Multi-scale nested UNet with transformer for colorectal polyp segmentation.

BACKGROUND: Polyp detection and localization are essential tasks for colonoscopy. U-shape network based convolutional neural networks have achieved remarkable segmentation performance for biomedical images, but lack of long-range dependencies modeling limits their receptive fields. PURPOSE: Our goal was to develop and test a novel architecture for polyp segmentation, which takes advantage of learning local information with long-range dependencies modeling. METHODS: A novel architecture combining with multi-scale nested UNet structure integrated transformer for polyp segmentation was developed. The proposed network takes advantage of both CNN and transformer to extract distinct feature information. The transformer layer is embedded between the encoder and decoder of a U-shape net to learn explicit global context and long-range semantic information. To address the challenging of variant polyp sizes, a MSFF unit was proposed to fuse features with multiple resolution. RESULTS: Four public datasets and one in-house dataset were used to train and test the model performance. Ablation study was also conducted to verify each component of the model. For dataset Kvasir-SEG and CVC-ClinicDB, the proposed model achieved mean dice score of 0.942 and 0.950 respectively, which were more accurate than the other methods. To show the generalization of different methods, we processed two cross dataset validations, the proposed model achieved the highest mean dice score. The results demonstrate that the proposed network has powerful learning and generalization capability, significantly improving segmentation accuracy and outperforming state-of-the-art methods. CONCLUSIONS: The proposed model produced more accurate polyp segmentation than current methods on four different public and one in-house datasets. Its capability of polyps segmentation in different sizes shows the potential clinical application.

Noncontact Manipulation of Intracellular Structure Based on Focused Surface Acoustic Waves.

Cell orientation is essential in many applications in biology, medicine, and chemistry, such as cellular injection, intracellular biopsy, and genetic screening. However, the manual cell orientation technique is a trial-and-error approach, which suffers from low efficiency and low accuracy. Although several techniques have improved these issues to a certain extent, they still face problems deforming or disrupting cell membranes, physical damage to the intracellular structure, and limited particle size. This study proposes a noncontact and noninvasive cell orientation method that rotates a cell using surface acoustic waves (SAWs). To realize the acoustic cell orientation process, we have fabricated a microdevice consisting of two pairs of focused interdigital transducers (FIDTs). Instead of rotating the entire cell, the proposed method rotates the intracellular structure, the cytoplasm, directly through the cell membrane by acoustic force. We have tested the rotational manipulation process on 30 zebrafish embryos. The system was able to orientate a cell to a target orientation with a one-time success rate of 93%. Furthermore, the postoperation survival rate was 100%. Our acoustic rotational manipulation technique is noninvasive and easy to use, which provides a starting point for cell-manipulation-essential tasks, such as single-cell analysis, organism studies, and drug discovery.

Human γδ T cells induce CD8+ T cell antitumor responses via antigen-presenting effect through HSP90-MyD88-mediated activation of JNK.

Human Vγ9Vδ2 T cells have attracted considerable attention as novel alternative antigen-presenting cells (APCs) with the potential to replace dendritic cells in antitumor immunotherapy owing to their high proliferative capacity and low cost. However, the utility of γδ T cells as APCs to induce CD8+ T cell-mediated antitumor immune response, as well as the mechanism by which they perform APC functions, remains unexplored. In this study, we found that activated Vγ9Vδ2 T cells were capable of inducing robust CD8+ T cell responses in osteosarcoma cells. Activated γδ T cells also effectively suppressed osteosarcoma growth by priming CD8+ T cells in xenograft animal models. Mechanistically, we further revealed that activated γδ T cells exhibited increased HSP90 production, which fed back to upregulate MyD88, followed by JNK activation and a subsequent improvement in CCL5 secretion, leading to enhanced CD8+ T cell cross-priming. Thus, our study suggests that Vγ9Vδ2 T cells represent a promising alternative APC for the development of γδ T cell-based tumor immunotherapy.

Compartmentalized Janus droplets of photoresponsive cholesteric liquid crystals and poly(dimethylsiloxane)-based oligomers.

