Fusion of convolutional neural network with XGBoost feature extraction for predicting multi-constituents in corn using near infrared spectroscopy.

Near-infrared (NIR) spectroscopy has been widely utilized to predict multi-constituents of corn in agriculture. However, directly extracting constituent information from the NIR spectra is challenging due to many issues such as broad absorption band, overlapping and non-specific nature. To solve these problems and extract implicit features from the raw data of NIR spectra to improve performance of quantitative models, a one-dimensional shallow convolutional neural network (CNN) model based on an eXtreme Gradient Boosting (XGBoost) feature extraction method was proposed in this paper. The leaf node feature information in the XGBoost was encoded and reconstructed to obtain the implicit features of raw data in the NIR spectra. A two-parametric Swish (TSwish or TS) activation function was proposed to improve the performance of CNN, and the elastic net (EN) was also applied to avoid the overfitting problem of the CNN model. Performance of the developed XGBoost-CNN-TS-EN model was evaluated using two public NIR spectroscopy datasets of corn and soil, and the obtained determination coefficients (R2) for moisture, oil, protein, and starch of the corn on test set were 0.993, 0.991, 0.998, and 0.992, respectively, with that of the soil organic matter being 0.992. The XGBoost-CNN-TS-EN model exhibits superior stability, good prediction accuracy, and generalization ability, demonstrating its great potentials for quantitative analysis of multi-constituents in spectroscopic applications.

Detection of PCBs and OCPs in the Irtysh River Water (GC-MS/MS) and ecological risk assessment.

This study optimized a gas chromatography-tandem triple quadrupole mass spectrometry (GC-MS/MS) method for the determination of 21 persistent organic pollutants (POPs) in Irtysh River water, including 14 organochlorines (OCPs) and 7 polychlorinated biphenyls (PCBs). Factors such as column temperature ramping, selection of qualitative and quantitative ion pairs and collision energy were considered to achieve perfect separation and accurate quantification of all 21 target compounds. The limits of detection (LOD) for PCBs and OCPs ranged from 0.21 to 1.18 ng/L. Applying this method to detect POPs in the Irtysh River revealed concentrations of OCPs ranging from ND to 20.2 ng/L and PCBs from ND to 0.411 ng/L. Source analysis indicated that POPs in the Irtysh River mainly originate from historical industrial and agricultural activities, particularly the deliberate use of pesticides. To ensure ecological safety and human health, expanding the range of target analytes and monitoring periods is necessary. This study provides:•Qualitative and quantitative analysis methods for 7 PCBs and 14 OCPs.•Recoveries achieved ranged between 74.6 to 109 % with RSD less than 15 %.•Analysis of sources, transport pathways, accumulation status, and ecological risks of PCBs and OCPs in the Irtysh River.

Hydrogel based on M1 macrophage lysate and alginate loading with oxaliplatin for effective immunomodulation to inhibit melanoma progression, recurrence and metastasis.

Despite the monumental success of immunotherapy in treating melanoma clinically, it still confronts significant challenges, chiefly that singular immunomodulatory tactics are insufficient to suppress the recurrence and metastasis of melanoma. Herein, these challenges are addressed by a hydrogel based on M1 macrophage lysate and alginate (M1LMHA) loaded with oxaliplatin (OXA), named M1LMHA@OXA.The results obtained from scanning electron microscopy and confocal microscopy indicate that the structure and morphology of M1LMHA@OXA remain unchanged. Flow cytometry results reveal that M1LMHA@OXA significantly promotes the maturation of dendritic cells (DCs) and enhances the proliferation of T lymphocytes. In a subcutaneous melanoma transplant model, M1LMHA@OXA effectively suppressed tumor growth in comparison to OXA alone and M1LMHA alone. Flow cytometry demonstrated that M1LMHA@OXA markedly increased the number of mature DCs and CD8+ T cells at the tumor site, while significantly reducing the quantity of M2-like tumor-associated macrophages (TAM) and enhancing the presence of M1 macrophages. Enzyme-linked immunosorbent assay (ELISA) results indicated that following treatment with M1LMHA@OXA, the levels of interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) in the bloodstream of mice were significantly elevated, whereas interleukin-10 (IL-10) exhibited no significant difference. This outcome further corroborates the ability of M1LMHA@OXA to substantially bolster the immune capability of mice. Similar results have also been observed in a melanoma subcutaneous transplantation recurrence model, and optical imaging of the lungs of mice revealed that M1LMHA@OXA inhibited tumor metastasis to the lungs. Notably, M1LMHA@OXA exhibits an exceptional therapeutic effect on the growth, post-surgical recurrence, and metastasis of the B16F10 melanoma. Therefore, this study provides a straightforward strategy that leverages the cooperative regulation of multiple immune cells to thwart the proliferation, recurrence, and spread of melanoma.

