Generation Sequencing Technologies Research Articles

Machine learning-based prediction of proteins’ architecture using sequences of amino acids and structural alphabets

In addition to the growth of protein structures generated through wet laboratory experiments and deposited in the PDB repository, AlphaFold predictions have significantly contributed to the creation of a much larger database of protein structures. Annotating such a vast number of structures has become an increasingly challenging task. CATH is widely recognized as one the most common platforms for addressing this challenge, as it classifies proteins based on their structural and evolutionary relationships, offering the scientific community an invaluable resource for uncovering various properties, including functional annotations. While CATH annotation involves – to some extent – human intervention, keeping up with the classification of the rapidly expanding repositories of protein structures has become exceedingly difficult. Therefore, there is a pressing need for a fully automated approach. On the other hand, the abundance of protein sequences stemming from next generation sequencing technologies, lacking structural annotations, presents an additional challenge to the scientific community. Consequently, 'pre-annotating’ protein sequences with structural features, ensuring a high level of precision, could prove highly advantageous. In this paper, after a thorough investigation, we introduce a novel machine-learning model capable of classifying any protein domain, whether it has a known structure or not, into one of the 40 main CATH Architectures. We achieve an F1 Score of 0.92 using only the amino acid sequence and a score of 0.94 using both the sequence of amino acids and the sequence of structural alphabets. Communicated by Ramaswamy H. Sarma

Gene sequencing technologies and their application in cancer research

The continuous development of gene sequencing technology has made the next-generation sequencing technology and the third-generation sequencing technology gradually applied to scientific research, which has greatly improved the efficiency and accuracy of sequencing and reduced the cost. The incidence of tumors in the human population continues to rise, making tumors gradually become one of the most serious diseases that endanger health. In view of the close relationship between gene mutations and tumorigenesis, the progress of gene sequencing technology has a profound impact on clinical research on tumors. In this thesis, literature analysis was used to introduce several gene sequencing technologies and compare them from multiple perspectives. In addition, the causes of tumorigenesis and the role of sequencing technology in the clinical research of human tumors were investigated. This paper found that the third-generation sequencing technology was more efficient than the next-generation sequencing technology, but it was difficult to be widely used due to its lower accuracy. Sequencing technology is of great help to tumor clinical research.

Nitrite Degradation by a Novel Marine Bacterial Strain Pseudomonas aeruginosa DM6: Characterization and Metabolic Pathway Analysis

High concentrations of nitrite in marine aquaculture wastewater not only pose a threat to the survival and immune systems of aquatic organisms but also contribute to eutrophication, thereby impacting the balance of coastal ecosystems. Compared to traditional physical and chemical methods, utilizing microorganism-mediated biological denitrification is a cost-effective and efficient solution. However, the osmotic pressure changes and salt-induced enzyme precipitation in high-salinity seawater aquaculture environments may inhibit the growth and metabolism of freshwater bacterial strains, making it more suitable to select salt-tolerant marine microorganisms for treating nitrite in marine aquaculture wastewater. In this study, a salt-tolerant nitrite-degrading bacterium, designated as DM6, was isolated from the seawater (salinity of 25–30‰) of Portunus trituberculatus cultivation. The molecular identification of strain DM6 was conducted using 16S rRNA gene sequencing technology. The impacts of various environmental factors on the nitrite degradation performance of strain DM6 were investigated through single-factor and orthogonal experiments, with the selected conditions considered to be the key factors affecting the denitrification efficiency of microorganisms in actual wastewater treatment. PCR amplification of key genes involved in the nitrite metabolism pathway of strain DM6 was conducted, including denitrification pathway-related genes narG, narH, narI, nirS, and norB, as well as assimilation pathway-related genes nasC, nasD, nasE, glnA, gltB, gltD, gdhB, and gdhA. The findings indicated that strain DM6 is classified as Pseudomonas aeruginosa and exhibits efficient nitrite degradation even under a salinity of 35‰. The optimal nitrite degradation efficiency of DM6 was observed when using sodium citrate as the carbon source, a C/N ratio of 20, a salinity of 13‰, pH 8.0, and a temperature of 35 °C. Under these conditions, DM6 could completely degrade an initial nitrite concentration of 156.33 ± 1.17 mg/L within 36 h. Additionally, the successful amplification of key genes involved in the nitrite denitrification and assimilation pathways suggests that strain DM6 may possess both denitrification and assimilation pathways for nitrite degradation simultaneously. Compared to freshwater strains, strain DM6 demonstrates higher salt tolerance and exhibits strong nitrite degradation capability even at high concentrations. However, it may be more suitable for application in the treatment of wastewater from marine aquaculture systems during summer, high-temperature, or moderately alkaline conditions.

