bluuebunny/crossref_metadata_2025 huggingface dataset:
In‑silico analysis predicting effects of some Protein conding SNPs of human tumor suppressor protein53 (TP53 gene) by using different Bioinformatic tools
Authors: Waheed Zainab Abdullah , Sarhan Nadia Habeeb , Hamzah Ahmed Ibrahim , Shaker Mustafa Mohammed
Published: July 2022

BackgroundTp53 gene encodes a tumor suppressor protein containing transcriptional activation, DNA binding, and oligomerization domains. The encoded protein responds to diverse cellular stresses to regulate expression of target genes, thereby inducing cell cycle arrest, apoptosis, senescence, DNA repair, or changes in metabolism. Mutations in this gene are associated with a variety of human cancers, including hereditary cancers such as Li-Fraumeni syndrome. Alternative splicing of this gene and the use of alternate promoters result in multiple transcript variants and isoformsAim of studyThe study is aimed to study the effect of some protein coding SNPs on human health and if it benign or neutral by using different bioinformatics tools (I-MUTANT 3. 0,PROVEAN,and SNPS&GO; PhD-snp)ResultsThe result shows that the protein sequence identification was as the following:MAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQMLLDLRWCYFLINSSanalysis of (10) SNPs shows that 5 SNPs(50%) having a nuclic acid change which result in a new amino acid formation and this change was considerd large increase stability according to I-Mutant while just 1SNP (1%)have neutral stability in the same tool but only 4(40%)SNPs showed large decrease stability in the analysis at the same tool which can be considered having effect on human health .While as in PhD-SNP,SNP&GO,PROVEAN showed 0(0%) increase stability but prdected that (50%,50%,40%)have neutral affect in the protein modification while(40%,40%,50%) had Large decrease stability according to PhD-SNP,SNP&GO,PROVEAN respectively which may lead to human disease.
Characteristic analysis of BpbZIP family genes and BpbZIP26 significantly enhanced triterpenoid production in Betula platyphylla under S-nitrosothiol treatment
Authors: Wang Bo , Yang Haixin , Gao Xinglei , Liu Huimin , Fan Guizhi
Published: July 2022

Background: Basic leucine zipper (bZIP) transcription factors are crucial in plant development, and response to environmental stress, etc. With the development of sequencing technology and bioinformatics analysis, the bZIP family genes has been screened and identified in many plant species, but bZIP family genes has not been systematically characterized and identified their function in B. platyphylla.Methods: B. platyphylla reference genome was used to characterize bZIP family genes. The physicochemical properties, chromosome distribution, gene structure, and syntenic relationships were analyzed by bioinformatics methods. The effect of BpbZIP26 on triterpenoid production was investigated using Agrobacterium-mediated transient transformation under N6022 treatment.Results: 51 bZIP family genes were identified in B. platyphylla, and named BpbZIP1~BpbZIP51 sequentially according to their positions on chromosomes. All BpbZIP genes were unevenly distributed on 14 chromosomes, and divided into 13 subgroups according to the classification of A. thaliana bZIP proteins. 12 duplication events were detected in the B. platyphylla genome, and 28 orthologs existed between B. platyphylla and A. thaliana, 83 orthologs existed between B. platyphylla and G. max, and 73 orthologs existed between B. platyphylla and P. trichocarpa. N6022 treatment changed gene expression levels of most BpbZIPs in seedlings of Betula platyphylla. Among of them, N6022 treatment significantly enhanced gene expression levels BpbZIP26 in leaves, stems and roots of B. platyphylla. BpbZIP26 mediated triterpenoid production, and N6022 treatment further enhanced triterpenoid production in BpbZIP26 overexpression calli of B. platyphylla using Agrobacterium-mediated transient transformation. Conclusion: This work highlights potential BpbZIP family genes responding to S-nitrosothiol and their roles in triterpenoid production.
Binding and dynamics demonstrate the destabilisation of ligand binding for the S688Y mutation in the NMDA receptor GluN1 subunit
Authors: Chen Zheng , Church W. Bret , Bastard Karine , Duff Anthony P. , Balle Thomas
Published: July 2022

Encephalopathies are brain dysfunctions which leads to cognitive, sensory, and motor development impairments. Recently, the identification of several mutations within the N-methyl-D-aspartate receptor (NMDAR) have been identified as significant in the aetiology of this group of conditions. However, a complete understanding of the underlying molecular mechanism and changes to the receptor due to these mutations has been elusive. We studied the molecular mechanisms by which one of the first mutation within the NMDAR GluN1 ligand binding domain, Ser688Tyr, cause the encephalopathies. We performed molecular docking, randomly seeded molecular dynamics simulations, and binding free energy calculations to determine the behaviour of the 2 major co-agonists: glycine and D-serine in both the wild-type and S688Y receptor. We observed that the Ser688Tyr mutation leads to instability of both ligands within the ligand binding site due to structural changes associated with the mutation. The binding free energy for both ligands was significantly more unfavourable in the mutated receptor. These results explain previously observed in vitro electrophysiological data and provide detailed aspects of ligand association, and its effects on receptor activity. Our study provides valuable insight into the consequences of mutations within the NMDAR GluN1 ligand binding domain.
The mechanism of action of carbon nanostructures in tribochemical reactions
Authors: Ozimina Dariusz , Kulczycki Andrzej , Janas Dawid , Desaniuk Tomasz , Dzięgielewski Wojciech
Published: July 2022