Robotic anatomical resection for hepatocellular carcinoma located within segment 7 using the Glissonean approach.

Worldwide use of robotic-assisted hepatectomy has increased dramatically over the past two decades. The role of robotic liver surgery is still controversial, especially with respect to its long-term oncological outcomes in treating early-stage hepatocellular carcinoma (HCC). The Glissonean approach is a fundamental technique for anatomical resection using open and laparoscopic liver surgery. To our knowledge, there have been few reports on purely robotic anatomical segmentectomy 7 for HCC using the Glissonean approach have been described. The present study describes the technical details and surgical outcomes of totally robotic segmentectomy 7 using the Glissonean approach. Fourteen patients with HCC limited to segment 7 underwent segmentectomy 7 from January 2019 through April 2023 in our hospital. The surgical techniques, peri-operative, and oncological outcomes were analyzed. Purely robotic anatomical segmentectomy 7 using the Glissonean approach was safe and feasible with the technology described herein in all of the 14 patients. The peri-operative and oncological outcomes were better and/or comparable with those of other similar hepatic resections using open approach and/or laparoscopic approach. The median follow-up time was 18 months. Intrahepatic recurrence occurred in 2 (14.3%) patient within one year following surgery. The 3-year overall survival rate was 81%. Although technically challenging, the purely robotic segmentectomy 7 could be performed safely and simultaneously with oncological radicality using the Glissonean approach.

Detection of Road Risk Sources Based on Multi-Scale Lightweight Networks.

Timely discovery and disposal of road risk sources constitute the cornerstone of road operation safety. Presently, the detection of road risk sources frequently relies on manual inspections via inspection vehicles, a process that is both inefficient and time-consuming. To tackle this challenge, this paper introduces a novel automated approach for detecting road risk sources, termed the multi-scale lightweight network (MSLN). This method primarily focuses on identifying road surfaces, potholes, and scattered objects. To mitigate the influence of real-world factors such as noise and uneven brightness on test results, pavement images were carefully collected. Initially, the collected images underwent grayscale processing. Subsequently, the median filtering algorithm was employed to filter out noise interference. Furthermore, adaptive histogram equalization techniques were utilized to enhance the visibility of cracks and the road background. Following these preprocessing steps, the MSLN model was deployed for the detection of road risk sources. Addressing the challenges associated with two-stage network models, such as prolonged training and testing times, as well as deployment difficulties, this study adopted the lightweight feature extraction network MobileNetV2. Additionally, transfer learning was incorporated to elevate the model's training efficiency. Moreover, this paper established a mapping relationship model that transitions from the world coordinate system to the pixel coordinate system. This model enables the calculation of risk source dimensions based on detection outcomes. Experimental results reveal that the MSLN model exhibits a notably faster convergence rate. This enhanced convergence not only boosts training speed but also elevates the precision of risk source detection. Furthermore, the proposed mapping relationship coordinate transformation model proves highly effective in determining the scale of risk sources.