Effects of Polymannuronic Acid on the Intestinal Microbiota in Mice after Long-Term Intragastric Administration.

Polymannuronic acid (PM) is an alginate oligosaccharide derived from brown algae with a characterized structure and excellent biological activities. Herein, mice were given different doses of PM through 30-day-long-term intragastric administration, and the contents of the jejunum, ileum, and colon were analyzed by 16S rRNA gene sequencing technology for microbial diversity, and relevant experiments were verified according to the analysis results so as to comprehensively evaluate the effects of PM on the intestinal flora. The PM (400 mg/kg and 100 mg/kg) could regulate the microflora balance at the phylum level and increase the microflora richness in the jejunum, ileum, and colon of the mice. The PM could induce more strains that are negatively correlated with Escherichia, thereby reducing the relative abundance of Escherichia. Analysis of bacterial function showed that high and low doses of PM could promote lipid metabolism in the bacterial communities. Moreover, the PM could reduce serum total cholesterol and cholesterol ester levels in a concentration-dependent manner. High-dose PM could lead to colonic intestinal inflammation by increasing the relative abundance of multiple bacterial groups in the jejunum, ileum, and colon. Moreover, high-dose PM could increase lipopolysaccharide-binding protein and interleukin-1β levels. Therefore, the dose of PM plays an important role in its efficacy, and its biological activity is dosedifferent.

Single locus HLA sequencing with the nanopore technology for HLA disease association diagnosis.

Associations between HLA genotype and disease susceptibility encompass almost all the classic HLA loci. The level of typing resolution enabling a correct identification of an HLA disease susceptibility gene depends on the disease itself and/or on the accumulated knowledge about the molecular involvement of the HLA allele(s) engaged. Therefore, the application of Next Generation Sequencing technologies to HLA disease association, which would improve typing resolution, could prove useful to better understand disease severity. In the present study, we tested a nanopore sequencing approach developed by Omixon Biocomputing Ltd, dedicated to on-demand locus typing for HLA and disease, as an alternative to the conventional widely used sequence specific oligoprobe (SSO) approach. A total of 145 DNA samples used in routine diagnosis by SSO were retrospectively analyzed with nanopore technology, for HLA-A*02 immunotherapy decision for A*29, B*27, B*51, B*57 identification in class I, and DRB1, DQA1, and DQB1 for bullous dermatosis, rheumatoid arthritis, diabetes, and celiac disease requests in class II. Each locus was typed in a separate experiment, except for DQB1 and DQA1, which were analyzed together. Concordance between typings reached 100% for all the loci tested. Ambiguities by nanopore were only found for missing exon coverage. This approach was found to be very well adapted to the routine flow imposed by the SSO technique. This study illustrates the use of the new NanoTYPE MONO kit for single locus HLA sequencing for HLA and disease association diagnosis.

Recent Advances towards the Understanding of Secondary Acute Myeloid Leukemia Progression.

