panel of cell shape descriptors (area, length, width, circularity, aspect ratio, roundness, solidity). The expression profiles of phenotypically relevant markers were quantified by ddPCR. Statistical analysis, multivariate data exploration, and projection-based modelling were used for identifying specific morphological fingerprints indicative of phenotype.

Results

Cell morphology was sensitive to both cell density and IL-1β. In both cell types, all shape descriptors correlated with expression of extracellular matrix (ECM)- and inflammatory-regulating genes. A hierarchical clustered image map revealed that individual samples sometimes responded differently in control or IL-1β conditions than the overall population. Despite these variances, discriminative projection-based modeling revealed distinct morphological fingerprints that discriminated between control and inflammatory chondrocyte phenotypes: the most essential morphological characteristics attributable to non-treated control cells was a higher cell aspect ratio in healthy bovine chondrocytes and roundness in OA human chondrocytes. In contrast, a higher circularity and width in healthy bovine chondrocytes and length and area in OA human chondrocytes indicated an inflammatory (IL-1β) phenotype. When comparing the two species/health conditions, bovine healthy and human OA chondrocytes exhibited comparable IL-1β-induced morphologies in roundness, a widely recognized marker of chondrocyte phenotype, and aspect ratio.

Discussion

Overall, cell morphology can be used as a biological fingerprint for describing chondrocyte phenotype. Quantitative single cell morphometry in conjunction with advanced methods for multivariate data analysis allows identifying morphological fingerprints that can discriminate between control and inflammatory chondrocyte phenotypes. This approach could be used to assess how culture conditions, inflammatory mediators, and therapeutic modulators regulate cell phenotype and function.
RNA-seq analysis reveals the effect of the metamorphic cue (juvenile oysters) on the Rapana venosa larvae
Authors: Yang Mei-Jie , Shi Ying , Lin Zhi-Shu , Shi Pu , Hu Zhi , Zhou Cong , Hu Peng-Peng , Yu Zheng-Lin , Zhang Tao , Song Hao
Published: February 2023

As a vital developmental event, metamorphosis controls the population dynamics of most marine invertebrates and affects the breeding of economic shellfish. Rapana venosa is an economically important species in China, but artificial aquaculture has hampered its metamorphosis process. Previous studies have found that juvenile oysters can effectively induce the metamorphosis of R. venosa, but the specific induction mechanism is not clear. Here, we investigated the mechanism underlying the response of R. venosa to juvenile oysters through the RNA-seq analysis. In this study, the gene set responses to metamorphosis cues (juvenile oysters) in R. venosa were identified, and GO and KEGG enrichment analyses were further performed on these gene sets. The results showed that the expression of the prototype of the class of immediate early genes, the transcription factor AP-1, was rapidly and significantly increased, and the molecular chaperone of NOS, HSP90, exhibited lower expression in the M12 group than in the control group. In contrast, the expression of inhibitors of apoptosis (IAPs) was significantly increased upon exposure to juvenile oysters. Additionally, the Wnt signaling pathway and MAPK signaling pathway were enriched in the trend analysis. These pathways may also play critical regulatory roles in the response to juvenile oysters. Taken together, the results show that competent larvae rapidly respond to the inducing effects of oysters via some immediate early genes, such as the transcription factor AP-1, which may further regulate downstream pathways such as the MAPK signaling pathway to cause subsequent changes, including a decrease in HSP90 and an increase in IAPs. These changes together may regulate the metamorphosis of R. venosa. This study provides further evidence that juvenile oysters are the metamorphosis cues of R. venosa, which may enhance our understanding of the metamorphosis mechanism in this marine invertebrate.
Design and experiment of cone disk centrifugal shellfish seeding device
Authors: Zhang Hanbing , Li Pengpeng , Zhang Haonan , Huang Wei , Zhang Guochen , Mu Gang , Li Xiuchen
Published: February 2023