Advances in the preparation and application of cyclodextrin derivatives in food and the related fields.

Cyclodextrin (CD) derivatives have recently gained worldwide attention, which have versatile advantages and restrained the defects of parent CDs. The superior properties of CD derivatives in encapsulation, stabilization, and solubilization facilitate their application in food, biomedicine, daily chemicals, and textiles. In this review, the preparation, classification, and main benefits of CD derivatives are systematically introduced. By introducing targeted groups into the parent CD molecule, they exhibit significant improvement in their required characteristic. Besides, the important point closely related to application, the safety assessment, has also been highlighted. Most tested CD derivatives have been verified to be relatively safe in a limited dosage. Then, the applications of CD derivatives have been described in detail from the food to its related field. In food field, CD derivatives play an important role in the stability and bioavailability of bioactive compounds, control flavor release, and improve the antimicrobial and antioxidant properties of packaging materials. These advantages can also be expanded to the related field, offering innovative solutions that enhance product quality, human health, and environmental sustainability. This review highlights the broad applications and potential of CD derivatives, underscoring their role in driving advancements across multiple industries.

Total flavonoids of litchi Seed alleviates schistosomiasis liver fibrosis in mice by suppressing hepatic stellate cells activation and modulating the gut microbiomes.

Infection with Schistosoma japonicum (S. japonicum) is an important zoonotic parasitic disease that causes liver fibrosis in both human and domestic animals. The activation of hepatic stellate cells (HSCs) is a crucial phase in the development of liver fibrosis, and inhibiting their activation can alleviate this progression. Total flavonoids of litchi seed (TFL) is a naturally extracted drug, and modern pharmacological studies have shown its anti-fibrotic and liver-protective effects. However, the role of TFL in schistosomiasis liver fibrosis is still unclear. This study investigated the therapeutic effects of TFL on liver fibrosis in S. japonicum infected mice and explored its potential mechanisms. Animal study results showed that TFL significantly reduced the levels of Interleukin-1ß (IL-1ß), Tumor Necrosis Factor-α (TNF-α), Interleukin-4 (IL-4), and Interleukin-6 (IL-6) in the serum of S. japonicum infected mice. TFL reduced the spleen index of mice and markedly improved the pathological changes in liver tissues induced by S. japonicum infection, decreasing the expression of alpha-smooth muscle actin (α-SMA), Collagen I and Collagen III protein in liver tissues. In vitro studies indicated that TFL also inhibited the activation of HCSs induced by Transforming Growth Factor-ß1 (TGF-ß1) and reduced the levels of α-SMA. Gut microbes metagenomics study revealed that the composition, abundance, and functions of the mice gut microbiomes changed significantly after S. japonicum infection, and TLF treatment reversed these changes. Therefore, our study indicated that TFL alleviated granulomatous lesions and improved S. japonicum induced liver fibrosis in mice by inhibiting the activation of HSCs and by improving the gut microbiomes.

Principle and application of self-transcribing active regulatory region sequencing in enhancer discovery research.

Self-transcribing active regulatory region sequencing (STARR-seq) is a high-throughput sequencing method capable of simultaneously discovering and validating all enhancers within the genome. In this method, candidate sequences are inserted into plasmid vectors and electroporated into cells. Acting as both enhancers and target genes, the self-transcription of these sequences will also be enhanced by themselves. By sequencing the transcriptome and comparing the results with the non-inserted control, the locations and activity of enhancers can be determined. In traditional enhancer discovery strategies, the chromatin open regions and transcription active regions were sequenced and predicted as enhancers. However, the activity of these putative enhancers could only be validated one by one without a high-throughput method. STARR-seq solved this limitation, allowing simultaneous enhancers discovery and activity validation in a high-throughput manner. Since the introduction of STARR-seq, it has been widely used to discover enhancers and validate enhancer activity in a number of organisms and cells. In this review, we present the traditional enhancer prediction methods and the basic principles, development history, specific applications of STARR-seq, and its future prospects, aiming to provide a reference for researchers in related fields conducting enhancer studies.

