Three-dimensional pseudo-continuous arterial spin-labelled perfusion imaging for diagnosing upper cervical lymph node metastasis in patients with nasopharyngeal carcinoma: a whole-node histogram analysis

AIM

To evaluate whole-node histogram parameters of blood flow (BF) maps derived from three-dimensional pseudo-continuous arterial spin-labelled (3D pCASL) imaging in discriminating metastatic from benign upper cervical lymph nodes (UCLNs) for nasopharyngeal carcinoma (NPC) patients.

MATERIALS AND METHODS

Eighty NPC patients with a total of 170 histologically confirmed UCLNs (67 benign and 103 metastatic) were included retrospectively. Pre-treatment 3D pCASL imaging was performed and whole-node histogram analysis was then applied. Histogram parameters and morphological features, such as minimum axis diameter (MinAD), maximum axis diameter (MaxAD), and location of UCLNs, were assessed and compared between benign and metastatic lesions. Predictors were identified and further applied to establish a combined model by multivariate logistic regression in predicting the probability of metastatic UCLNs. Receiver operating characteristic (ROC) curves were used to analyse the diagnostic performance.

RESULTS

Metastatic UCLNs had larger MinAD and MinAD/MaxAD ratio, greater energy and entropy values, and higher incidence of level II (upper jugular group), but lower BF10th value than benign nodes (all p<0.05). MinAD, BF10th, energy, and entropy were validated as independent predictors in diagnosing metastatic UCLNs. The combined model yielded an area under the curve (AUC) of 0.932, accuracy of 84.42 %, sensitivity of 80.6 %, and specificity of 90.29 %.

CONCLUSIONS

Whole-node histogram analysis on BF maps is a feasible tool to differentiate metastatic from benign UCLNs in NPC patients, and the combined model can further improve the diagnostic efficacy.

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.

SNP-based and haplotype-based genome-wide association on drug dependence in Han Chinese

BACKGROUND

Drug addiction is a serious problem worldwide and is influenced by genetic factors. The present study aimed to investigate the association between genetics and drug addiction among Han Chinese.

METHODS

A total of 1000 Chinese users of illicit drugs and 9693 healthy controls were enrolled and underwent single nucleotide polymorphism (SNP)-based and haplotype-based association analyses via whole-genome genotyping.

RESULTS

Both single-SNP and haplotype tests revealed associations between illicit drug use and several immune-related genes in the major histocompatibility complex (MHC) region (SNP association: log10BF = 15.135, p = 1.054e-18; haplotype association: log10BF = 20.925, p = 2.065e-24). These genes may affect the risk of drug addiction via modulation of the neuroimmune system. The single-SNP test exclusively reported genome-wide significant associations between rs3782886 (SNP association: log10BF = 8.726, p = 4.842e-11) in BRAP and rs671 (SNP association: log10BF = 7.406, p = 9.333e-10) in ALDH2 and drug addiction. The haplotype test exclusively reported a genome-wide significant association (haplotype association: log10BF = 7.607, p = 3.342e-11) between a region with allelic heterogeneity on chromosome 22 and drug addiction, which may be involved in the pathway of vitamin B12 transport and metabolism, indicating a causal link between lower vitamin B12 levels and methamphetamine addiction.

CONCLUSIONS

These findings provide new insights into risk-modeling and the prevention and treatment of methamphetamine and heroin dependence, which may further contribute to potential novel therapeutic approaches.

Deciphering temporal gene expression dynamics in multiple coral species exposed to heat stress: Implications for predicting resilience

Coral reefs are facing unprecedented threats due to global climate change, particularly elevated sea surface temperatures causing coral bleaching. Understanding coral responses at the molecular level is crucial for predicting their resilience and developing effective conservation strategies. In this study, we conducted a comprehensive gene expression analysis of four coral species to investigate their long-term molecular response to heat stress. We identified distinct gene expression patterns among the coral species, with laminar corals exhibiting a stronger response compared to branching corals. Heat shock proteins (HSPs) showed an overall decreasing expression trend, indicating the high energy cost associated with sustaining elevated HSP levels during prolonged heat stress. Peroxidases and oxidoreductases involved in oxidative stress response demonstrated significant upregulation, highlighting their role in maintaining cellular redox balance. Differential expression of genes related to calcium homeostasis and bioluminescence suggested distinct mechanisms for coping with heat stress among the coral species. Furthermore, the impact of heat stress on coral biomineralization varied, with downregulation of carbonic anhydrase and skeletal organic matrix proteins indicating reduced capacity for biomineralization in the later stages of heat stress. Our findings provide insights into the molecular mechanisms underlying coral responses to heat stress and highlight the importance of considering species-specific responses in assessing coral resilience. The identified biomarkers may serve as indicators of heat stress and contribute to early detection of coral bleaching events. These findings contribute to our understanding of coral resilience and provide a basis for future research aimed at enhancing coral survival in the face of climate change.

Automated detection of MRI-negative temporal lobe epilepsy with ROI-based morphometric features and machine learning

Objective

Temporal lobe epilepsy (TLE) predominantly originates from the anteromedial basal region of the temporal lobe, and its prognosis is generally favorable following surgical intervention. However, TLE often appears negative in magnetic resonance imaging (MRI), making it difficult to quantitatively diagnose the condition solely based on clinical symptoms. There is a pressing need for a quantitative, automated method for detecting TLE.

Methods

This study employed MRI scans and clinical data from 51 retrospective epilepsy cases, dividing them into two groups: 34 patients in TLE group and 17 patients in non-TLE group. The criteria for defining the TLE group were successful surgical removal of the epileptogenic zone in the temporal lobe and a favorable postoperative prognosis. A standard procedure was used for normalization, brain extraction, tissue segmentation, regional brain partitioning, and cortical reconstruction of T1 structural MRI images. Morphometric features such as gray matter volume, cortical thickness, and surface area were extracted from a total of 20 temporal lobe regions in both hemispheres. Support vector machine (SVM), extreme learning machine (ELM), and cmcRVFL+ classifiers were employed for model training and validated using 10-fold cross-validation.

Results

The results demonstrated that employing ELM classifiers in conjunction with specific temporal lobe gray matter volume features led to a better identification of TLE. The classification accuracy was 92.79%, with an area under the curve (AUC) value of 0.8019.

