Shanghai Academy of Science & Technology

DNA methylation in short homeobox gene 2 (SHOX2) and RAS association domain family protein 1 (RASSF1A) shows significant auxiliary diagnostic value for early-stage lung cancer. However, the detection accuracy is frequently compromised because of the complexity of the analytical procedures. This pilot external quality assessment (EQA) study evaluated the performance of methylated SHOX2 (mSHOX2) and methylated RASSF1A (mRASSF1A) detection across clinical laboratories in China. A sample panel was prepared containing two mSHOX2-positive samples, one mRASSF1A-positive sample, one mSHOX2 and mRASSF1A double-positive sample, and one negative sample. The panel was randomly coded and distributed to clinical laboratories for mSHOX2 and mRASSF1A detection in 2023 and 2024. The returned results were compared and scored to evaluate laboratory performance. The sample panel demonstrated sufficient stability and applicability. Results were collected from 21 laboratories in 2023 and 29 laboratories in 2024. Approximately 90.5 % (19/21) and 75.9 % (22/29) laboratories achieved correct results in 2023 and 2024, respectively. Out of the 105 results in 2023 and 145 results in 2024, 1 false negative and 3 false positives were observed in 2023 and 6 false negatives and 12 false positives in2024. This two-round EQA study in China emphasizes the need for improvement in the performance of mSHOX2 and mRASSF1A methylation detection. These results underscore the critical role of EQA schemes in monitoring and improving the detection quality in clinical laboratories. To address the challenges in mSHOX2 and mRASSF1A detection, targeted recommendations are proposed to enhance detection accuracy and reliability.

Zero-knowledge proof (ZKP) is a widely used privacy-preserving technology, where multiscalar multiplication (MSM) accounts for over 70% of the computational workload. The acceleration of MSM can enhance the overall performance of ZKP, making it a focal point of community attention. However, in practical applications involving the deployment of multiple MSM accelerators, existing designs often overlook strategies for optimizing bandwidth and area efficiency. To address this, we propose Myosotis, an efficiently pipelined and parameterized MSM architecture. By sharing input data and allocating cache effectively, it mitigates average transmission bandwidth in runtime. Myosotis also supports the use of multiple point addition (PADD) units to achieve performance gains, balancing area overhead and latency for improved area efficiency. Different parameter selection enables a tradeoff between the performance, area, and bandwidth of the MSM accelerator. When benchmarking with MSM degrees between <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$2^{18}$ </tex-math></inline-formula> and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$2^{26}$ </tex-math></inline-formula>, our proposed baseline design achieves up to <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$3.32\times $ </tex-math></inline-formula> and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$6.72\times $ </tex-math></inline-formula> speedups over state-of-the-art FPGA and ASIC designs. Compared to the baseline, Myosotis with two window MSMs and one PADD unit reduces bandwidth demand by 43% while maintaining similar area and latency. On the other hand, Myosotis with three window MSMs and two PADD units decreases latency by 43% and bandwidth by 17%, with only a 9% area increase.

Abstract The objective of this study was to analyze the status of insect diversity in Shirpur, Dhule of Maharashtra. Various insect orders were collected and identified to assess their abundance and diversity across different habitats in Shirpur. Specimens were collected using net sweeping, yellow pan trapping, and host rearing methods from agricultural fields, recreation parks and forest areas. Over the course of the survey during 2022 to 2024, a total of 2,781 insects representing 21 different orders were collected. Hymenopterans dominated the diversity accounting for 516 specimens, followed by Hemipterans (478), Coleopterans (446), and Lepidopterans (395). Mecopterans were least represented while Collembola and Anoplura represented five specimens each. Crop-pests dominated the collection accounting for 54% followed by 34% beneficial insects, 7% household pests and 5% domestic animal pests. High crop-pest population and fairly rich beneficial insect populations signify co-evolution of pest-beneficial insect interactions in this agro-ecosystem.

Laser shock peening is an effective surface technology for improving the surface mechanical properties of metals. Many studies have been performed to process different kinds of metallic material that can induce compressive residual stress in the top layer of samples, which would extend the fatigue life of metal parts in the industry. The titanium alloy samples are treated by laser shock peening with water layer as constraint layer and without protective coating in this research, after which the titanium alloy samples are observed and analyzed with a scanning electron microscope, hardness tester, laser confocal microscope, and wear tester. The surface roughness, surface microstructure, and other properties of untreated and treated titanium alloy are compared to study the effect on titanium alloy of laser shock peening process without protective coating.