High-sensitivity narrow­band T-shaped cantilever Fabry-perot acoustic sensor for photoacoustic spectroscopy.

Photoacoustic spectroscopy (PAS) has been rapidly developed and applied to different detection scenarios. The acoustic pressure detection is an important part in the PAS system. In this paper, an ultrahigh sensitivity Fabry-Perot acoustic sensor with a T-shaped cantilever was proposed. To achieve the best acoustic pressure effect, the dimension of the cantilever structure was designed and optimized by finite element analysis using COMSOL Multiphysics. Simulation results showed that the sensitivity of such T-shaped cantilever was 1.5 times higher than that based on a rectangular cantilever, and the resonance frequency of T-shaped cantilever were able to modulate from 800 Hz to 1500 Hz by adjusting the multi-parameter characteristics. Experimental sensing results showed that the resonance frequency of T-shaped Fabry-Perot acoustic sensor was 1080 Hz, yielding a high sensitivity of 1.428 µm/Pa, with a signal-to-noise ratio (SNR) of 84.8 dB and a detectable pressure limit of 1.9 µPa/Hz1/2@1 kHz. We successfully used such acoustic sensor to measure acetylene (C2H2) concentration in the PAS. The sensitivity of PAS for C2H2 gas was 3.22 pm/ppm with a concentration range of 50 ppm ∼100 ppm, and the minimum detection limit was 24.91ppb.

Enhancing cancer therapy: the integration of oncolytic virus therapy with diverse treatments.

As one of the significant challenges to human health, cancer has long been a focal point in medical treatment. With ongoing advancements in the field of medicine, numerous methodologies for cancer therapy have emerged, among which oncolytic virus therapy has gained considerable attention. However, oncolytic viruses still exhibit limitations. Combining them with various therapies can further enhance the efficacy of cancer treatment, offering renewed hope for patients. In recent research, scientists have recognized the promising prospect of amalgamating oncolytic virus therapy with diverse treatments, potentially surmounting the restrictions of singular approaches. The central concept of this combined therapy revolves around leveraging oncolytic virus to incite localized tumor inflammation, augmenting the immune response for immunotherapeutic efficacy. Through this approach, the patient's immune system can better recognize and eliminate cancer cells, simultaneously reducing tumor evasion mechanisms against the immune system. This review delves deeply into the latest research progress concerning the integration of oncolytic virus with diverse treatments and its role in various types of cancer therapy. We aim to analyze the mechanisms, advantages, potential challenges, and future research directions of this combination therapy. By extensively exploring this field, we aim to instill renewed hope in the fight against cancer.

Nano-enabled regulation of DNA damage in tumor cells to enhance neoantigen-based pancreatic cancer immunotherapy.

Low-expression antigens, especially neoantigens, pose a significant challenge in immunotherapy for low immunogenicity pancreatic cancer. Increasing the tumor mutation burden is crucial to enhance the expression of tumor antigens and improve tumor immunogenicity. However, the incomplete intervention in DNA stability hampers effective elevation of the tumor mutation burden, thus reducing the probability of neoantigen. To address this issue, we have developed a novel nano-regulator that intervenes in the DNA stability of tumor cells, thereby enhancing tumor mutations. This nano-regulator comprises metal-organic frameworks (MOFs) encapsulating DNA damage agent doxorubicin and DNA damage repair inhibitor siRNA-ATR, enabling simultaneous induction of DNA mutations and inhibition of their repair. Importantly, this regulator, named as MOFDOX&siATR, can modulate the tumor gene expression profile, induce the production of neoantigens of Atp8b1, and enhance the immunogenicity of pancreatic cancer. The characteristics of DNA stability intervention by MOFDOX&siATR hold promise for augmenting the immune response in low immunogenic tumors, making it a potential nanomedicine for the treatment of pancreatic cancer.

