Deep-Cloud: A Deep Neural Network-Based Approach for Analyzing Differentially Expressed Genes of RNA-seq Data

Presently, the field of analyzing differentially expressed genes (DEGs) of RNA-seq data is still in its infancy, with new approaches constantly being proposed. Taking advantage of deep neural networks to explore gene expression information on RNA-seq data can provide a novel possibility in the biomedical field. In this study, a novel approach based on a deep learning algorithm and cloud model was developed, named Deep-Cloud. Its main advantage is not only using a convolutional neural network and long short-term memory to extract original data features and estimate gene expression of RNA-seq data but also combining the statistical method of the cloud model to quantify the uncertainty and carry out in-depth analysis of the DEGs between the disease groups and the control groups. Compared with traditional analysis software of DEGs, the Deep-cloud model further improves the sensitivity and accuracy of obtaining DEGs from RNA-seq data. Overall, the proposed new approach Deep-cloud paves a new pathway for mining RNA-seq data in the biomedical field.

Epigallocatechin-3-gallate derived polymer coated Prussian blue for synergistic ROS elimination and antibacterial therapy

Reactive oxygen species (ROS) play a vital role in wound healing process by fighting against invaded bacteria. However, excess ROS at the wound sites lead to oxidative stress that can trigger deleterious effects, causing cell death, tissue damage and chronic inflammation. Therefore, we fabricated a core-shell structured nanomedicine with antibacterial and antioxidant properties via a facile and green strategy. Specifically, Prussian blue (PB) nanozyme was fabricated and followed by coating a layer of epigallocatechin-3-gallate (EGCG)-derived polymer via polyphenolic condensation reaction and self-assembly process, resulting in PB@EGCG. The introduction of PB core endowed EGCG-based polyphenol nanoparticles with excellent NIR-triggered photothermal properties. Besides, owing to multiple enzyme-mimic activity of PB and potent antioxidant capacity of EGCG-derived polymer, PB@EGCG exhibited a remarkable ROS-scavenging ability, mitigated intracellular ROS level and protected cells from oxidative damage. Under NIR irradiation (808 nm, 1.5 W/cm2), PB@EGCG (50 µg/mL) exerted synergistic EGCG-derived polymer-photothermal antibacterial activity against Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus aureus (S. aureus). In vivo therapeutic effect was evaluated using a S. aureus-infected rat model indicated PB@EGCG with a prominent bactericidal ability could modulate the inflammatory microenvironment and accelerate wound healing. Overall, this dual-functional nanomedicine provides a promising strategy for efficient antibacterial therapy.

A simple joint detection platform for high-throughput single-cell heterogeneity screening

Single cell heterogeneity plays an important role in many biological phenomena and distinguishing cells that exhibit certain mutation in sample could benefit clinical diagnose and drug screening. Typical single cell detection methods such as flow cytometry, in-situ hybridization, real-time amplification or sequencing test either protein or nucleic acid as target and usually require specialized instruments. Joint measurement of the both types of targets could be done by combining the above strategies precisely but also unwieldly. Methods for rapidly and parallelly screening single cells with target genotype and antigen is needed. In this study, we describe a gel plate platform to distinguish cell types based on their phenotypes on target gene and antigen with low equipment requirement. Integrated cell lysis and immobilization were done in the gel solidification step, after which antibody hybridization and real-time amplification were sequentially carried out without losing the original loci information of individual single cells so the three types of information of individual single cells could be combined to distinguished cells with expected genotype and phenotype. The easy-to-use gel platform has potential in point-of-care circumstances and single-cell stimulation response that have high requirements on efficiency and simplicity.

Thrombin and Thrombin-Incorporated Biomaterials for Disease Treatments

Thrombin, a coagulation-inducing protease, has long been used in the hemostatic field. During the past decades, many other therapeutic uses of thrombin have been developed. For instance, burn treatment, pseudoaneurysm therapy, wound management, and tumor vascular infarction (or tumor vasculature blockade therapy) can all utilize the unique and powerful function of thrombin. Based on their therapeutic effects, many thrombin-associated products have been certificated by the Food and Drug Administration, including bovine thrombin, human thrombin, recombinant thrombin, fibrin glue, etc. Besides, several thrombin-based drugs are currently undergoing clinical trials. In this article, the therapeutic uses of thrombin (from the initial hemostasis to the latest cancer therapy), the commercially available drugs associated with thrombin, and the pros and cons of thrombin-based therapeutics (e.g., adverse immune responses related to bovine thrombin, thromboinflammation, and vasculogenic "rebounds") are summarized. Further, the current challenges and possible future research directions of thrombin-incorporated biomaterials and therapies are discussed. It is hoped that this review may provide a valuable reference for researchers in this field and help them to design safer and more effective thrombin-based drugs for fighting against various intractable diseases.

Extracellular RNA: A new perspective on the human pre-implantation embryos

It is currently a challenge to perform noninvasive molecular biological analysis of in vitro fertilized embryos. In this issue of Cell Genomics, Wu et al.1 developed a non-invasive method to evaluate human pre-implantation embryos by characterizing the extracellular RNAs in spent media from the culture of in vitro fertilization embryos.

Recent advances in droplet sequential monitoring methods for droplet sorting

Droplet microfluidics is an attractive technology to run parallel experiments with high throughput and scalability while maintaining the heterogeneous features of individual samples or reactions. Droplet sorting is utilized to collect the desired droplets based on droplet characterization and in-droplet content evaluation. A proper monitoring method is critical in this process, which governs the accuracy and maximum frequency of droplet handling. Until now, numerous monitoring methods have been integrated in the microfluidic devices for identifying droplets, such as optical spectroscopy, mass spectroscopy, electrochemical monitoring, and nuclear magnetic resonance spectroscopy. In this review, we summarize the features of various monitoring methods integrated into droplet sorting workflow and discuss their suitable condition and potential obstacles in use. We aim to provide a systematic introduction and an application guide for choosing and building a droplet monitoring platform.

2D Covalent Organic Frameworks with Kagome Lattice: Synthesis and Applications

2D covalent organic frameworks with Kagome (kgm) topology are a promising class of crystalline frameworks that possess both triangular and hexagonal pores. These dual-pore structures enable kgm COFs to exhibit unique advantages in selective separation, mass transfer, and targeted drug release. However, the synthesis of 2D kgm COFs has been hindered by the reliance on empirical methods. This review systematically summarizes the conventional macrocycle-to-framework strategy, typical [4+2] co-polymerization synthetic strategy, and bifunctional molecules self-condensation approach for constructing 2D kgm COFs. Factors influencing the formation of kgm lattice are surveyed, such as monomer type, solvent polarity, substrate concentration, etc., and highlight the representative examples on targeted synthesis. Additionally, applications of 2D kgm COFs and relationships between structure and performances are summarized. Finally, key fundamental perspectives are proposed to accelerate the further development of this intriguing material.