Conclusion

The method proposed in this study can significantly assist in the preoperative identification of TLE patients. By employing this method, TLE can be included in surgical criteria, which could alleviate patient symptoms and improve prognosis, thereby bearing substantial clinical significance.

[Effect of recombinant human thrombin for hemostasis in liver resection: a randomized controlled phase Ⅲ clinical trial]

Objective: To evaluate the hemostatic efficacy, safety and immunogenicity of recombinant human thrombin in the treatment of liver wounds that still ooze after conventional surgical hemostasis. Methods: A multicenter, stratified randomized, double-blind, placebo-controlled phase Ⅲ trial with a planned enrollment of 510 subjects at 33 centers, with a 2∶1 randomization to the thrombin group versus the placebo group. An interim analysis will be conducted after approximately 70% of the subjects have completed the observation period. The primary efficacy endpoint was the rate of hemostasis within 6 minutes at the point of bleeding that could be evaluated. Safety analysis was performed one month after surgery, and the positive rates of anti-drug antibody (ADA) and neutralizing antibody were evaluated. Results: At the interim analysis, a total of 348 subjects had been randomized and received the study drug (215 were male and 133 were female). They were aged 19-69 (52.9±10.9)years. Among them, 232 were in the thrombin group and 116 were in the placebo group, with balanced and comparable demographics and baseline characteristics between the two groups. The hemostasis rate at 6 minutes was 71.6% (95%CI:65.75%-77.36%) in the thrombin group and 44.0% (95%CI: 34.93%-53.00%) in the placebo group, respectively (P<0.001). No grade≥3 drug-related adverse events and no drug-related deaths were reported from the study.No recombinant human thrombin-induced immunologically-enhanced ADA or immunologically-induced ADA was detected after topical use in subjects. Conclusion: Recombinant human thrombin has shown significant hemostatic efficacy and good safety in controlling bleeding during liver resection surgery, while also demonstrating low immunogenicity characteristics.

Comparative transcriptome analysis reveals deep molecular landscapes in stony coral Montipora clade

Introduction: Coral reefs, among the most invaluable ecosystems in the world, face escalating threats from climate change and anthropogenic activities. To decipher the genetic underpinnings of coral adaptation and resilience, we undertook comprehensive transcriptome profiling of two emblematic coral species, Montipora foliosa and Montipora capricornis, leveraging PacBio Iso-Seq technology. These species were strategically selected for their ecological significance and their taxonomic proximity within the Anthozoa class. Methods: Our study encompassed the generation of pristine transcriptomes, followed by thorough functional annotation via diverse databases. Subsequently, we quantified transcript abundance and scrutinized gene expression patterns, revealing notable distinctions between the two species. Results: Intriguingly, shared orthologous genes were identified across a spectrum of coral species, highlighting a substantial genetic conservation within scleractinian corals. Importantly, a subset of genes, integral to biomineralization processes, emerged as exclusive to scleractinian corals, shedding light on their intricate evolutionary history. Furthermore, we discerned pronounced upregulation of genes linked to immunity, stress response, and oxidative-reduction processes in M. foliosa relative to M. capricornis. These findings hint at the presence of more robust mechanisms in M. foliosa for maintaining internal equilibrium and effectively navigating external challenges, underpinning its potential ecological advantage. Beyond elucidating genetic adaptation in corals, our research underscores the urgency of preserving genetic diversity within coral populations. Discussion: These insights hold promise for informed conservation strategies aimed at safeguarding these imperiled ecosystems, bearing ecological and economic significance. In synthesis, our study seamlessly integrates genomic inquiry with ecological relevance, bridging the gap between molecular insights and the imperative to conserve coral reefs in the face of mounting threats.

Measurement of the Positive Muon Anomalous Magnetic Moment to 0.20 ppm

We present a new measurement of the positive muon magnetic anomaly, a_{μ}≡(g_{μ}-2)/2, from the Fermilab Muon g-2 Experiment using data collected in 2019 and 2020. We have analyzed more than 4 times the number of positrons from muon decay than in our previous result from 2018 data. The systematic error is reduced by more than a factor of 2 due to better running conditions, a more stable beam, and improved knowledge of the magnetic field weighted by the muon distribution, ω[over ˜]_{p}^{'}, and of the anomalous precession frequency corrected for beam dynamics effects, ω_{a}. From the ratio ω_{a}/ω[over ˜]_{p}^{'}, together with precisely determined external parameters, we determine a_{μ}=116 592 057(25)×10^{-11} (0.21 ppm). Combining this result with our previous result from the 2018 data, we obtain a_{μ}(FNAL)=116 592 055(24)×10^{-11} (0.20 ppm). The new experimental world average is a_{μ}(exp)=116 592 059(22)×10^{-11} (0.19 ppm), which represents a factor of 2 improvement in precision.

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.

The Role of Radiation Therapy for Metastatic Cervical Cancer

PURPOSE/OBJECTIVE(S)

Survival rates for women with metastatic cervical cancer (CC) are low, with limited management options. Radiation therapy (RT) for metastatic disease has led to prolonged survival in other malignancies, however, the data are scarce in CC. Herein, we evaluated the effect of RT for metastatic CC.

MATERIALS/METHODS

A total of 58 patients with metastatic CC between September 2019 and January 2023 were retrospectively analyzed. All the patients were treated with platinum-based chemotherapy combined with targeted therapy or immunotherapy followed with or without RT (NRT). The recent efficacy, survival status and prognostic factors were analyzed statistically.

RESULTS

Objective response rate (ORR) was 63.6% with one complete and twenty partial responses in RT group (n = 33) and 40.0% with two complete and eight partial responses in NRT group (n = 25), respectively (p = 0.074). Disease control rate (DCR) of the RT and NRT groups were 79.4% vs 80.0%, respectively (p = 0.861). Median follow-up time was 17 months (3-39months). In RT group, 11(33.3%) patients experienced local regional or distant failure and 9 (27.3%) patients were dead. In NRT group, 15(60%) patients had progression and 8 (32%) patients dead. There was no significant difference between the two groups in overall survival (OS); however, RT group displayed superior progression-free survival (PFS) (1-year OS: 72.7% vs. 68.0%, p = 0.460; 1-year PFS: 66.7% vs. 40.0%, p = 0.039). The multivariate analysis showed that RT, immunotherapy, lymph node metastasis only relevant predictor of superior PFS but not OS. In subgroup analysis, patients treated with RT appeared to have a better PFS in some specific cohorts, such as age>45 years (72.0% vs 36.4% P = 0.015), squamous carcinoma histology (71.0% vs 40.9% P = 0.017), metastatic at diagnosis (75.0% vs 47.6% P = 0.012), non-targeted therapy (72.4% vs 43.8% P = 0.040). No significant increase in treatment-related toxicity was observed in the RT group compared with the NRT group.