Sodium alginate hydrogel encapsulating microglia cell lysate subjected to serum starvation for mitigating glioma cells.

Glioma is the most common malignant tumor in the brain, accounting for over 80% of all primary intracranial tumors. The current clinical treatment has shown certain limitations. Although M1 type microglia can secrete various pro-inflammatory cytokines and are expected to be used for glioma treatment, direct use of microglia may lead to overactivation and trigger immune storms. Therefore, we first found that serum starvation can stimulate the transformation of microglia into M1 type. Subsequently, we found through comparative experiments that the inhibitory effect of microglial cell lysis medium on glioma cells was stronger than that of microglial cell culture medium. Finally, we successfully prepared sodium alginate hydrogel loaded with microglia lysis solution to achieve sustained inhibitory effect on the growth of glioma and avoid its proliferation.

Chemotactic recruitment of genetically engineered cell membrane-camouflaged metal-organic framework nanoparticles for ischemic osteonecrosis treatment.

Ischemic osteonecrosis, particularly glucocorticoid-induced osteonecrosis of the femoral head (GIONFH), is primarily due to the dysfunction of osteogenesis and angiogenesis. miRNA, as a therapeutic system with immense potential, plays a vital role in the treatment of various diseases. However, due to the unique microenvironmental structure of bone tissue, especially in the case of GIONFH, where there is a deficiency in the vascular system, it is challenging to effectively target and deliver to the ischemic osteonecrosis area. A drug delivery system assisted by genetically engineered cell membranes holds promise in addressing the challenge of targeted miRNA delivery. Herein, we leverage the potential of miR-21 in modulating osteogenesis and angiogenesis to design an innovative biomimetic nanoplatform system. First, we employed metal-organic frameworks (MOFs) as the core structure to load miR-21-m (miR-21-m@MOF). The nanoparticles were further coated with the membrane of bone marrow mesenchymal stem cells overexpressing CXCR4 (CM-miR-21-m@MOF), enhancing their ability to target ischemic bone areas via the CXCR4-SDF1 axis. These biomimetic nanocomposites possess both bone-targeting and ischemia-guiding capabilities, actively targeting GIONFH lesions to release miR-21-m into target cells, thereby silencing PTEN gene and activating the PI3K-AKT signaling pathway to regulate osteogenesis and angiogenesis. This innovative miRNA delivery system provides a promising therapeutic avenue for GIONFH and potentially other related ischemic bone diseases. STATEMENT OF SIGNIFICANCE.

Copper(II)-Based Nano-Regulator Correlates Cuproptosis Burst and Sequential Immunogenic Cell Death for Synergistic Cancer Immunotherapy.

Immunogenic cell death (ICD) of tumor cells serves as a crucial initial signal in the activation of anti-tumor immune responses, holding marked promise in the field of tumor immunotherapy. However, low immunogenicity tumors pose challenges in achieving complete induction of ICD, thereby limiting the response rates of immunotherapy in clinical patients. The emergence of cuproptosis as a new form of regulated cell death has presented a promising strategy for enhanced immunotherapy of low immunogenic tumors. To trigger cuproptosis, copper-ionophore elesclomol (ES) had to be employed for the copper-transporting-mediated process. Herein, we proposed a copper(II)-based metal-organic framework nanoplatform (Cu-MOF) to facilitate a cooperative delivery of encapsulated ES and copper (ES-Cu-MOF) to induce cuproptosis burst and enhance ICD of fibrosarcoma. Our results showed that the ES-Cu-MOF nano-regulator could effectively release Cu2+ and ES in response to the intracellular environment, resulting in elevated mitochondrial ROS generation and initiated cuproptosis of tumor cells. Furthermore, sequential ICDs were significantly triggered via the ES-Cu-MOF nano-regulator to activate the anti-tumor immune response. The results of tumor inhibition experiment indicated that the nano-regulator of ES-Cu-MOF obviously accumulated in the tumor site, inducing ICD for dendritic cell activation. This enabled an increased infiltration of cytotoxic CD8+ T cells and consequently enhanced antitumor immune responses for successfully suppressing fibrosarcoma growth. Thus, the copper(II)-based metal-organic framework nano-regulator offered a promising approach for inducing cuproptosis and cuproptosis-stimulated ICD for cancer immunotherapy.