Secondary acute myeloid leukemia (sAML) is a heterogeneous malignant hematopoietic disease that arises either from an antecedent hematologic disorder (AHD) including myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), aplastic anemia (AA), or as a result of exposure to genotoxic chemotherapeutic agents or radiotherapy (therapy related AML, tAML). sAML is diagnosed when the number of blasts is ≥20% in the bone marrow or peripheral blood, and it is characterized by poor prognosis, resistance to therapy and low overall survival rate. With the recent advances in next generation sequencing technologies, our understanding of the molecular events associated with sAML evolution has significantly increased and opened new perspectives for the development of novel therapies. The genetic aberrations that are associated with sAML affect genes involved in processes such as splicing, chromatin modification and genome integrity. Moreover, non-coding RNAs' emerged as an important contributing factor to leukemogenesis. For decades, the standard treatment for secondary AML has been the 7 + 3 regimen of cytarabine and daunorubicin which prolongs survival for several months, but modifications in either dosage or delivery has significantly extended that time. Apart from traditional chemotherapy, hematopoietic stem cell transplantation, CAR-T cell therapy and small molecule inhibitors have also emerged to treat sAML.

Efficient crop straws biotreatment using the fungus Cerrena Unicolor GC.u01

Lignin is main composition of agricultural biomass which can be decomposed through enzymatic hydrolysis by fungi. However, there are still needs to identify more efficient and effective fungal stain for biomass valorization. In this study, lignin degrading fungi from birch forest were screened for sustainable degradation of waste agricultural straws. The most effective strain was identified as Cerrena unicolor GC.u01 using 18 S rDNA gene-sequencing technology. Three different crop straws (corn stalk, rice and wheat straws) were used for the biotreatment studies. The activities of lignin degrading enzymes, laccase (Lac), cellulase and xylanase, secreted by C. unicolor were also determined. Scanning electron microscopy (SEM), fourier transform infrared spectroscopy (FTIR) and thermal gravimetric analyzer (TGA) were further used to monitor the effects of the biotreatment process. The results showed that C. unicolor degraded 34.3% rice straw lignin, a percentage which was higher than other isolated strains after 15 d straw liquid fermentation. The highest Lac activity (8.396 U•mL− 1) was observed with corn stalk on the 7 d. Cellulase and xylanase activities, in the same biomass, were higher than those of wheat and rice straws after 15 d. Furthermore, SEM, FTIR and TGA analyses showed that C. unicolor pretreatment process had significant effects on corn stalk, rice and wheat straws’ structures. The newly isolated stain of C. unicolor demonstrated high lignin degradation potential that can provide effective, ecofriendly means of valorizing biomass to industrial useable raw-material.

The underlying molecular mechanism of ciliated epithelium dysfunction and TGF-β signaling in children with congenital pulmonary airway malformations

The aim of this study was to investigate the variation in gene expression in the complete transcripts of Congenitalpulmonary airwaymalformation (CPAM) of the lung using Next Generation Sequencing (NGS) technology. There were 20 cases involving children with CPAM were used for selection of study sample. NGS was used to establish RNA-Seq libraries for the two groups of samples separately, and both groups were conducted to differential expression analysis and Gene Ontology (GO) functional enrichment analysis. The pathways of the differential genes were analyzed to find the enriched target pathways. A total of 592 genes were expressed with significant differences (CPAM vs. normal tissue, P < 0.05). GO functional analysis of DEGs indicated that abnormal ciliary function played a role in the development of CPAM. Subsequently, analysis of these genes pathways showed the TGF-β signaling pathway was significantly enriched. Finally, the results of immunohistochemical analysis of some DEGs showed that a significant reduction in the expression of SMAD6, a gene related to the TGF-β signaling pathway, led to abnormal activation of the pathway. TGF-β signaling pathway involved in the evolution of the disease obtained by DEGs enrichment pathway analysis. SMAD6, a gene involved in this pathway, might be a potential biomarker for the diagnosis and treatment of CPAM.