CONCLUSION

RT provided superior PFS in metastatic CC patients compared to NRT, and well tolerated. Moreover, RT, immunotherapy, lymph node metastasis only were independent significant prognostic factors for PFS. Subgroup analysis showed that combination of RT and chemotherapy obtained favorable PFS in metastatic CC patients with age>45 years, squamous carcinoma histology, metastatic at diagnosis, non-targeted therapy. Studies with a larger sample size and longer follow-up are warranted.

Radiation Induced Lung Injury in Rats after Pre-Oxygenation Radiotherapy

PURPOSE/OBJECTIVE(S)

Deep inspiratory breath holding (DIBH) has been widely used during the radiotherapy of thoracic tumors. The main disadvantage of voluntary DIBH is the short duration of each breath hold. The hypocapnia induced by hyperoxia (oxygen concentration > 50%) pre-oxygenation (PreO2) combined with mechanical hyperventilation has been reported to prolong the duration of single breath hold, but its safety remains controversial, especially the sensitivity of lung tissue to radiation damage under hyperoxia exposure has not been elucidated. In this study, we aim to investigate the changes of radiation induced lung injury in rats after PreO2 radiation.

MATERIALS/METHODS

We evaluated the lung tissue of rats at different time points (48h, 2w, 4w, 8w, 12w) after thoracic radiation (15Gy single fraction to the right lung), and sequenced the transcriptome of lung tissue at 48 hours after irradiation. Rat cohorts (n = 7/group): 1. Control (Con); 2. Radiation group (RT); 3. Pre-oxygenation (oxygen concentration > 90%) for 8 hours before thoracic radiation (PreO2).

RESULTS

The inflammatory exudation emerged in the pulmonary interstitium at 48 hours, and reached the most serious alveolitis after four weeks of irradiation (the comparison of alveolitis scores in RT4w vs Con4w and PreO2(4w) vs Con4w, P<0.001) on hematoxylin-eosin staining. While the alveolitis scores in RT group and PreO2 group were not statistically different at each time point. Masson staining showed that the pulmonary fibrosis in the RT group and the PreO2 group reached an obvious pathological change at 12 weeks after irradiation, but the difference between the two groups was not significant. Transcriptome sequencing showed that the number of differential genes in PreO2 vs Con was 559 (302 up-regulated genes and 257 down-regulated genes). The GO enrichment analysis indicated that chromosome segregation was the most significant functional item with P value in the comparative analysis, and the KEGG enrichment analysis suggested that cell division was the most significant enrichment pathway of these differential genes. While there was a small quantity of differential genes in PreO2 vs RT group (3 up-regulated genes and 12 down-regulated genes). Pentose and glucuronate conversions were the most significant enrichment pathway of these differential genes.

CONCLUSION

This study demonstrated that PreO2 radiotherapy did not increase the severity of radiation induced lung injury in rats compared to conventional radiotherapy. Further study should be conducted to confirm these results and to investigate the regulatory mechanism of pneumonia caused by PreO2 radiotherapy.

Deep Learning-Based Multi-Modality Segmentation of Primary Gross Tumor Volume in CT and MRI for Nasopharyngeal Carcinoma

PURPOSE/OBJECTIVE(S)

The delineation of primary gross tumor volume (GTV) of nasopharyngeal carcinoma (NPC) is an essential step for radiotherapy planning. In clinical practice, radiation oncologists manually delineate the GTV in planning CT with the help of diagnostic MRI. This is because NPC tumors are closely adjacent to many important anatomic structures, and CT and MRI provide complementary strength to accurately determine the tumor extension boundary. Manual delineation is time-consuming with the potential registration errors between MRI and CT decreasing the delineation accuracy. In this study, we propose a fully automated GTV segmentation method based on CT and MRI by first aligning MRI to CT, and then, segmenting the GTV using a multi-modality deep learning model.

MATERIALS/METHODS

We collected 104 nasopharyngeal carcinoma patients with both planning CT and diagnostic MRI scans (T1 & T2 phases). An experienced radiation oncologists manually delineated the GTV, which was further examined by another senior radiation oncologist. Then, a coarse to fine cross-modality registration from MRI to CT was conducted as follows: (1) A rigid transformation was performed on MRI to roughly align MRI to CT with similar anatomic position. (2) Then, the region of interest (RoI) on both CT and rigid-transformed MRI were cropped. (3) A leading cross-modality deformable registration algorithm, named DEEDS, was applied on the cropped MRI and CT RoIs to find an accurate local alignment. Next, using CT and registered MRI as the combined input, a multi-modality deep segmentation network based on nnUNet was trained to generate the GTV prediction. 20% patients were randomly selected as the unseen testing set to quantitatively evaluate the performance.

RESULTS

The quantitative NPC GTV segmentation performance is summarized in Table 1. The deep segmentation model using CT alone achieved reasonable high performance with 76.6% Dice score and 1.34mm average surface distance (ASD). When both CT and registered MRI were used, the segmentation model further improved the performance by 0.9% Dice score increase and 11% relative ASD error reduction, demonstrating the complementary strength of CT and MRI in determining NPC GTV. Notably, the achieved 77.5% Dice score and 1.19mm ASD by the multimodality model is among the top performing results reported in recent automatic NPC GTV segmentation using either CT or MRI modality.

CONCLUSION

We developed a fully automated multi-modal deep-learning model for NPC GTV segmentation. The developed model can segment the NPC GTV in high accuracy. With further optimization and validation, this automated model has potential to standardize the NPC GTV segmentation and significantly decrease the workload of radiation oncologists in clinical practice.

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.

