The application of 3D-printed auto-stable artificial vertebral body in en bloc resection and reconstruction of thoracolumbar metastases

BACKGROUND

Nerve compression symptoms and spinal instability, resulting from spinal metastases, significantly impact the quality of life for patients. A 3D-printed vertebral body is considered an effective approach to reconstruct bone defects following en bloc resection of spinal tumors. The advantage of this method lies in its customized shape and innermost porous structure, which promotes bone ingrowth and leads to reduced postoperative complications.

OBJECTIVE

The purpose of this study is to assess the effectiveness of 3D-printed auto-stable artificial vertebrae in the en bloc resection and reconstruction of thoracolumbar metastases.

METHODS

This study included patients who underwent en bloc resection of thoracolumbar metastases based on the Weinstein-Boriani-Biagini surgical staging system, between January 2019 and April 2021. The patients were divided into two groups: the observation group, which was reconstructed using 3D-printed auto-stable vertebral bodies, and the control group, treated with titanium cages and allograft bone. Evaluation criteria for the patients included assessment of implant subsidence, instrumentation-related complications, VAS score, and Frankel grading of spinal cord injury.

RESULTS

The median follow-up period was 21.8 months (range 12-38 months). Among the patients, 10 received a customized 3D-printed artificial vertebral body, while the remaining 10 received a titanium cage. The observation group showed significantly lower operation time, intraoperative blood loss, and postoperative drainage compared to the control group (P < 0.05). At the final follow-up, the average implant subsidence was 1.8 ± 2.1 mm for the observation group and 5.2 ± 5.1 mm for the control group (P < 0.05). The visual analog scale (VAS) scores were not statistically different between the two groups at preoperative, 24 h, 3 months, and 1 year after the operation (P < 0.05). There were no statistically significant differences in the improvements of spinal cord functions between the two groups.

CONCLUSION

The utilization of a 3D-printed auto-stable artificial vertebra for reconstruction following en bloc resection of thoracolumbar metastases appears to be a viable and dependable choice. The low occurrence of prosthesis subsidence with 3D-printed prostheses can offer immediate and robust stability.

Integration of Metabolomics and Transcriptomics Reveals Major Metabolic Pathways and Potential Biomarkers Involved in Pulmonary Tuberculosis and Pulmonary Tuberculosis-Complicated Diabetes

Pulmonary tuberculosis (PTB) and diabetes mellitus (DM) are common chronic diseases that threaten human health. Patients with DM are susceptible to PTB, an important factor that aggravates the complications of diabetes. However, the molecular regulatory mechanism underlying the susceptibility of patients with DM to PTB infection remains unknown. In this study, healthy subjects, patients with primary PTB, and patients with primary PTB complicated by DM were recruited according to inclusion and exclusion criteria. Peripheral whole blood was collected, and alteration profiles and potential molecular mechanisms were further analyzed using integrated bioinformatics analysis of metabolomics and transcriptomics. Transcriptional data revealed that lipocalin 2 (LCN2), defensin alpha 1 (DEFA1), peptidoglycan recognition protein 1 (PGLYRP1), and integrin subunit alpha 2b (ITGA2B) were significantly upregulated, while chloride intracellular channel 3 (CLIC3) was significantly downregulated in the group with PTB and DM (PTB_DM) in contrast to the healthy control (HC) group. Additionally, the interleukin 17 (IL-17), phosphatidylinositol 3-kinase (PI3K)-AKT, and peroxisome proliferator-activated receptor (PPAR) signaling pathways are important for PTB infection and regulation of PTB-complicated diabetes. Metabolomic data showed that glycerophospholipid metabolism, carbon metabolism, and fat digestion and absorption processes were enriched in the differential metabolic analysis. Finally, integrated analysis of both metabolomic and transcriptomic data indicated that the NOTCH1/JAK/STAT signaling pathway is important in PTB complicated by DM. In conclusion, PTB infection altered the transcriptional and metabolic profiles of patients with DM. Metabolomic and transcriptomic changes were highly correlated in PTB patients with DM. Peripheral metabolite levels may be used as biomarkers for PTB management in patients with DM. IMPORTANCE The comorbidity of diabetes mellitus (DM) significantly increases the risk of tuberculosis infection and adverse tuberculosis treatment outcomes. Most previous studies have focused on the relationship between the effect of blood glucose control and the outcome of antituberculosis treatment in pulmonary tuberculosis (PTB) with DM (PTB_DM); however, early prediction and the underlying molecular mechanism of susceptibility to PTB infection in patients with DM remain unclear. In this study, transcriptome sequencing and untargeted metabolomics were performed to elucidate the key molecules and signaling pathways involved in PTB infection and the susceptibility of patients with diabetes to PTB. Our findings contribute to the development of vital diagnostic biomarkers for PTB or PTB_DM and provide a comprehensive understanding of molecular regulation during disease progression.

Synthetic phylogenetically diverse communities promote denitrification and stability

Denitrification is an important process of the global nitrogen cycle as some of its intermediates are environmentally important or related to global warming. However, how the phylogenetic diversity of denitrifying communities affects their denitrification rates and temporal stability remains unclear. Here we selected denitrifiers based on their phylogenetic distance to construct two groups of synthetic denitrifying communities: one closely related (CR) group with all strains from the genus Shewanella and the other distantly related (DR) group with all constituents from different genera. All synthetic denitrifying communities (SDCs) were experimentally evolved for 200 generations. The results showed that high phylogenetic diversity followed by experimental evolution promoted the function and stability of synthetic denitrifying communities. Specifically, the productivity and denitrification rates were significantly (P < 0.05) higher with Paracocus denitrificans as the dominant species (since the 50th generation) in the DR community than those in the CR community. The DR community also showed significantly (t = 7.119, df = 10, P < 0.001) higher stability through overyielding and asynchrony of species fluctuations, and showed more complementarity than the CR group during the experimental evolution. This study has important implications for applying synthetic communities to remediate environmental problems and mitigate greenhouse gas emissions.

