HpGAN: Sequence Search with Generative Adversarial Networks

Sequences play an important role in many engineering applications and systems. Searching sequences with desired properties has long been an interesting but also challenging research topic. This article proposes a novel method, called HpGAN, to search desired sequences algorithmically using generative adversarial networks (GAN). HpGAN is based on the idea of zero-sum game to train a generative model, which can generate sequences with characteristics similar to the training sequences. In HpGAN, we design the Hopfield network as an encoder to avoid the limitations of GAN in generating discrete data. Compared with traditional sequence construction by algebraic tools, HpGAN is particularly suitable for intractable problems with complex objectives which prevent mathematical analysis. We demonstrate the search capabilities of HpGAN in two applications: 1) HpGAN successfully found many different mutually orthogonal complementary code sets (MOCCS) and optimal odd-length Z-complementary pairs (OB-ZCPs) which are not part of the training set. In the literature, both MOCSSs and OB-ZCPs have found wide applications in wireless communications. 2) HpGAN found new sequences which achieve four-times increase of signal-to-interference ratio--benchmarked against the well-known Legendre sequence--of a mismatched filter (MMF) estimator in pulse compression radar systems. These sequences outperform those found by AlphaSeq.Comment: 12 pages, 16 figure

Global trends in the research of biodegradable biomedical magnesium-based materials: a bibliometric analysis

Background: In recent years, there has been a notable surge in the interest surrounding biodegradable materials, particularly in the context of biomedical applications. This has led to a significant rise in the number of research studies focusing on the utilization of biodegradable magnesium-based materials in the field of biomedicine. However, a dearth of comprehensive assessment exists regarding the body of research concerning biodegradable biomedical magnesium-based materials. In this study, a bibliometric approach was used to illustrate the current state of research and global trends pertaining to biodegradable magnesium-based materials for biomedical applications.Methods: We conducted a search of the Web of Science core collection database for the past decade (2013–2022). VOSviewer software and the bibliometric online analysis platform were employed for bibliometric analysis and visualization.Results: Correspondingly, 1267 documents were retrieved. We discovered that the number of papers in the field of degradable biomedical magnesium-based materials research has increased annually. In addition, China and the Chinese Academy of Sciences have published the largest number of papers in the field of biodegradable biomedical magnesium-based materials. Papers related to biodegradable magnesium-based materials for biomedical use were mainly published in acta biomaterialia, materials science and engineering c-materials for biological applications and materials journals. Keyword co-occurrence analysis showed that “corrosion"and “mechanical-properties” appear more frequently. The top 10 common keywords include corrosion, mechanical-properties, microstructure, biocompatibility, behavior, magnesium, magnesium alloys, degradation magnesium alloy, in vitro.Conclusion: Research on biodegradable magnesium-based materials for biomedical use continues to increase steadily. China maintains a leading position in the world, and the Chinese Academy of Sciences represents a notable contribution to the research of biodegradable magnesium-based materials for biomedical use. Subsequently, “corrosion” and “mechanical-properties” were identified as the current research hotspots in the area of biodegradable biomedical magnesium-based materials

Identification of genes regulated by Wnt/β-catenin pathway and involved in apoptosis via microarray analysis

BACKGROUND: Wnt/β-catenin pathway has critical roles in development and oncogenesis. Although significant progress has been made in understanding the downstream signaling cascade of this pathway, little is known regarding Wnt/β-catenin pathway modification of the cellular apoptosis. METHODS: To identify potential genes regulated by Wnt/β-catenin pathway and involved in apoptosis, we used a stably integrated, inducible RNA interference (RNAi) vector to specific inhibit the expression and the transcriptional activity of β-catenin in HeLa cells. Meanwhile, we designed an oligonucleotide microarray covering 1384 apoptosis-related genes. Using oligonucleotide microarrays, a series of differential expression of genes was identified and further confirmed by RT-PCR. RESULTS: Stably integrated inducible RNAi vector could effectively suppress β-catenin expression and the transcriptional activity of β-catenin/TCF. Meanwhile, depletion of β-catenin in this manner made the cells more sensitive to apoptosis. 130 genes involved in some important cell-apoptotic pathways, such as PTEN-PI3K-AKT pathway, NF-κB pathway and p53 pathway, showed significant alteration in their expression level after the knockdown of β-catenin. CONCLUSION: Coupling RNAi knockdown with microarray and RT-PCR analyses proves to be a versatile strategy for identifying genes regulated by Wnt/β-catenin pathway and for a better understanding the role of this pathway in apoptosis. Some of the identified β-catenin/TCF directed or indirected target genes may represent excellent targets to limit tumor growth

PTEN in kidney diseases: a potential therapeutic target in preventing AKI-to-CKD transition

Renal fibrosis, a critical factor in the development of chronic kidney disease (CKD), is predominantly initiated by acute kidney injury (AKI) and subsequent maladaptive repair resulting from pharmacological or pathological stimuli. Phosphatase and tensin homolog (PTEN), also known as phosphatase and tensin-associated phosphatase, plays a pivotal role in regulating the physiological behavior of renal tubular epithelial cells, glomeruli, and renal interstitial cells, thereby preserving the homeostasis of renal structure and function. It significantly impacts cell proliferation, apoptosis, fibrosis, and mitochondrial energy metabolism during AKI-to-CKD transition. Despite gradual elucidation of PTEN’s involvement in various kidney injuries, its specific role in AKI and maladaptive repair after injury remains unclear. This review endeavors to delineate the multifaceted role of PTEN in renal pathology during AKI and CKD progression along with its underlying mechanisms, emphasizing its influence on oxidative stress, autophagy, non-coding RNA-mediated recruitment and activation of immune cells as well as renal fibrosis. Furthermore, we summarize prospective therapeutic targeting strategies for AKI and CKD-treatment related diseases through modulation of PTEN