Magnetic Bead Spherical Nucleic Acid Microstructure for Reliable DNA Preservation and Repeated DNA Reading

DNA is an attractive medium for long-term data storage because of its density, ease of copying, sustainability, and longevity. Recent advances have focused on the development of new encoding algorithms, automation, and sequencing technologies. Despite progress in these subareas, the most challenging hurdle in the deployment of DNA storage remains the reliability of preservation and the repeatability of reading. Herein, we report the construction of a magnetic bead spherical nucleic acid (MB-SNA) composite microstructure and its use as a cost-effective platform for reliable DNA preservation and repeated reading. MB-SNA has an inner core of silica@γ-Fe2O3@silica microbeads and an outer spherical shell of double-stranded DNA (dsDNA) with a density as high as 34 pmol/cm2. For MB-SNA, each strand of dsDNA stored a piece of data, and the high-density packing of dsDNA achieved high-capacity storage. MB-SNA was advantageous in terms of reliable preservation over free DNA. By accelerated aging tests, the data of MB-SNA is demonstrated to be readable after 0.23 million years of preservation at -18 °C and 50% relative humidity. Moreover, MB-SNA facilitated repeated reading by facile PCR-magnetic separation. After 10 cycles of PCR access, the retention rate of dsDNA for MB-SNA is demonstrated to be as high as 93%, and the accuracy of sequencing is more than 98%. In addition, MB-SNA makes cost-effective DNA storage feasible. By serial dilution, the physical limit for MB-SNA to achieve accurate reading is probed to be as low as two microstructures.

MineProt: a stand-alone server for structural proteome curation

AlphaFold-like systems are rapidly expanding the scale of proteome structuring, and MineProt provides an effective solution for custom curation of these novel high-throughput data. It enables researchers to build their own server in simple steps, run almost out-of-the-box scripts to annotate and curate their proteins, analyze their data via a user-friendly online interface, and utilize plugins to extend the functionality of server. It is expected to support researcher productivity and facilitate data sharing in the new era of structural proteomics. Database URL MineProt is open-source software available at https://github.com/huiwenke/MineProt.

Context-aware deep network for coronary artery stenosis classification in coronary CT angiography

Automatic coronary artery stenosis grading plays an important role in the diagnosis of coronary artery disease. Due to the difficulty of learning the informative features from varying grades of stenosis, it is still a challenging task to identify coronary artery stenosis from coronary CT angiography (CCTA). In this paper, we propose a context-aware deep network (CADN) for coronary artery stenosis classification. The proposed method integrates 3D CNN with Transformer to improve the feature representation of coronary artery stenosis in CCTA. We evaluate the proposed method on a multicenter dataset (APOLLO study with NCT05509010). Experimental results show that our proposed method can achieve the accuracy of 0.84, 0.83, and 0.86 for stenosis diagnosis on the lesion, artery, and patient levels, respectively.

Polyp-Canal Reconstruction Reveals Evolution Toward Complexity in Corals

Modern scleractinian corals are classified into robust, complex, and basal clades through comparative molecular studies. However, only few morphological or biological criteria can systematically determine the evolutionary trajectories of these major scleractinian coral clades. Here, we obtained the structural information of 21 scleractinian coral species representing robust and complex clades: High-resolution micro-computed tomography was used to reconstruct the polyp-canal systems in their colonies and to visualize the dynamic polyp growth processes. We found that the emergence of mesh-like canals may distinguish representatives of complex and robust clades. The differences in polyp-canal connections suggest distinct evolutionary trajectories among coral species: The formation of the canal network promoted the development of more complex coral structures, and coral polyps within this network formed calices of very similar volume, following precise axial growth directions. The influence of individual polyps on the coral colony becomes less significant as coral structures become more complex, and coral species with more complicated polyp-canal systems occupied niches more efficiently. This work supplements current evolutionary studies on reef-building corals, providing insight for further studies on coral growth patterns.

Development and validation of a survival prediction model and risk stratification for pancreatic neuroendocrine neoplasms

PURPOSE

We explored risk variables associated with cancer-specific survival (CSS) in patients with pancreatic neuroendocrine neoplasms (PNENs) and created a network dynamic nomogram model to predict patient survival time.

METHODS

A total of 7750 patients with PNENs were included in this analysis, including 134 with functional PNENs and 7616 with nonfunctional PNENs. Clinical feature and prognosis differences between functional and nonfunctional PNENs were compared. Independent prognostic factors affecting CSS were analyzed by univariate and multifactorial Cox regression. Nomogram and web-based prognosis prediction of PNENs were developed and validated by C indices, decision curve analysis, and calibration plots.

RESULTS

Patients with functional PNENs were younger at diagnosis than those with nonfunctional PNENs. Functional PNENs had better prognoses than nonfunctional PNENs (5-year survival rates: 78.55% and 71.10%, respectively). Univariate and multifactorial Cox regression analyses showed that tumor infiltration (T), nodal metastasis (N), metastasis (M), tumor site, differentiation grade, age, marital status, and surgical treatment were independent prognostic risk factors for CSS, which were included in the prognostic nomogram and web-based prognosis calculator. The calibration plots and decision curve analysis showed that the nomogram had excellent prediction and clinical practical ability. The C indices for CSS in the training and validation cohorts were 0.848 (95% CI 0.838-0.8578) and 0.823 (95% CI 0.807-0.839), respectively. We scored all patients according to the nomogram and divided patients into three different risk groups. The prognosis of the low-risk population was significantly better than those of the middle- and high-risk populations based on Kaplan-Meier survival curve.

CONCLUSION

We analyzed the clinical features of PNENs and developed a convenient and web dynamic nomogram to predict CSS.

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.

Association of residential greenness with the risk of metabolic syndrome in Chinese older adults: a longitudinal cohort study

AIMS

We aimed to investigate the association between residential greenness and MetS in older Chinese adults.

METHODS

Longitudinal data on sociodemographic characteristics and lifestyle were collected from the Shenzhen Healthy Ageing Research (SHARE) cohort. Greenness exposure was assessed through satellite-derived Normalized Difference Vegetation Index (NDVI) values in the 250-m, 500-m, and 1250-m radius around the residential address for each participant. MetS was defined by standard guidelines for the Chinese population.

RESULTS

A total of 49,893 older Chinese adults with a mean age of 70.96 (SD = 5.26) years were included in the study. In the fully adjusted models, participants who lived in the highest quartile of NDVI_250-m, NDVI_500-m, and NDVI_1250-m had a 15% (odds ratio, OR = 0.85, 95% confidence interval, CI: 0.80-0.90), 12% (OR = 0.88, 95% CI: 0.83-0.93), and 11% (OR = 0.89, 95% CI: 0.85-0.95) lower incidence of MetS, respectively, than those living in the lowest quartile (all p-_trend < 0.01). Interactions and subgroup analyses showed that age, sex, smoking status, and drinking status were significant effect modifiers (p-_interaction for all NDVI < 0.05).