The association between physical activity and fear of falling among community-dwelling older women in China: the mediating role of physical fitness

Background

This study aimed to explore the association between physical activity (PA) and fear of falling (FOF) and to determine whether this relationship was mediated by physical fitness (PF) in community-dwelling older women.

Methods

For this cross-sectional study, a total of 1,108 older women were recruited. Moderate-to-vigorous physical activity (MVPA) and light physical activity (LPA) were objectively measured by accelerometers. Physical fitness indicators including body mass index (BMI), forced vital capacity, choice reaction time, grip strength, sit and reach, and five times sit-to-stand were measured. FOF was evaluated by the Chinese version of the activities-specific balance confidence scale. A stepwise linear regression model analysis was used for mediation analysis, and bootstrap analysis was used to verify the mediation effects.

Result

The Pearson correlation coefficient results suggested that MVPA was significantly and negatively correlated with FOF while LPA was not correlated with FOF. Logistic regression analysis suggested a significant association between MVPA, BMI, forced vital capacity, choice reaction time, sit and reach, grip strength, five times sit-to-stand, and FOF. The mediation analysis showed a negative relationship between MVPA and FOF. BMI completely mediated the relationship between MVPA and FOF while sit and reach, five times sit-to-stand, and forced vital capacity partially mediated the relationship between MVPA and FOF.

Conclusion

Accumulation of more daily MVPA was associated with reducing the odds of FOF in community-dwelling older women. PF indicators fully or partially mediate the relationship between MVPA and FOF. Therefore, more intervention efforts should focus on the promotion of MVPA to improve PF and thus reduce FOF among older women.

Research on machine vision and deep learning based recognition of cotton seedling aphid infestation level

Aphis gossypii Glover is a major insect pest in cotton production, which can cause yield reduction in severe cases. In this paper, we proposed the A. gossypii infestation monitoring method, which identifies the infestation level of A. gossypii at the cotton seedling stage, and can improve the efficiency of early warning and forecasting of A. gossypii, and achieve precise prevention and cure according to the predicted infestation level. We used smartphones to collect A. gossypii infestation images and compiled an infestation image data set. And then constructed, trained, and tested three different A. gossypii infestation recognition models based on Faster Region-based Convolutional Neural Network (R-CNN), You Only Look Once (YOLO)v5 and single-shot detector (SSD) models. The results showed that the YOLOv5 model had the highest mean average precision (mAP) value (95.7%) and frames per second (FPS) value (61.73) for the same conditions. In studying the influence of different image resolutions on the performance of the YOLOv5 model, we found that YOLOv5s performed better than YOLOv5x in terms of overall performance, with the best performance at an image resolution of 640×640 (mAP of 96.8%, FPS of 71.43). And the comparison with the latest YOLOv8s showed that the YOLOv5s performed better than the YOLOv8s. Finally, the trained model was deployed to the Android mobile, and the results showed that mobile-side detection was the best when the image resolution was 256×256, with an accuracy of 81.0% and FPS of 6.98. The real-time recognition system established in this study can provide technical support for infestation forecasting and precise prevention of A. gossypii.

A wide megafauna gap undermines China's expanding coastal ecosystem conservation

To fulfill sustainable development goals, many countries are expanding efforts to conserve ecologically and societally critical coastal ecosystems. Although megafauna profoundly affect the functioning of ecosystems, they are neglected as a key component in the conservation scheme for coastal ecosystems in many geographic contexts. We reveal a rich diversity of extant megafauna associated with all major types of coastal ecosystems in China, including 218 species of mammals, birds, reptiles, cephalopods, and fish across terrestrial and marine environments. However, 44% of these species are globally threatened, and 78% have not yet been assessed in China for extinction risk. More worrisome, 73% of these megafauna have not been designated as nationally protected species, and <10% of their most important habitats are protected. Filling this wide "megafauna gap" in China and globally would be a leading step as humanity strives to thrive with coastal ecosystems.

Context-aware augmentation for liver lesion segmentation: shape uniformity, expansion limit and fusion strategy

Background

Data augmentation with context has been an effective way to increase the robustness and generalizability of deep learning models. However, to our knowledge, shape uniformity, expansion limit, and fusion strategy of context have yet to be comprehensively studied, particularly in lesion segmentation of medical images.

Methods

To examine the impact of these factors, we take liver lesion segmentation based on the well-known deep learning architecture U-Net as an example and thoroughly vary the context shape, the expansion bandwidth as well as three representative fusion methods. In particular, the context shape includes rectangular, circular and polygonal, the expansion bandwidth is scaled by a maximum value of 2 compared to the lesion size, and the context fusion weighting strategy is composed of average, Gaussian and inverse Gaussian.

Results

Studies conducted on a newly constructed high-quality and large-volume dataset show that (I) uniform context improves lesion segmentation, (II) expanding the context with either 5 or 7 pixels yields the highest performance for liver lesion segmentation, depending on the lesion size, and (III) an unevenly distributed weighting strategy for context fusion is appreciated but in the opposite direction, depending on lesion size as well.

Conclusions

Our findings and newly constructed dataset are expected to be useful for liver lesion segmentation, especially for small lesions.

Protective Effects of Different Hypothermal Preservation Solutions on Structure and Function of Isolated Rat Arteries

OBJECTIVE

With the increasing application of vascular reconstruction in surgical procedures, allogeneic vessels are becoming more popular in clinical practice due to their abundant sources, precise diameter matching, improved histocompatibility, and higher long-term patency rate. This study aimed to investigate the protective effect of various preservation solutions on the function and structure of the isolated rat abdominal aorta preserved under hypothermal conditions.

METHODS

The study utilized a total of 150 Sprague-Dawley (SD) rats, with 144 rats allocated to the experimental groups and 6 rats allocated to the control groups. The abdominal aorta of the rats was chosen as the subject of our research. The aorta in the experimental groups were randomly assigned to 4 groups: University of Wisconsin (UW) solution group, histidine-tryptophan-ketoglutarate (HTK) solution group, normal saline (NS) group, and sodium lactate Ringer's solution (RS) group. Samples were subjected to examination after preservation periods of 1 day, 3 days, 5 days, 7 days, 14 days, 30 days, and 90 days. Evaluation of vascular physiological function involved detecting and assessing vasoconstriction ability and measuring cell viability through the MTT test. Evaluation of the vascular wall structure involved tension tolerance tests and pathological staining.