The aim of this article is to experimentally verify the modified Arrhenius equation for catalytic reactions. The theoretical mathematical reactivity model proposed in the authors’ previous articles assumes that: a) the catalytic reaction rate constant depends not only on the temperature at which the reaction occurs but also on the additional energy supplied to the reactants as a result of the flow of electrons emitted by the catalyst, b) the catalytic reaction rate constant changes in a periodic manner. The research focused on two areas of catalyst applications: controlling tribological processes and converting methanol to hydrogen under visible light irradiation. The article proposes a new interpretation of the earlier findings in tribology and photocatalytic decomposition of methanol. The experimental data show that graphene and nanotubes (CNTs) act as catalysts in tribochemical reactions and that catalytic reactions are initiated by light energy. The key feature of the mechanism by which the nanostructures behave is that they absorb various forms of energy from the surroundings, which are to be stored, transported, or released as pulses back to the surroundings when a catalyzed reaction takes place.
Clinical outcome of drug-coated balloons in patients with femoropopliteal chronic total occlusive lesions: results from the multicenter EAGLE study
Authors: Hayakawa Naoki , Takahara Mitsuyoshi , Nakama Tatsuya , Horie Kazunori , Takanashi Keisuke , Kanagami Teruaki , Ichihara Shinya , Arakawa Masataka , Tobita Kazuki , Mori Shinsuke , Iwata Yo , Suzuki Kenji , Kanda Junji
Published: July 2022

Background: Several studies have reported the efficacy of drug-coated balloons (DCB) for simple femoropopliteal (FP) lesions. However, the effectiveness of DCB for FP chronic total occlusive lesions (CTO) is controversial. The present study investigated the clinical outcomes of DCB for FP-CTO.Materials and methods: We retrospectively analyzed 359 limbs of 318 patients who underwent EVT with DCB for FP-CTO between July 2017 and February 2021 at seven cardiovascular centers. The primary endpoint was 12-month primary patency. The secondary endpoints were the 12-month rates of freedom from: (1) clinically-driven target lesion revascularization (CD-TLR), and (2) re-occlusion. The association of baseline characteristics with the 12-month restenosis risk was investigated using the Cox proportional hazards regression model.Results: The 12-month rate of primary patency was 79.8% (95% confidence interval [95%CI], 75.1% to 84.8%), whereas the corresponding rates of freedom from CD-TLR and re-occlusion were 86.4% (95%CI: 82.6% to 90.4%) and 88.5% (95%CI: 84.7% to 92.4%), respectively. The bailout stent rate was 8.9%. Independent risk factors for restenosis were hemodialysis (adjusted hazard ratio, 2.18 [1.39 to 3.45]; P=0.001), chronic limb-threatening ischemia (CLTI) (2.02 [1.33 to 3.07]; P=0.001), and restenosis lesion (2.02 [1.32 to 3.08]; P=0.001). Use of dual antiplatelet therapy (DAPT) was identified as a protective factor for restenosis (0.54 [0.35 to 0.82]; P=0.003).Conclusion: Despite the low rate of bailout stent, DCB treatment for FP-CTO was effective in real-world clinical practice. Hemodialysis, CLTI, and restenosis lesion were independent risk factors for 12-month restenosis, and the use of DAPT significantly attenuated the risk of 12-month restenosis.
Automatic Segmentation of Hepatic Metastases on DWI images Based on a Deep Learning Method: Assessment of Tumor Treatment Response According to the RECIST 1.1 Criteria
Authors: Liu Xiang , Wang Rui , Zhu Zemin , Wang Kexin , Gao Yue , Li Jialun , Zhang Yaofeng , Wang Xiangpeng , Zhang Xiaodong , Wang Xiaoying
Published: July 2022

Background
Evaluation of treated tumors according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria is an important but time-consuming task in medical imaging. Deep learning methods are expected to automate the evaluation process and improve the efficiency of imaging interpretation.
Objective
To develop an automated algorithm for segmentation of liver metastases based on a deep learning method and assess its efficacy for treatment response assessment according to the RECIST 1.1 criteria.
Methods
One hundred and sixteen treated patients with clinically confirmed liver metastases were enrolled. All patients had baseline and post-treatment MR images. They were divided into an initial (n = 86) and validation cohort (n = 30) according to the examined time. The metastatic foci on DWI images were annotated by two researchers in consensus. Then the treatment responses were assessed by the two researchers according to RECIST 1.1 criteria. A 3D U-Net algorithm was trained for automated liver metastases segmentation using the initial cohort. Based on the segmentation of liver metastases, the treatment response was assessed automatically with a rule-based program according to the RECIST 1.1 criteria. The segmentation performance was evaluated using the Dice similarity coefficient (DSC), volumetric similarity (VS), and Hausdorff distance (HD). The area under the curve (AUC) and Kappa statistics were used to assess the accuracy and consistency of the treatment response assessment by the deep learning model and compared with two radiologists [attending radiologist (R1) and fellow radiologist (R2)] in the validation cohort.
Results
In the validation cohort, the mean DSC, VS, and HD were 0.85 ± 0.08, 0.89 ± 0.09, and 25.53 ± 12.11 mm for the liver metastases segmentation. The accuracies of R1, R2 and automated segmentation-based assessment were 0.77, 0.65, and 0.74, respectively, and the AUC values were 0.81, 0.73, and 0.83, respectively. The consistency of treatment response assessment based on automated segmentation and manual annotation was moderate [K value: 0.60 (0.34–0.84)].
Conclusion
The deep learning-based liver metastases segmentation was capable of evaluating treatment response according to RECIST 1.1 criteria, with comparable results to the junior radiologist and superior to that of the fellow radiologist.
Prevalence and Nucleotide sequence relatedness among Wenyonia species (Cestoda: Caryophyllidea) in Synodontis clarias from Lekki Lagoon, Lagos, Nigeria
Authors: Koledoye Toluwani Yemi , Abazuh Uchenna Desmond , Akinsanya Bamidele , Adekoya Khalid Olajide
Published: July 2022