Ensiled diet improved the growth performance of Tibetan sheep by regulating the rumen microbial community and rumen epithelial morphology.

The aim of this study was to investigate the effects of ensiled agricultural byproducts from Qinghai-Tibet plateau on growth performance, rumen microbiota, ruminal epithelium morphology, and nutrient transport-related gene expression in Tibetan sheep. Fourteen male Tibetan sheep were randomly assigned to one of two diets: an untreated diet (without silage inoculum, CON, n = 7) or an ensiled diet (with silage inoculum, ESD, n = 7). The total experimental period lasted for 84 d, including early 14 d as adaption period and remaining 70 d for data collection. The ESD increased average daily gain (P = 0.046), dry matter intake (P < 0.001), ammonia nitrogen (P = 0.045), microbial crude protein (P = 0.034), and total volatile fatty acids concentration (P < 0.001), and decreased ruminal pH value (P = 0.014). The proportion of propionate (P = 0.006) and the copy numbers of bacteria (P = 0.01) and protozoa (P = 0.002) were higher, while the proportion of acetate (P = 0.028) was lower in the sheep fed ESD compared to CON. Pyrosequencing of the 16S ribosomal RNA gene revealed that ESD increased the relative abundance of Firmicutes, Ruminococcus, Lachnospiraceae_AC2044_group, Lachnospiraceae_XPB1014_group, and Christensenellaceae_R-7_group in the rumen (P < 0.05), while decreased the relative abundance of Bacteroidota, Prevotellaceae_UCG-003, and Veillonellaceae_UCG-001 (P < 0.05). Analyses with PICRUSt2 and STAMP indicated that the propionate metabolism pathway was enriched in the sheep fed ESD (P = 0.026). The ESD increased the rumen papillae height (P = 0.012), density (P = 0.036), and surface area (P = 0.001), and improved the thickness of the total epithelia (P = 0.018), stratum corneum (P = 0.040), stratum granulosum (P = 0.042), and stratum spinosum and basale (P = 0.004). The relative mRNA expression of cyclin-dependent Kinase 2, CyclinA2, CyclinD2, zonula occludens-1, Occludin, monocarboxylate transporter isoform 1 (MCT1), MCT4, sodium/potassium pump, and sodium/hydrogen antiporter 3 were higher in the rumen epithelial of sheep fed ESD than CON (P < 0.05). Conversely, the relative mRNA expressions of Caspase 3 and B-cell lymphoma-2 were lower in the sheep fed ESD than CON (P < 0.05). In conclusion, compared with an untreated diet, feeding an ensiled diet altered the rumen microbial community, enhanced nutrient transport through rumen epithelium, and improved the growth performance of Tibetan sheep.

Tibetan sheep on the Qinghai-Tibet Plateau experience significant nutrient stress while a substantial amount of agricultural byproducts in the region go discarded and wasted. In this study, agricultural byproducts were ensiled and fed to the Tibetan sheep to investigate their effects on growth performance, rumen microorganisms, and nutrient transport through rumen epithelial tissues. Fourteen male Tibetan sheep were randomly assigned to one of two diets: untreated diet (without silage inoculum, CON, n = 7) or ensiled diet (with silage inoculum, ESD, n = 7). After 70 d of feeding, the ESD-fed sheep had a higher body weight than CON. The ensiled diet changed the rumen microbial community and increased the relative abundance of cellulolytic bacteria in the rumen. In addition, the ensiled diet also promoted the development of rumen epithelia and improved the relative expression of gene related to nutrient transport. Overall, the ensiled diet optimized the use of agricultural byproducts and significantly contributed to the production of Tibetan sheep.