RESULTS

The pathogen-positive rate in the HTK group and NS group at 1 month was 16.7%. Regarding the vascular skeleton structure, both the UW group and HTK group exhibited intact structures after 2 weeks of preservation, with slightly edematous collagen and elastic fibers, which was significantly better than that of the NS group and RS group. In terms of cell activity and contractile function, all preservation groups showed similar effects within 2 weeks. However, after 2 weeks, the UW group showed the most favorable preservation effect (P<0.05). In terms of vascular tension, different groups exhibited similar effects within 1 week. However, after 2 weeks, the UW group showed the best preservation effect (P<0.05).

CONCLUSION

All 4 types of preservation solution had a preservation effect on the structure and function of isolated blood vessels during short-term hypothermal preservation. However, after 2-week preservation, the UW solution was found to be the most suitable solution for the preservation of blood vessels.

Effects of different preservation schemes on isolated rat artery

Allogeneic blood vessels are regarded as one of the best natural substitutes for diseased blood vessels due to their good vascular compliance and histocompatibility. Since the supply and demand of allograft blood vessels do not always match in time and space, a good preservation scheme for isolated blood vessels is essential. The abdominal aortas of 110 male Sprague-Dawley (SD) rats were randomly divided into three groups, including cold storage group (4°C) (CSG), frozen storage group (FSG) and ambient storage group (25 ± 2°C) (ASG). Seven time points of preservation for 1, 3, 5, 7, 14, 30 and 90 days were set for detection. The changes in vascular physiological function were evaluated by MTT test and vasoconstriction ability detection, and the changes in vascular wall structure were evaluated by the tension tolerance test and pathological staining. The vascular function of CSG was better than FSG within first the 7 days, but the result was opposite since the 14th day. The vascular wall structure, collagen and elastic fibres of vessels, in CSG, showed oedema within 30 days, and continuous disintegration and rupture at 90 days. The vessel wall structure of FSG remained intact within 90 days. The tensile strength of the vessels in CSG was better than that in FSG within 5 days, and there was no statistical difference between the two groups between the 7th and 30th day, and then, the FSG was higher than CSG on the 90th day. Both cold storage and frozen storage could be applied as safe and effective preservation schemes for isolated rat artery within first 30 days. Cold storage is recommended when the storage time is <14 days, and then, frozen storage is better.

The genome of okra (Abelmoschus esculentus) provides insights into its genome evolution and high nutrient content

Okra (Abelmoschus esculentus) is an important vegetable crop with high nutritional value. However, the mechanism underlying its high nutrient content remains poorly understood. Here, we present a chromosome-scale genome of okra with a size of 1.19 Gb. Comparative genomics analysis revealed the phylogenetic status of A. esculentus, as well as whole-genome duplication (WGD) events that have occurred widely across the Malvaceae species. We found that okra has experienced three additional WGDs compared with the diploid cotton Gossypium raimondii, resulting in a large chromosome number (2n = 130). After three WGDs, okra has undergone extensive genomic deletions and retained substantial numbers of genes related to secondary metabolite biosynthesis and environmental adaptation, resulting in significant differences between okra and G. raimondii in the gene families related to cellulose synthesis. Combining transcriptomic and metabolomic analysis, we revealed the relationship between gene expression and metabolite content change across different okra developmental stages. Furthermore, the sinapic acid/S-lignin biosynthesis-related gene families have experienced remarkable expansion in okra, and the expression of key enzymes involved in the sinapic acid/S-lignin biosynthesis pathway vary greatly across developmental periods, which partially explains the differences in metabolite content across the different stages. Our study gains insights into the comprehensive evolutionary history of Malvaceae species and the genetic basis that underlies the nutrient content changes in okra, which will facilitate the functional study and genetic improvement of okra varieties.

KRP-DS: A Knowledge Graph-Based Dialogue System with Inference-Aided Prediction

With the popularity of ChatGPT, there has been increasing attention towards dialogue systems. Researchers are dedicated to designing a knowledgeable model that can engage in conversations like humans. Traditional seq2seq dialogue models often suffer from limited performance and the issue of generating safe responses. In recent years, large-scale pretrained language models have demonstrated their powerful capabilities across various domains. Many studies have leveraged these pretrained models for dialogue tasks to address concerns such as safe response generation. Pretrained models can enhance responses by carrying certain knowledge information after being pre-trained on large-scale data. However, when specific knowledge is required in a particular domain, the model may still generate bland or inappropriate responses, and the interpretability of such models is poor. Therefore, in this paper, we propose the KRP-DS model. We design a knowledge module that incorporates a knowledge graph as external knowledge in the dialogue system. The module utilizes contextual information for path reasoning and guides knowledge prediction. Finally, the predicted knowledge is used to enhance response generation. Experimental results show that our proposed model can effectively improve the quality and diversity of responses while having better interpretability, and outperforms baseline models in both automatic and human evaluations.

Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum

BACKGROUND

Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. However, the mechanisms underlying these advantageous traits remain largely unexplored. Here, we present a high-quality genome assembly of the allotetraploid P. giganteum aiming at providing insights into biomass accumulation.

RESULTS

Our assembly has a genome size 2.03 Gb and contig N50 of 88.47 Mb that was further divided into A and B subgenomes. Genome evolution analysis revealed the evolutionary relationships across the Panicoideae subfamily lineages and identified numerous genome rearrangements that had occurred in P. giganteum. Comparative genomic analysis showed functional differentiation between the subgenomes. Transcriptome analysis found no subgenome dominance at the overall gene expression level; however, differentially expressed homoeologous genes and homoeolog-specific expressed genes between the two subgenomes were identified, suggesting that complementary effects between the A and B subgenomes contributed to biomass accumulation of P. giganteum. Besides, C4 photosynthesis-related genes were significantly expanded in P. giganteum and their sequences and expression patterns were highly conserved between the two subgenomes, implying that both subgenomes contributed greatly and almost equally to the highly efficient C4 photosynthesis in P. giganteum. We also identified key candidate genes in the C4 photosynthesis pathway that showed sustained high expression across all developmental stages of P. giganteum.

