Biomedical subjects

Bin Meng

Publications and source records attributed to Bin Meng.

6 recordsLinked to original sources

PubMed2026

NanoSSL: attention mechanism-based self-supervised learning method for protein identification using nanopores.

MOTIVATION: Nanopores are cutting-edge interdisciplinary tools that can analyze biomolecules at the single-molecule level for many applications, e.g. DNA sequencing. Efforts are underway to extend nanopores to proteomics, including the development of machine learning algorithms for protein sequencing and identification. However, single-molecule data are intrinsically noisy and hard to process. Moreover, the development and performance of machine learning for nanopore is jeopardized by data scarcity. Self-supervised learning is an emerging method that may yield advantages in nanopore scenarios. RESULTS: We propose and experimentally validate Nanopore analysis using Self-Supervised Learning (NanoSSL), a generative self-supervised learning framework based on attention mechanisms for the identification of protein signals from nanopores. Leveraging a two-step approach consisting of self-supervised pre-training and supervised fine-tuning, NanoSSL learns useful feature representations from empirical data to facilitate downstream classification tasks. Inspired by the concept of fragmentation in conventional protein sequencing technologies, during pretraining each translocation event is split into multiple non-overlapping fragments of equal size, some of which are randomly masked and reconstructed using a masked autoencoder. Learning the feature representations of the reconstructed nanopore events facilitates molecular identification in fine-tuning. In this study, we retested a publicly available nanopore multiplexed protein sensing dataset for model iteration, and subsequently measured Alzheimer's disease biomarker Aβ1-42 using homemade solid-state nanopores. Empirical results indicated NanoSSL achieved an unprecedented performance across four metrics: accuracy, precision, recall, and F1 score, when classifying two mutated Aβ1-42, E22G and G37R. The self-supervised learning and attention mechanism were verified as the source of performance gains. AVAILABILITY AND IMPLEMENTATION: The main program is available at https://doi.org/10.5281/zenodo.17172822.

Nanopores↗

PubMed2005

[Analysis on the multi-distribution and the major influencing factors on severe acute respiratory syndrome in Beijing].

OBJECTIVE: To analyse the multi-dimension nature of severe acute respiratory syndrome (SARS) transmission. METHODS: Based on the data of SARS in 2003 and the geographic information system of Beijing, as well as under the broad range of the theorems and techniques of data-driven and model-driven knowledge mining, hierarchical techniques were used to test the hot spots. Wavelet technique was also used to decompose Moran's I frequency to survey the spatial clustering process of SARS. For factors analysis, BW test was used to distinguish factors which influencing SARS process. In temporal aspects, susceptive-infective-removal model (SIR) without Taylor expansion was solved by a genetic-simulated annealing algorithm, that directly provided a new approach to obtain epidemic parameters from the SIR model. RESULTS: Different order of spatial hot spots were noticed and the clustering were relevant with the means of transportation. Diffusion dynamics were changed along with the temporal process of SARS. Regarding factor analysis, geographic relationship, population density, the amount of doctors and hospitals appeared to be the key elements influencing the transmission of SARS. The predictable number of SARS cases evolving with time were also calculated. CONCLUSIONS: Cluster detection of close contacts of SARS infective in Beijing revealed the spatial characters of urban population flow and having important implications in the prevention and control of this communicable diseases. Some human and physical environment factors played statistical significant roles in different periods during SARS epidemics. An efficient algorithm was developed to solve SIR model directly, enabling the estimation of epidemic parameters from SIR and early forecast.

Algorithms↗

PubMed2005

[Selectivity and individualization of transpedicular balloon kyphoplasty for aged osteoporotic spinal fractures].

OBJECTIVE: To investigate the selectivity and individualization of transpedicular balloon kyphoplasty for aged osteoporotic spinal fracture. METHODS: Twenty-two consecutive procedures were performed in 17 aged patients with osteoporotic spinal compression fractures from April 2002 to June 2004. The signal changes in different sequences were confirmed by magnetic resonance imaging before the procedures. This operation involved the percutaneous insertion of two inflatable bone tamps into a fractured vertebral body transpedicularly under fluoroscopic guidance. Every patient was treated individually, according to the results of radiography and CT scan before operation. Preoperative and postoperative complications, visual analogue scale, and radiographic findings such as vertebral height and Cobb angle were recorded and analyzed. RESULTS: All patients tolerated the procedure well with immediate relief of their back pain in 24 hours. There was no leakage of cement into the epidura. The mean loss percent of the anterior and middle vertebral heights were (35.32 +/- 13.15)% and (27.53 +/- 12.61)% before operation, and (14.21 +/- 12.43)% and (16.2 +/- 7.5)% after operation. The height restoration of vertebra was confirmed by X-ray after the procedure (P < 0.01). The mean kyphosis was improved from (25.3 +/- 4.2) degrees to (8.6 +/- 5.1) degrees. No complications occurred. No patient had nerve injury. The patients were allowed to walk next day after the procedure. CONCLUSION: The selectivity and individualization of transpedicular balloon kyphoplasty for aged osteoporotic spinal fractures has satisfactory short-term clinical efficacy. It is also an effective way to prevent complications.