Effect of symbiotic fungi-Armillaria gallica on the yield of Gastrodia elata Bl. and insight into the response of soil microbial community

Armillaria members play important roles in the nutrient supply and growth modulation of Gastrodia elata Bl., and they will undergo severe competition with native soil organisms before colonization and become symbiotic with G. elata. Unraveling the response of soil microbial organisms to symbiotic fungi will open up new avenues to illustrate the biological mechanisms driving G. elata’s benefit from Armillaria. For this purpose, Armillaria strains from four main G. elata production areas in China were collected, identified, and co-planted with G. elata in Guizhou Province. The result of the phylogenetic tree indicated that the four Armillaria strains shared the shortest clade with Armillaria gallica. The yields of G. elata were compared to uncover the potential role of these A. gallica strains. Soil microbial DNA was extracted and sequenced using Illumina sequencing of 16S and ITS rRNA gene amplicons to decipher the changes of soil bacterial and fungal communities arising from A. gallica strains. The yield of G. elata symbiosis with the YN strain (A. gallica collected from Yunnan) was four times higher than that of the GZ strain (A. gallica collected from Guizhou) and nearly two times higher than that of the AH and SX strains (A. gallica collected from Shanxi and Anhui). We found that the GZ strain induced changes in the bacterial community, while the YN strain mainly caused changes in the fungal community. Similar patterns were identified in non-metric multidimensional scaling analysis, in which the GZ strain greatly separated from others in bacterial structure, while the YN strain caused significant separation from other strains in fungal structure. This current study revealed the assembly and response of the soil microbial community to A. gallica strains and suggested that exotic strains of A. gallica might be helpful in improving the yield of G. elata by inducing changes in the soil fungal community

Clostridium butyricum ameliorates indomethacin-induced enteropathy by promoting MUC2 secretion via suppressing the Notch pathway

Nonsteroidal anti-inflammatory drug (NSAID) enteropathy is a serious clinical complication with no effective treatments available. Modulating the intestinal microbiota through dietary and nutritional targets is a promising strategy for preventing NSAID enteropathy. This study aimed to investigate the protective effect and underlying mechanisms of the probiotic Clostridium butyricum (CB) on indomethacin (IND)-induced enteropathy. C57BL/6J mice received CB treatment for 14 days along with concurrent IND gavage for the final 7 days. Caco2 cells were stimulated with IND to evaluate the effect of CB supernatant (CBS) on the intestinal barrier function, and LS174T cells were used to validate the modulatory action of CBS on the Notch signaling pathway. Our findings revealed that CB treatment prevented anorexia and weight loss, reduced the severity of enteropathy, and decreased the inflammatory response of the small intestine. CB also increased the expression of tight junction proteins and reduced permeability in mice and Caco2 cells. Additionally, CB suppressed apoptosis and promoted proliferation in the small intestine. Further research found that CB increased the number of goblet cells and MUC2 secretion. Mechanistically, CB may promote MUC2 secretion by suppressing the Notch signaling pathway, consistent with the results of intervention in LS174T cells with CBS. In conclusion, CB might prevent NSAID enteropathy by increasing MUC2 secretion through the inhibition of the Notch pathway. Our study identified the potential efficacy of CB as a preventive strategy against NSAID enteropathy and showed promising prospects for CB as a food supplement

Evaluate how steaming and sulfur fumigation change the microstructure, physicochemical properties and in vitro digestibility of Gastrodia elata Bl. starch

The sulfur dioxide gas (SO2) generated by sulfur burning can improve the appearance quality of food and enhance the storage time. However, excessive sulfur dioxide will pollute the environment and cause deterioration of food quality, and even the high residual levels can increase the risk of cancer. As Gastrodia elata Blume is prone to corruption during processing, sulfur fumigation is often used for preservation. In this study, spectral analysis and Texture Profile Analysis (TPA) were used to investigate the effects of traditional sulfur fumigation processing on the morphology quality, edible quality and structural characteristics of G. elata. The results showed that compared with direct drying, the pH decreased by 0.399 of the sulfur fumigated after steamed treatment G. elata, and the morphology quality, pasting ability and gel edible quality of the starch were significantly improved. In addition, it was suggested that sulfur fumigation after steaming could promote the release of molecular chains from starch granules and thus enhance the cross-linking between molecules, which explained the reason for the improve of starch edible quality. This study can provide technical and theoretical support for improving the quality of starch rich foods, replacing sulfur fumigation and reducing potential environmental hazards

The <i>Sinocyclocheilus</i> cavefish genome provides insights into cave adaptation

BACKGROUND: An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. RESULTS: The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. CONCLUSION: As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0223-4) contains supplementary material, which is available to authorized users

A noninvasive model for chronic kidney disease screening and common pathological type identification from retinal images

Chronic kidney disease (CKD) is a global health challenge, but invasive renal biopsies, the gold standard for diagnosis and prognosis, are often clinically constrained. To address this, we developed the kidney intelligent diagnosis system (KIDS), a noninvasive model for renal biopsy prediction using 13,144 retinal images from 6773 participants. The KIDS achieves an area under the receiver operating characteristic curve (AUC) of 0.839–0.993 for CKD screening and accurately identifies the five most common pathological types (AUC: 0.790–0.932) in a multicenter and multi-ethnic validation, outperforming nephrologists by 26.98% in accuracy. Additionally, the KIDS further predicts disease progression based on pathological classification. Given its flexible strategy, the KIDS can be adapted to local conditions to provide a tailored tool for patients. This noninvasive model has the potential to improve CKD clinical management, particularly for those who are ineligible for biopsies