CONCLUSIONS

Our study provides important genomic resources for elucidating the genetic basis of advantageous traits in polyploid species, and facilitates further functional genomics research and genetic improvement of P. giganteum.

Improving the identification of miRNA-disease associations with multi-task learning on gene-disease networks

MicroRNAs (miRNAs) are a family of non-coding RNA molecules with vital roles in regulating gene expression. Although researchers have recognized the importance of miRNAs in the development of human diseases, it is very resource-consuming to use experimental methods for identifying which dysregulated miRNA is associated with a specific disease. To reduce the cost of human effort, a growing body of studies has leveraged computational methods for predicting the potential miRNA-disease associations. However, the extant computational methods usually ignore the crucial mediating role of genes and suffer from the data sparsity problem. To address this limitation, we introduce the multi-task learning technique and develop a new model called MTLMDA (Multi-Task Learning model for predicting potential MicroRNA-Disease Associations). Different from existing models that only learn from the miRNA-disease network, our MTLMDA model exploits both miRNA-disease and gene-disease networks for improving the identification of miRNA-disease associations. To evaluate model performance, we compare our model with competitive baselines on a real-world dataset of experimentally supported miRNA-disease associations. Empirical results show that our model performs best using various performance metrics. We also examine the effectiveness of model components via ablation study and further showcase the predictive power of our model for six types of common cancers. The data and source code are available from https://github.com/qwslle/MTLMDA.

Precise in-field molecular diagnostics of crop diseases by smartphone-based mutation-resolved pathogenic RNA analysis

Molecular diagnostics for crop diseases can guide the precise application of pesticides, thereby reducing pesticide usage while improving crop yield, but tools are lacking. Here, we report an in-field molecular diagnostic tool that uses a cheap colorimetric paper and a smartphone, allowing multiplexed, low-cost, rapid detection of crop pathogens. Rapid nucleic acid amplification-free detection of pathogenic RNA is achieved by combining toehold-mediated strand displacement with a metal ion-mediated urease catalysis reaction. We demonstrate multiplexed detection of six wheat pathogenic fungi and an early detection of wheat stripe rust. When coupled with a microneedle for rapid nucleic acid extraction and a smartphone app for results analysis, the sample-to-result test can be completed in ~10 min in the field. Importantly, by detecting fungal RNA and mutations, the approach allows to distinguish viable and dead pathogens and to sensitively identify mutation-carrying fungicide-resistant isolates, providing fundamental information for precision crop disease management.

A causal effects of gut microbiota in the development of migraine

BACKGROUND

The causal association between the gut microbiome and the development of migraine and its subtypes remains unclear.

METHODS

The single nucleotide polymorphisms concerning gut microbiome were retrieved from the gene-wide association study (GWAS) of the MiBioGen consortium. The summary statistics datasets of migraine, migraine with aura (MA), and migraine without aura (MO) were obtained from the GWAS meta-analysis of the International Headache Genetics Consortium (IHGC) and FinnGen consortium. Inverse variance weighting (IVW) was used as the primary method, complemented by sensitivity analyses for pleiotropy and increasing robustness.

RESULTS

In IHGC datasets, ten, five, and nine bacterial taxa were found to have a causal association with migraine, MA, and MO, respectively, (IVW, all P < 0.05). Genus.Coprococcus3 and genus.Anaerotruncus were validated in FinnGen datasets. Nine, twelve, and seven bacterial entities were identified for migraine, MA, and MO, respectively. The causal association still exists in family.Bifidobacteriaceae and order.Bifidobacteriales for migraine and MO after FDR correction. The heterogeneity and pleiotropy analyses confirmed the robustness of IVW results.

CONCLUSION

Our study demonstrates that gut microbiomes may exert causal effects on migraine, MA, and MO. We provide novel evidence for the dysfunction of the gut-brain axis on migraine. Future study is required to verify the relationship between gut microbiome and the risk of migraine and its subtypes and illustrate the underlying mechanism between them.

Removal of per- and polyfluoroalkyl substances by nanofiltration: Effect of molecular structure and coexisting natural organic matter

This study investigates the removal efficiency of anionic, cationic, and zwitterionic per- and polyfluoroalkyl substances (PFAS) by nanofiltration (NF) in the presence of three representative natural organic matter (NOM) types: bovine serum albumin (BSA), humic acid (HA), and sodium alginate (SA). In particular, effects of PFAS molecular structure and coexisting NOM on the transmission and adsorption efficiency of PFAS during NF treatment were analyzed. The results indicate that NOM types dominate membrane fouling behavior despite the coexistence of PFAS. SA exhibits the most significant fouling propensity, resulting in maximum water flux decline. NF effectively removed both ether and precursor PFAS. The effects of the three typical NOM on the membrane-passing behavior of PFAS were consistent for all PFAS investigated. Generally, PFAS transmission decreased in the order of SA-fouled > pristine > HA-fouled > BSA-fouled, indicating that the presence of HA and BSA enhanced PFAS removal while SA declined. Furthermore, reduced PFAS transmission was observed with increased perfluorocarbon chain length or molecular weight (MW), regardless of the presence or type of the NOM. The impacts of NOM on PFAS filtration diminished when the PFAS van der Waals radius was > 4.0 Å, MW > 500 Da, polarization > 20 Å, or LogKow > 3. These findings suggest that both steric repulsion and hydrophobic interactions, especially the former, play important roles in PFAS rejection by NF. This study provides insights into the specific applicability and performance of membrane-based processes for eliminating PFAS during drinking and wastewater treatments, and highlighting the importance of coexisting NOM.