The high morbidity and mortality of heart disease present a significant threat to human health. The development of methods for the quick and accurate diagnosis of heart diseases, enabling their effective treatment, has become a key issue of concern. Right ventricular (RV) segmentation from cine cardiac magnetic resonance (CMR) images plays a significant role in evaluating cardiac function for clinical diagnosis and prognosis. However, due to the complex structure of the RV, traditional segmentation methods are ineffective for RV segmentation. In this paper, we propose a new deep atlas network to improve the learning efficiency and segmentation accuracy of a deep learning network by integrating multi-atlas. First, a dense multi-scale U-net (DMU-net) is presented to acquire transformation parameters from atlas images to target images. The transformation parameters map the atlas image labels to the target image labels. Second, using a spatial transformation layer, the atlas images are deformed based on these parameters. Finally, the network is optimized by backpropagation with two loss functions where the mean squared error function (MSE) is used to measure the similarity of the input images and transformed images. Further, the Dice metric (DM) is used to quantify the overlap between the predicted contours and the ground truth. In our experiments, 15 datasets are used in testing, and 20 cine CMR images are selected as atlas. The mean values and standard deviations for the DM and Hausdorff distance are 0.871 and 4.67mm, 0.104 and 2.528mm, respectively. The correlation coefficients of endo-diastolic volume, endo-systolic volume, ejection fraction, and stroke volume are 0.984, 0.926, 0.980, and 0.991, respectively, and the mean differences between all of the mentioned parameters are 3.2, -1.7, 0.02, and 4.9, respectively. Most of these differences are within the allowable range of 95%, indicating that the results are acceptable and show good consistency. The segmentation results obtained in this method are compared with those obtained by other methods that provide satisfactory performance. The other methods provide better segmentation effects at the base, but either no segmentation or the wrong segmentation at the top, which demonstrate that the deep atlas network can improve top-area segmentation accuracy. Our results indicate that the proposed method can achieve better segmentation results than the previous methods, with both high relevance and consistency, and has the potential for clinical application.

Abstract Adolescent idiopathic scoliosis (AIS) is the most common pediatric musculoskeletal disorder worldwide, characterized by atypical spine curvatures in otherwise healthy children. Human genetic studies have identified candidate genes associated with AIS, however, only a few of these genes have been shown to recapitulate adult-viable scoliosis in animal models. To further define susceptibility loci for AIS, we performed whole exome sequencing on a cohort of 195 Han Chinese AIS patients and 229 healthy controls. We identified members of the axonemal dynein family associated with both sporadic and familial AIS. We demonstrate that disruption of the dynein axonemal heavy chain 10 (dnah10) gene results in recessive adult-viable scoliosis in zebrafish. These dnah10 mutant zebrafish display reduced ependymal cilia beating and a disassembly of the Reissner fiber in the hindbrain and spinal canal, concurrent with the onset of body curvatures. Altogther, these results demonstrate that mutations in axonemal dynein genes are linked with human AIS and suggest that ependymal cell cilia function plays an essential role in maintaining spine alignment in humans.

The classification of immune subtypes was based on immune signatures highlighting the tumor immuno-microenvironment. It was found that immune subtypes associated with mutation and expression patterns in the tumor. How the intrinsic genetic and transcriptomic alterations contribute to the immune subtypes and how to select drug combinations from both targeted drugs and immune therapeutic drugs according to different immune subtypes are still not clear. Through statistical analysis of genetic alterations and transcriptional profiles of breast invasive carcinoma (BRCA) samples, we found significant differences in the number of somatic missense mutations and frameshift deletions among the different immune subtypes. The high mutation load for somatic missense mutations and frameshift deletions may be explained by the high frequency of mutations and high expression of DNA double-strand break repair pathway genes. Extensive analysis of signaling pathways in both the genetic and transcriptomic levels reveals significantly altered pathways such as tumor protein Tumor Protein P53 (TP53) and receptor tyrosine kinase (RTK)/RAS signaling pathways among different subtypes. Drug targets in the signaling pathways such as mitogen-activated protein kinase kinase kinase 1 (MAP3K1) and Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Alpha (PIK3CA) show genetic alteration in specific subtypes, which may be potential targets for patients of a specific subtype. More drug targets which show transcriptional difference among immune subtypes were discovered, such as cyclin-dependent kinase (CDK)4, CDK6, Erb-B2 receptor tyrosine kinase 2 (ERBB2), etc. Moreover, differences in functional activity between tumor growth and immune-related pathways also elucidate the extrinsic factors of differences in prognosis and suggest potential drug combinations for different immune subtypes. These results help to explain how intrinsic alterations are associated with the immune subtypes and provide clues for possible combination therapy for different immune subtypes.