This paper designed a centrifugal shellfish seeding device with a conical disc structure to improve the seeding efficiency and uniformity of the centrifugal shellfish seeding device. The dynamic model of the shellfish seedling moving on the conical disk is established, and the main parameters affecting the shellfish seedling’s movement characteristics are determined as the cone angle of the impeller, the speed of the impeller, and the offset angle of the blade. Using the EDEM software and the shellfish seedlings blanking rate as the influencing factors, a single factor simulation test was performed. The research found that the variation trend of shellfish seedlings distribution in a single statistical area gradually decreased along the horizontal direction of both sides, with the origin being the center of the seedling sowing device. Test orthogonal rotation simulations using the variation coefficient of seedlings distribution uniformity and the effective job width as evaluation indicators. Use Design Expert software to optimize the structure of the seedling sowing device based on the test results, and determine the optimal structure with the maximum width and the minimum variation coefficient as constraints: the impeller cone angle is 7.72°, and the blade offset angle is -0.9°. Use the above-mentioned seeding device for simulation and actual seeding testing. The simulation results show that when the impeller speed is 750r/min and the blanking rate is 0.65kg/s, the variation coefficient of seedlings distribution uniformity and the effective job width are 12.84% and 24.98m, respectively, while the actual test results are 13.77% and 23.25m, respectively. The object of the seeding performance test was commonly used size shellfish seedlings of the Philippines clam. The results showed that the impeller speed, blanking rate, quadratic term of shellfish seedling size, quadratic term of blanking rate, and interactive term of impeller speed and blanking rate had significant effects on the variation coefficient of the distribution uniformity of shellfish seedlings (P<0.01). Shellfish seedling size, impeller speed, and interactive term of impeller speed and blanking rate all had a significant impact on job width (P<0.01). The results of this study provide a reference for the mechanized design of shellfish seeding.
Finite element analysis and optimization of foam filled fender under quasi static and dynamic responses
Authors: Djamaluddin F.
Published: February 2023

Mainly composed of elastic materials, ship fenders are utilised on all kinds of vessels for the protection of berthing structures and the prevention of damage due to heavy crash loads. This study aims to enhance deformation mode and crash performance of foam-filled fenders under quasi-static and dynamic loadings. Six models of ship fender’s structure are chosen for simulation test. The fenders are examined for crashworthiness parameters such as crushing force efficiency (CFE) and specific energy absorption (SEA). Finite element analysis is conducted for estimating crash responses then compared to an appropriate reference and experiment result. Four design variables are considered for instance height, foam density, thickness, and material for optimization. Non-dominated Sorting Genetic Algorithm II as multi-objective optimization approach are used to obtain the maximum of Specific Energy Absorption (SEA) and the minimum of Crushing Force Efficiency (CFE). Based on the results of the optimization, the best performance is observed in model 5, however it can be replaced the traditional fender design.
Morphea: The 2023 update
Authors: Papara Cristian , De Luca David A. , Bieber Katja , Vorobyev Artem , Ludwig Ralf J.
Published: February 2023

Morphea, also known as localized scleroderma, is a chronic inflammatory connective tissue disorder with variable clinical presentations, that affects both adults and children. It is characterized by inflammation and fibrosis of the skin and underlying soft tissue, in certain cases even of the surrounding structures such as fascia, muscle, bone and central nervous system. While the etiology is still unknown, many factors may contribute to disease development, including genetic predisposition, vascular dysregulation, TH1/TH2 imbalance with chemokines and cytokines associated with interferon-γ and profibrotic pathways as well as certain environmental factors. Since the disease may progress to permanent cosmetic and functional sequelae, it is crucial to properly assess the disease activity and to initiate promptly the adequate treatment, thus preventing subsequent damage. The mainstay of treatment is based on corticosteroids and methotrexate. These, however, are limited by their toxicity, especially if applied long-term. Furthermore, corticosteroids and methotrexate often do not sufficiently control the disease and/or the frequent relapses of morphea. This review presents the current understanding of morphea by discussing its epidemiology, diagnosis, management and prognosis. In addition, it will describe recent pathogenetic findings, thus proposing potential novel targets for therapeutic development in morphea.
Group B streptococcus virulence factors associated with different clinical syndromes: Asymptomatic carriage in pregnant women and early-onset disease in the newborn
Authors: Schindler Yulia , Rahav Galia , Nissan Israel , Treygerman Orit , Prajgrod George , Attia Bracha Zukerman , Raz Ronit , Valenci Gal Zizelski , Tekes-Manova Dorit , Maor Yasmin
Published: February 2023

Background

Group B streptococcus (GBS) harbors many virulence factors but there is limited data regarding their importance in colonization in pregnancy and early-onset disease (EOD) in the newborn. We hypothesized that colonization and EOD are associated with different distribution and expression of virulence factors.

Methods

We studied 36 GBS EOD and 234 GBS isolates collected during routine screening. Virulence genes (pilus-like structures-PI-1, PI-2a, PI-2b; rib and hvgA) presence and expression were identified by PCR and qRT-PCR. Whole genome sequencing (WGS) and comparative genomic analyses were used to compare coding sequences (CDSs) of colonizing and EOD isolates.