Unexpected reactivity of cyclometalated iridium(III) dimers. Direct synthesis of a mononuclear luminescent complex

A new synthetic method has been developed for the preparation of unexpected emissive iridium(III) complexes (A and B), directly obtained from the established [Ir(ppy)2(μ-Cl)]2 dimer, under reaction conditions in which such compounds are usually considered stable. Complex A ([Ir(ppy)2(Oppy)], where Hppy = 2-phenylpyridine and HOppy = 2-(o-hydroxyphenyl)pyridine) was obtained from the dimer without the addition of further ancillary ligands in the reaction environment, but in the presence of a basic water environment in 2-ethoxyethanol as solvent at 165 °C. The complex evidences the unexpected insertion of an oxygen atom between the iridium(III) center and the carbon atom of one ppy moiety. Under specific reaction conditions, the mer-[Ir(ppy)3] complex (B) was obtained. The presence of the right amount of water is important to maximize the formation of A relative to B. Both compounds were fully characterized by NMR spectroscopy and mass spectrometry (MS), and the X-ray structure of A was also determined. DFT calculations were used to shed light on the reaction mechanism leading to the unexpected formation of A, suggesting that the Oppy ligand is generated intramolecularly once the [Ir(ppy)2(μ-OH)]2 dimer is formed. The process is probably assisted by a redox reaction involving the second iridium(III) center in the dimer. The electrochemical and photophysical properties of complexes A and B were investigated in comparison with the well-known fac-[Ir(ppy)3] analogue (C). Complex A displays a green emission (λmax = 545 nm) with a photoluminescence quantum yield (PLQY) of nearly 40%, whereas the oxygen-free counterpart B is poorly emissive, exhibiting an orange emission (λmax = 605 nm) with a PLQY below 10%. These findings may pave the way for the direct synthesis of neutral luminescent complexes with the general formula [Ir(C^N)2(OC^N)], even using dimers with non-commercial or highly substituted C^N ligands, without the need for synthesizing the corresponding hydroxyl-substituted ancillary ligand, which may be hardly obtainable.

Spatial Transcriptomic Analysis Reveals Regional Transcript Changes in Early and Late Stages of rd1 Model Mice with Retinitis Pigmentosa

Retinitis pigmentosa (RP) is the leading cause of inherited blindness with a genetically heterogeneous disorder. Currently, there is no effective treatment that can protect vision for those with RP. In recent decades, the rd1 mouse has been used to study the pathological mechanisms of RP. Molecular biological studies using rd1 mice have clarified the mechanism of the apoptosis of photoreceptor cells in the early stage of RP. However, the pathological changes in RP over time remain unclear. The unknown pathology mechanism of RP over time and the difficulty of clinical treatment make it urgent to perform more refined and spatially informed molecular biology studies of RP. In this study, spatial transcriptomic analysis is used to study the changes in different retinal layers of rd1 mice at different ages. The results demonstrate the pattern of photoreceptor apoptosis between rd1 mice and the control group. Not only was oxidative stress enhanced in the late stage of RP, but it was accompanied by an up-regulation of the VEGF pathway. Analysis of temporal kinetic trends has further identified patterns of changes in the key pathways of the early and late stages, to help understand the important pathogenesis of RP. Overall, the application of spatial transcriptomics to rd1 mice can help to elucidate the important pathogenesis of RP involving photoreceptor apoptosis and retinal remodeling.

Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data

MOTIVATION

Multiple displacement amplification (MDA) has become the most commonly used method of whole genome amplification, generating a vast amount of DNA with higher molecular weight and greater genome coverage. Coupling with long-read sequencing, it is possible to sequence the amplicons of over 20 kb in length. However, the formation of chimeric sequences (chimeras, expressed as structural errors in sequencing data) in MDA seriously interferes with the bioinformatics analysis but its influence on long-read sequencing data is unknown.

RESULTS

We sequenced the phi29 DNA polymerase-mediated MDA amplicons on the PacBio platform and analyzed chimeras within the generated data. The 3rd-ChimeraMiner has been constructed as a pipeline for recognizing and restoring chimeras into the original structures in long-read sequencing data, improving the efficiency of using TGS data. Five long-read datasets and one high-fidelity long-read dataset with various amplification folds were analyzed. The result reveals that the mis-priming events in amplification are more frequently occurring than widely perceived, and the propor tion gradually accumulates from 42% to over 78% as the amplification continues. In total, 99.92% of recognized chimeric sequences were demonstrated to be artifacts, whose structures were wrongly formed in MDA instead of existing in original genomes. By restoring chimeras to their original structures, the vast majority of supplementary alignments that introduce false-positive structural variants are recycled, removing 97% of inversions on average and contributing to the analysis of structural variation in MDA-amplified samples. The impact of chimeras in long-read sequencing data analysis should be emphasized, and the 3rd-ChimeraMiner can help to quantify and reduce the influence of chimeras.

AVAILABILITY AND IMPLEMENTATION

The 3rd-ChimeraMiner is available on GitHub, https://github.com/dulunar/3rdChimeraMiner.

Genome-wide identification of the heat shock transcription factor gene family in two kiwifruit species

High temperatures have a significant impact on plant growth and metabolism. In recent years, the fruit industry has faced a serious threat due to high-temperature stress on fruit plants caused by global warming. In the present study, we explored the molecular regulatory mechanisms that contribute to high-temperature tolerance in kiwifruit. A total of 36 Hsf genes were identified in the A. chinensis (Ac) genome, while 41 Hsf genes were found in the A. eriantha (Ae) genome. Phylogenetic analysis revealed the clustering of kiwifruit Hsfs into three distinct groups (groups A, B, and C). Synteny analysis indicated that the expansion of the Hsf gene family in the Ac and Ae genomes was primarily driven by whole genome duplication (WGD). Analysis of the gene expression profiles revealed a close relationship between the expression levels of Hsf genes and various plant tissues and stress treatments throughout fruit ripening. Subcellular localization analysis demonstrated that GFP-AcHsfA2a/AcHsfA7b and AcHsfA2a/AcHsfA7b -GFP were localized in the nucleus, while GFP-AcHsfA2a was also observed in the cytoplasm of Arabidopsis protoplasts. The results of real-time quantitative polymerase chain reaction (RT-qPCR) and dual-luciferase reporter assay revealed that the majority of Hsf genes, especially AcHsfA2a, were expressed under high-temperature conditions. In conclusion, our findings establish a theoretical foundation for analyzing the potential role of Hsfs in high-temperature stress tolerance in kiwifruit. This study also offers valuable information to aid plant breeders in the development of heat-stress-resistant plant materials.