Background: Wenyonia Woodland, 1923 represents a monophyletic lineage of Caryophyllidean tapeworms that exclusively infect mochokid catfishes of the genus Synodontis. In Nigeria, information on the molecular characterization of Wenyonia sp tracing the phylogenetic relationship within the genus is lacking. This study was therefore aimed to evaluate the genetic relatedness between and among Wenyonia species based on the partial nucleotide sequence of the D1-D3 region of the 28SrRNA gene and the mt region (trnK + nad3 + trnS + trnW + cox1) genes.Methods and results: One hundred and twenty Synodontis clarias from the Lekki Lagoon were purchased fresh at the Oluwo market Epe, Lagos, Nigeria between November 2020 and April 2021. Total genomic DNA of identified Wenyonia species recovered from the fishes were extracted. PCR was done to amplify the divergent domains (D1-D3) region of the 28SrRNA gene and the mt region (trnK + nad3 + trnS + trnW + cox1) genes in the Wenyonia species, and PCR products sequenced. The nucleotide sequences obtained were verified using BLAST and they were subsequently analyzed using the Molecular Evolutionary Genetic Analysis (MEGA 7.0). Wenyonia sp are abundant in Synodontis clarias with W. virilis the most prevalent and W. minuta the least prevalent. The phylogenetic tree based on the D1-D3 region of the partial 28SrRNA gene nucleotide sequence revealed three main clusters that indicated that W. minuta and W. youdeoweii are more genetically related than W. virilis. W. longicauda, however, showed more intermediate relatedness between and among the 5 Wenyonia species used in the tree. W. acuminuta showed the least genetically relatedness among the 5 Wenyonia species. Based on the partial mt region comprising trnK+ nad3+ trnS+ trnW+ cox1, W. acuminuta showed more genetic relatedness with W. longicauda than with W. youdeoweii. Conclusion: The study therefore revealed that Wenyonia sp are abundant in Synodontis clarias and that the species are genetically closely related as revealed by the taxonomical classification. However, some individual among these species may have been evolving.
Milling chatter detection of thin-walled parts based on GA-SE-SCK-VMD and RCMDE
Authors: Liu Xianli , Wang Hanbin , Li Maoyue , Wang Zhixue , Meng Boyang
Published: July 2022

In the milling process, it is easy to produce chatter due to the low rigidity of thin-walled structure, which leads to the deterioration of workpiece surface quality and reduces the service life of cutting tools and machine tools. Therefore, a new chatter detection method for thin-walled parts based on optimal variational mode decomposition (OVMD) and refined composite multiscale dispersion entropy (RCMDE) is proposed in this paper. Firstly, to solve the problem that the decomposition effect of the variational mode decomposition (VMD) algorithm is greatly affected by its parameter, genetic algorithm (GA) is used to iteratively optimize the parameter of the VMD algorithm, and a new index, square envelope spectral correlated kurtosis (SE-SCK), is introduced as the fitness function of the genetic algorithm. Then, the energy ratio of the decomposed signal is calculated as the principle of selecting sub-components, and the sub-components with rich chatter information are selected for signal reconstruction. To solve the problem that the multiscale dispersion entropy (MDE) will miss some information in the multi-scale process, RCMDE is introduced to detect milling chatter. Finally, the experiment of the variable cutting depth in side milling of titanium alloy thin-walled parts is carried out. The experimental results show that the OVMD algorithm proposed can solve the problem of difficult separation of chatter frequency bands caused by mode aliasing, and lay a foundation for subsequent chatter feature extraction. RCMDE is more conducive to chatter detection than the single-scale DE when the scale factor is 4. The distinguishing effect of RCMDE on the machining state is more than 50% higher than that of MDE when the scale factor is 4.
Development of high-performance nickel-based catalysts for production of hydrogen and carbon nanotubes from biogas
Authors: Saconsint Supanida , Sae-tang Nonthicha , Sr Atthapon , Koo-Amornpattana Wanida , Assabumrungrat Suttichai , Fukuhara Choji , Ratchahat Sakhon
Published: July 2022