Results

Serotype III (ST17) was significantly associated with EOD and serotype VI (ST1) with colonization. hvgA and rib genes were more prevalent among EOD isolates (58.3 and 77.8%, respectively; p < 0.01). The pilus loci PI-2b and PI-2a were more prevalent among EOD isolates (61.1%, p < 0.01), while the pilus loci PI-2a and PI-1 among colonizing isolates (89.7 and 93.1% vs. 55.6 and 69.4%, p < 0.01). qRT PCR analysis revealed that hvgA was barely expressed in colonizing isolates, even though the gene was detected. Expression of the rib gene and PI-2b was two-fold higher in EOD isolates compared to colonizing isolates. Transcription of PI-2a was three-fold higher in colonizing isolates compared to EOD isolates. ST17 isolates (associated with EOD) had a smaller genome size compared ST1 and the genome was more conserved relative to the reference strain and ST17 isolates. In a multivariate logistic regression analysis virulence factors independently associated with EOD were serotype 3, and PI-1 and PI-2a was protective.

Conclusion

There was a significant difference in the distribution of hvg A, rib, and PI genes among EOD (serotype III/ST17) and colonizing (serotype VI/ST1) isolates suggesting an association between invasive disease and these virulence factors. Further study is needed to understand the contribution of these genes to GBS virulence.
Inhibitory effect of lactobacilli supernatants on biofilm and filamentation of Candida albicans, Candida tropicalis, and Candida parapsilosis
Authors: Poon Yeuklan , Hui Mamie
Published: February 2023

Introduction

Probiotic Lactobacillus strains had been investigated for the potential to protect against infection caused by the major fungal pathogen of human, Candida albicans. Besides antifungal activity, lactobacilli demonstrated a promising inhibitory effect on biofilm formation and filamentation of C. albicans. On the other hand, two commonly isolated non-albicans Candida species, C. tropicalis and C. parapsilosis, have similar characteristics in filamentation and biofilm formation with C. albicans. However, there is scant information of the effect of lactobacilli on the two species.

Methods

In this study, biofilm inhibitory effects of L. rhamnosus ATCC 53103, L. plantarum ATCC 8014, and L. acidophilus ATCC 4356 were tested on the reference strain C. albicans SC5314 and six bloodstream isolated clinical strains, two each of C. albicans, C. tropicalis, and C. parapsilosis.

Results and Discussion:

Cell-free culture supernatants (CFSs) of L. rhamnosus and L. plantarum significantly inhibited in vitro biofilm growth of C. albicans and C. tropicalis. L. acidophilus, conversely, had little effect on C. albicans and C. tropicalis but was more effective on inhibiting C. parapsilosis biofilms. Neutralized L. rhamnosus CFS at pH 7 retained the inhibitory effect, suggesting that exometabolites other than lactic acid produced by the Lactobacillus strain might be accounted for the effect. Furthermore, we evaluated the inhibitory effects of L. rhamnosus and L. plantarum CFSs on the filamentation of C. albicans and C. tropicalis strains. Significantly less Candida filaments were observed after co-incubating with CFSs under hyphae-inducing conditions. Expressions of six biofilm-related genes (ALS1, ALS3, BCR1, EFG1, TEC1, and UME6 in C. albicans and corresponding orthologs in C. tropicalis) in biofilms co-incubated with CFSs were analyzed using quantitative real-time PCR. When compared to untreated control, the expressions of ALS1, ALS3, EFG1, and TEC1 genes were downregulated in C. albicans biofilm. In C. tropicalis biofilms, ALS3 and UME6 were downregulated while TEC1 was upregulated. Taken together, the L. rhamnosus and L. plantarum strains demonstrated an inhibitory effect, which is likely mediated by the metabolites secreted into culture medium, on filamentation and biofilm formation of C. albicans and C. tropicalis. Our finding suggested an alternative to antifungals for controlling Candida biofilm.
Does diet or macronutrients intake drive the structure and function of gut microbiota?
Authors: Li Yuhang , Yan Yujie , Fu Hengguang , Jin Shiyu , He Shujun , Wang Zi , Dong Guixin , Li Baoguo , Guo Songtao
Published: February 2023

Shift of ingestive behavior is an important strategy for animals to adapt to change of the environment. We knew that shifts in animal dietary habits lead to changes in the structure of the gut microbiota, but we are not sure about if changes in the composition and function of the gut microbiota respond to changes in the nutrient intake or food items. To investigate how animal feeding strategies affect nutrient intakes and thus alter the composition and digestion function of gut microbiota, we selected a group of wild primate group for the study. We quantified their diet and macronutrients intake in four seasons of a year, and instant fecal samples were analyzed by high-throughput sequencing of 16S rRNA and metagenomics. These results demonstrated that the main reason that causes seasonal shifts of gut microbiota is the macronutrient variation induced by seasonal dietary differences. Gut microbes can help to compensate for insufficient macronutrients intake of the host through microbial metabolic functions. This study contributes to a deeper understanding of the causes of seasonal variation in host-microbial variation in wild primates.
Discrimination of psychrophilic enzymes using machine learning algorithms with amino acid composition descriptor
Authors: Huang Ailan , Lu Fuping , Liu Fufeng
Published: February 2023

Introduction

Psychrophilic enzymes are a class of macromolecules with high catalytic activity at low temperatures. Cold-active enzymes possessing eco-friendly and cost-effective properties, are of huge potential application in detergent, textiles, environmental remediation, pharmaceutical as well as food industry. Compared with the time-consuming and labor-intensive experiments, computational modeling especially the machine learning (ML) algorithm is a high-throughput screening tool to identify psychrophilic enzymes efficiently.