CONCLUSIONS

Residential greenness is associated with a lower risk of MetS in Chinese older adults, especially for young older adults, females, non-smokers, and non-drinkers.

Analysis of mutational genotyping using correctable decoding sequencing with superior specificity

The ability to accurately identify SNPs or low-abundance mutations is important for early clinical diagnosis of diseases, but the existing high-throughput sequencing platforms are limited in terms of their accuracy. Here, we propose a correctable decoding sequencing strategy that may be used for high-throughput sequencing platforms. This strategy is based on adding a mixture of two types of mononucleotides, natural nucleotide and cyclic reversible termination (CRT), for cyclic sequencing. Using the synthetic characteristic of CRTs, about 75% of the calls are unambiguous for a single sequencing run, and the remaining ambiguous sequence can be accurately deduced by two parallel sequencing runs. We demonstrate the feasibility of this strategy, and its cycle efficiency can reach approximately 99.3%. This strategy is proved to be effective for correcting errors and identifying whether the sequencing information is correct or not. And its conservative theoretical error rate was determined to be 0.0009%, which is lower than that of Sanger sequencing. In addition, we establish that the information of only a single sequencing run can be used to detect samples with known mutation sites. We apply this strategy to accurately identify a mutation site in mitochondrial DNA from human cells.

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.

Utilizing an artificial intelligence system to build the digital structural proteome of reef-building corals

BACKGROUND

Reef-building corals play an important role in the marine ecosystem, and analyzing their proteomes from a structural perspective will exert positive effects on exploring their biology. Here we integrated mass spectrometry with newly published ColabFold to obtain digital structural proteomes of dominant reef-building corals.

RESULTS

Of the 8,382 homologous proteins in Acropora muricata, Montipora foliosa, and Pocillopora verrucosa identified, 8,166 received predicted structures after about 4,060 GPU hours of computation. The resulting dataset covers 83.6% of residues with a confident prediction, while 25.9% have very high confidence.

CONCLUSIONS

Our work provides insight-worthy predictions for coral research, confirms the reliability of ColabFold in practice, and is expected to be a reference case in the impending high-throughput era of structural proteomics.

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.

Plasma amyloid-beta levels and risk of new-onset atrial fibrillation in the general population

Background

Atrial fibrillation (AF) is a major health burden worldwide, with significant sex differences in epidemiology and risk factors. Amyloid-β40 (Aβ40) and Amyloid-β42 (Aβ42), the hallmark of cerebral amyloid angiopathy, have recently been linked to prevalence and prognosis of several cardiovascular outcomes including stroke and coronary heart disease. However, whether these biomarkers are associated with incident AF remains largely unknown.

Purpose

To investigate the associations between plasma concentrations of Aβ40 and Aβ42 with new-onset AF.

Methods

4,134 participants without a history of AF at baseline (from 2002 to 2005) with qualified plasma samples in the Rotterdam Study were included in this study. AF was diagnosed by electrocardiograms, general practitioners' and hospital records. Cox proportional hazards regression models with natural cubic splines were used to assess the linear/nonlinear association between biomarkers and risk of new-onset AF. All models were adjusted for traditional cardiovascular risk factors.

Results

Mean age was 71.3±7.2 years and 2,383 (57.6%) were women. Median follow-up time was 9.2 years. In the fully adjusted model, higher levels of Aβ40 [hazard ratio, 95% confidence interval: 1.16 (1.05–1.28)] and Aβ42 [1.19 (1.09–1.31)], as well as Amyloid-β42 to β40 ratio (Aβ42/40) [1.09 (1.02–1.17)] were significantly associated with incident AF. The observed association between Aβ40 and AF attenuated after mutual adjustment for Aβ42 [1.05 (0.92–1.19)]. In addition, a J-shaped association was found between Aβ40 and AF with the lowest AF risk at Aβ40 values of 212.5 pg/ml.

Conclusions

Both Aβ40 and Aβ42 were independently significantly associated with new-onset AF in the general population independent of cardiovascular risk factors. Findings also suggest a stronger association between AF onset and Aβ42 and AF onset, compared to Aβ40. A nonlinear association was found between Aβ40 and AF, reflecting a substantially increased AF risk among participants with severely increased Aβ40 values.

Funding Acknowledgement

Type of funding sources: None.

Cardiometabolic multimorbidity and lifetime risk of atrial fibrillation among men and women

Background

Atrial fibrillation (AF) is the most common cardiac arrythmia worldwide, with an increased risk of comorbidity, and significant sex differences in pathophysiology and prognosis. Cardiometabolic disorders, including obesity, hypertension, diabetes mellitus, coronary heart disease, stroke, and heart failure commonly coexist with AF. However, the sex-specific patterns and (combined) impact of cardiometabolic disorders on the risk of new-onset AF remains largely unknown.

Purpose

To examine the association between patterns of cardiometabolic multimorbidity and new-onset AF and lifetime risk of AF incidence among men and women.

Methods

4,113 men and 5,432 women free of prevalent AF at baseline (from 1996 to 2008) from the Rotterdam Study were included. AF incidents were assessed by electrocardiograms and general practitioners' and hospital records, and followed up to January 1st, 2014. Sex-specific Cox proportional hazards regression models were used to assess the association between the amount of cardiometabolic disorders and risks of new-onset AF. Models were adjusted for traditional cardiovascular risk factors. Remaining lifetime risk for AF was estimated across the cardiometabolic multimorbidity groups at index ages of 55, 65, and ≥75 years up to age 108.

Results

Mean age at baseline was 65.5±9.4 years. Median follow-up time was 10.8 years. In the fully-adjusted model, a significant association was found between the amount of cardiometabolic disorders and incident AF among women but not men. Compared to women without cardiometabolic disorders, women with 3 (hazard ratios, 95% conference intervals: 2.17 (1.24–3.79)) and ≥4 comorbidities (4.58 (2.22–9.48)) had higher AF risks. The lifetime risk for AF was significantly increased with the number of cardiometabolic disorders among both men and women. At index age of 55 years, the lifetime risks (95% confidence interval) for AF were 25.2% (17.1–33.4), 24.2% (20.0–28.9), 27.1% (23.2–31.0), 30.0% (24.3–35.7) and 34.1% (22.4–45.7), for 0, 1, 2, 3, and ≥4 comorbid cardiometabolic disorders among men, respectively. Corresponding risks were 16.3% (6.68–25.9), 20.3% (16.3–24.3), 27.6% (24.1–31.2), 23.6% (17.8–29.4) and 33.3% (16.0–50.2) among women.