Selecting a suitable catalyst for implementing both simultaneous productions of hydrogen-rich syngas and multi-walled carbon nanotubes (MWCNTs) through the integration of dry reforming and methane decomposition reactions has recently gained great interests. In this study, a series of bimetallic (NiMo/MgO) and trimetallic (CoNiMo/MgO, FeNiMo/MgO, CoFeMo/MgO) catalysts was prepared and evaluated for a catalytic activity of CH4 and CO2 conversions of biogas in a fixed bed reactor at 800°C and atmospheric pressure. Among the catalysts investigated for directly converting biogas process, the bimetallic NiMo/MgO catalyst showed the outstanding catalytic performance with 86.4% CH4 conversion and 95.6% CO2 conversion as well as producing the highest syngas purity of 90.0% with H2/CO ratio = 1.1. Moreover, the characterization of the synthesized CNTs proved that the well-aligned structured morphology, high purity, and excellent textural properties were obtained using NiMo/MgO catalyst. On the other hand, using trimetallic catalysts which have the composition of Co and Fe particles leads to severe deactivation. This could be elucidated by the influence of the catalyst oxidation with CO2 in biogas, resulting in the transformation of metal into large metal oxide. The integrative process through using NiMo/MgO catalysts is regarded as a promising pathway, which has potentially useful for directly converting biogas into a high value-added product and provides a management approach for the enormous amounts of wastes.
Fatty Infiltrate and Neck Muscle Volume in Individuals with Chronic Whiplash Associated Disorders Compared to Healthy Controls
Authors: Lund Nils , Leinhard Olof Dahlqvist , Elliott Jim , Peterson Gunnel , Borga Magnus , Zsigmond Peter , Karlsson Anette , Peolsson Anneli
Published: July 2022

The underlying pathophysiological mechanisms of chronic Whiplash Associated Disorders (WAD) are not fully understood, and more knowledge of morphology is needed to better understand the disorder, improve diagnostics and treatments. The aim was to investigate muscle fat infiltration (MFI) and muscle volume (MV) in dorsal neck musculature among participants with chronic WAD grade II-III compared to matched healthy controls, and in relation to functional severity of WAD measured with Neck Disability Index (NDI). MV and MFI at spinal segments C4 through C7 in both sexes with mild- to moderate chronic WAD, severe chronic WAD, and age- and sex matched healthy controls was compared. Muscles: trapezius, splenius, semispinalis capitis and semispinalis cervicis were segmented by a blinded assessor and analyzed, showing statistically significantly higher MFI in right trapezius among participants with severe chronic WAD compared to healthy controls (p=0.007). No other statistically significant differences were found for MFI (p=0.22-0.95) or MV (p=0.20-0.76). In conclusion, there are quantifiable changes in muscle composition of right trapezius, the side of dominant pain, among participants with severe chronic WAD. Further research is needed to better understand chronic WAD pathophysiology, muscle morphological changes, and its’ relation to neck disability.
Reduced expression of PRX2/ATPRX1, PRX8, PRX35, and PRX73 affects cell elongation, vegetative growth, and vasculature structures in Arabidopsis thaliana
Authors: Jeong Yu Jeong , Kim Young-Cheon , Lee June Seung , Kim Dong-Gwan , Lee Jeong Hwan
Published: July 2022

Class III peroxidases (PRXs) are involved in a broad spectrum of physiological and developmental processes throughout the life cycle of plants. However, the specific function of each PRX member in the family remains largely unknown. In this study, we selected four class III peroxidase genes (PRX2/ATPRX1, PRX8, PRX35, and PRX73) from a previous genome-wide transcriptome analysis, and performed phenotypic and morphological analyses, including histochemical staining in PRX2RNAi, PRX8RNAi, PRX35RNAi, and PRX73RNAi plants. The reduced mRNA levels of corresponding PRX genes in PRX2RNAi, PRX8RNAi, PRX35RNAi, and PRX73RNAi seedlings resulted in elongated hypocotyls and roots, and slightly faster vegetative growth. To investigate internal structural changes in the vasculature, we performed histochemical staining, which revealed alterations in cell wall structures in the main vasculature of hypocotyls, stems, and roots of each PRXRNAi plant compared to wild-type (Col-0) plants. Furthermore, we found that PRX35RNAi plants displayed the decrease in lignified cell wall in vascular region, which were involved in downregulation of lignin biosynthesis and biosynthesis-regulated genes’ expression. Taken together, these results indicated that the reduced expression levels of PRX2/ATPRX1, PRX8, PRX35, and PRX73 affected hypocotyl and root elongation, vegetative growth, and the vasculature structures in hypocotyl, stem, and root tissues, suggesting that the four class III PRX genes play roles in plant developmental processes.
Diversity and plasticity of simultaneously expressing extracellular protease inhibitors from four marine Streptomyces spp. isolated from West coast of India
Authors: Shintre Neha , Deshpande Neelima , Patwardhan Rajashree , Tamhane Vaijayanti
Published: July 2022

Streptomyces have long been studied for their defense metabolites and Protease Inhibitors (PIs) they secrete for mediating biotic interactions. Current study focuses on diversity of extracellular PIs obtained from four marine Streptomyces species isolated from intertidal regions of West Coast of India. Streptomyces PIs showed strong inhibition of subtilisin followed by trypsin and chymotrypsin. Using shotgun proteomics approach, we identified 15 Streptomyces PIs belonging to 4 PI families namely Streptomyces subtilisin inhibitor (SSI), Potato peptidase inhibitor, Ovomucoid and Serpin. This is a first report of identification of Ovomucoid and Potato peptidase inhibitor families from Streptomyces. Amongst the 15 PIs, 12 were SSIs with 20-75% sequence similarity and variations in the conserved 73rd aa residue. Moreover, 10 SSI isoforms were co-expressed in a single species S. longispororuber. In-silico and in-vitro assays with proteases from microbial, bovine and insect sources suggested that the Streptomyces PIs had a broad-spectrum inhibitory activity. In co-culture of Streptomyces with other protease producing bacteria, cellular secretions differentially affected growth, sporulation and/or pigment production. Present study elucidates the diversity and plasticity of extracellular PIs from marine Streptomyces spp. Further, their role in chemical ecology of the bacterial communities as well as their potential applications in therapeutics are discussed.
Histopathology pattern and survival analysis of patients with kidney biopsy in the Top End of Northern Australia from 2007 to 2020
Authors: Goh Kim Ling , Abeyaratne Asanga , Priyadarshana Kelum
Published: July 2022