Phytoextraction of per- and polyfluoroalkyl substances (PFAS) by weeds: Effect of PFAS physicochemical properties and plant physiological traits

Phytoextraction is a promising technology that uses plants to remediate contaminated soil. However, its feasibility for per- and polyfluoroalkyl substances (PFAS) and the impact of PFAS properties and plant traits on phytoextraction efficacy remains unknown. In this study, we conducted greenhouse experiment and evaluated the potential of weeds for phytoextraction of PFAS from soil and assessed the effects of PFAS properties and plant traits on PFAS uptake via systematic correlation analyses and electron probe microanalyzer with energy dispersive spectroscopy (FE-EPMA-EDS) imaging. The results showed that 1) phytoextraction can remove 0.04%- 41.4%wt of PFAS from soil, with extracted PFAS primarily stored in plant shoots; 2) Weeds preferentially extracted short-chain PFAS over long-chain homologues from soil. 3) PFAS molecular size and hydrophilicity determined plant uptake behavior, while plant morphological traits, particularly root protein and lipid content, influenced PFAS accumulation and translocation. Although plants with thin roots and small leaf areas exhibited greater PFAS uptake and storage ability, the impact of PFAS physicochemical properties was more significant. 4) Finally, short-chain PFAS were transported quickly upwards in the plant, while uptake of long-chain PFOS was restricted.

[Efficacy and safety of bendamustine-rituximab combination therapy for newly diagnosed indolent B-cell non-Hodgkin's lymphoma and elderly mantle cell lymphoma: a multi-center prospective phase II clinical trial in China]

Objectives: This study aimed to assess the efficacy and safety of bendamustine in combination with rituximab (BR regimen) for the treatment of newly diagnosed indolent B-cell non-Hodgkin's lymphoma (B-iNHL) and elderly mantle cell lymphoma (eMCL) . Methods: From December 1, 2020 to September 10, 2022, a multi-center prospective study was conducted across ten Grade A tertiary hospitals in Shandong Province, China. The BR regimen was administered to evaluate its efficacy and safety in newly diagnosed B-iNHL and eMCL patients, and all completed at least four cycles of induction therapy. Results: The 72 enrolled patients with B-iNHL or MCL were aged 24-74 years, with a median age of 55 years. Eastern Cooperative Oncology Group (ECOG) performance status scores of 0-1 were observed in 76.4% of patients, while 23.6% had scores of 2. Disease distribution included follicular lymphoma (FL) (51.4% ), marginal zone lymphoma (MZL) (33.3% ), eMCL (11.1% ), and the unknown subtype (4.2% ). According to the Ann Arbor staging system, 16.7% and 65.3% of patients were diagnosed with stage Ⅲ and stage Ⅳ lymphomas, respectively. Following four cycles of BR induction therapy, the overall response rate was 98.6%, with a complete response (CR) rate of 83.3% and a partial response (PR) rate of 15.3%. Only one eMCL patient experienced disease progression during treatment, and only one FL patient experienced a relapse. Even when evaluated using CT alone, the CR rate was 63.9%, considering the differences between PET/CT and CT assessments. The median follow-up duration was 11 months (range: 4-22), with a PFS rate of 96.8% and an OS rate of 100.0%. The main hematologic adverse reactions included grade 3-4 leukopenia (27.8%, with febrile neutropenia observed in 8.3% of patients), grade 3-4 lymphopenia (23.6% ), grade 3-4 anemia (5.6% ), and grade 3-4 thrombocytopenia (4.2% ). The main non-hematologic adverse reactions such as fatigue, nausea/vomiting, rash, and infections occurred in less than 20.0% of patients. Conclusion: Within the scope of this clinical trial conducted in China, the BR regimen demonstrated efficacy and safety in treating newly diagnosed B-iNHL and eMCL patients.

Ultrasmall Pt NPs-modified flasklike colloidal motors with high mobility and enhanced ion tolerance

Chemically powered colloidal motors propelled by the self-phoretic effect have attracted widespread attention. However, the low motion efficiency and ion tolerance hinder their application in complex media. Herein, we report a scalable and simple method to synthesize 2.6 nm Platinum nanoparticles (Pt NPs) in the nanoporous wall of carbonaceous flasklike colloidal motors in a ligand-free manner. The obtained Pt NPs-modified flasklike colloidal motors (Pt-FCMs) are propelled by the catalytic decomposition of H₂O₂ fuels. They exhibit ultrafast mobility with an instantaneous velocity of 134 μm s^-1 at 5% H₂O₂, which is equivalent to 180 bodylengths per second. Particularly, these Pt-FCMs have an enhanced ion tolerance, due to the higher catalytic activity of small-sized Pt NPs in the carbonaceous wall. Furthermore, the direction of motion could be reversed by adding cationic surfactant cetyltrimethylammonium bromide. Such ultrasmall Pt NPs funtionalized flasklike colloidal motors exhibit a great potential utilization in the field of biomedicines and environmental technology.

Therapeutically targeting essential metabolites to improve immunometabolism manipulation after liver transplantation for hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the most prevalent primary liver malignancy worldwide and is associated with a poor prognosis. Sophisticated molecular mechanisms and biological characteristics need to be explored to gain a better understanding of HCC. The role of metabolites in cancer immunometabolism has been widely recognized as a hallmark of cancer in the tumor microenvironment (TME). Recent studies have focused on metabolites that are derived from carbohydrate, lipid, and protein metabolism, because alterations in these may contribute to HCC progression, ischemia-reperfusion (IR) injury during liver transplantation (LT), and post-LT rejection. Immune cells play a central role in the HCC microenvironment and the duration of IR or rejection. They shape immune responses through metabolite modifications and by engaging in complex crosstalk with tumor cells. A growing number of publications suggest that immune cell functions in the TME are closely linked to metabolic changes. In this review, we summarize recent findings on the primary metabolites in the TME and post-LT metabolism and relate these studies to HCC development, IR injury, and post-LT rejection. Our understanding of aberrant metabolism and metabolite targeting based on regulatory metabolic pathways may provide a novel strategy to enhance immunometabolism manipulation by reprogramming cell metabolism.