Bacterial diversity in cheese wastewater using Next-Generation Sequencing (NGS)

Abstract. Estikomah SA, Suranto, Susilowati A, Masykuri M. 2024. Bacterial diversity in cheese wastewater using Next-Generation Sequencing (NGS). Biodiversitas 25: 482-490. Cheese wastewater (whey) has a high content of organic substances, including lactose, protein, and fat. The lactose in whey wastewater can also be used as a bacterial growth medium. Bacterial community structure is an essential aspect of microbial water quality. The bacterial diversity data obtained can then be used to evaluate the existence of bacteria that might be useful for making microbiological products. This research employs Next Generation Sequencing (NGS) technology to determine the diversity and abundance of bacteria based on 16S rRNA gene amplicons for further processing of whey wastewater. The NGS-based technique overcomes the limitations of conventional bacterial culture techniques. The effectiveness and accuracy of microbial diversity analysis employing NGS technology are high. The research method includes the steps of sample preparation, DNA extraction using a ZymoBIOMICS DNA Microprep Kit (D4300), PCR amplification of the V3-V4 16S rRNA gene region, DNA sequencing, and a bioinformatics-statistical analysis. The results show that bacterial diversity in whey wastewater was found to have an average number of Operational Taxon Units (OTUs) of 259 tags. The metagenomics study of the microbial community in whey wastewater successfully detected the dominant genus of bacteria, which can benefit the management of whey wastewater. The presence of Lactobacillus and Acetobacter confirms that cheese whey wastewater exists in Yogyakarta Province. Acetobacter can oxidize ethanol to produce acetic acid, a pungent odor characteristic that causes environmental pollution. On the other hand, the presence of Lactobacillus and Acetobacter shows that whey wastewater can be reprocessed to produce fermented beverages, thereby improving their value and minimizing the impact of environmental pollution.

Understanding genomic medicine for thoracic aortic disease through the lens of induced pluripotent stem cells.

Thoracic aortic disease (TAD) is often silent until a life-threatening complication occurs. However, genetic information can inform both identification and treatment at an early stage. Indeed, a diagnosis is important for personalised surveillance and intervention plans, as well as cascade screening of family members. Currently, only 20% of heritable TAD patients have a causative mutation identified and, consequently, further advances in genetic coverage are required to define the remaining molecular landscape. The rapid expansion of next generation sequencing technologies is providing a huge resource of genetic data, but a critical issue remains in functionally validating these findings. Induced pluripotent stem cells (iPSCs) are patient-derived, reprogrammed cell lines which allow mechanistic insights, complex modelling of genetic disease and a platform to study aortic genetic variants. This review will address the need for iPSCs as a frontline diagnostic tool to evaluate variants identified by genomic discovery studies and explore their evolving role in biological insight through to drug discovery.

Investigation of the therapeutic effect of Hedan tablets on high-fat diet-induced obesity in rats by GC-MS technology and 16S ribosomal RNA gene sequencing.

Obesity is a persistent metabolic condition resulting from the excessive accumulation or abnormal distribution of body fat. This study aimed to establish an experimental rat model of obesity. The efficacy of treating obesity with Hedan tablets (HDT) was assessed by monitoring changes in weight, blood lipid levels, analyzing inflammatory factors, evaluating organ indices, and observing liver tissue pathology. Furthermore, we utilized 16S ribosomal RNA gene sequencing technology to explore changes in intestinal flora. In addition, GC-MS was used to measure fecal short-chain fatty acid (SCFA) content. The onset of obesity led to a significant decrease in the relative abundance of beneficial bacteria. Conversely, the administration of HDT demonstrated a substantial ability to increase the relative abundance of beneficial bacteria. Obesity resulted in a noteworthy reduction in total SCFAs, a trend significantly reversed in the HDT group. Through correlation analysis, it was determined that HDT mitigated the inflammatory response and improved blood lipid levels by augmenting the abundance of Lactobacillus, Limosilactobacillus, Ruminococcus, and Enterococcus. These particular intestinal flora were identified as regulators of SCFA metabolism, thereby ameliorating metabolic abnormalities associated with obesity. Moreover, HDT intervention elevated the overall fecal concentration of SCFAs, thereby improving metabolic disorders induced by obesity. The anti-obesity effects of HDT are likely attributable to their capacity to influence the composition of intestinal flora and boost SCFA levels in the intestine.