A new kind of Janus droplet containing photoresponsive cholesteric liquid crystals (CLCs) was fabricated for the first time and their formation, compartment structure, mesophase texture and function were thoroughly investigated. In the droplets, the CLC compartments included a typical nematic LC (4'-pentyl-4-biphenylcarbonitrile) doped with an azobenzene-containing chiral dopant, and the other compartments were formed of a poly(dimethylsiloxane)-based oligomer. Janus droplets were fabricated through microphase separation of the incompatible components in chloroform solution dispersed in an aqueous medium, induced by slow evaporation of chloroform. The mesophase structures of the CLC phase in Janus droplets, both suspended in aqueous medium and spreading on substrates, were controlled by the bulk elastic free energy of the CLC phase, surface anchoring and confining geometries. The helix pitch of the cholesteric phase in the droplets was determined by the doping concentration of the chiral dopant. For the suspended Janus droplets with the helix pitch obviously smaller than the droplet sizes, the CLC compartments mainly possessed a bipolar structure instead of the Frank-Pryce structure typically observed on CLC droplets. After the Janus droplets spread on the substrates, the CLC compartments changed to crescent shapes due to the different wettability characteristics of the two compartments, and the formed stable and metastable CLC configurations were distinctively different from those in the suspensions. Interestingly, when the Janus droplets spreading on substrates were irradiated with a laser beam (λ = 488 nm) of low intensity, the directors in the CLC compartments rearranged to form fingerprint structures with minimum total energy.

Photoinduced mass transfer of azo polymers from micrometer to submillimeter studied by a real-time single particle strategy.

Photoinduced mass transfer of azo polymers is a fascinating function with potential applications in areas ranging from photonics and nanofabrication to cell biology. However, the true nature of this unique effect still remains elusive in many aspects due to its puzzling mechanism and lack of a way for real-time observation. This work presents a new strategy to study the photoinduced mass transfer through in situ optical microscopic observation and videoing on single particles under laser irradiation. By inspecting the shape evolution processes of the particles from the side view, both the scale and direction of the mass transfer can be well characterized in a real-time manner, which shows great advantages for carrying out the systematic investigation. The mass transfer behaviour was thus investigated using the microspheres with diameters (D) ranging from micrometer to submillimeter. The mass transfer in the direction of the electric vibration was observed to occur in different scales for azo polymers with different degrees of functionalization (DFs) controlled by the light penetration depths. With the varied combinations of particle sizes and DFs, the particles with diversified shape-anisotropy and complex morphologies were generated by the mass transfer. For the microspheres with sizes in micrometer and submillimeter scales, those formed from the azo polymers with extremely high DF (100%) and extremely low DF (1%) respectively exhibited the most efficient mass transfer to cause significant shape deformations. With the optical and thermal simulations, these observations are well rationalized by considering the optical power distribution, energy utilization efficiency and heat dissipation route. This study not only provides deep insight into the photoinduced mass transfer behavior, but also extends the mass transfer scale of the particles from micrometer to submillimeter for the first time.

Bone combined cement grafting in giant cell tumor around the knee reduces mechanical failure.

OBJECTIVES: The aims of our study are (1) to explore the risk factors of mechanical failure (MF), (2) to figure out an index to evaluate this risk, and (3) to select an optimal reconstruction strategy to reduce this risk. METHODS: We retrospectively reviewed 104 patients from Dec. 2008 to Mar. 2016, undergone extensive knee curettages in our institution. Radiographs and post-operative interviews were used to classified cases of MF. Relative factors (age, tumor location, the invaded area, etc.) were also collected and analyzed by SPSS software. RESULTS: Thick subchondral bony layer (p = 0.006) and combined grafting of the cement and bone (p = 0.006) had lower risk of mechanical failure. Mechanical failure appeared to happen in the femur (p = 0.012) more easily. The ROC curve (AUC = 0.722) reveals that less post-operative bony layer (≤ 3.3 mm) is more likely to cause mechanical failure. The Kaplan-Meier survival curve showing increased survival in those patients after a combination grafting surgery (HR, 3.799; p = 0.006). CONCLUSION: Based on our study results, combined grafting of the cement and bone reduced the risk of mechanical failure in the knee due to the thin subchondral bone layer (SCB), especially in the femur.