Conclusions

We observed a significant combined impact of cardiometabolic disorders on AF risk, most evidently among women. Participants with cardiometabolic multimorbidity had a significantly increased lifetime risk of AF, especially at a young index age.

Funding Acknowledgement

Type of funding sources: None.

Constructing the boundary between potent and ineffective siRNAs by MG-algorithm with C-features

BACKGROUND

In siRNA based antiviral therapeutics, selection of potent siRNAs is an indispensable step, but these commonly used features are unable to construct the boundary between potent and ineffective siRNAs.

RESULTS

Here, we select potent siRNAs by removing ineffective ones, where these conditions for removals are constructed by C-features of siRNAs, C-features are generated by MG-algorithm, Icc-cluster and the different combinations of some commonly used features, MG-algorithm and Icc-cluster are two different algorithms to search the nearest siRNA neighbors. For the ineffective siRNAs in test data, they are removed from test data by I-iteration, where I-iteration continually updates training data by adding these successively removed siRNAs. Furthermore, the efficacy of siRNAs of test data is predicted by their nearest neighbors of training data.

CONCLUSIONS

By siRNAs of Hencken dataset, results show that our algorithm removes almost ineffective siRNAs from test data, gives the clear boundary between potent and ineffective siRNAs, and accurately predicts the efficacy of siRNAs also. We suggest that our algorithm can provide new insights for selecting the potent siRNAs.

Lithium chloride promotes neural functional recovery after local cerebral ischaemia injury in rats through Wnt signalling pathway activation

BACKGROUND

Lithium chloride (LiCl) has a significant neuroprotective effect in cerebral ischaemia. However, to date, there is a paucity of evidence on the role of LiCl in neural restoration after brain ischaemia and the signalling pathways involved remain unclear.

MATERIALS AND METHODS

Therefore, to address this gap, the middle cerebral artery occlusion (MCAO) rat model was used to simulate human ischaemia stroke. Male Sprague-Dawley rats were given MCAO for 90 min followed by reperfusion, and Dickkopf-1 (DKK1, 5.0 μg/kg) was administered half an hour before MCAO. Rats were then treated with hypodermic injection of LiCl (2.0 mmol/kg) twice a day for 1 week. After treatment, cognitive impairment was assessed by the Morris water maze test. Neurological deficit score, 2,3,5-triphenyl tetrazolium chloride staining, brain water content, and histopathology were used to evaluate brain damage. Enzyme-linked immunosorbent assay was used to measure oxidative stress damage and inflammatory cytokines. Apoptosis of the hippocampal neurons was tested by western blot. The key factors of Wnt signalling pathway in the ischaemic penumbra were detected by immunofluorescence staining and quantitative real-time polymerase chain reaction.

RESULTS

Current experimental results showed that LiCl treatment significantly improved the impaired spatial learning and memory ability, suppressed oxidative stress, inflammatory reaction, and neuron apoptosis accompanied by attenuating neuronal damage, which subsequently decreased the brain oedema, infarct volume and neurological deficit. Furthermore, the treatment of LiCl activated Wnt signalling pathway. Interestingly, the aforementioned effects of LiCl treatment were markedly reversed by administration of DKK1, an inhibitor of Wnt signalling pathway.

CONCLUSIONS

These results indicate that LiCl exhibits neuroprotective effects in focal cerebral ischaemia by Wnt signalling pathway activation, and it might have latent clinical application for the prevention and treatment of ischaemic stroke.

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.

P-382 Decrease of serum estradiol prior to human chorionic gonadotrophin administration have an impact on live birth in IVF/ICSI cycles

Study question

Whether decrease of serum estradiol prior to human chorionic gonadotrophin administration have an impact on live birth in IVF/ICSI cycles?

Summary answer

The E2 change before the day of hCG administration had significant correlation with live birth. The live birth rate decreased with decreasing serum E2 level.

What is known already

The objective of this study was to assess the effects of a decrease of estradiol (E2) levels on the day of human chorionic gonadotrophin (hCG) administration on in vitro fertilization /intracytoplasmic sperm injection (IVF/ICSI) outcomes, including cycles with long, antagonist and micro stimulus protocols.

Study design, size, duration

In this retrospective cohort study, 1303 patients who received IVF/ICSI non-donor treatment were identified. Patients were divided into two groups according to live birth and the characteristics of IVF/ICSI cycles were compared between groups, including baseline infertility parameters, ovarian stimulation characteristics and embryo laboratory manipulation parameters.

Participants/materials, setting, methods

In this retrospective cohort study, 1303 patients who received IVF/ICSI non-donor treatment were identified. Patients were divided into two groups according to live birth and the characteristics of IVF/ICSI cycles were compared between groups, including baseline infertility parameters, ovarian stimulation characteristics and embryo laboratory manipulation parameters. The multivariate logistic regression model was performed to adjust potential confounders and assess correlation between E2 dynamics before hCG administration and live birth.

Main results and the role of chance

Our results revealed that patients without live birth had higher age (32.13 ± 4.33 vs. 30.21 ± 3.71, P &lt; 0.001) and pervious miscarriages (0.57 ± 0.95 vs. 0.46 ± 0.83, P = 0.0295), while had lower number of oocytes retrieved (8.95 ± 4.69 vs. 12.36 ± 5.54, P &lt; 0.001), day of hCG E2 (8269.53 ± 4104.22 vs. 9580.71 ± 3534.11, P &lt; 0.001) and endometrium thickness (10.37 ± 3.66 vs. 11.50 ± 3.40, P &lt; 0.001) compared with patients with live birth. Additionally, the multivariate logistic regression analysis displayed significant impact of serum E2 change on the live birth, and the achievement of live birth [OR (95%CI) 0.81 (0.71, 0.92), P = 0.001] decreased with the decreasing level of serum E2 before hCG trigger day. Estradiol stratification analyses displayed the OR and 95% CI for the association between △E2 and live birth among patients with different levels of estradiol decline (&lt;25%, 25%–50%, 50%–75%, &gt;75%). Compared with the &lt;25% decline and 25%–50% decline groups, the ORs of 50%–75% and &gt;75% decline groups were 1.66 (95% CI: 1.12-2.45, P = 0.012) and 2.00 (95% CI: 1.39-2.89, P &lt; 0.001), respectively, after adjusting potential confounders.