Influencing factors and prognostic value of left ventricular systolic dysfunction in patients with complete occlusion of the left anterior descending artery reperfused by primary percutaneous coronary intervention

BACKGROUND

The aim of this study was to perform a retrospective analysis of patients with acute anterior wall ST-segment elevation myocardial infarction (AAW-STEMI) whose left anterior descending (LAD) artery was completely occluded and reperfused by primary percutaneous coronary intervention (PPCI) and to determine the influencing factors and prognostic value of left ventricular systolic dysfunction (LVSD) in the acute phase of acute myocardial infarction (AMI).

METHODS

A total of 304 patients with AAW-STEMI were selected. The selected patients were divided into two groups: the preserved left ventricular ejection fraction (pLVEF) group (LVEF ≥ 50%, n = 185) and the reduced left ventricular ejection fraction (rLVEF) group (LVEF < 50%, n = 119). The influencing factors of LVSD and their predictive value for LVSD were analyzed. Patients were followed up by examining outpatient records and via telephone. The predictive value of LVSD for the cardiovascular mortality of patients with AAW-STEMI was analyzed.

RESULTS

Age, heart rate (HR) at admission, number of ST-segment elevation leads (STELs), peak creatine kinase (CK) and symptom to wire-crossing (STW) time were independent risk factors for LVSD (P < 0.05). The receiver operating characteristic (ROC) analysis showed that the peak CK had the strongest predictive value for LVSD, with an area under the curve (AUC) of 0.742 (CI, 0.687 to 0.797) as the outcome. At a median follow-up of 47 months (interquartile range, 27 to 64 months), the Kaplan‒Meier survival curves up to 6-year follow-up revealed a total of 8 patients succumbed to cardiovascular disease, with 7 (6.54%) in the rLVEF group and 1 (0.56%) in the pLVEF group, respectively (hazard ratio: 12.11, [P = 0.02]). Univariate and multivariate Cox proportional hazards regression analysis demonstrated that rLVEF was an independent risk predictor of cardiovascular death in patients with AAW-STEMI discharged after PPCI (P < 0.01).

CONCLUSIONS

Age, HR at admission, number of STELs, peak CK, and STW time may be used to identify patients with a high risk of heart failure (HF) in a timely manner and initiate early standard therapy for incident LVSD in the acute phase of AAW-STEMI reperfused by PPCI. A trend toward increased cardiovascular mortality at follow-up was significantly linked to LVSD.

Pituitary metastasis of hepatocellular carcinoma as the initial presentations: a case report and review of the literature

Background

Extrahepatic metastasis of hepatocellular carcinoma (HCC) is common. However, pituitary metastasis of HCC is extremely rare. Our case may be helpful to extend the understanding of the disease.

Case presentation

A 65-year-old man presented to the outpatient department for unexplained headache and ptosis for 1 month. Brain imaging showed a slight enhancement tumor in the pituitary fossa, and the endocrinological assessment showed normal results. We considered the tumor as a non-functioning pituitary adenoma before surgery. Then, the tumor was resected by an endonasal endoscopic transsphenoidal approach. The histopathological examination results revealed the pituitary metastasis of HCC. Additional abdominal imaging revealed tumors were located in the left and right liver lobes with portal vein invasion and bilateral ilium metastases. After multidisciplinary cooperation, the patient chose chemotherapy.

Conclusion

We report a case of HCC metastasis to the pituitary gland that initially presented with neurological symptoms. We should consider the possibility of pituitary metastasis in HCC patients.

Coffee intake and risk of diabetic nephropathy: a Mendelian randomization study

Rationale and objective

A causal relationship concerning coffee intake and diabetic nephropathy (DN) is controversial. We conducted a Mendelian randomization study to assess the causal nature of these associations.

Methods

40 independent single nucleotide polymorphisms (SNPs) associated with coffee intake were selected from the UK Biobank study. Summary-level data for diabetic nephropathy were obtained from publicly available genome-wide association studies (GWAS) and the FinnGen consortium. Inverse variance weighted (IVW), MR-Egger, and weighted median (WM) methods were used to examine a causal association. Sensitivity analyses included Cochran's Q test, the intercept of MR-Egger, MR-PRESSO, and the Outlier method. Leave-One-Out sensitivity analyses were also conducted to reduce the heterogeneity.

Results

Our current study demonstrated positive associations of genetically predicted coffee intake with diabetic nephropathy (OR=1.939; P = 0.045 and type 2 diabetes with renal complications (OR = 2.787, P= 0.047). These findings were robust across several sensitivity analyses.

Conclusions

This study found a positive correlation between coffee consumption and the risk of diabetic nephropathy using genetic data. For a more accurate and trustworthy conclusion, subgroup analysis on coffee intake, including preparing method, variety of coffee, and quantity, is required.

Adipose-derived stem cell exosomes regulate Nrf2/Keap1 in diabetic nephropathy by targeting FAM129B

BACKGROUND

Exosomes from adipose-derived stem cells (ADSCs-Exos) have exhibited a therapeutic role in diabetic nephropathy (DN). Further studies are needed to investigate how ADSCs-Exos regulate oxidative stress and inflammation in high glucose-induced podocyte injury.

METHODS

An enzyme-linked immunosorbent assay (ELISA) was used to detect cellular inflammation. Reactive oxygen species (ROS) levels were assessed using flow cytometry in podocytes with different treatments. A malondialdehyde (MDA) kit was used to evaluate the lipid peroxidation levels in podocytes and kidney tissues of mice. Western blotting and co-immunoprecipitation were performed to detect protein expression and protein-protein interactions.