HepaRG culture in tethered spheroids as an in vitro three-dimensional model for drug safety screening.

Conventional two-dimensional (2D) monolayer cultures of HepaRG cells allow in vitro maintenance of many liver-specific functions. However, cellular dedifferentiation and functional deterioration over an extended culture period in the conventional 2D HepaRG culture have hampered its applications in drug testing. To address this issue, we developed tethered spheroids of HepaRG cells on Arg-Gly-Asp (RGD) and galactose-conjugated substratum with an optimized hybrid ratio as an in vitro three-dimensional (3D) human hepatocyte model. The liver-specific gene expression level and drug metabolizing enzyme activities in HepaRG-tethered spheorids were markedly higher than those in 2D cultures throughout the culture period of 7 days. The inducibility of three major cytochrome P450 (CYP) enzymes, namely CYP1A2, CYP2B6 and CYP3A4, was improved in both mRNA and activity level in tethered spheroids. Drug-induced cytotoxic responses to model hepatotoxins (acetaminophen, chlorpromazine and ketoconazole) in tethered spheroids were comparable to 2D cultures as well as other studies in the literature. Our results suggested that the HepaRG-tethered spheroid would be an alternative in vitro model suitable for drug safety screening.

Design, synthesis and biological evaluation of metronidazole-thiazole derivatives as antibacterial inhibitors.

A series of metronidazole­thiazole derivatives has been designed, synthesized and evaluated as potential antibacterial inhibitors. All the synthesized compounds were determined by elemental analysis, (1)H NMR and MS. They were also tested for antibacterial activity against Escherichia coli, Bacillus thuringiensis, Bacillus subtilis and Pseudomonas aeruginosa as well as for the inhibition to FabH. The results showed that compound 5 e exhibited the most potent inhibitory activity against E. coli FabH with IC50 of 4.9 lM. Molecular modeling simulation studies were performed in order to predict the biological activity of proposed compounds. Toxicity assay of compounds 5 a, 5 b, 5 d, 5 e, 5 g and 5 i showed that they were noncytotoxic against human macrophage. The results revealed that these compounds offered remarkable viability.

Design, synthesis and biological evaluation of metronidazole-thiazole derivatives as antibacterial inhibitors.

A series of metronidazole-thiazole derivatives has been designed, synthesized and evaluated as potential antibacterial inhibitors. All the synthesized compounds were determined by elemental analysis, 1H NMR and MS. They were also tested for antibacterial activity against Escherichia coli, Bacillus thuringiensis, Bacillus subtilis and Pseudomonas aeruginosa as well as for the inhibition to FabH. The results showed that compound 5e exhibited the most potent inhibitory activity against E. coli FabH with IC50 of 4.9µM. Molecular modeling simulation studies were performed in order to predict the biological activity of proposed compounds. Toxicity assay of compounds 5a, 5b, 5d, 5e, 5g and 5i showed that they were noncytotoxic against human macrophage. The results revealed that these compounds offered remarkable viability.

Colorectal polyp segmentation with denoising diffusion probabilistic models.

Early detection of polyps is essential to decrease colorectal cancer(CRC) incidence. Therefore, developing an efficient and accurate polyp segmentation technique is crucial for clinical CRC prevention. In this paper, we propose an end-to-end training approach for polyp segmentation that employs diffusion model. The images are considered as priors, and the segmentation is formulated as a mask generation process. In the sampling process, multiple predictions are generated for each input image using the trained model, and significant performance enhancements are achieved through the use of majority vote strategy. Four public datasets and one in-house dataset are used to train and test the model performance. The proposed method achieves mDice scores of 0.934 and 0.967 for datasets Kvasir-SEG and CVC-ClinicDB respectively. Furthermore, one cross-validation is applied to test the generalization of the proposed model, and the proposed methods outperformed previous state-of-the-art(SOTA) models to the best of our knowledge. The proposed method also significantly improves the segmentation accuracy and has strong generalization capability.

