Non-contact and label-free biomechanical imaging: Stimulated Brillouin microscopy and beyond

Brillouin microscopy based on spontaneous Brillouin scattering has emerged as a unique elastography technique because of its merit of non-contact, label-free, and high-resolution mechanical imaging of biological cell and tissue. Recently, several new optical modalities based on stimulated Brillouin scattering have been developed for biomechanical research. As the scattering efficiency of the stimulated process is much higher than its counterpart in the spontaneous process, stimulated Brillouin-based methods have the potential to significantly improve the speed and spectral resolution of existing Brillouin microscopy. Here, we review the ongoing technological advancements of three methods, including continuous wave stimulated Brillouin microscopy, impulsive stimulated Brillouin microscopy, and laser-induced picosecond ultrasonics. We describe the physical principle, the representative instrumentation, and biological application of each method. We further discuss the current limitations as well as the challenges for translating these methods into a visible biomedical instrument for biophysics and mechanobiology

Bigeye tuna fishing ground in relation to thermocline in the Western and Central Pacific Ocean using Argo data

444-451The relationship beween thermocline and bigeye tuna (Thunnus obesus) fishing grounds in the Western and Central Pacific Ocean was evaluated by Argo data and monthly CPUE (catch per unit effort). The generalized additive model indicated evidence of nonlinear relationships between CPUE and six thermocline characteristics. The results suggested that the fishing grounds distributed where the upper boundary temperature was about 26 ºC and the upper boundary depth values between 70 and 100 m. The fishing grounds located between the two high value shapes of the lower boundary depth of thermocline, if the depth was >300 or <150 m, the CPUE tended to be low. The lower boundary temperature of the thermocline in the fishing grounds was lower than 13 ºC. Conversely, if the temperature was higher than 17 ºC, the hooking rates were very low. The strongest relationship between CPUE with thermocline thickness and thermocline strength was approximately at 60 m and 0.1 ºC/m. The optimum ranges for the upper boundary thermocline temperature and depth and the lower boundary thermocline temperature and depth, thermocline thickness and thermocline strength were between 26-29 ºC, 70-110 m, 11-13 ºC, 200-280 m, and 0.01-0.15 ºC/m, 60-80 m, respectively

Calculation of Nearly Singular Boundary Element Integrals in Thin Structures Using an Improved Exponential Transformation

In this work, an improved exponential transformation is presented for nearly singular boundary element integrals in problems of thin structures. Accurate evaluation of nearly singular integrals is an important issue in the implementation of boundary element method (BEM) for thin structures. In this paper, the exponential transformation, which was firstly developed to evaluate nearly singular integrals arising in 2D BEM, is extended into 3D BEM to deal with nearly singular integrals. Firstly, a novel (α,β) coordinate system is introduced. Then, the conventional distance function is modified into a new form in (α,β) coordinate system. Based on the refined distance function, finally, an improved exponential transformation is employed in the new coordinate system. Furthermore, to perform integrations on irregular elements, an adaptive integration scheme considering both the shape of element and the projection point associated with the improved transformation is proposed. Numerical examples are presented to verify the proposed method. Results demonstrate the accuracy and efficiency of our method. Moreover, the accuracy of our method is less sensitive to the position of the projection point than that of the traditional methods

Provable Representation with Efficient Planning for Partial Observable Reinforcement Learning

In most real-world reinforcement learning applications, state information is only partially observable, which breaks the Markov decision process assumption and leads to inferior performance for algorithms that conflate observations with state. Partially Observable Markov Decision Processes (POMDPs), on the other hand, provide a general framework that allows for partial observability to be accounted for in learning, exploration and planning, but presents significant computational and statistical challenges. To address these difficulties, we develop a representation-based perspective that leads to a coherent framework and tractable algorithmic approach for practical reinforcement learning from partial observations. We provide a theoretical analysis for justifying the statistical efficiency of the proposed algorithm, and also empirically demonstrate the proposed algorithm can surpass state-of-the-art performance with partial observations across various benchmarks, advancing reliable reinforcement learning towards more practical applications.Comment: The first two authors contribute equall