RESULTS

ADSCs-Exos reversed oxidative stress and inflammation in podocytes and kidney tissues of DN mice induced by high glucose levels in vitro and in vivo. Interference with heme oxygenase-1 expression could reverse the improvement effect of ADSCs-Exos on oxidative stress induced by high glucose levels. Furthermore, high glucose inhibited nuclear factor erythroid 2-related factor 2 (Nrf2) protein expression and promoted Kelch-like ECH-associated protein 1 (Keap1) protein expression in podocytes, as well as their binding ability. As a potential target for Nrf2/Keap1 pathway regulation, FAM129B expression in podocytes is regulated by high glucose and ADSCs-Exos. Moreover, FAM129B siRNA blocked the inhibitory effect of ADSCs-Exos on intracellular ROS and MDA upregulation induced by high glucose in podocytes.

CONCLUSION

ADSCs-Exos regulate the Nrf2/Keap1 pathway to alleviate inflammation and oxidative stress in DN by targeting FAM129B, which may provide a potential therapeutic strategy for DN.

Automatic brain structure segmentation for 18F-fluorodeoxyglucose positron emission tomography/magnetic resonance images via deep learning

Background

Brain structure segmentation is of great value in diagnosing brain disorders, allowing radiologists to quickly acquire regions of interest and assist in subsequent analyses, diagnoses and treatment. Current brain structure segmentation methods are usually applied to magnetic resonance (MR) images, which provide higher soft tissue contrast and better spatial resolution. However, fewer segmentation methods are conducted on a positron emission tomography/magnetic resonance imaging (PET/MRI) system that combines functional and structural information to improve analysis accuracy.

Methods

In this paper, we explore a dual-modality image segmentation model to segment brain ¹⁸F-fluorodeoxyglucose (¹⁸F-FDG) PET/MR images based on the U-Net architecture. This model takes registered PET and MR images as parallel inputs, and four evaluation metrics (Dice score, Jaccard coefficient, precision and sensitivity) are used to evaluate segmentation performance. Moreover, we also compared the proposed approach with other single-modality segmentation strategies, including PET-only segmentation and MRI-only segmentation.

Results

The experiments were conducted on the clinical head data of 120 patients, and the results show that the proposed algorithm accurately delineates brain volumes of interest (VOIs), achieving superior performance with 84.24%±1.44% Dice score, 74.36%±2.40% Jaccard, 84.33%±1.56% precision and 84.73%±1.56% sensitivity. Furthermore, compared with directly using the FreeSurfer toolkit, the proposed method reduced the segmentation time, which only needs 20 seconds to segment the whole brain for each patient.

Conclusions

We present a deep learning-based method for the joint segmentation of anatomical and functional PET/MR images. Compared with other single-modality methods, our method greatly improved the accuracy of brain structure delineation, which shows great potential for brain analysis.

Highly inhibited transport of dissolved thallium(I) in manganese oxide-coated sand: Chemical condition effects and retention mechanisms

Thallium contamination in water can cause great danger to the environment. In this study, we synthesized manganese oxide-coated sand (MOCS) and investigated the transport and retention behaviors of Tl(I) in MOCS under different conditions. Characterization methods combined with a two-site nonequilibrium transport model were applied to explore the retention mechanisms. The results showed that Tl(I) mobility was strongly inhibited in MOCS media, and the retention capacity calculated from the fitted model was 510.41 mg/g under neutral conditions. The retention process included adsorption and oxidative precipitation by the manganese oxides coated on the sand surface. Cotransport with the same concentration of Mn(II) led to halving Tl(I) retention due to competition for reactive sites. Enhanced Tl(I) retention was observed under alkaline conditions, as increasing pH promoted electronegativity on the media surface. Moreover, the competitive cation Ca²⁺ significantly weakened Tl(I) retention by occupying adsorption sites. These findings provide new insights into understanding Tl(I) transport behavior in water-saturated porous media and suggest that manganese oxide-coated sand can be a cost-effective filter media for treating Tl-contaminated water.

DIALIZE China: A Phase IIIb, Randomized, Placebo-Controlled Study to Reduce Predialysis Hyperkalemia With Sodium Zirconium Cyclosilicate in Chinese Patients

PURPOSE

The DIALIZE China study (Reduce Incidence of Pre-Dialysis Hyperkalaemia With Sodium Zirconium Cyclosilicate in Chinese Subjects) (NCT04217590) evaluated sodium zirconium cyclosilicate (SZC) for the management of hyperkalemia in Chinese patients undergoing hemodialysis.

METHODS

In the double-blind, Phase IIIb DIALIZE China study, Chinese adults with kidney failure and predialysis hyperkalemia (predialysis serum potassium [sK+] concentration >5.4 mmol/L after the long interdialytic interval [LIDI] and >5.0 mmol/L after ≥1 short interdialytic interval) who were receiving hemodialysis 3 times weekly were randomized to placebo or SZC 5 g once daily on nondialysis days. Doses were titrated towards maintaining normokalemia for 4 weeks (titration period) in 5-g increments up to 15 g. Primary efficacy was the proportion of responders during the 4-week evaluation period following the titration period (ie, those with a predialysis sK+ of 4.0-5.0 mmol/L for at least 3 of 4 hemodialysis visits following the LIDI) who did not require urgent rescue therapy.

FINDINGS

Overall, 134 adults (mean [SD] age, 55 [11.3] years) were randomized to SZC or placebo (n = 67 each). There were significantly more responders with SZC (37.3%) versus placebo (10.4%; estimated odds ratio [OR] = 5.10; 95% CI, 1.90-15.12; P < 0.001). The probability of all predialysis sK+ concentrations being 3.5 to 5.5 mmol/L was significantly higher with SZC versus placebo (estimated OR = 6.41; 95% CI, 2.71-15.12; P < 0.001). A greater proportion of patients achieved an sK+ of 3.5 to 5.5 mmol/L on at least 3 of 4 LIDI visits during evaluation with SZC (73.1%) versus placebo (29.9%). Serious adverse events occurred in 9.1% and 11.9% of patients in the SZC and placebo groups, respectively.

IMPLICATIONS

SZC treatment for predialysis hyperkalemia is effective and well tolerated in Chinese patients with kidney failure receiving hemodialysis.