Structure and evolution of DNA transposons of the &lt;i&gt;L31&lt;/i&gt; superfamily of bivalves

DNA transposons of the IS630/Tc1/mariner (ITm) are widespread representatives of DNA transposons that make a significant contribution to the evolution of eukaryotic genomes. With the start of large-scale application of next generation sequencing (NGS) technologies and the emergence of many new whole genome sequences of organisms in nucleotide collections, ITm elements have been identified in most taxa of the eukaryotic tree of life. Despite the rather detailed study of the diversity of ITm representatives, elements are still found that contribute to the expansion and revision of the classification of this group of DNA transposons. This paper presents for the first time a detailed analysis of the L31 elements of bivalves, which resulted in a description of the structure, diversity, distribution, and phylogenetic position among the ITm elements. It was found that L31 transposons are an independent superfamily in the ITm group, which has an ancient origin. Within the L31 clade, rather high diversity was observed: five phylogenetic clusters were identified. At the moment, the presence of L31 transposons in molluscs has been revealed only in bivalves in the subclass Autobranchia, with a predominance in diversity and quantity in the infraclass Pteriomorphia. It has also been shown that the protein encoded by the second open reading frame (ORF2) is an integral structural component of almost all full-length L31 elements. The data obtained contribute to a better understanding of the evolution of representatives of ITm transposons. Further study of L31 transposons in other taxa (cnidaria), as well as the study of the function of the second ORF protein, will provide an opportunity to better understand the evolution of DNA transposons, the mechanisms of horizontal transfer, and the contribution to eukaryotic biodiversity.

Revealing Medicinal Constituents of Bistorta vivipara Based on Non-Targeted Metabolomics and 16S rDNA Gene Sequencing Technology.

Bistorta vivipara is a medicinal plant with a long history, but there are few studies on the effects of its medicinal components and endophytic bacteria on the accumulation of secondary metabolites. Therefore, in this study, non-targeted metabolomics techniques and 16s rDNA techniques were used to study B. vivipara from different regions. A total of 1290 metabolites and 437 differential metabolites were identified from all samples. Among them, flavonoids, isoflavonoids, and benzopyrans are the main medicinal components of B. vivipara; these have potential anticancer, antiviral, and antioxidant properties, as well as potential applications for the treatment of atrial fibrillation. In addition, irigenin, an important medicinal component, was identified for the first time. The endophytic bacterial communities in the root tissues of B. vivipara from different regions were also different in composition and richness. Hierarchical clustering heat map analysis showed that Proteobacteria and Actinobacteriota bacteria significantly affected the accumulation of many medicinal components in the roots of B. vivipara.

A randomized optimal k-mer indexing approach for efficient parallel genome sequence compression

Next Generation Sequencing (NGS) technology generates massive amounts of genome sequence that increases rapidly over time. As a result, there is a growing need for efficient compression algorithms to facilitate the processing, storage, transmission, and analysis of large-scale genome sequences. Over the past 31 years, numerous state-of-the-art compression algorithms have been developed. The performance of any compression algorithm is measured by three main compression metrics: compression ratio, time, and memory usage. Existing k-mer hash indexing systems take more time, due to the decision-making process based on compression results. In this paper, we propose a two-phase reference genome compression algorithm using optimal k-mer length (RGCOK). Reference-based compression takes advantage of the inter-similarity between chromosomes of the same species. RGCOK achieves this by finding the optimal k-mer length for matching, using a randomization method and hashing. The performance of RGCOK was evaluated on three different benchmark data sets: novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Homo sapiens, and other species sequences using an Amazon AWS virtual cloud machine. Experiments showed that the optimal k-mer finding time by RGCOK is around 45.28 min, whereas the time for existing state-of-the-art algorithms HiRGC, SCCG, and HRCM ranges from 58 min to 8.97 h.

The Impact of Probiotic Bifidobacterium on Liver Diseases and the Microbiota.