Limitations, reasons for caution

There was concealment of randomization and blinding of outcome assessments reducing the risk of selection and measurement bias.

Wider implications of the findings

In summary, the E2 change before the day of hCG administration had significant correlation with live birth, and the live birth decreased with the decreasing level of serum E2 before hCG trigger day. The patients with a greater decline in the E2 level more likely to had poor clinical outcomes.

Trial registration number

Chi CTR1900026088

Symbiodiniaceae microRNAs and their targeting sites in coral holobionts: A transcriptomics-based exploration

Corals should make excellent models for cross-kingdom research because of their natural animal-photobiont holobiont composition, yet a lack of studies and experimental data restricts their use. Here we integrate new full-length transcriptomes and small RNAs of four common reef-building corals with the published Cladocopium genomes to gain deeper insight into gene regulation in coral-Symbiodiniaceae holobionts. Eleven novel Symbiodiniaceae miRNAs get identified, and enrichment results of their target genes show that they might play a role in downregulating rejection from host coral cells, protecting symbiont from autophagy and apoptosis in parallel. This work provides evidence for the early origin of cross-kingdom regulation as a mechanism of self-defense autotrophs can use against heterotrophs, sheds more light on coral-Symbiodiniaceae holobionts, and contributes valuable data for further coral research.

Trends in Methamphetamine Use in the Mainland of China, 2006-2015

Background

Methamphetamine is the most prevalent drug in the mainland of China, yet few studies on the non-medical use of methamphetamine nationwide have been conducted. This study aimed to examine the trends in the prevalence of non-medical methamphetamine use and to explore the flow pattern of internal migrant methamphetamine users in the mainland of China.

Methods

Data were extracted from the National Dynamic Management and Control Database for Drug Users (NDMCD). Joinpoint regressions were used to examine trends in the prevalence and population size of methamphetamine use.

Results

A total of 1,821,468 methamphetamine use cases registered in NDMCD from 2006 to 2015 were identified. The number of methamphetamine use cases presented an increasing trend in all age subgroups, and among them, the elderly increased the fastest [annual percent change (APC_2006−2015), 122.9; 95% CI, 113.0–133.3; p < 0.001]. The prevalence of methamphetamine use increased from 4.69 per 100,000 population in 2008 to 45.38 per 100,000 population in 2015 (APC_2008−2015, 36.1; 95% CI, 31.9–40.6; p < 0.001). The regions of the Pearl River Delta, Yangtze River Delta, and Beijing-Tianjin-Hebei Urban Agglomeration absorbed over 96% of all internal migrant methamphetamine use cases, and the number of migrant methamphetamine use cases presented increased trends in these three regions.

Conclusions

The increasing trends in methamphetamine use have become a threat to all age groups in China. Substance use prevention programs should focus on internal migrant drug users, especially in economically developed regions.

Transmembrane transport process and endoplasmic reticulum function facilitate the role of gene cel1b in cellulase production of Trichoderma reesei

Background

A total of 11 β-glucosidases are predicted in the genome of Trichoderma reesei, which are of great importance for regulating cellulase biosynthesis. Nevertheless, the relevant function and regulation mechanism of each β-glucosidase remained unknown.

Results

We evidenced that overexpression of cel1b dramatically decreased cellulase synthesis in T. reesei RUT-C30 both at the protein level and the mRNA level. In contrast, the deletion of cel1b did not noticeably affect cellulase production. Protein CEL1B was identified to be intracellular, being located in vacuole and cell membrane. The overexpression of cel1b reduced the intracellular pNPGase activity and intracellular/extracellular glucose concentration without inducing carbon catabolite repression. On the other hand, RNA-sequencing analysis showed the transmembrane transport process and endoplasmic reticulum function were affected noticeably by overexpressing cel1b. In particular, some important sugar transporters were notably downregulated, leading to a compromised cellular uptake of sugars including glucose and cellobiose.

Conclusions

Our data suggests that the cellulase inhibition by cel1b overexpression was not due to the β-glucosidase activity, but probably the dysfunction of the cellular transport process (particularly sugar transport) and endoplasmic reticulum (ER). These findings advance the knowledge of regulation mechanism of cellulase synthesis in filamentous fungi, which is the basis for rationally engineering T. reesei strains to improve cellulase production in industry.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01809-1.

Women-specific risk factors and risk of incident atrial fibrillation in UK Biobank

Funding Acknowledgements

Type of funding sources: None.

Background

Atrial fibrillation (AF) is the most common cardiac arrhythmia worldwide and carries a large morbidity and mortality risk. Recent evidence suggests differences in epidemiology and pathophysiology of AF between women and men and underscores a poorer prognosis of AF among women. This calls for further investigation regarding the impact of women-specific risk factors on AF development.

Purpose

To investigate the association between women-specific risk factors and new-onset AF.

Methods

235,191 women (mean [standard deviation] age: 55.7 [8.1] years) free of AF and without a history of hysterectomy and/or bilateral oophorectomy from the UK Biobank were included. Various women-specific risk factors were assessed from 2006 to 2010. Follow-up of new-onset AF occurred through October 2020. Cox proportional hazards analyses were performed to investigate prospective associations between each risk factor and incident AF. Additionally, natural splines were used to identify any potential nonlinear associations.

Results

After a median follow-up of 11.6 (interquartile range: 10.9–12.3) years, 4,629 (2%) women experienced new-onset AF. In fully adjusted models, having experienced irregular menstrual cycle was significantly associated with increased new-onset AF risk [hazard ratio (HR); 95% confidence interval (CI): 1.34; 1.01-1.79]. In addition, nonlinear associations were found between menopausal age, menarcheal age, number of live births, and number of total reproductive years with incident AF. Compared to the reference, early menopause (menopause &lt;45 years of age) or delayed menopause (&gt;60 years) significantly increased risks of incident AF (HR; 95CI: 1.24; 1.10-1.39 and 1.34; 1.01-1.78, respectively). Compared to the reference, both early menarche (menarche ≤11 years) and late menarche (menarche ≥13 years) were associated with AF incidence (HR; 95CI: 1.10; 1.00-1.21 and 1.08; 1.00-1.17, respectively). Compared to women with one or two children, having no children (HR; 95CI: 1.13; 1.04-1.24), or more than six children (HR; 95%CI: 1.67; 1.03-2.70) were associated with higher AF risks. Having reproductive years ≤20 years was significantly associated with incident AF (HR; 95CI: 1.74; 1.07-2.86).