LncRNA CDKN2B-AS1 interacts with LIN28B to exacerbate sepsis-induced acute lung injury by inducing HIF-1α/NLRP3-mediated pyroptosis

Sepsis-associated acute lung injury (ALI) is a life-threatening condition in intensive care units with high mortality. LncRNAs have been confirmed to participate in the underlying pathogenesis of septic ALI. This study investigated the biological functions of lncRNA CDKN2B-AS1 in septic ALI and its potential mechanism.BEAS-2B cells were challenged with lipopolysaccharide (LPS) and mice were subjected to caecal ligation and puncture (CLP) to induce septic ALI in vitro and in vivo. The expression levels of CDKN2B-AS1, LIN28B, HIF-1α, and pyroptosis-related molecules were assessed by qRT-PCR or Western blotting. The production of IL-1β and IL-18 was detected by ELISA. BEAS-2B cell pyroptosis was examined by flow cytometry. The interaction between LIN28B and CDKN2B-AS1/HIF-1α was validated by RIP and RNA pull-down assays. Colocalization of CDKN2B-AS1 and LIN28B was observed by FISH. ALI was determined by HE staining, the lung wet-to-dry (W/D) weight ratio, inflammatory cell numbers, and total protein concentration in bronchoalveolar lavage fluid (BALF). Caspase-1 expression in the lung tissues was examined by immunohistochemical staining.CDKN2B-AS1 was upregulated in BEAS-2B cells after LPS stimulation. CDKN2B-AS1 knockdown inhibited pyroptosis in LPS-exposed BEAS-2B cells in vitro and the lung tissues of septic mice in vivo. Mechanistically, CDKN2B-AS1 interacted with LIN28B to enhance HIF-1α stability. Rescue experiments showed that HIF-1α overexpression counteracted the inhibitory effect of sh-CDKN2B-AS1 on LPS-induced pyroptosis. CDKN2B-AS1 bound to LIN28B to trigger NLRP3-mediated pyroptosis by stabilizing HIF-1α, which promoted sepsis-induced ALI. CDKN2B-AS1 might be a novel therapeutic target for this disease.

[Clinical presentation and prognosis in children over 10-year-old with primary nephrotic syndrome]

Objective: To summary the clinical presentation and prognosis of primary nephrotic syndrome (PNS) in teenagers. Methods: The clinical data, renal pathological types and prognosis of 118 children over 10-year-old with PNS treated in the Department of Nephrology of the Children's Hospital Affiliated to Capital Institute of Pediatrics from January 2010 to December 2020 were retrospectively analyzed, with 408 children ≤10-year-old as control group synchronously. Chi-square test was used to compare the difference of clinical types, pathologic types, response to steroids and tubulointerstitial changes between the groups. The teenagers with steroid resistant nephrotic syndrome (SRNS) were divided into initial non-responder group and late non-responder group. Kaplan-Meier method was used to compare the difference of persistent proteinuria, and Fisher's exact test for the histological types. Results: There were 118 children >10-year-old, including 74 males and 44 females, with the onset age of 12.1 (10.8, 13.4) years; and 408 children ≤10-year-old with the onset age of 4.5 (3.2, 6.8) years. The proportion of SRNS was significantly higher in patients >10-year-old than those ≤10-year-old (24.6% (29/118) vs. 15.9% (65/408), χ²=4.66, P=0.031). There was no statistical difference in the pathological types between >10-year-old and ≤10-year-old (P>0.05), with minimal change disease the most common type (56.0% (14/25) vs. 60.5% (26/43)). The percentage of cases with renal tubulointerstitial lesions was significantly higher in children >10-year-old compared to those ≤10-year-old (60.0% (15/25) vs. 23.3% (10/43), χ²=9.18, P=0.002). There were 29 cases presented with SRNS in PNS over 10-year-old, including 19 initial non-responders and 10 late non-responders. Analyzed by Kaplan-Meier curve, it was shown that the percentage of persistent proteinuria after 6 months of immunosuppressive treatments was significantly higher in initial non-responders than those of the late non-responders ((22±10)% vs. 0, χ²=14.68, P<0.001); the percentage of minimal change disease was significantly higher in patients of late non-responders than those of the initial non-responders (5/6 vs. 3/13, P=0.041). Of the 63 >10-year-old with steroid-sensitive nephrotic syndrome followed up more than one year, 38 cases (60.3%) had relapse, and 14 cases (22.2%) were frequent relapse nephrotic syndrome and steroid dependent nephrotic syndrome. Among the 45 patients followed up over 18-year-old, 22 cases (48.9%) had recurrent proteinuria continued to adulthood, 3 cases of SRNS progressed to kidney insufficiency, and one of them developed into end stage kidney disease and was administrated with hemodialysis. Conclusions: Cases over 10-year-old with PNS tend to present with SRNS and renal tubulointerstitial lesions. They have a favorable prognosis, but are liable to relapse in adulthood.

[Clinicopathological and gene mutation characteristics of uterine carcinosarcoma]

To explore the clinicopathological characteristics, immunophenotype, diagnosis and differential diagnosis of uterine carcinosarcoma (UCS), and to explore the gene mutation characteristics and tumor mutation burden (TMB) of UCS. The clinical imaging, pathomorphological data and immunohistochemical expression of 4 cases of UCS, which were archived in the Department of Pathology of the Second Affiliated Hospital of Soochow University from January 2021 to May 2022 were retrospectively analyzed. All exon groups of 4 cases of UCS were sequenced. All the 4 patients were female, aged 47-81 years. The maximum diameter of the tumor was 4.0-13.0 cm, and the boundary was unclear. Microscopically, the tumor was composed of malignant epithelium and sarcoma. Immunohistochemistry showed that the epithelial components of 4 patients expressed broad-spectrum cytokeratin (AE1/E3), the sarcoma components expressed Vimentin, PAX8, ER, PR were expressed to varying degrees, and Ki-67 positive index was high (60%-90%). There were 3 p53 missense mutations, 1 nonsense mutation, 4 MLH1, PMS2, MSH2, MSH6 were positive and PD-L1 was negative. The sequencing results of the whole exon group of 4 UCS patients showed that TP53, BCL9L, BRD4, CLTCLI, PSMD1I, PLEC genes showed a high mutation ratio, which was 3/4, 2/4, 2/4, 2/4, 2/4, 2/4, respectively. TMB analysis showed that the TMB of 4 cases of UCS was<5 mut/Mb. UCS is a rare and highly malignant endometrial tumor. The sequencing results of the whole exon group suggested that TP53, BCL9L, BRD4 and other genes had high mutation rates, suggesting that the occurrence and development of UCS may be closely related to Wnt signaling pathway. Molecular typing indicated that 3 cases of UCS were of high copy number type/p53 mutation type, and 1 case had POLD1 mutation. Microsatellite stability, low PD-L1 expression and TMB results suggested that UCS patients have no obvious advantage in immunotherapy.

Cytosine base editors (CBEs) for inducing targeted DNA base editing in Nicotiana benthamiana

BACKGROUND

The base editors can introduce point mutations accurately without causing double-stranded DNA breaks or requiring donor DNA templates. Previously, cytosine base editors (CBEs) containing different deaminases are reported for precise and accurate base editing in plants. However, the knowledge of CBEs in polyploid plants is inadequate and needs further exploration.

RESULTS

In the present study, we constructed three polycistronic tRNA-gRNA expression cassettes CBEs containing A3A, A3A (Y130F), and rAPOBEC1(R33A) to compare their base editing efficiency in allotetraploid N. benthamiana (n = 4x). We used 14 target sites to compare their editing efficiency using transient transformation in tobacco plants. The sanger sequencing and deep sequencing results showed that A3A-CBE was the most efficient base editor. In addition, the results showed that A3A-CBE provided most comprehensive editing window (C₁ ~ C₁₇ could be edited) and had a better editing efficiency under the base background of TC. The target sites (T2 and T6) analysis in transformed N. benthamiana showed that only A3A-CBE can have C-to-T editing events and the editing efficiency of T2 was higher than T6. Additionally, no off-target events were found in transformed N. benthamiana.