Methods

In this study, the influence of 4 ML methods (support vector machines, K-nearest neighbor, random forest, and naïve Bayes), and three descriptors, i.e., amino acid composition (AAC), dipeptide combinations (DPC), and AAC + DPC on the model performance were systematically analyzed.

Results and discussion

Among the 4 ML methods, the support vector machine model based on the AAC descriptor using 5-fold cross-validation achieved the best prediction accuracy with 80.6%. The AAC outperformed than the DPC and AAC + DPC descriptors regardless of the ML methods used. In addition, amino acid frequencies between psychrophilic and non-psychrophilic proteins revealed that higher frequencies of Ala, Gly, Ser, and Thr, and lower frequencies of Glu, Lys, Arg, Ile,Val, and Leu could be related to the protein psychrophilicity. Further, ternary models were also developed that could classify psychrophilic, mesophilic, and thermophilic proteins effectively. The predictive accuracy of the ternary classification model using AAC descriptor via the support vector machine algorithm was 75.8%. These findings would enhance our insight into the cold-adaption mechanisms of psychrophilic proteins and aid in the design of engineered cold-active enzymes. Moreover, the proposed model could be used as a screening tool to identify novel cold-adapted proteins.
PREDICTOR: A Physical emulatoR enabling safEty anD ergonomICs evaluation and Training of physical human-rObot collaboRation
Authors: Sunesson Carl Emil , Schøn Daniel Tofte , Hassø Christopher Nybo Ploug , Chinello Francesco , Fang Cheng
Published: February 2023

Safety and ergonomics of Physical Human-Robot Collaboration (PHRC) are crucial to make human-robot collaborative systems trustworthy and make a significant impact in real-world applications. One big obstacle to the development of relevant research is the lack of a general platform for evaluating the safety and ergonomics of proposed PHRC systems. This paper aims to create a Physical emulatoR enabling safEty anD ergonomICs evaluation and Training of physical human-rObot collaboRation (PREDICTOR). PREDICTOR consists of a dual-arm robot system and a VR headset as its hardware and contains physical simulation, haptic rendering and visual rendering modules as its software. The dual-arm robot system is used as an integrated admittance-type haptic device, which senses the force/torque applied by a human operator as an input to drive the simulation of a PHRC system and constrains the handles' motion to match their virtual counterparts in the simulation. The motion of the PHRC system in the simulation is fed back to the operator through the VR headset. PREDICTOR combines haptics and VR to emulate PHRC tasks in a safe environment since the interactive forces are monitored to avoid any risky events. PREDICTOR also brings flexibility as different PHRC tasks can be easily set up by changing the PHRC system model and the robot controller in the simulation. The effectiveness and performance of PREDICTOR were evaluated by experiments.
The role of ATP1A3 gene in epilepsy: We need to know more
Authors: Zou Shuang , Lan Yu-Long , Gong Yiwei , Chen Zhong , Xu Cenglin
Published: February 2023

The ATP1A3 gene, which encodes the Na+/K+-ATPase α3 catalytic subunit, plays a crucial role in both physiological and pathological conditions in the brain, and mutations in this gene have been associated with a wide variety of neurological diseases by impacting the whole infant development stages. Cumulative clinical evidence suggests that some severe epileptic syndromes have been linked to mutations in ATP1A3, among which inactivating mutation of ATP1A3 has been intriguingly found to be a candidate pathogenesis for complex partial and generalized seizures, proposing ATP1A3 regulators as putative targets for the rational design of antiepileptic therapies. In this review, we introduced the physiological function of ATP1A3 and summarized the findings about ATP1A3 in epileptic conditions from both clinical and laboratory aspects at first. Then, some possible mechanisms of how ATP1A3 mutations result in epilepsy are provided. We think this review timely introduces the potential contribution of ATP1A3 mutations in both the genesis and progression of epilepsy. Taken that both the detailed mechanisms and therapeutic significance of ATP1A3 for epilepsy are not yet fully illustrated, we think that both in-depth mechanisms investigations and systematic intervention experiments targeting ATP1A3 are needed, and by doing so, perhaps a new light can be shed on treating ATP1A3-associated epilepsy.