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.

Chimera: The spoiler in multiple displacement amplification

Multiple displacement amplification (MDA) based on isothermal random priming and high fidelity phi29 DNA polymerase-mediated processive extension has revolutionized the field of whole genome amplification by enabling the amplification of minute amounts of DNA, such as from a single cell, generating vast amounts of DNA with high genome coverage. Despite its advantages, MDA has its own challenges, one of the grandest being the formation of chimeric sequences (chimeras), which presents in all MDA products and seriously disturbs the downstream analysis. In this review, we provide a comprehensive overview of current research on MDA chimeras. We first reviewed the mechanisms of chimera formation and chimera detection methods. We then systematically summarized the characteristics of chimeras, including overlap, chimeric distance, chimeric density, and chimeric rate, as found in independently published sequencing data. Finally, we reviewed the methods used to process chimeric sequences and their impacts on the improvement of data utilization efficiency. The information presented in this review will be useful for those interested in understanding the challenges with MDA and in improving its performance.

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.