Hepatic artery restriction operation combined with ALPPS (HARO-ALPPS), a novel ALPPS procedure for the treatment of hepatocellular carcinoma with severe fibrosis: retrospective clinical cohort study.

BACKGROUND: Associating liver partition with portal vein ligation for staged liver resection (ALPPS) has been used in the treatment of patients with advanced or massive liver cancer without sufficient future liver remnant, but concerns remain regarding tumor outcomes and surgical safety. This study aims to evaluate the efficacy and safety of a new procedure, hepatic artery restriction operation combined with ALPPS (HARO-ALPPS), in the treatment of hepatocellular carcinoma (HCC) patients especially with severe fibrosis. METHODS: This retrospective study analyzed 8 patients who underwent HARO-ALPPS for HCC and compared their outcomes with 64 patients who underwent conventional ALPPS. The primary outcomes assessed were liver regeneration ability (measured by relative and absolute kinetic growth rates), postoperative complications, and mortality. The secondary outcomes included overall survival and disease-free survival. RESULTS: HARO-ALPPS significantly restricted the blood supply of the hepatic artery. One week after surgery, the blood flow of the right hepatic artery dropped to 62.1%. At the same time, HARO-ALPPS shows superior liver regeneration ability, which is particularly prominent in the background of liver fibrosis. No serious complications occurred after HARO-ALPPS. The overall survival rate of HARO-ALPPS was 75%, which was higher than that of ALPPS (64%, P =0.816). CONCLUSION: Compared to conventional ALPPS, HARO-ALPPS exhibits a better liver regeneration ability, and favorable long-term outcomes. Further prospective studies are needed to validate these findings and evaluate the long-term oncologic outcomes of this novel procedure.

MR2CPPIS: Accurate prediction of protein-protein interaction sites based on multi-scale Res2Net with coordinate attention mechanism.

Proteins play a vital role in various biological processes and achieve their functions through protein-protein interactions (PPIs). Thus, accurate identification of PPI sites is essential. Traditional biological methods for identifying PPIs are costly, labor-intensive, and time-consuming. The development of computational prediction methods for PPI sites offers promising alternatives. Most known deep learning (DL) methods employ layer-wise multi-scale CNNs to extract features from protein sequences. But, these methods usually neglect the spatial positions and hierarchical information embedded within protein sequences, which are actually crucial for PPI site prediction. In this paper, we propose MR2CPPIS, a novel sequence-based DL model that utilizes the multi-scale Res2Net with coordinate attention mechanism to exploit multi-scale features and enhance PPI site prediction capability. We leverage the multi-scale Res2Net to expand the receptive field for each network layer, thus capturing multi-scale information of protein sequences at a granular level. To further explore the local contextual features of each target residue, we employ a coordinate attention block to characterize the precise spatial position information, enabling the network to effectively extract long-range dependencies. We evaluate our MR2CPPIS on three public benchmark datasets (Dset 72, Dset 186, and PDBset 164), achieving state-of-the-art performance. The source codes are available at https://github.com/YyinGong/MR2CPPIS.

Estimates on age, growth, and mortality of Leuciscus chuanchicus (Kessler 1876) in the Ningxia section of the upper reaches of the Yellow River, China.