CONCLUSIONS

All in all, we conclude that A3A-CBE is the most suitable vector for specific C to T conversion in N. benthamiana. Current findings will provide valuable insights into selecting an appropriate base editor for breeding polyploid plants.

Regulation of capsule spine formation in castor

Castor (Ricinus communis L.) is a dicotyledonous oilseed crop that can have either spineless or spiny capsules. Spines are protuberant structures that differ from thorns or prickles. The developmental regulatory mechanisms governing spine formation in castor or other plants have remained largely unknown. Herein, using map-based cloning in 2 independent F2 populations, F2-LYY5/DL01 and F2-LYY9/DL01, we identified the RcMYB106 (myb domain protein 106) transcription factor as a key regulator of capsule spine development in castor. Haplotype analyses demonstrated that either a 4,353-bp deletion in the promoter or a single nucleotide polymorphism leading to a premature stop codon in the RcMYB106 gene could cause the spineless capsule phenotype in castor. Results of our experiments indicated that RcMYB106 might target the downstream gene RcWIN1 (WAX INDUCER1), which encodes an ethylene response factor known to be involved in trichome formation in Arabidopsis (Arabidopsis thaliana) to control capsule spine development in castor. This hypothesis, however, remains to be further tested. Nevertheless, our study reveals a potential molecular regulatory mechanism underlying the spine capsule trait in a nonmodel plant species.

Insights and future trends in bioanalysis: an interview with Jing Tu

Jack Lodge, Commissioning Editor of Bioanalysis, and Neil Spooner, Editor in Chief, speak to Jing Tu.

Discriminating Single Nucleotide Variations in Solid-State Nanopores by Evaluating the Combination Efficiency between DNA Polymerase and Its Substrate

A single nucleotide variant present between two otherwise identical nucleic acids will have unexpected functional consequences frequently. Here, a neoteric single nucleotide variation (SNV) detection assay that integrates two complementary nanotechnology systems, nanoassembly technology and an ingenious nanopore biosensing platform, has been applied to this research. Specifically, we set up a detection system to reflect the binding efficiency of the polymerase and nanoprobe through the difference of nanopore signals and then explore the effect of base mutation at the binding site. In addition, machine learning based on support vector machines is used to automatically classify characteristic events mapped by nanopore signals. Our system reliably discriminates single nucleotide variants at binding sites, even possessing the recognition among transitions, transversions, and hypoxanthine (base I). Our results demonstrate the potential of solid-state nanopore detection for SNV and provide some ideas for expanding solid-state nanopore detection platforms.

Impact of metacognition on attitudes toward epilepsy in medical students

PURPOSE

This study evaluated medical students' knowledge and attitudes toward epilepsy and the influence of metacognition thereon.

METHOD

Valid questionnaires were administered to medical students including undergraduate, professional postgraduate, and standardized residency training students (N = 503). The questionnaire had 4 parts: demographic information, knowledge of epilepsy, attitudes toward epilepsy, and metacognitive assessment. The Chinese Public Attitudes Toward Epilepsy scale and 30-Item Metacognition Questionnaire were used to assess attitudes and metacognition, respectively.

RESULTS

Almost all participants had heard of epilepsy; 38.8% had witnessed a seizure and 25% were acquainted with a person with epilepsy. The proportion of correct answers to epilepsy-related knowledge ranged from 40.6% (Putting an object into the mouth of a person experiencing an epileptic seizure) to 97% (Convulsion is a symptom of epilepsy). However, knowledge of epilepsy was not able to affect attitudes toward epilepsy. Age, years of clinical experience, having witnessed a seizure, positive belief of worry, and need to control thinking were correlated with the different domains of attitude toward epilepsy. When participants were divided into 2 groups-i.e., those with high and low knowledge of epilepsy, participants in the former group who had a positive belief of worry or had not witnessed any seizures were more likely to have negative attitudes toward epilepsy.

CONCLUSION

Medical students showed good awareness of the etiology and symptoms of epilepsy. Overall, attitudes toward epilepsy were negative. A positive belief of worry was associated with a more negative attitude toward epilepsy among respondents with greater knowledge of epilepsy.

Two Bacillus spp. Strains Improve the Structure and Diversity of the Rhizosphere Soil Microbial Community of Lilium brownii var. viridulum

Lily Fusarium wilt disease caused by Fusarium spp. spreads rapidly and is highly destructive, leading to a severe reduction in yield. In this study, lily (Lilium brownii var. viridulum) bulbs were irrigated after planting with suspensions of two Bacillus strains that effectively control lily Fusarium wilt disease to assess their effects on the rhizosphere soil properties and microbial community. A high-throughput sequencing of microorganisms in the rhizosphere soil was performed and the soil physicochemical properties were measured. The FunGuild and Tax4Fun tools were used for a functional profile prediction. The results showed that Bacillus amyloliquefaciens BF1 and B. subtilis Y37 controlled lily Fusarium wilt disease with control efficacies of 58.74% and 68.93%, respectively, and effectively colonized the rhizosphere soil. BF1 and Y37 increased the bacterial diversity and richness of the rhizosphere soil and improved the physicochemical properties of the soil, thereby favoring the proliferation of beneficial microbes. The relative abundance of beneficial bacteria was increased and that of pathogenic bacteria was decreased. Bacillus abundance in the rhizosphere was positively correlated with most soil physicochemical properties, whereas Fusarium abundance was negatively correlated with most physicochemical properties. Functional prediction revealed that irrigation with BF1 and Y37 significantly upregulated glycolysis/gluconeogenesis among metabolism and absorption pathways. This study provides insights into the mechanism by which two Bacillus strains with antifungal activity, BF1 and Y37, antagonize plant pathogenic fungi and lays the foundation for their effective application as biocontrol agents.

PHMB modified photothermally triggered nitric oxide release nanoplatform for precise synergistic therapy of wound bacterial infections

Bacterial infection has been considered as a significant obstacle for wound healing. Nitric oxide (NO), as a novel alternative for antibiotics, has emerged as a promising antibacterial agent. However, the precise spatiotemporal controlled release of NO still remains a major challenge. Herein, a near-infrared (NIR) light triggered NO release nanoplatform (designated as PB-NO@PDA-PHMB) with enhanced broad-spectrum antibacterial and anti-biofilm properties was constructed. Given that PB-NO@PDA-PHMB has strong absorption in the NIR region and exhibits excellent photothermal effect, it can rapidly trigger NO release by NIR irradiation. PB-NO@PDA-PHMB can effectively contact and capture bacteria, and then exhibit synergistic effect of photothermal and gas therapy. In vitro and in vivo experiments indicated that PB-NO@PDA-PHMB exhibited excellent biocompatibility, satisfactory synergistic antibacterial efficacy and the capability of accelerating wound healing. Under NIR irradiation (808 nm, 1 W cm^-2, 7 min), PB-NO@PDA-PHMB (80 μg mL^-1) achieved 100% bactericidal activity against both Gram-negative bacteria Escherichia coli (E. coli) and Gram-positive bacteria Staphyloccocus aureus (S. aureus), removed 58.94% of S. aureus biofilm. Therefore, this all-in-one antibacterial nanoplatform with high NIR responsiveness provides a promising antibiotic-free strategy for bacterial infection treatment.