Aim: Royal Darwin Hospital (RDH) is the main tertiary hospital that has performed more than 600 biopsies since its establishment. Although Aboriginal people in Australia’s Northern Territory has the highest rate of renal replacement therapy, the histopathology pattern of their renal diseases is still under discussed. We aimed to analyse the histopathology pattern of patients undergoing renal biopsy in RDH from June 2007 to June 2020. Secondary aims include clinical indication and survival analysis of patients with kidney biopsies. Methods: We conducted a retrospective cohort study on all native kidney biopsy reports from patients over the age of 16, from June 2007 to June 2020. Descriptive statistics was used to summarise age, sex, indigeneity, histopathological pattern, and mortality. Categorical values were expressed as absolute frequencies and percentages. Survival analysis was performed using multivariate analyses and Cox proportional hazard regression model. Results: There were 364 native renal biopsies included in the analysis. Sub-nephrotic proteinuria was the most common clinical indication for kidney biopsy (n=160,47.8%). Diabetes nephropathy (DN) was the most common pathological finding (n=71,12.8%). Indigenous population who had dialysis performs poorly compared to their non-indigenous counterpart (HR 2.37,95% CI 1.53-3.67,p<0.001). Conclusion: Diabetic nephropathy is the most common native kidney biopsy in the NT with higher mortality among indigenous patients. This study supports the previous findings of indigenous female excess, younger age of kidney disease requiring kidney biopsy, and excess of diabetic nephropathy in the top-end of the NT. It can be speculated that some diabetic patients had atypical features prompting a biopsy.
A Novel Prognostic Model for Hepatocellular Carcinoma Patients Based on Signature Ferroptosis-Immune Microenvironment-Related Genes
Authors: Yin Xisheng , Tang Jiayi , Yang Qian , Xu Ke , Chen Shi , He Miao , Yang Yuhan , Luo Jincheng , Li Yunyue , Wang Xiaoyu , Liu Xin , Chi Hao , Li Xiaosong
Published: July 2022

Background
Hepatocellular carcinoma (HCC) is one of the leading malignancies in the world due to its progressively increasing incidence. Nonetheless, the impact of ferroptosis and immune microenvironment on prognosis of HCC remains unclear. This research work aims to identify ferroptosis-immune microenvironment-related genes (FIMRGs) which influence the prognosis of HCC, providing a theoretical basis for an in-depth understanding of the pathogenesis and prognosis of HCC.
Methods
TCGA-LIHC cohort and GSE14520 cohort were enrolled in this study. 167 ferroptosis-related genes (FRGs) were retrieved from the FerrDb data resource. Consensus clustering assessment, immune infiltration assessment, weighted gene co-expression network analysis (WGCNA), Pearson correlation analysis along with Cox regression were used to identify and establish FIMRGs signature in HCC. Univariate coupled with multivariate regression assessment were executed to ascertain the independent prognostic worthiness of the risk score. The tumor microenvironment (TME) and drug sensitivity profiling were compared between the high-HCC risk and low-HCC risk groups. Subsequently, the drugs or molecular compounds targeting each prognostic gene were predicted via the DGIdb database.
Results
Based on 15 DEFRGs related with prognosis in individuals with HCC, the two clusters with significant prognostic differences have been mined. 9 genes (PTPRO, CRHBP, HMOX1, FABP5, TREM2, ADAMTS14, LILRA6, CAPG, and RGS2) have been identified from 55 FIMRGs, which were adopted to generate and verify the risk score model in the training along with the validation set. Cox regression assessment manifested the risk score to be independent predictive factor. TME analysis and drug sensitivity profiling exhibited remarkable differences in the immune microenvironment between high-HCC and low-HCC risk groups, with the low-HCC risk group being more likely to benefit from chemotherapy. Furthermore, A miRNA-mRNA regulatory network consisting of four prognostic genes and five prognostic miRNAs was formed. Finally, there were four drugs targeting HMOX1, one drug targeting RGS2, CAPG and CRHBP respectively, which have been extracted from the DGIdb database.
Conclusion
This study proposed a novel and promising prognostic gene signature, which could provide us a panoramic view of the prediction of prognosis for HCC patients.
Valve design considerations in liquid hydrogen systems to prevent failure
Authors: Sotoodeh Karan , Gudmestad Ove
Published: July 2022

Hydrogen has potential as an alternative source of energy (energy carrier) because it can be converted, stored, and used efficiently, with a wide range of applications. It can be created from renewable energy sources and can thus serve as storage of renewable energy like wind- and sun-power. It has been several decades since liquid hydrogen has been used as a fuel in space technology, however, the Space Shuttle Challenger disaster in 1986, was caused by seals leaking due to low outside temperature; the night of January 28th 1986 was freezing cold. This underlines the importance of cautious use of hydrogen.It shall be noted that Hydrogen liquefies at -252.9°C (-423°F), so cryogenic systems and sophisticated insulation techniques are necessary. Furthermore, steel is susceptible to hydrogen induced cracking. Control of the flow has always been carried out by valve assemblies in processing plants. The proper design of industrial valves in every industry, including hydrogen systems, can significantly improve the safety and reliability of the valves specifically, as well as the plant as a whole. An overview of various previous studies is presented in this paper, discussing important design concepts for cryogenic valves. The main research question is to determine what are the main design considerations for valves used in liquid hydrogen, so as to minimize the risk of leakage from the valves to ensure required safety. In this study, different aspects of valve design for liquid hydrogen are examined, such as selection of steel materials, steel wall thickness calculations, stem design, sealing material selection, fire-safe design, cavity over-pressure protection, and body and bonnet extension. The effects of the outside temperature will also be discussed.
Estimation of marine algal biomass using a coverage analysis
Authors: Jung Seung Wook , Choi Chang Geun
Published: July 2022