A SAW-Based Programmable Controlled RNA Detecting Device: Rapid In Situ Cytolysis-RNA Capture-RNA Release-PCR in One Mini Chamber.

Viral RNA detection is crucial in preventing and treating early infectious diseases. Traditional methods of RNA detection require a large amount of equipment and technical personnel. In this study, proposed a programmable controlled surface acoustic wave (SAW)-based RNA detecting device has been proposed. The proposed device can perform the entire viral RNA detection process, including cell lysis by cell-microparticle collision through SAW-induced liquid whirling, RNA capture by SAW-suspended magnetic beads, RNA elution through SAW-induced high streaming force, and PCR thermal cycling through SAW-generated heat. The device has completed all RNA detection steps in one mini chamber, requiring only 489 µl reagents for RNA extraction, much smaller than the amount used in manual RNA extraction (2065 µl). The experimental results have shown that PCR results from the device are comparable to those achieved via commercial qPCR instrumental detection. This work has demonstrated the potential of SAW-based lab-on-a-chip devices for point-of-care testing and provided a novel approach for rapidly detecting infectious diseases.

An On-Demand Collaborative Innate-Adaptive Immune Response to Infection Treatment.

Deep tissue infection is a common clinical issue and therapeutic difficulty caused by the disruption of the host antibacterial immune function, resulting in treatment failure and infection relapse. Intracellular pathogens are refractory to elimination and can manipulate host cell biology even after appropriate treatment, resulting in a locoregional immunosuppressive state that leads to an inadequate response to conventional anti-infective therapies. Here, a novel antibacterial strategy involving autogenous immunity using a biomimetic nanoparticle (NP)-based regulating system is reported to induce in situ collaborative innate-adaptive immune responses. It is observed that a macrophage membrane coating facilitates NP enrichment at the infection site, followed by active NP accumulation in macrophages in a mannose-dependent manner. These NP-armed macrophages exhibit considerably improved innate capabilities, including more efficient intracellular ROS generation and pro-inflammatory factor secretion, M1 phenotype promotion, and effective eradication of invasive bacteria. Furthermore, the reprogrammed macrophages direct T cell activation at infectious sites, resulting in a robust adaptive antimicrobial immune response to ultimately achieve bacterial clearance and prevent infection relapse. Overall, these results provide a conceptual framework for a novel macrophage-based strategy for infection treatment via the regulation of autogenous immunity.

Multiple influence of immune cells in the bone metastatic cancer microenvironment on tumors.

Bone is a common organ for solid tumor metastasis. Malignant bone tumor becomes insensitive to systemic therapy after colonization, followed by poor prognosis and high relapse rate. Immune and bone cells in situ constitute a unique immune microenvironment, which plays a crucial role in the context of bone metastasis. This review firstly focuses on lymphatic cells in bone metastatic cancer, including their function in tumor dissemination, invasion, growth and possible cytotoxicity-induced eradication. Subsequently, we examine myeloid cells, namely macrophages, myeloid-derived suppressor cells, dendritic cells, and megakaryocytes, evaluating their interaction with cytotoxic T lymphocytes and contribution to bone metastasis. As important components of skeletal tissue, osteoclasts and osteoblasts derived from bone marrow stromal cells, engaging in 'vicious cycle' accelerate osteolytic bone metastasis. We also explain the concept tumor dormancy and investigate underlying role of immune microenvironment on it. Additionally, a thorough review of emerging treatments for bone metastatic malignancy in clinical research, especially immunotherapy, is presented, indicating current challenges and opportunities in research and development of bone metastasis therapies.

Osteocyte mitochondria inhibit tumor development via STING-dependent antitumor immunity.

Bone is one of the most common sites of tumor metastases. During the last step of bone metastasis, cancer cells colonize and disrupt the bone matrix, which is maintained mainly by osteocytes, the most abundant cells in the bone microenvironment. However, the role of osteocytes in bone metastasis is still unclear. Here, we demonstrated that osteocytes transfer mitochondria to metastatic cancer cells and trigger the cGAS/STING-mediated antitumor response. Blocking the transfer of mitochondria by specifically knocking out mitochondrial Rho GTPase 1 (Rhot1) or mitochondrial mitofusin 2 (Mfn2) in osteocytes impaired tumor immunogenicity and consequently resulted in the progression of metastatic cancer toward the bone matrix. These findings reveal the protective role of osteocytes against cancer metastasis by transferring mitochondria to cancer cells and potentially offer a valuable therapeutic strategy for preventing bone metastasis.