Research progress and prospects of utilizing carbon-based nanomaterials in enhanced oil recovery

Carbon-based nanomaterials have received heightened global interest by petroleum researchers because of their abundant stocks of necessary raw materials, ease of size control, readiness for modification, and high stability. In light of the practical demand for oil development, this study reviews the recent progress in the research of enhancing oil recovery using carbon-based nanomaterials of various dimensions, including carbon dots, carbon nanotubes, carbon nanofibers, and graphene and its derivatives. Moreover, the study elaborates on the application of these materials in high-efficiency oil displacement, profile control and water shutoff, as well as the fracturing process. The related challenges and solutions in practical oil exploration and development are analyzed, and the application prospects of these materials in future oil reservoirs and oilfields are predicted. This review provides valuable theoretical and experimental references for the large-scale application of carbon-based nanomaterials.Document Type: Invited reviewCited as: Shen, M., Zhang, C., Yan, X., Wang, L., Wu, Y., Jin, X. Research progress and prospects of utilizing carbon-based nanomaterials in enhanced oil recovery. Advances in Geo-Energy Research, 2024, 14(3): 201-214. https://doi.org/10.46690/ager.2024.12.0

Application of non-invasive methods of radiology to the osteoporosis

Early screening and timely treatment can effectively reduce the morbidity and mortality of the osteoporotic fractures, and hence efficient and accurate non-invasive radiological method is crucial. Non-invasive imaging methods of radiology frequently encounter less resistance in the promotion of therapeutic activities than invasive procedures like bone biopsy and perfusion imaging. Although dual-energy X-ray absorption has been established as the primary diagnostic method for osteoporosis, its efficacy is relatively constrained due to various parameters, and it is challenging to accurately depict the true status of bone structure. In recent years, radiological techniques have developed rapidly. Computed tomography, magnetic resonance imaging, quantitative ultrasound and other imaging techniques have been widely used in the diagnosis of osteoporosis in the research and clinical practices, which provides more comprehensive and detailed information about bone mineral density and bone structure for early diagnosis, treatment design and prognosis monitoring. As clinic and computer science crosstalk closely, it will become possible for artificial intelligence to assist or even independently perform imaging analysis and disease screening in image data base. This article reviews the individual characteristics and latest research progress of the non-invasive radiological techniques for the osteoporosis

25(OH)VitD and human endocrine and functional fertility parameters in women undergoing IVF/ICSI

Background: Vitamin D plays an important role in reproduction. Evidence shown that free 25-hydroxyvitamin D (25(OH)VitD) was more accurate than total 25(OH)VitD in reflecting the status of 25(OH)VitD during pregnancy. However, the relationship between free 25(OH)VitD and female fertility parameters has not been reported yet. Therefore, this study aims to compare the correlation of free and total 25(OH)VitD with fertility parameters in infertility females undergoing in vitro fertilization and embryo transfer (IVF-ET) or intracytoplasmic sperm injection (ICSI). Methods: According to the inclusion and exclusion criteria, 2569 infertility patients who received IVF-ET or ICSI treatment for the first time participated in this study. Five milliliter peripheral blood samples of the patients were collected on the day before embryo transfer (ET). Enzyme linked immunosorbent assay (ELISA) kits was used to detect free 25(OH)VitD and total 25(OH)VitD, and clinical information was collected. Spearman’s rho was used to evaluate the association between the variables. Results: The median (IQR) of free 25(OH)VitD was 4.71 (4.11-5.31) pg/mL and total 25(OH)VitD was 19.54 (16.52-22.83) ng/m. The correlation between them, however, was week (rho=0.311). Compared to total 25(OH)VitD, free 25(OH)VitD was slightly better correlated with basal follicle-stimulating hormone (FSH) (rho=0.041, P=0.036), basal estradiol (E2) (rho=0.089, P<0.001), anti-Müllerian hormone (AMH) (rho=-0.057, P=0.004), antral follicle count (AFC) (rho=-0.053, P=0.007), E2 (rho=-0.080, P<0.001), number of oocytes retrieval (rho=-0.079, P<0.001) and progesterone (P)/E2 on hCG trigger day (rho=0.081, P<0.001). Conclusions: Overall, there was only a rather weak correlation of free as well as total 25(OH)VitD with human endocrine and functional fertility parameters in women undergoing IVF/ICSI. Neither free nor total 25(OH)VitD seems to play a major role in human embryo implantation