Aged↗

PubMed2004

[The contrast study between single and double balloon bilateral dilatation of kyphoplasty].

OBJECTIVE: To contrast single and double balloon-inflated kyphoplasty for vertebral compression fractures (VCFs) and evaluate its clinical efficacy. METHODS: From May 2000 to May 2004, 90 consecutive procedures were performed in 58 patients who suffered from painful vertebral compression fractures, transferring tumour and angioma. Ninety vertebrae were inflated while 62 as A group were double balloon and 28 as B group were single balloon, fracture reduction and bone cement augmentation. Preoperative and postoperative symptom levels, variables, complications were recorded and the vertebral height and Cobb angle were measured and analyzed. RESULTS: All patients' pain was alleviated or disappeared without syndrome, and the vertebral height and Cobb angle of both groups were improved. The average recovery rate was 72.6% (22.9% approximately 100%), Cobb angle from 17.9 degrees (3.1 degrees approximately 31.6 degrees ) were corrected to 9.6 degrees (0.6 degrees approximately 28.2 degrees ), the average angle was 8.7 degrees (0.3 degrees approximately 27.2 degrees ), and the contrast between preoperative and postoperative showed obvious differences (P <0.001). The average recovery rate of A group was 77.6% (55.3% approximately 100%), B group was 64.3% (22.9% approximately 100%). The average postoperative Cobb angle of A group was 9.9 degrees (0.3 degrees approximately 27.2 degrees ), B group was 8.6 degrees (0.6 degrees approximately 19.8 degrees ) (P >0.05). CONCLUSIONS: As a promising minimally invasive surgery, balloon kyphoplasty can provide early relief of pain and improve the function as well as spinal alignment in treatment of painful compression fracture owing to recovering the vertebral height and Cobb angle of the vertebral body. Single balloon-inflated kyphoplasty can improve VCFs as double balloon.

Adult↗

PubMed2004

Exploratory spatial data analysis for the identification of risk factors to birth defects.

BACKGROUND: Birth defects, which are the major cause of infant mortality and a leading cause of disability, refer to "Any anomaly, functional or structural, that presents in infancy or later in life and is caused by events preceding birth, whether inherited, or acquired (ICBDMS)". However, the risk factors associated with heredity and/or environment are very difficult to filter out accurately. This study selected an area with the highest ratio of neural-tube birth defect (NTBD) occurrences worldwide to identify the scale of environmental risk factors for birth defects using exploratory spatial data analysis methods. METHODS: By birth defect registers based on hospital records and investigation in villages, the number of birth defects cases within a four-year period was acquired and classified by organ system. The neural-tube birth defect ratio was calculated according to the number of births planned for each village in the study area, as the family planning policy is strictly adhered to in China. The Bayesian modeling method was used to estimate the ratio in order to remove the dependence of variance caused by different populations in each village. A recently developed statistical spatial method for detecting hotspots, Getis's 7, was used to detect the high-risk regions for neural-tube birth defects in the study area. RESULTS: After the Bayesian modeling method was used to calculate the ratio of neural-tube birth defects occurrences, Getis's statistics method was used in different distance scales. Two typical clustering phenomena were present in the study area. One was related to socioeconomic activities, and the other was related to soil type distributions. CONCLUSION: The fact that there were two typical hotspot clustering phenomena provides evidence that the risk for neural-tube birth defect exists on two different scales (a socioeconomic scale at 6.84 km and a soil type scale at 22.8 km) for the area studied. Although our study has limited spatial exploratory data for the analysis of the neural-tube birth defect occurrence ratio and for finding clues to risk factors, this result provides effective clues for further physical, chemical and even more molecular laboratory testing according to these two spatial scales.

Bayes Theorem↗

PubMed2002

DNA cleavage by aromatic amines.

A series of aryl amines was found to induce cleavage of DNA. Subsequent refinement led to an efficient family of dimeric derivatives capable of cleavage at low concentration. Initial investigations suggest this is an unprecedented mode of DNA cleavage, which may be ultimately applied to the development of sequence-specific agents.

Amines↗