Surface-Acoustic-Wave (SAW)-Driven Device for Three-Dimensional Cell Manipulation.

Cell orientation is a necessary step in micromanipulation, which significantly affects the outcomes of cell manipulation. Existing cell orientation techniques include the trial-and-error manual approach that suffers from low efficiency, the mechanical contact approaches that have problems of being invasive, and non-contact approaches that are difficult to set up. OBJECTIVE: This paper proposes a system with a surface-acoustic wave (SAWs) to perform noninvasive cell orientation. METHODS: The system employed a SAW chip with a pair of interdigital transducers (IDTs) to rotate embryos around the X and Y axis using acoustic streaming force. Instead of rotating the entire embryos like other methods, the proposed system rotates the cytoplasm alone through the cell chorion. RESULTS: We evaluated the cellular structure recognition algorithm and the rotation control using 100 embryo images and 30 zebrafish embryos. The system successfully recognized all required cellar structures for visual feedback. Furthermore, it rotated all cells into the desired position, including 26 cases completed within 10s with an orientation angle error of less than 4°. All 30 embryos hatched after manipulation. CONCLUSION: The proposed technique can automatically rotate the cytoplasm through the cell chorion noninvasively. SIGNIFICANCE: The system provides a starting point for noninvasive cell manipulation tasks, such as fast intracellular structure scanning and analysis, and microinjection.

14, 15-EET alleviates neurological impairment through maintaining mitochondrial dynamics equilibrium via AMPK/SIRT1/FoxO1 signal pathways in mice with cerebral ischemia reperfusion.

AIM: To explore whether 14, 15-EET regulates mitochondrial dynamics to exert neuroprotective effects after cerebral ischemia-reperfusion and its underlying mechanisms. METHODS: The mouse middle cerebral artery occlusion reperfusion model was used to observe brain infarct volume and neuronal apoptosis by TTC staining and Tunel assay, modified neurological severity score to detect neurological impairment, HE staining and Nissl staining to observe neuron damage, western blot and immunofluorescence methods to detect the expression of mitochondrial dynamics-related proteins, transmission electron microscopy, and Golgi-Cox staining to detect mitochondrial morphology and neuronal dendritic spines. RESULTS: 14, 15-EET reduced the neuronal apoptosis and cerebral infarction volume induced by middle cerebral artery occlusion reperfusion (MCAO/R), inhibited the degradation of dendritic spines, maintained the structural integrity of neurons, and alleviated neurological impairment. Cerebral ischemia-reperfusion induces mitochondrial dynamics disorders, upregulates the expression of the mitochondrial division protein Fis 1, and inhibits the expression of mitochondrial fusion proteins MFN1, MFN2, and OPA1, while 14, 15-EET treatment reverses this process. Mechanistic studies have shown that 14, 15-EET promotes the phosphorylation of AMPK, upregulates the expression of SIRT1 and phosphorylation of FoxO1, thereby inhibiting mitochondrial division and promoting mitochondrial fusion, preserving mitochondrial dynamics, maintaining neuronal morphological and structural integrity, and alleviating neurological impairment induced by middle cerebral artery occlusion reperfusion. Compound C treatment diminishes the neuroprotective effect of 14, 15-EET following MCAO/R in mice. CONCLUSION: This study elucidates the novel neuroprotective mechanism of 14, 15-EET, providing a novel approach for the development of drugs based on mitochondrial dynamics.

Survey of open science practices and attitudes in the social sciences.