ViMIC 2.0: an updated database of human disease-related viral mutations, integration sites, and multi-omics data

ViMIC 2.0 is an updated database that provides comprehensively curated data on virus mutations (VMs), viral integration sites (VISs), and multi-omics datasets related to human diseases. Leveraging expanding public data, ViMIC 2.0 significantly enhanced data scale, diversity, and analytical capabilities compared to the previous version. In terms of data volume, the number of virus types has increased from 8 to 28, VM entries have grown from 31 712 to 64 168, virus-related diseases expanded from 77 to 177, literature rose from 2539 to 6433, and omics datasets have substantially increased from 28 sets of single expression profile data to 255 sets of multi-omics data. In addition, ViMIC 2.0 has updated 9409 VISs, 173 048 sequences, newly incorporated sequencing types such as single-cell transcriptomic sequencing (scRNA-seq), and genome binding/occupancy profiling. Regarding the visualization module, ViMIC 2.0 now provides results of differential gene expression analysis for bulk RNA-seq or array, cell type annotation and gene feature plot for scRNA-seq data, and differential methylation analysis for methylation profiling, as well as peak annotation for ChIP-seq/ChIP-on-chip/ATAC-seq data. In summary, ViMIC 2.0 serves as a user-friendly, up-to-date, and well-maintained resource for the virology research community. ViMIC 2.0 is freely accessible at http://www.biomedinfo.cn/ViMIC2.0/index.php

Impact of apolipoprotein A1 on tumor immune microenvironment, clinical prognosis and genomic landscape in hepatocellular carcinoma

Background: Current knowledge on apolipoprotein A1 (APOA1) in hepatocellular carcinoma (HCC) is fragmented and even contradictory. Multi-dimensional analyses are required to comprehensively elucidate its value and underlying mechanism. Methods: We collected 49 RNA-seq datasets, 40 cell line types data and 70 scRNA pan-cancer datasets public available, including 17 HCC datasets (1754 tumor samples), and enrolled 73 pairs of HCC tissue and 516 blood samples independently from our clinics. APOA1 impacting on the HCC tumor microenvironment (TME) was analyzed using intensive data mining. Methylation sequencing, flow cytometry, quantitative PCR, western blot, immunohistochemistry and clinical chemistry assays were conducted for wet experimental investigation. Results: The APOA1 ontology fingerprint indicated that it played various crucial biological roles in HCC, primarily involved in cholesterol efflux. Consistent findings at histology, serology, and clinical follow-up revealed that high APOA1 was a good prognosis indicator of HCC. Hypermethylation in the APOA1 promoter region was found in clinical samples which is in accordance with the reduction of APOA1 in HCC. The cell cycle, DNA replication, mismatch repair pathways, and tumor cell proliferation were less observed in the HCC APOA1high subgroup. The favorable immunoregulatory abilities of APOA1 showed interesting findings: A positive correlation between APOA1 and anti-Tumor immune cells (NK, CD8+ T cells) and a negative association with immune cells exerting immunosuppressive effects, including M2 macrophages. Conclusion: This is an integrative multidimensional exploration of APOA1 using bioinformatics and experiments. Both the prognostic value and anti-Tumor effects based on APOA1 panoramic exploration in the HCC TME demonstrate a new potential clinical target for HCC assessment and intervention in the future.</p