This study was conducted to assess the feasibility of biomass estimation by non-destructive sampling, determine whether the results derived from various types of marine algae are reliable, and a newly proposed method. A quantitative survey was conducted on marine algae communities distributed in the subtidal zone in 67 coastal regions in Korea. Regression analyses were conducted on 11,642 fresh weight datasets covering of 135 species of marine algae. The linear function was FW = 17.721C (adj r2 = 0.745, p < 0.001) and the power function was FW = 4.48C1.251 (adj r2 = 0.891, p < 0.001). Our analysis accounted for the fact that there were three vertically distributed layers of a marine algal assemblages with various shapes (i.e., the Ecklonia complex, the Sargassum and Undaria complex, and the understory complex). For the Ecklonia complex, the linear function was FW = 27.360C (adj r2 = 0.886, p < 0.001) and the power function was FW = 9.626C1.223 (adj r2 = 0.909, p < 0.001). For the Sargassum and Undaria complex, the linear function was FW = 18.389C (adj r2 = 0.916, p < 0.001) and the power function was FW = 6.567C1.255 (adj r2 = 0.942, p < 0.001). For the understory complex, the linear function was FW = 10.419C (adj r2 = 0.737, p < 0.001) and the power function was FW = 4.377C1.182 (adj r2 = 0.871, p < 0.001). Our findings demonstrated that the proposed method can accurately estimate the primary productivity of a wide range of coastal ecosystems based on remote sensing and non-destructive surveys of small-scale marine algal communities.
Characteristics of Wind Flow Around a University Campus Settlement Estimated by CFD Simulation
Authors: Gorgulu Yasin Furkan , Hazer Aysegul
Published: July 2022

Performing a computational fluid dynamics (CFD) analysis of a settlement can present many parameters such as determining the wind load, predicting the temperature distribution, determining the turbulence formations about how that settlement should be located, to the scientists in the architectural and engineering departments. In this study, a CFD analysis has been done using a commercial analysis program “Ansys Fluent” and the geometry has been created using an architectural program known as “SketchUp”. Istanbul Health and Technology University Merter Campus buildings have been taken as the reference models. Streamlines, velocity, pressure, temperature and turbulence kinetic energy distribution contours have been projected. The highest flow velocities and turbulence density were observed between the campus buildings, and when the temperature distributions were examined, dramatic decreases were found in the building temperatures on the windward facade. The maximum wind loads, temperature distributions and so on have been detected and according to the results, recommendations have been made.
Study on Typhoon Disaster Assessment by Mining Data from Social Media Based on Artificial Neural Network
Authors: Li Shaopan , Wang Yan , Huang Hong , Huang Lida , Chen Yang
Published: July 2022

Typhoon disaster is a major threat to the economy and personnel safety in coastal areas. After the disaster, the objective assessment of typhoon disaster economic losses can provide an important reference for the post-disaster rescue and reconstruction and improve the scientific decision-making. In this study, social media data, disaster causing factors, disaster bearing carriers (exposure and vulnerability) and other factors in traditional disasters were combined to achieve rapid disaster assessment. Convolutional neural networks were used to train a text classifier and perform automatic text classification of social media data. The correlations were discussed between various texts and disaster economic losses. It was found that there was a strong correlation between the geographical distribution of texts describing disaster damage and disaster economic losses. A Back Propagation neural network was used for supervised learning to realize disaster loss assessment. To prove the reliability and applicability of the evaluation model, typhoons “Mangkhut” and “Lekima” were selected as study cases to realize the whole process from information collection to final assessment. The introduction of social media data modified the assessment results obtained by traditional methods and reduced the difference between the estimated disaster loss value and the actual value.
Protective effect of peroxisome proliferator-activated receptor-α in regulating the early inflammation response to extended hepatectomy from a comparative transcriptomic analysis
Authors: Shi Cheng-Cheng , Bai Yang , Yan Xin , Cheng Nuo , Guo Wen-Zhi , Zhang Shui-Jun , Shi Ji-Hua
Published: July 2022