Photothermal/lysozyme-catalyzed hydrolysis dual-modality therapy via halloysite nanotube-based platform for effective bacterial eradication

Bacterial biofilm seriously impedes the healing of infected wound, remaining a major challenge in wound repair. Antibiotic-free antibacterial strategies based on nanotechnology are emerging as promising tools to combat bacterial infections. Here, halloysite nanotube (HNT), as a natural clay mineral, was employed to fabricate a multifunctional platform (designated as HNTs@CuS@PDA-Lys) through a layer-by-layer strategy for treating bacterial infections by utilizing synergistic lysozyme (Lys)-photothermal therapy (PTT). Specifically, amino-modified HNTs were first decorated with copper sulfide (CuS), followed by coated with a polydopamine (PDA) layer, then functionalized with antimicrobial enzyme Lys onto the surface of PDA via cation-π interactions. The as-prepared HNTs@CuS@PDA-Lys at a low dose (200 μg/mL) exhibited excellent synergistic Lys-photothermal bactericidal activity against Escherichia coli (E. coli) (100.0 ± 0.2 %) and Staphyloccocus aureus (S. aureus) (99.9 ± 0.1 %), eliminated 75.9 ± 2.0 % of S. aureus biofilm under near-infrared (NIR) irradiation (808 nm, 1.5 W/cm²). In vivo experiments using a S. aureus-infected rat model showed HNTs@CuS@PDA-Lys could rapidly kill bacteria and accelerate wound healing process. Overall, this multifunctional nanoplatform combines the advantages of PTT and Lys, providing a cost-efficient, environmental friendly strategy for bacterial and biofilm eradication, demonstrating the potential applications in the field of biomedicine.

Nanopore sensors for single molecular protein detection: Research progress based on computer simulations

As biological macromolecules, proteins are involved in important cellular functions ranging from DNA replication and biosynthesis to metabolic signalling and environmental sensing. Protein sequencing can help understand the relationship between protein function and structure, and provide key information for disease diagnosis and new drug design. Nanopore sensors are a novel technology to achieve the goal of label-free and high-throughput protein sequencing. In recent years, nanopore-based biosensors have been widely used in the detection and analysis of biomolecules such as DNA, RNA, and proteins. At the same time, computer simulations can describe the transport of proteins through nanopores at the atomic level. This paper reviews the applications of nanopore sensors in protein sequencing over the past decade and the solutions to key problems from a computer simulation perspective, with the aim of pointing the way to the future of nanopore protein sequencing.

A case of limb shaking transient ischaemic attack due to internal carotid artery dissection: an unusual presentation of fibromuscular dysplasia

BACKGROUND

Fibromuscular dysplasia (FMD) has a high prevalence of associated nontraumatic carotid artery dissection, which could further result in transient ischaemic attack (TIA) or stroke. Limb shaking TIA is an unusual form of TIA that is commonly discribed in elderly patients with atherosclerotic backgrounds, while there are limited data about it in patients with FMD. Furthermore, discussions of limb shaking TIA in nonelderly patients are scarce.

CASE PRESENTATION

An Asian 47-year-old female presented with intermittent involuntary movement of the left upper limb accompanied by neck torsion. The episode stopped soon after changing to the supine position. On native source images of time-of-flight magnetic resonance angiography (TOF-MRA), the right internal carotid artery showed a "dual lumen sign" with an intimal flap. On contrast-enhanced magnetic resonance angiography and sagittal black-blood T1WI, an intravascular haematoma with irregular lumen stenosis was observed, which overall indicated right internal carotid artery dissection. Digital subtraction angiography showed the characteristic "string-of-beads" appearance in the left internal carotid artery, and the presence of this sign pointed to the diagnosis of FMD. The patient was finally diagnosed with limb shaking TIA due to internal carotid dissection with fibromuscular dysplasia. The patient was prescribed dual anti-platelet therapy. The limb shaking vanished soon after admission with no reoccurrence in the three-month follow-up.

CONCLUSIONS

This case demonstrates that limb shaking TIA can present in patients with FMD. Limb shaking TIA in nonelderly patients can be caused by multiple diseases, and more detailed patient guidance is required in clinical practice.

G-quadruplex structures are key modulators of somatic structural variants in cancers

G-quadruplexes (G4s) are non-canonical secondary genome structures. Aberrant formation of G4s can impair genome integrity. Investigation of the relationship between G4s and somatic structural variants (SVs) in cancers could provide a better understanding of the role of G4 formation in cancer development and progression. In this study, we combined bioinformatic approaches and multi-omics data to investigate the connection between G4s and the somatic SVs. Somatic SV breakpoints were significantly enriched in G4 regions, regardless of SV subtypes. This enrichment was only observed in regions demonstrated to form G4s in cells ("active quadruplexes"), rather than in regions with a sequence compatible with G4 formation but without confirmed G4 formation ("potential quadruplexes"). Several genomic features impacted the connection between G4s and SVs, with the enrichment being notably strengthened at the boundary of topologically associated domains. Somatic breakpoints were also preferentially associated with G4 regions with earlier replication timing and open chromatin status. In cancer patients with homologous recombination repair defects, G4s and somatic breakpoints were substantially more strongly associated. Machine learning models were constructed that showed that G4 propensity is a potent feature for predicting the density of SV breakpoints. Altogether, these findings suggest that the G4 structures play a critical role in modulating the production of somatic SVs in cancers.

Genome-Wide Identification of Kiwifruit SGR Family Members and Functional Characterization of SGR2 Protein for Chlorophyll Degradation

The STAY-GREEN (SGR) proteins play an important role in chlorophyll (Chl) degradation and are closely related to plant photosynthesis. However, the availability of inadequate studies on SGR motivated us to conduct a comprehensive study on the identification and functional dissection of SGR superfamily members in kiwifruit. Here, we identified five SGR genes for each of the kiwifruit species [Actinidia chinensis (Ac) and Actinidia eriantha (Ae)]. The phylogenetic analysis showed that the kiwifruit SGR superfamily members were divided into two subfamilies the SGR subfamily and the SGRL subfamily. The results of transcriptome data and RT-qPCR showed that the expression of the kiwifruit SGRs was closely related to light and plant developmental stages (regulated by plant growth regulators), which were further supported by the presence of light and the plant hormone-responsive cis-regulatory element in the promoter region. The subcellular localization analysis of the AcSGR2 protein confirmed its localization in the chloroplast. The Fv/Fm, SPAD value, and Chl contents were decreased in overexpressed AcSGR2, but varied in different cultivars of A. chinensis. The sequence analysis showed significant differences within AcSGR2 proteins. Our findings provide valuable insights into the characteristics and evolutionary patterns of SGR genes in kiwifruit, and shall assist kiwifruit breeders to enhance cultivar development.

Effect of Multicomponent Intervention on Functional Decline in Chinese Older Adults: A Multicenter Randomized Clinical Trial

OBJECTIVES

To confirm whether multicomponent exercise following vivifrail recommendations was an effective method for improving physical ability, cognitive function, gait, balance, and muscle strength in Chinese older adults.