Conclusions

Having experienced early or delayed menopause, early or late menarche, or irregular menstrual cycles conferred higher risks of incident AF among women in the UK Biobank. Interestingly, both nulliparity and multiparity, compared to having one or two children, were associated with an increased AF risk. Our results highlight the importance of knowledge regarding the reproductive history of women in devising screening strategies for AF prevention.

Full-Length Transcriptome Sequencing Reveals Tissue-Specific Gene Expression Profile of Mangrove Clam Geloina erosa

Mollusca is the second largest animal phylum and represents one of the most evolutionarily successful animal groups. Geloina erosa, a species of Corbiculidae, plays an important role in mangrove ecology. It is highly adaptable and can withstand environmental pollution and microbial infections. However, there is no reference genome or full-length transcriptome available for G. erosa. This impedes the study of the biological functions of its different tissues because transcriptome research requires reference genome or full-length transcriptome as a reference to improve accuracy. In this study, we applied a combination of Illumina and PacBio single-molecule real-time sequencing technologies to sequence the full-length transcriptomes of G. erosa tissues. Transcriptomes of nine samples obtained from three tissues (hepatopancreas, gill, and muscle) were sequenced using Illumina. Furthermore, we obtained 87,310 full-length reads non-chimeric sequences. After removing redundancy, 22,749 transcripts were obtained. The average Q score of 30 was 94.48%. In total, 271 alternative splicing events were predicted. There were 14,496 complete regions and 3,870 lncRNAs. Differential expression analysis revealed tissue-specific physiological functions. The gills mainly express functions related to filtration, metabolism, identifying pathogens and activating immunity, and neural activity. The hepatopancreas is the main tissue related to metabolism, it also involved in the immune response. The muscle mainly express functions related to muscle movement and control, it contains more energy metabolites that gill and hepatopancreas. Our research provides an important reference for studying the gene expression of G. erosa under various environmental stresses. Moreover, we present a reliable sequence that will provide an excellent foundation for further research on G. erosa.

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.

Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs

Background

Amphioxus is a model organism for vertebrate evolutionary research. The significant contrast between morphological phenotypic similarity and high-level genetic polymorphism among amphioxus populations has aroused scientists' attention. Here we resequenced 21 amphioxus genomes to over 100X depth and mapped them to a haploid reference.

Results

More than 11.5 million common SNPs were detected in the amphioxus population, which mainly affect genes enriched in ion transport, signal transduction and cell adhesion, while protein structure analysis via AlphaFold2 revealed that these SNPs fail to bring effective structural variants.

Conclusions

Our work provides explanation for “amphioxus polymorphism paradox” in a micro view, and generates an enhanced genomic dataset for amphioxus research.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-022-01038-w.

Soil causes gut microbiota to flourish and total serum IgE levels to decrease in mice

Traditional farm environments induce protection from allergic diseases. In this study, farm environmental factors were classified into three categories, environmental microbes, soil, and organic matter. To explore the impact of soil and environmental microorganisms on gut microbiota and immune function, mice were fed sterilized soil and inhaling microbes, soil microbes, or non-sterilized soil. Metagenomic sequencing results showed the intake of sterile soil i.e. inhaling a small amount of soil microbes in the air increased gut microbial diversity and the abundance of type III secretion system (T3SS) genes, and decreased serum immune IgE levels induced by 2-4-dinitrofluorobenzene(DNFB). The intake of soil microbes increased the abundance of genes involved in the metabolism of short chain fatty acids and amino acid biosynthesis. Meanwhile, the intake of soil increased gut microbial diversity, the abundance of T3SS genes and related infectious elements, and genes associated with the metabolism of short chain fatty acids and amino acid biosynthesis, and decreased serum IgE levels. Therefore, soil may be useful as a potential "prebiotic" promoting the reproduction and growth of some intestinal microorganisms that harbor bacterial secretion system genes, especially those of T3SS, whose abundance was positively and significantly correlated with innate immune function of mice. This article is protected by copyright. All rights reserved.

Extended XOR algorithm with biotechnology constraints for Data Security in DNA Storage

Background:

DNA storage is becoming a global research hotspot in recent years and today, most researches are focused on storage density and big data. The security of DNA storage needs to be observed. Some DNA-based security methods were introduced for traditional information security problems. However, few encryption algorithm considered the limitation of biotechnology and applied it for DNA storage. The difference between DNA cryptography and the traditional one is that the former is based on the limitation of biotechnology, which is unrelated to numeracy.

Objective:

An extended XOR algorithm (EXA) was introduced for encryption with constriants of biotechnology, which can solve the problems of synthesis and sequencing partly, such as GC content and homopolymer in DNA storage..

Methods:

The target file was converted by a quaternary DNA storage model to maximize the storage efficiency. The key file could be ‘anything’ converted into DNA sequence by a binary DNA storage model to make the best utilization for the length of the key file.

Results:

The input files were encrypted into DNA storage and decrypted to error-free output files.

Conclusion:

This meant error-free encryption DNA storage is feasible and EXA paves the way for encryption in large-scale DNA storage.

Fate of thiamethoxam from treated seeds in mesocosms and response of aquatic invertebrate communities

Thiamethoxam is a neonicotinoid insecticide widely applied in the Canadian Prairies. It has been detected in surface waters of agro-ecosystems, including wetlands, but the potential effects on non-target invertebrate communities in these wetlands have not been well characterized. In an effort to understand better the fate of thiamethoxam in wetlands and the response of invertebrates (zooplankton and emergent insects), model systems were used to mimic wetland flooding into planted fields. Outdoor mesocosms were treated with a single application of thiamethoxam-treated canola seeds at three treatment levels based on a recommended seeding rate (i.e., 6 kg/ha; 1×, 10×, and 100× seeding rate) and monitored over ten weeks. The mean half-life of thiamethoxam in the water column was 6.2 d. There was no ecologically meaningful impact on zooplankton abundances or community structure among treatments. Statistically significant differences were observed in aquatic insect abundance between control mesocosms and the two greatest thiamethoxam treatments (10× and 100× seeding rate). The observed results indicate exposure to thiamethoxam at environmentally relevant concentrations likely does not represent a significant ecological risk to abundance and community structure of wetland zooplankton and emergent insects.