Background
The regulation mechanism of post-operative hepatic failure and small-for-size syndrome remains unclear. Thus, we aimed to analyze the molecular profiles following extended hepatectomy and identify the therapeutic target.
Methods
Major hepatectomy and extended hepatectomy were performed in the rat model, and the remnant livers were obtained dynamically for the high-throughput transcriptome analysis to identify the differentially expressed genes (DEGs). The general framework for weighted gene co-expression network analysis (WGCNA) was employed to explore the expression patterns of DEGs. The expression and function of the selected DEG from the WGCNA was further verified following hepatectomy in the human and rat.
Results
DEGs after major hepatectomy and extended hepatectomy were detected by transcriptomics. WGCNA identified 10 distinct gene co-expression modules according to the correlation between module eigengene and different postoperative time-points. The magenta module (gene count: 289) and the lightcyan module (gene count: 484) were found positively correlated with major hepatectomy instead of extended hepatectomy. In the lightcyan module, peroxisome proliferator-activated receptor-α (PPARα) was selected and found the down-regulation in the remnant liver following extended (marginal) hepatectomy in rats and humans. Besides, administration of PPARα agonist attenuated hepatic inflammation injury while PPARα antagonist increased liver inflammation injury after extended hepatectomy in rats, marked by the significantly changed aminotransferases, tumor necrosis factor-α and interleukin-6 levels in the plasm, and histological Suzuki criteria.
Conclusion
DEGs and their molecular profiles after extended hepatectomy were identified, and PPARα could be a potential therapy target for small-for-size syndrome.
Adeno-Associated Virus based Caveolin-1 Delivery via Different Routes for the Prevention of Cholesterol Gallstone Formation
Authors: Li Sha , Chen Hongtan , Jiang Xin , Hu Fengling , Li Yiqiao , Xu Guoqiang
Published: July 2022

Background
The hepatic caveolin1 (CAV1) was reduced in cholesterol gallstone disease (CGD). And mice with CAV1 deficiency were prone to develop CGD. However, it remains unknown whether the restored hepatic CAV1 expression would prevent the development of CGD.
Methods
C57BL/6 mice were injected with adeno-associated virus 2/8 (AAV2/8) vectors carrying CAV1 gene (AAV2/8CAV1) via intravenous (i.v.) or intraperitoneal (i.p.) route and then were subjected to a lithogenic diet (LD) for 8 weeks. Uninjected mice were used as control. The functional consequences of rescuing CAV1 expression by either i.v. or i.p. AAV2/8CAV1 treatment on CGD prevention and its subsequent molecular mechanisms were examined.
Results
The CAV1 expression was reduced in liver and gallbladder of LD-fed-induced CGD mice. We discovered that AAV2/8CAV1 i.p. delivery results in higher transduction efficiency in the gallbladder than tail vein administration. And although either i.v. or i.p. injection of AAV2/8CAV1 improved the liver lipid metabolic abnormalities in CGD mice, they did not affect LD feeding-induced bile cholesterol supersaturation. In comparison with i.v. administration route, i.p. administration of AAV2/8CAV1 obviously increased CAV1 protein levels in the gallbladder of LD-fed mice. And i.p. delivery of AAV2/8CAV1 would partially improve gallbladder cholecystokinin receptor (CCKAR) responsiveness and impede bile cholesterol nucleation, via the activation of adenosine monophosphate-activated protein kinase (AMPK) signaling induced a reduction of gallbladder mucin-1 (MUC1) and MUC5ac expression and gallbladder cholesterol accumulation.
Conclusions
CGD prevention by i.p. AAV2/8CAV1 injection in LD-fed mice was associated with the improvement of gallbladder stasis, which again supported the notion that supersaturated bile is required but not sufficient for the formation of cholesterol gallstones. Additionally, AAV treatment via local i.p. injection offers particular advantages over the systemic i.v. route for much more effective gallbladder gene delivery, which will be an excellent tool for conducting preclinical functional studies on the maintenance of normal gallbladder function to prevent CGD.
A 2-D numerical study of contact angle effect on transient falling-film flow over horizontal tubes
Authors: Kandukuri Prudviraj , Deshmukh Sandip , Katiresan Supradeepan
Published: July 2022

The coverage of the liquid film over the horizontal tubes, particularly the wetting ratio, is important for heat transfer mechanism of gravity-driven evaporators and absorbers. A 2D, two-phase CFD model was developed to examine the falling-film hydrodynamics and transient flow mechanism for Reynolds numbers ranging from 100-500, contact angles spanning from 0°/30°/60°/90°, and inter tube spacing of 10 mm. The VOF method is used in this article to capture the gas-liquid interface. The findings showed that the complete spreading of the liquid film is difficult at low Reynolds numbers and high contact angles. The formation of dry regions on the tube wall as a result of insufficient liquid supply, liquid film breakage, and liquid film shrinkage. Furthermore, as the Reynolds number increases and contact angle decrease, the wetting ratio over the tube surface increases. It was worth noting that each contact angle must have a minimum Reynolds number in order to keep the surface completely wet. The research also found that for higher Reynolds numbers, the influence of contact angle on wettability of tube wall can be ignored. The liquid propagation time required to wet the tube surface increases as the contact angle value increases for the same Reynolds number. Fouling over the tubes can be aided by the formation of air voids near the lower stagnation zone.
Targeted, actionable and fair: reviewer reports as feedback and its effect on ECR career choices
Authors: Derrick Gemma , Zimmermann Alessandra , Greaves Helen , Best Jonathan , Klavans Richard
Published: July 2022