METHODS

This was a multicenter and randomized clinical trial conducted in Jiangsu, China, from April 2021 to April 2022. Intervention lasted for 12 weeks and 104 older adults with functional declines were enrolled. All participants were randomly assigned to a control (usual care plus health education) or exercise group (usual care plus health education plus exercise). Primary outcomes were the change score of Short Physical Performance Battery (SPPB) and activities of daily living (ADL). The secondary outcomes included instrumental activities of daily living, Tinetti scores, Frailty score, short-form Mini Nutritional Assessment, Mini-Mental State Examination, Geriatric Depression Scale-15, the 12-item Short Form Survey, 4-meter gait speed test, 6-min walking distance, grip strength, and body composition analysis.

RESULTS

Among the participants, the average age was 85 (82, 88) years. After 12 weeks of follow-up, the exercise group showed a significant improvement in SPPB, with a change of 2 points (95% confidence interval [0, 3.5], P<0.001) compared to control. In contrast, SPPB remained stable in the control group. Compared to the control group, ADL improved in the exercise group, as did instrumental activities of daily living, Tinetti, Frailty, Short Form Survey, 4-meter gait speed test, and 6-min walking distance. Although there was no significant difference between groups in body composition analysis after post-intervention, the exercise group still improved in soft lean mass (P=0.002), fat-free mass (P=0.002), skeletal muscle mass index (P<0.001), fat-free mass index (P=0.004), appendicular skeletal muscle mass (P<0.001), and leg muscle mass (P<0.001), while the control group had no significant increase. No difference was observed in adverse events during trial period.

CONCLUSIONS

The multicomponent exercise intervention following vivifrail recommendations is an effective method for older adults with functional decline and can reverse the functional decline and improve gait, balance, and muscle strength. Additionally, the 12-week multicomponent exercise method provides guidance for Chinese medical professionals working in the field of geriatrics and is a promising method to improve physical function in the general population.

Value of machine learning-based transrectal multimodal ultrasound combined with PSA-related indicators in the diagnosis of clinically significant prostate cancer

OBJECTIVE

To investigate the effect of transrectal multimodal ultrasound combined with serum prostate-specific antigen (PSA)-related indicators and machine learning for the diagnosis of clinically significant prostate cancer.

METHODS

Based on Gleason score of postoperative pathological results, the subjects were divided into clinically significant prostate cancer groups(GS>6)and non-clinically significant prostate cancer groups(GS ≤ 6). The independent risk factors were obtained by univariate logistic analysis. Artificial neural network (ANN), logistic regression (LR), support vector machine (SVM), decision tree (DT), random forest (RF), and K-nearest neighbor (KNN) machine learning models were combined with clinically significant prostate cancer risk factors to establish the machine learning model, calculate the model evaluation indicators, construct the receiver operating characteristic curve (ROC), and calculate the area under the curve (AUC).

RESULTS

Independent risk factor items (P< 0.05) were entered into the machine learning model. A comparison of the evaluation indicators of the model and the area under the ROC curve showed the ANN model to be best at predicting clinically significant prostate cancer, with a sensitivity of 80%, specificity of 88.6%, F1 score of 0.897, and the AUC was 0.855.

CONCLUSION

Establishing a machine learning model by rectal multimodal ultrasound and combining it with PSA-related indicators has definite application value in predicting clinically significant prostate cancer.

A molecular dynamics investigation of Taq DNA polymerase and its complex with a DNA substrate using a solid-state nanopore biosensor

Proteins have a small volume difference by the diversity of amino acids, which make protein detection and identification a great challenge. Solid-state nanopore as label-free biosensors has attracted attention with high sensitivity. In this work, we investigated the Taq DNA polymerase before and after combining it with a DNA substrate on a solid-state nanopore through molecular dynamics. In simulation, we analyzed the contribution source of nanopore current blockage. In addition to considering the traditional physical exclusion volume model, the non-covalent interaction between the protein molecules and the pore wall also showed to affect the current blockage in the nanopore. When choosing pores of comparable size to protein molecules, the two states of Taq DNA polymerase produce differentiated non-covalent interactions with the pore wall, which enhanced the amplitude difference in current blockage. As a result, the two DNA polymerases can be distinguished through the distinct current blockage. However, when applying additional pulling force or increasing the pore size of the nanopore, the differences between the current blockages are not significant enough to distinguish. The introduction of the non-covalent interaction makes it clear to understand the current blockage differences, which guide the mechanism between molecules with similar structures or volumes.

The Mechanism of Overflow Amplitude in Nanopore Experiments and Its Application in Molecule Detection

The investigation of abnormal experimental phenomena observed in nanopore research improves our understanding of nanopores. In this article, we report and explore the unusual phenomenon that the amplitude of current blockage decreases beyond zero baseline (overflow amplitudes), which was observed in the translocation behavior of 100 bp double-stranded DNA molecules through SiN_x nanopores. In our experiments, the overflow amplitude decreases with the increase of salt concentration and also decreases when the dwell time is shortened as the normalized amplitude of the overflow current showed a reduction with the increase of voltage. Upon analyzing the electric double layer meanwhile, the overflow amplitudes were shown to be positively correlated with the depth of the electric double layer and the duration of interaction between biological molecules. The formation of overflow amplitude can be attributed to the double electric layer ionic perturbation and reconfiguration, which are the results of the interaction between the biomolecule and the electric bilayer. The validation of the assumption using biomolecules containing different charges demonstrated that the overflow amplitude increased with the increase of the charge. It was concluded that proteins that pass through the nanopore with different orientation were differentiated based on their different overflow amplitude patterns. The investigation of overflow amplitude helps to enhance the understanding and the performance of nanopores.

Extracellular cell-free RNA profile in human large follicles and small follicles

Background: Previous studies have shown that a large number of valuable and functional cell-free RNAs (cfRNAs) were found in follicular fluid. However, the species and characteristics of follicular fluid cfRNAs have not been reported. Furthermore, their implications are still barely understood in the evaluation of follicular fluid from follicles of different sizes, which warrants further studies.

Objective: This study investigated the landscape and characteristics of follicular fluid cfRNAs, the source of organization, and the potential for distinguishing between follicles of different sizes.

Methods: Twenty-four follicular fluid samples were collected from 20 patients who received in vitro fertilization (n = 9) or ICSI (n = 11), including 16 large follicular fluid and 8 small follicular fluid samples. Also, the cfRNA profile of follicular fluid samples was analyzed by RNA sequencing.

Results: This result indicated that the concentration of follicular fluid cfRNAs ranged from 0.78 to 8.76 ng/ml, and fragment length was 20–200 nucleotides. The concentration and fragment length of large follicular fluid and small follicular fluid samples were not significantly different (p &gt; 0.05). The technical replica correlation of follicular fluid samples ranged from 0.3 to 0.9, and the correlation of small follicular fluid samples was remarkably (p &lt; 0.001) lower than that of large follicular fluid samples. Moreover, this study found that cfRNAs of the follicular fluid could be divided into 37 Ensembl RNA biotypes, and a large number of mRNAs, circRNAs, and lncRNAs were observed in the follicular fluid. The number of cfRNAs in large follicular fluid was remarkably (p &lt; 0.05) higher than that of small follicular fluid. Furthermore, the follicular fluid contained a large amount of intact mRNA and splice junctions and a large number of tissue-derived RNAs, which are at a balanced state of supply and elimination in the follicular fluid. KEGG pathway analysis showed that differentially expressed cfRNAs were enriched in several pathways, including thyroid hormone synthesis, the cGMP-PKG signaling pathway, and inflammatory mediator regulation of TRP channels. In addition, we further showed that four cfRNAs (TK2, AHDC1, PHF21A, and TTYH1) serve as a potential indicator to distinguish the follicles of different sizes. The ROC curve shows great potential to predict follicular fluid from follicles of different sizes [area under the curve (AUC) &gt; 0.88].