Open science practices such as posting data or code and pre-registering analyses are increasingly prescribed and debated in the applied sciences, but the actual popularity and lifetime usage of these practices remain unknown. This study provides an assessment of attitudes toward, use of, and perceived norms regarding open science practices from a sample of authors published in top-10 (most-cited) journals and PhD students in top-20 ranked North American departments from four major social science disciplines: economics, political science, psychology, and sociology. We observe largely favorable private attitudes toward widespread lifetime usage (meaning that a researcher has used a particular practice at least once) of open science practices. As of 2020, nearly 90% of scholars had ever used at least one such practice. Support for posting data or code online is higher (88% overall support and nearly at the ceiling in some fields) than support for pre-registration (58% overall). With respect to norms, there is evidence that the scholars in our sample appear to underestimate the use of open science practices in their field. We also document that the reported lifetime prevalence of open science practices increased from 49% in 2010 to 87% a decade later.

A deep supervised transformer U-shaped full-resolution residual network for the segmentation of breast ultrasound image.

PURPOSE: Breast ultrasound (BUS) is an important breast imaging tool. Automatic BUS image segmentation can measure the breast tumor size objectively and reduce doctors' workload. In this article, we proposed a deep supervised transformer U-shaped full-resolution residual network (DSTransUFRRN) to segment BUS images. METHODS: In the proposed method, a full-resolution residual stream and a deep supervision mechanism were introduced into TransU-Net. The residual stream can keep full resolution features from different levels and enhance features fusion. Then, the deep supervision can suppress gradient dispersion. Moreover, the transformer module can suppress irrelevant features and improve feature extraction process. Two datasets (dataset A and B) were used for training and evaluation. The dataset A included 980 BUS image samples and the dataset B had 163 BUS image samples. RESULTS: Cross-validation was conducted. For the dataset A, the proposed DSTransUFRRN achieved significantly higher Dice (91.04 ± 0.86%) than all compared methods (p < 0.05). For the dataset B, the Dice was lower than that for the dataset A due to the small number of samples, but the Dice of DSTransUFRRN (88.15% ± 2.11%) was significantly higher than that of other compared methods (p < 0.05). CONCLUSIONS: In this study, we proposed DSTransUFRRN for BUS image segmentation. The proposed methods achieved significantly higher accuracy than the compared previous methods.

Enhancement of T cell infiltration via tumor-targeted Th9 cell delivery improves the efficacy of antitumor immunotherapy of solid tumors.

Insufficient infiltration of T cells severely compromises the antitumor efficacy of adoptive cell therapy (ACT) against solid tumors. Here, we present a facile immune cell surface engineering strategy aiming to substantially enhance the anti-tumor efficacy of Th9-mediated ACT by rapidly identifying tumor-specific binding ligands and improving the infiltration of infused cells into solid tumors. Non-genetic decoration of Th9 cells with tumor-targeting peptide screened from phage display not only allowed precise targeted ACT against highly heterogeneous solid tumors but also substantially enhanced infiltration of CD8+ T cells, which led to improved antitumor outcomes. Mechanistically, infusion of Th9 cells modified with tumor-specific binding ligands facilitated the enhanced distribution of tumor-killing cells and remodeled the immunosuppressive microenvironment of solid tumors via IL-9 mediated immunomodulation. Overall, we presented a simple, cost-effective, and cell-friendly strategy to enhance the efficacy of ACT against solid tumors with the potential to complement the current ACT.

Cancer cells reprogram to metastatic state through the acquisition of platelet mitochondria.

Metastasis is the major cause of cancer deaths, and cancer cells evolve to adapt to various tumor microenvironments, which hinders the treatment of tumor metastasis. Platelets play critical roles in tumor development, especially during metastasis. Here, we elucidate the role of platelet mitochondria in tumor metastasis. Cancer cells are reprogrammed to a metastatic state through the acquisition of platelet mitochondria via the PINK1/Parkin-Mfn2 pathway. Furthermore, platelet mitochondria regulate the GSH/GSSG ratio and reactive oxygen species (ROS) in cancer cells to promote lung metastasis of osteosarcoma. Impairing platelet mitochondrial function has proven to be an efficient approach to impair metastasis, providing a direction for osteosarcoma therapy. Our findings demonstrate mitochondrial transfer between platelets and cancer cells and suggest a role for platelet mitochondria in tumor metastasis.