Recent studies have shown the promising potential of probiotics, especially the bacterial genus Bifidobacterium, in the treatment of liver diseases. In this work, a systematic review was conducted, with a focus on studies that employed advanced Next Generation Sequencing (NGS) technologies to explore the potential of Bifidobacterium as a probiotic for treating liver pathologies such as Non-Alcoholic Fatty Liver Disease (NAFLD), Non-Alcoholic Steatohepatitis (NASH), Alcoholic Liver Disease (ALD), Cirrhosis, and Hepatocelullar Carcinoma (HCC) and its impact on the microbiota. Our results indicate that Bifidobacterium is a safe and effective probiotic for treating liver lesions. It successfully restored balance to the intestinal microbiota and improved biochemical and clinical parameters in NAFLD, ALD, and Cirrhosis. No significant adverse effects were identified. While more research is needed to establish its efficacy in treating NASH and HCC, the evidence suggests that Bifidobacterium is a promising probiotic for managing liver lesions.

Integrated characterizations of intestinal bacteria and transcriptomics revealed the acute stress response to carbonate alkalinity in white shrimp Penaeusvannamei

The impact of carbonate alkalinity in saline-alkaline water on aquatic organisms, particularly Penaeus vannamei, a significant species in aquaculture, remains a critical area of study. To elucidate the acute response mechanisms of P. vannamei to elevated carbonate alkalinity environments, we utilized 16S rRNA gene and transcriptome sequencing technologies to analyze intestinal bacteria and gene expressions within various tissues. Our investigation revealed notable changes in specific intestinal bacterial OTUs, whose abundances varied preceding the overall bacterial community, indicating the sensitivity to carbonate alkalinity exposure. These shifts are accompanied by a simplification in bacterial networks and alterations in pathogenic OTUs, notably Aeromonas OTU. Concurrently, gene expression variations were observed across the hepatopancreas, gills, muscles, and intestines, with decreasing numbers of DEGs in the mentioned order. Annotation of these DEGs revealed enrichments in pathways related to transport, catabolism, immune responses, circulatory functions, and lipid metabolism. Notably, correlations between specific intestinal bacterial OTUs and gene expression shifts were identified across these tissues. Several OTUs, attributed to Rhizobiales, Saccharimonadales, Acidovora, and Aeromona, exhibited a correlation with DEGs in all four tissues, primarily associated with amino acid metabolism, signal transduction, and transport and catabolism pathways. Our study provides comprehensive insights into the dynamic responses of P. vannamei to elevated carbonate alkalinity stress. These findings contribute crucial knowledge for effective P. vannamei cultivation in saline-alkaline water, advancing our understanding in this field.

Dupilumab-associated ocular surface disease is characterized by a shift from Th2/Th17 toward Th1/Th17 inflammation.

Dupilumab is used for the treatment of atopic dermatitis (AD). Approximately one third of AD patients develop a dupilumab-associated ocular surface disease (DAOSD), of which the pathomechanism is poorly understood. This study aimed at investigating inflammatory markers in tear fluids of patients on dupilumab therapy. Tear fluids were collected from AD patients with DAOSD (ADwDAOSD), AD patients without DAOSD (ADw/oDAOSD), and non-AD patients before and during dupilumab therapy, and analyzed using a specialized proteomic approach quantifying inflammatory markers. The ocular surface microbiome was determined by next generation sequencing technology. Upon dupilumab therapy, an upregulation of 31 inflammatory markers was observed in DAOSD tear fluids compared to baseline in AD patients. While IL-12B was upregulated in both ADwDAOSD and ADw/oDAOSD groups, the pattern of inflammatory markers significantly differed between groups and over time. In the ADwDAOSD group, a shift from a mixed Th2/Th17 pattern at baseline toward a Th1/Th17 profile under dupilumab was observed. Furthermore, an upregulation of remodeling and fibrosis markers was seen in DAOSD. Semantic map and hierarchical cluster analyses of baseline marker expression revealed four clusters distinguishing between AD and non-AD as well as ADwDAOSD and ADw/oDAOSD patient groups. In a pilot study, dupilumab therapy was associated with a decrease in richness of the ocular surface microbiome. DAOSD is characterized by a Th1/Th17 cytokine profile and an upregulation of markers known to promote remodeling and fibrosis. The expression pattern of inflammatory markers in tear fluids at baseline might serve as a prognostic factor for DAOSD.