Conclusion: Overall, our study revealed that a large number of cfRNAs could be detected in follicular fluid and could serve as a potential non-invasive biomarker in distinguishing between follicles of different sizes. These results may inform the study of the utility and implementation of cfRNAs in clinical practice.

Molecular Typing Based on Oxidative Stress Genes and Establishment of Prognostic Characteristics of 7 Genes in Lung Adenocarcinoma

Oxidative stress could maintain different biological processes in human cancer. However, the effect of oxidative stress on lung adenocarcinoma (LUAD) should be studied. This study analyzed the expression and clinical importance of oxidative stress in LUAD in detail. The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were employed for obtaining LUAD expression profiles. Based on oxidative stress-related genes, molecular subtypes substantially correlated with the LUAD prognosis were discovered with ConsensusClusterPlus. Differentially expressed genes (DEGs) among subtypes were found using the Limma software package. Least absolute shrinkage and selection operator- (Lasso-) Cox analysis was employed to create the polygenic risk model. RiskScore and clinically relevant features were used to create nomograms. By utilizing oxidative stress-related genes and reliable clustering, stable molecular subtypes were first discovered. The prognosis, clinical characteristics, route characteristics, and immunological characteristics of these three molecular subtypes were all different. Subsequently, by using differential expression genes among molecular subtypes and Lasso, 7 main genes linked with the oxidative stress phenotype were discovered. A prognostic risk model was also built on the basis of major genes associated with the oxidative stress phenotype. The model demonstrated a high level of resilience and was unaffected by clinical-pathological features. It played a stable predictive role in independent datasets. Ultimately, to improve the prognosis model and survival prediction, RiskScore (RS) was combined with clinicopathological variables, and a decision tree model was used. The model exhibited a high prediction accuracy as well as the ability to predict survival. This research found that oxidative stress-related genes have a major involvement in the onset and progression of LUAD and that they may influence LUAD susceptibility to immunotherapy and standard chemotherapy. Furthermore, the identified risk models for 7 genes linked with oxidative stress exhibited could assist clinical treatment decisions and prognosis prediction. The classifier could be used as a molecular diagnostic tool for assessing LUAD patients' prognosis risk.

Machine learning prediction of prostate cancer from transrectal ultrasound video clips

Objective

To build a machine learning (ML) prediction model for prostate cancer (PCa) from transrectal ultrasound video clips of the whole prostate gland, diagnostic performance was compared with magnetic resonance imaging (MRI).

Methods

We systematically collated data from 501 patients—276 with prostate cancer and 225 with benign lesions. From a final selection of 231 patients (118 with prostate cancer and 113 with benign lesions), we randomly chose 170 for the purpose of training and validating a machine learning model, while using the remaining 61 to test a derived model. We extracted 851 features from ultrasound video clips. After dimensionality reduction with the least absolute shrinkage and selection operator (LASSO) regression, 14 features were finally selected and the support vector machine (SVM) and random forest (RF) algorithms were used to establish radiomics models based on those features. In addition, we creatively proposed a machine learning models aided diagnosis algorithm (MLAD) composed of SVM, RF, and radiologists’ diagnosis based on MRI to evaluate the performance of ML models in computer-aided diagnosis (CAD). We evaluated the area under the curve (AUC) as well as the sensitivity, specificity, and precision of the ML models and radiologists’ diagnosis based on MRI by employing receiver operator characteristic curve (ROC) analysis.

Results

The AUC, sensitivity, specificity, and precision of the SVM in the diagnosis of PCa in the validation set and the test set were 0.78, 63%, 80%; 0.75, 65%, and 67%, respectively. Additionally, the SVM model was found to be superior to senior radiologists’ (SR, more than 10 years of experience) diagnosis based on MRI (AUC, 0.78 vs. 0.75 in the validation set and 0.75 vs. 0.72 in the test set), and the difference was statistically significant (p< 0.05).

Conclusion

The prediction model constructed by the ML algorithm has good diagnostic efficiency for prostate cancer. The SVM model’s diagnostic efficiency is superior to that of MRI, as it has a more focused application value. Overall, these prediction models can aid radiologists in making better diagnoses.

Characterization of the Intestinal Fungal Microbiome in HIV and HCV Mono-Infected or Co-Infected Patients

Intestinal mycobiome dysbiosis plays an important role in the advancement of HIV- and HCV-infected patients. Co-infection with HCV is an important risk factor for exacerbating immune activation in HIV-infected patients, and gut fungal microbial dysbiosis plays an important role. However, no systematic study has been conducted on the intestinal fungal microbiome of HIV/HCV co-infected patients to date. Patients infected with HIV and HCV, either alone or in combination, and healthy volunteers were included. Stool samples were collected for fungal ITS sequencing and for further mycobiome statistical analysis. We found that the abundance of fungal species significantly decreased in the HIV/HCV co-infection group compared to in the healthy control group, while no significant differences were found in the mono-infection groups. Low-CD4 + T-cell patients in the HIV group and high-ALT-level patients in the HCV group were discovered to have a more chaotic fungal community. Furthermore, the opportunistic pathogenic fungal profiles and fungal inter-correlations in the co-infection group became less characteristic but more complicated than those in the mono-infection groups. Intestinal fungal dysregulation occurs in HIV- and HCV-infected patients, and this dysregulation is further complicated in HIV/HCV co-infected patients.

Iron deposition in the precuneus is correlated with mild cognitive impairment in patients with cerebral microbleeds: A quantitative susceptibility mapping study

Purpose

The purpose of this study was to define whether mild cognitive impairment (MCI) is associated with iron deposition in rich-club nodes distant from cerebral microbleeds (CMBs) in patients with cerebral small vessel disease (CSVD).

Methods

A total of 64 participants underwent magnetic resonance imaging (MRI) scanning and were separated into three groups, namely, CMB(+), CMB(–), and healthy controls (HCs). We compared their characteristics and susceptibility values of rich-club nodes [e.g., superior frontal gyrus (SFG), precuneus, superior occipital gyrus (SOG), thalamus, and putamen]. We then divided the CMB(+) and CMB(–) groups into subgroups of patients with or without MCI. Then, we analyzed the relationship between iron deposition and MCI by comparing the susceptibility values of rich-club nodes. We assessed cognitive functions using the Montreal Cognitive Assessment (MoCA) and quantified iron content using quantitative susceptibility mapping (QSM).

Results

In the putamen, the CMB(+) and CMB(–) groups had significantly different susceptibility values. Compared with the HCs, the CMB(+) and CMB(–) groups had significantly different susceptibility values for the SFG and SOG. In addition, we found significant differences in the putamen susceptibility values of the CMB(+)MCI(+) group and the two CMB(–) groups. The CMB(+)MCI(+) and CMB(+)MCI(–) groups had significantly different precuneus susceptibility values. The binary logistic regression analysis revealed that only higher susceptibility values of precuneus were associated with a cognitive decline in patients with CMBs, and it indicated statistical significance.