To investigate the age structure, growth pattern, mortality and exploitation rates of Leuciscus chuanchicus in the upstream Ningxia section of the Yellow River, four sampling surveys were conducted between 2022 and 2023. A total of 472 individuals were measured for their total length (TL) and body weight (W). Age determination was performed using otoliths. The collected samples had a range of total lengths from 4.52 to 37.45 cm, body weights ranging from 0.68 to 552.43 g, and ages ranging from 1 to 7 years old. The relationship between total length and body weight was expressed as W = 0.0052 L3.19 for all samples, which indicates that the growth of L. chuanchicus adheres to allometry. The Von Bertalanffy growth equation revealed that the fish had an asymptotic total length (L∞) of approximately 37.9 cm with a growth coefficient (K) value of approximately 0.461 yr-1. Using the age-based catch curve method, the calculated total instantaneous mortality rate (Z) for all samples was determined as being equal to approximately 1.1302 yr-1. Additionally, three methods were used to estimate the average instantaneous rate of natural mortality (M), resulting in an approximate value of 0.7167 yr-1 for all samples. Furthermore, the instantaneous rate of fishing mortality (F) for all samples was calculated as 0.4134 yr-1, leading us to determine that the exploitation rate (E) is 0.3658. It was concluded that the growth rate of L. chuanchicus in the upstream of the Yellow River is relatively fast, and L. chuanchicus has not been subjected to excessive exploitation, yet its relatively high natural mortality rate underscores the need for targeted management measures aimed at preserving its habitat.

A cross-linked macropore hydrogel based on M1 macrophage lysate and alginate regulates tumor-associated macrophages for the treatment of melanoma.

Pro-inflammatory M1 macrophages possess the ability to change the immunosuppressive tumor microenvironment by releasing various inflammatory factors simultaneously, which can effectively inhibit tumor progression and relapse. Promoting macrophage polarization towards M1 may be an effective way to treat Melanoma. However, the risk of cytokine storm caused by the proliferation and excessive activation of M1 macrophages greatly limits it as a biosafety therapeutic strategy in anti-tumor immunotherapy. Therefore, how to engineer natural M1 macrophage to a biocompatible biomaterial that maintains the duration time of tumor suppressive property duration time still remains a huge challenge. To achieve this goal, we developed an injectable macroporous hydrogel (M1LMHA) using natural M1 macrophage lysates and alginate as raw materials. M1LMHA had excellent biocompatibility, adjustable degradation rate and could sustainably release varieties of natural inflammatory factors, such as tumor necrosis factor-α (TNF-α), interferon-gamma (IFN-γ), and interleukin-12 (IL-12), etc. M1LMHA could repolarize anti-inflammatory M2 macrophages to M1 macrophages by the synergistic effect of released tiny inflammatory factors via the NF-κB pathway. This study supported that M1LMHA might be an effective and safe tool to activate tumor-associated immune cells, improving the efficiency of anti-tumor immunotherapy.

Engineering Efferocytosis-Mimicking Nanovesicles to Regulate Joint Anti-Inflammation and Peripheral Immunosuppression for Rheumatoid Arthritis Therapy.

Rheumatoid arthritis (RA) is an autoimmune disorder characterized by chronic inflammation of the synovial joints and the dysfunction of regulatory T cells (Tregs) in the peripheral blood. Therefore, an optimal treatment strategy should aim to eliminate the inflammatory response in the joints and simultaneously restore the immune tolerance of Tregs in peripheral blood. Accordingly, we developed an efferocytosis-mimicking nanovesicle that contains three functional factors for immunomodulating of efferocytosis, including "find me" and "eat me" signals for professional (macrophage) or non-professional phagocytes (T lymphocyte), and "apoptotic metabolite" for metabolite digestion. We showed that efferocytosis-mimicking nanovesicles targeted the inflamed joints and spleen of mice with collagen-induced arthritis, further recruiting and selectively binding to macrophages and T lymphocytes to induce M2 macrophage polarization and Treg differentiation and T helper cell 17 (Th17) recession. Under systemic administration, the efferocytosis-mimicking nanovesicles effectively maintained the pro-inflammatory M1/anti-inflammatory M2 macrophage balance in joints and the Treg/Th17 imbalance in peripheral blood to prevent RA progression. This study demonstrates the potential of efferocytosis-mimicking nanovesicles for RA immunotherapy.