Background: Previous studies of the use of peer review for the allocation of competitive funding agencies have concentrated on questions of efficiency and how to make the ‘best’ decision, by ensuring that successful applicants are also the more productive or visible in the long term. This paper examines the components of feedback received from an unsuccessful grant application, is associated with motivating applicants career decisions to persist (reapply for funding), or to switch (not to reapply, or else leave academia).Methods: This study combined data from a survey of all applicants to ECR funding calls of The Wellcome Trust 2009-2019; with interviews with unsuccessful applicants (n=19), and manual coding of reviewer comments received by applicants (n=81).Results: Survey results show a high proportion of resubmissions, with 50% of unsuccessful applicants at T0 reapplying at T1, and with 35% of these achieving success with this reapplication. Here, peer-review-comments-as-feedback sends signals to applicants to encourage them to persist (continue) or switch (not continue) even when the initial application has failed. Feedback associated by unsuccessful applicants as motivating their decision to resubmit had 3 characteristics: actionable; targeted; and fair.Conclusions: The results lead to identification of standards of feedback for funding agencies and peer-reviewers to promote when providing reviewer feedback to applicants as part of their peer review process. The provision of quality reviewer-reports-as-feedback to applicants, ensures that peer review acts as a participatory research governance tool focused on supporting the development of individuals and their future research plans.
Non metastasis protein 2 (NME2) is a potential target for leukemia-specific immunotherapy
Authors: Däbritz Tobias , TSCHIEDEL Sabine , CROSS Michael , NIEDERWIESER Dietger
Published: July 2022

Background: NME2 is an immunogenic overexpressed tumor-associated antigen in chronic myeloid leukemia (CML). We evaluated NME2’s antigenicity in common HLA-backgrounds as a potential target for CML-specific immunotherapy. Methods: NME2-specific cytotoxic T-lymphocytes (CTL) were generated by stimulating cultured PBMCs with artificial antigen presenting cells (aAPC) expressing NME2 and the appropriate HLA-A antigen. Cultured PBMCs were obtained from healthy donors or CML-patients and priming with aAPCs was repeated weekly. IFNγ production from CD8+CTLs was evaluated by ELISpot assays. Results: NME2-specific CTLs were successfully generated both from healthy donors and from CML patients after hematopoietic stem cell transplantation. NME2-specific recognition by CTLs was HLA class I restricted (HLA-A 02, 03, 24) with no significant differences between the HLA-A backgrounds tested. The T315I TKI resistance mutation BCR::ABL1 did not affect susceptibility to CTL-mediated killing.Conclusions: NME2-specific CTLs can eradicate CML progenitor cells remaining after TKI-therapy or HSCT. Immunotherapy targeting NME2 may complement existing therapies.
Effect of Atmospheric Pressure Cold Plasma Gliding Arc Discharge Remote Treatment on Microbiological and Physicochemical Properties of Black Peppercorns (Piper nigrum)
Authors: Silva A. B.G.C.J. , Weerasinghe W. A.B.S. , Weeratunge H. D. , Milani M.D.Y. , Amunugoda P. N.R.J. , Gunawardena S. H. P. , de Alwis A.A.P.
Published: July 2022

The authors have requested that this preprint be removed from Research Square.
Prenatal diagnosis and genetic counseling of an inherited unbalanced chromosome abnormalities in a Chinese family
Authors: Zhang Ying , Chen Juan , Feng Zonghui , Li Wencheng
Published: July 2022

Background: Unbalanced chromosome abnormalities (UBCA) are either gains or losses or large genomic regions, but the affected person is not or only minimally clinically affected. Copy number variants (CNVs) are an important source of normal and pathogenic genome variations. CNVs and UBCA identified in prenatal cases need careful considerations and correct interpretation if those are harmless or harmful variants from the norm.Case presentation: A 25-year-old, gravida 1, para 0, woman underwent amniocentesis at 18 weeks of gestation because the noninvasive prenatal testing (NIPT) results revealed a 6.8 Mb duplication from 2q11.1 to 2q11.2. Chromosomal microarray analysis (CMA) was performed on uncultured amniocytes. GTG-banding karyotype analysis on cultured amniocytes was performed. Results: Chromosomal GTG-banding of the cultured amniocytes revealed a karyotype of 46,XX. CMA detected a 6.8-Mb chromosomal duplication in the region of 2q11.1q11.2 (arr[GRCh37] 2q11.1q11.2(95,327,873_102,088,148)x3).Conclusion: Chromosomal microdeletions and microduplications are difficult to detect by conventional cytogenetics, combination of prenatal ultrasound, karyotype analysis, NIPT, CMA and genetic counseling is helpful for the prenatal diagnosis of UBCA and chromosomal microdeletions/microduplications..
Storage-induced changes in plasticizer emigration and structural properties of soybean isolate protein-based composite films
Authors: Zhu Tingwei , Fan Peipei , Li Qianyu , Ma Luyan , Wei Qian , Guo Xingfeng , Chen Fusheng
Published: July 2022

Previous study found soybean isolate protein (SPI)-based composite films added by corn starch (CS) (SPI:CS (4:1) composite film, SPI:CS (1:1) composite film) exhibited good mechanical property and better stability during the short-term storage pre-experiment. These properties were related to internal structure changes. In order to accordingly understanding the causes driving stability changes in performance and then controlling long-term stability of the SPI-based composite films, plasticizer emigration and structural properties of SPI-based composite films stored at different temperatures (5 ℃, 20 ℃, 35 ℃) and 54% relative humidity were systematically investigated over a period of time. High storage temperature (＞ 20 ℃) accelerated plasticizer emigration which reflected in increased migration rate of glycerol molecules and decreased moisture content. During the storage of SPI-based composite films, the decreased free SH partly formed new disulfide bonds and non-covalent inter-molecular interactions like hydrogen bonds changes significantly weakened the protein structure, which influenced mechanical properties changes during storage. PAGE and FTIR results explained the protein aggregation was bond with disulfide bonds and the reorganization of protein structure with prevalence of extended β-sheet conformation.