Conclusion

Iron deposition in the precuneus is an independent risk factor for MCI in patients with CMBs. CMBs might influence iron content in remote rich-club nodes and be relevant to MCI.

[Application and Inspiration of Information System used in National Health and Nutrition Examination Survey of America]

The National Health and Nutrition Examination Survey (NHANES) of America has been running for more than 60 years and has achieved many significant achievements with international influence. The application of modern information technologies in NHANES provides a supplementary tool for the project's high quality and refined implementation. This paper introduces the information system of NHANES from seven aspects: project management, survey participant interview, physical examination, laboratory examination, field follow-up, data sharing, and social services. The construction and application prospects of the China National Health Survey Information System, suitable for China's native conditions, are also discussed in this article.

Prediction of Time-Series Transcriptomic Gene Expression Based on Long Short-Term Memory with Empirical Mode Decomposition

RNA degradation can significantly affect the results of gene expression profiling, with subsequent analysis failing to faithfully represent the initial gene expression level. It is urgent to have an artificial intelligence approach to better utilize the limited data to obtain meaningful and reliable analysis results in the case of data with missing destination time. In this study, we propose a method based on the signal decomposition technique and deep learning, named Multi-LSTM. It is divided into two main modules: One decomposes the collected gene expression data by an empirical mode decomposition (EMD) algorithm to obtain a series of sub-modules with different frequencies to improve data stability and reduce modeling complexity. The other is based on long short-term memory (LSTM) as the core predictor, aiming to deeply explore the temporal nonlinear relationships embedded in the sub-modules. Finally, the prediction results of sub-modules are reconstructed to obtain the final prediction results of time-series transcriptomic gene expression. The results show that EMD can efficiently reduce the nonlinearity of the original data, which provides reliable theoretical support to reduce the complexity and improve the robustness of LSTM models. Overall, the decomposition-combination prediction framework can effectively predict gene expression levels at unknown time points.

Genome-Wide Identification and Structural Characterization of Growth-Regulating Factors (GRFs) in Actinida eriantha and Actinidia chinensis

Growth-regulating factors (GRFs) encode plant-specific transcription factors that play a vital role in regulation of plant growth, development, and stress response. Although GRFs have been identified in various plants, there is no reported work available in Actinidia (commonly known as kiwifruit) so far. In the present study, we identified 22 GRF genes on A. chinensis (hereafter A. chinensis is referred to as Ac, and GRF genes in A. chinensis are referred to as AcGRF) distributed on 17 chromosomes and one contig, and 26 GRF genes in A. eriantha (hereafter A. eriantha is referred to as Ae, and GRF genes in A. eriantha are referred to as AeGRF) distributed on 21 chromosomes. Phylogenetic analysis showed that kiwifruit GRF proteins were clustered into five distinct groups. Additionally, kiwifruit GRFs showed motif composition and gene structure similarities within the same group. Synteny analysis showed that whole-genome duplication played a key role in the expansion of the GRF family in kiwifruit. The higher expression levels of kiwifruit GRFs in young tissues and under stress conditions indicated their regulatory role in kiwifruit growth and development. We observed two genes in Ae (AeGRF6.1, AeGRF 6.2) and two genes in Ac (AcGRF 6.1, AeGRF 6.2) significantly upregulated in different RNA-seq datasets. The presence of conserved protein structures and cis-regulatory elements caused functional divergence in duplicated gene pairs. The subcellular localization indicated the presence of kiwifruit GRFs in the nucleus of the plant cell. Protein-protein interaction analysis predicted AtGIF protein orthologs for AcGRFs and AeGRFs. Taken together, we systematically analyzed the characterization of kiwifruit GRF family members for their potential role in kiwifruit development and Pseudomonas syringae pv. actinidiae (Psa.) invasion response. Further functional studies of kiwifruit GRFs in plant growth, development, and stress response will provide valuable insights for kiwifruit breeders.

Genome-Wide Identification of the LHC Gene Family in Kiwifruit and Regulatory Role of AcLhcb3.1/3.2 for Chlorophyll a Content

Light-harvesting chlorophyll a/b-binding (LHC) protein is a superfamily that plays a vital role in photosynthesis. However, the reported knowledge of LHCs in kiwifruit is inadequate and poorly understood. In this study, we identified 42 and 45 LHC genes in Actinidia chinensis (Ac) and A. eriantha (Ae) genomes. Phylogenetic analysis showed that the kiwifruit LHCs of both species were grouped into four subfamilies (Lhc, Lil, PsbS, and FCII). Expression profiles and qRT-PCR results revealed expression levels of LHC genes closely related to the light, temperature fluctuations, color changes during fruit ripening, and kiwifruit responses to Pseudomonas syringae pv. actinidiae (Psa). Subcellular localization analysis showed that AcLhcb1.5/3.1/3.2 were localized in the chloroplast while transient overexpression of AcLhcb3.1/3.2 in tobacco leaves confirmed a significantly increased content of chlorophyll a. Our findings provide evidence of the characters and evolution patterns of kiwifruit LHCs genes in kiwifruit and verify the AcLhcb3.1/3.2 genes controlling the chlorophyll a content.

Sensitive and Low-Bias Transcriptome Sequencing Using Agarose PCR

Transcriptome sequencing has emerged as an important research tool for exploring the mysteries of life at the single-cell level. However, its wide application is limited by the bias associated with the amplification reactions which is essential for library building of trace RNA. In this study, low-melting-point agarose was added to the amplification reactions to take advantage of its molecular crowding effect and polymer cross-linked structure to improve the sensitivity of the reactions and reduce bias. To further evaluate the performance of the method, it was applied to transcriptome sequencing of microregion samples from brain tissue sections of mice with Parkinson's disease at the single cell level. The results showed that agarose PCR had better performance than in-tube PCR. Further application of agarose PCR to transcriptome library sequencing could obtain data closer to that of unamplified. With the addition of low melting point agarose, the sensitivity of the amplification reaction was significantly increased, while homogeneity was increased by approximately 2-fold. Not only that, but this work also provides 11% sensitivity improvement for spatial transcriptomic study on Parkinson's disease-associated gene detection. The agarose PCR provides a new tool for efficient and homogeneous amplification of trace samples and can be widely used for spatial transcriptome library sequencing and studies.

Sensitivity to copy number variation analysis in single cell genomics

While previous studies have given some guidance, the sensitivity of copy number calling in single-cell genomics is still not comprehensive. We studied the impact of sequencing depth and other factors on single-cell copy number analysis. Sequencing Data from 26 datasets were retrieved, and 2946 single cells passed the filter. Thirty-eight single cells were independently downscaled to evaluate copy number variation (CNV) detection sensitivity at different bin sizes. The sensitivity of whole genome amplification (WGA) approaches and cell types to CNV calling were evaluated using downsampling of 101 and 70 cells. Cluster analysis based on t-SNE was executed to evaluate CNV calling performance. Our results suggest 0.75× sequencing depth with moderate resolution (250 kb bin size) may be a practical guideline considering both sequencing cost and performance of copy number calling, which can be appropriately optimized based on amplification approach, cell type, and sample complexity.