The Correlation of Gene Mutation and Clinical Characteristics in Patients with Myelodysplastic Syndrome and Prognostic Analysis

To explore the correlation between gene mutations and clinical characteristics, prognosis of myelodysplastic syndromes (MDS). Clinical data of 131 patients with MDS were collected from the First Hospital of Lanzhou University from June 2015 to February 2023, which 19 of them developed into secondary acute myeloid leukemia (sAML) during follow-up time. Second generation sequencing technology was used to detect the mutation types of MDS disease-related genes, drawn gene maps, and analyzed their correlation and prognosis based on the clinical data of patients. The median age of 131 MDS patients was 58(17-86) years old. The ratio of male to female was 1.3∶1. A total of 148 gene mutations and 25 types were found in the center. U2AF1 and ASXL1 were often co-mutations with other genes, which were accompanied by 20q- and normal karyotype (NK) respectively. SETBP1 and SRSF2 were more common in patients over 60 years old, while NPM1 and WT1 under 60 years. Older patients had a higher the number of genetic mutations than younger patients. The incidence of SF3B1 and RUNX1 in males was higher than females and DNMT3A in females was higher than males. The number of gene mutations in sAML was higher than MDS (1.8 vs 1.0, P =0.006). The univariate and multivariate analysis showed that IPSS-R prognostic score≥3.5, TP53 were adverse factors for poor prognosis in MDS patients. Patients with monoallelic mutation（ma-TP53）and wild-type（wt-TP53） TP53 had OS better than biallelic mutation（bi-TP53）(P =0.003). The OS of MDS patients was better than sAML(P =0.01) and transplant patients was significantly better than nontransplant patients(P =0.036). Gene mutation is closely related to cytogenetic indexes and clinical features (peripheral blood cell count, sex, age). IPSS-R prognostic score and TP53 were risk factors affecting OS in MDS patients.

MMGK: Multimodality Multiview Graph Representations and Knowledge Embedding for Mild Cognitive Impairment Diagnosis

The diagnosis of mild cognitive impairment (MCI), which is an early stage of Alzheimer’s disease (AD), has great clinical significance. Medical imaging and gene sequencing technologies have provided sufficient multimodality data for MCI diagnostic studies. However, how to effectively extract the rich representations from multimodality data remains a challenging task. To address this challenging task, we propose a new multimodality multiview graph representations and knowledge embedding (MMGK) framework to diagnose MCI. First, to obtain rich information from multimodality data, we extract multiview feature representations from magnetic resonance imaging (MRI) and genetic data. Afterward, considering the correlations between subjects, all subjects are constructed into a graph based on the different single-view feature representations, respectively. To further enrich the correlations between subjects, demographic data are utilized through knowledge embedding. Finally, to perform MCI diagnosis on multiview graphs, graph convolutional networks (GCNs) are utilized. In addition, to further improve the performance of MCI diagnosis, a two-step ensemble learning method is proposed. The proposed framework is evaluated on 188 subjects from the AD Neuroimaging Initiative (ADNI). Experimental results show that our proposed framework achieves good performance with accuracy reaching 0.888, and outperforms some state-of-the-art (SOTA) methods. In addition, the proposed framework is applied to Parkinson’s disease (PD) diagnosis and achieves 0.856 accuracy. Overall, our proposed method has potential for clinical application in MCI diagnosis and other diseases via integrating MRI, genetic data, and demographic data. Our code is available at: https://github.com/miacsu/MMGK.

Statement of Retraction: The role of second generation sequencing technology and nanomedicine in the monitoring and treatment of lower extremity deep vein thrombosis susceptibility genes

Statement of Retraction: The role of second generation sequencing technology and nanomedicine in the monitoring and treatment of lower extremity deep vein thrombosis susceptibility genes