CLINICALTRIALS

gov identifier: NCT04217590.

Comprehensive investigation on volatile and non-volatile metabolites in low-salt doubanjiang with different fermentation methods

Doubanjiang is a well-known fermented condiment in China, but the high-salt concentration in its traditional manufacture process greatly lengthens the fermentation time, and leads to potential health risks. Here, the effects of salt reduction and co-inoculated starters (Tetragenococcus halophilus and Zygosaccharomyces rouxii) on the volatile metabolites (VMs) and non-volatile metabolites (NVMs) of doubanjiang were investigated using metabolomics technology and chemometrics analysis. Results showed that 75 VMs were identified, and 12 of them had significant aroma contribution (ROVAs ≥ 1). In addition, 106 NVMs were defined as significantly different metabolites (p < 0.05; VIP ≥ 1). Salt reduction could significantly increase the concentrations of VMs, but this strategy also promoted some undesirable odors like 2-phetylfuran and hexanoic acid, which could be totally suppressed by inoculation of starter. Moreover, the two starters improved amino acid, ester, and acid metabolites. This study provides a deeper insight into the development of low-salt fermented foods.

Wash-Free and High-Contrast Imaging of Single-Nucleotide Variation in Single Cells Using Transcription-Amplified Light-Up RNA Aptamer

Single-nucleotide variation (SNV) imaging can indicate cellular heterogeneity and spatial pattern, but it remains challenging to produce high-gain signal while also yielding single-nucleotide resolution. Herein, we developed a light-up strategy for visualizing SNVs based on transcription amplification, enabling wash-free and high-contrast imaging of SNVs inside cells. The discrimination of SNVs is achieved by ligase-assisted transcription reaction. Employing a light-up RNA aptamer as a reporter eliminates nonspecific probe binding and the washing process and contributes to a 2-fold improvement of signal gain compared to that using the fluorescence in situ hybridization (FISH) method. The method allowed us to precisely quantify drug-resistant strains in the bacteria mixture and identify drug-resistant Salmonella enterica (S. enterica) isolated from poultry farm. Using this approach, we explored the colonization features of drug-resistant and drug-sensitive S. enterica in the mice intestinal tract and screened the prebiotics for Salmonella colonization inhibition. The SNV imaging method promises for the interrogation of genotypes in physiological and pathological states at the single-cell level.

The vertically-stratified resistomes in mangrove sediments was driven by the bacterial diversity

Early evidence has elucidated that the spread of antibiotic (ARGs) and metal resistance genes (MRGs) are mainly attributed to the selection pressure in human-influenced environments. However, whether and how biotic and abiotic factors mediate the distribution of ARGs and MRGs in mangrove sediments under natural sedimentation is largely unclear. Here, we profiled the abundance and diversity of ARGs and MRGs and their relationships with sedimental microbiomes in 0-100 cm mangrove sediments. Our results identified multidrug-resistance and multimetal-resistance as the most abundant ARG and MRG classes, and their abundances generally decreased with the sediment depth. Instead of abiotic factors such as nutrients and antibiotics, the bacterial diversity was significantly negatively correlated with the abundance and diversity of resistomes. Also, the majority of resistance classes (e.g., multidrug and arsenic) were carried by more diverse bacterial hosts in deep layers with low abundances of resistance genes. Together, our results indicated that bacterial diversity was the most important biotic factor driving the vertical profile of ARGs and MRGs in the mangrove sediment. Given that there is a foreseeable increasing human impact on natural environments, this study emphasizes the important role of biodiversity in driving the abundance and diversity of ARGs and MRGs.

Synthetic Denitrifying Communities Reveal a Positive and Dynamic Biodiversity-Ecosystem Functioning Relationship during Experimental Evolution

Biodiversity is vital for ecosystem functions and services, and many studies have reported positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships in plant and animal systems. However, if the BEF relationship exists and how it evolves remains elusive in microbial systems. Here, we selected 12 Shewanella denitrifiers to construct synthetic denitrifying communities (SDCs) with a richness gradient spanning 1 to 12 species, which were subjected to approximately 180 days (with 60 transfers) of experimental evolution with generational changes in community functions continuously tracked. A significant positive correlation was observed between community richness and functions, represented by productivity (biomass) and denitrification rate, however, such a positive correlation was transient, only significant in earlier days (0 to 60) during the evolution experiment (180 days). Also, we found that community functions generally increased throughout the evolution experiment. Furthermore, microbial community functions with lower richness exhibited greater increases than those with higher richness. Biodiversity effect analysis revealed positive BEF relationships largely attributable to complementary effects, which were more pronounced in communities with lower richness than those with higher richness. This study is one of the first studies that advances our understanding of BEF relationships and their evolutionary mechanisms in microbial systems, highlighting the crucial role of evolution in predicting the BEF relationship in microbial systems. IMPORTANCE Despite the consensus that biodiversity supports ecosystem functioning, not all experimental models of macro-organisms support this notion with positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships reported. The fast-growing, metabolically versatile, and easy manipulation nature of microbial communities allows us to explore well the BEF relationship and further interrogate if the BEF relationship remains constant during long-term community evolution. Here, we constructed multiple synthetic denitrifying communities (SDCs) by randomly selecting species from a candidate pool of 12 Shewanella denitrifiers. These SDCs differ in species richness, spanning 1 to 12 species, and were monitored continuously for community functional shifts during approximately 180-day parallel cultivation. We demonstrated that the BEF relationship was dynamic with initially (day 0 to 60) greater productivity and denitrification among SDCs of higher richness. However, such pattern was reversed thereafter with greater productivity and denitrification increments in lower-richness SDCs, likely due to a greater accumulation of beneficial mutations during the experimental evolution.

A graph-based genome and pan-genome variation of the model plant Setaria

Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established the Setaria pan-genome by assembling 110 representative genomes from a worldwide collection. The pan-genome is composed of 73,528 gene families, of which 23.8%, 42.9%, 29.4% and 3.9% are core, soft core, dispensable and private genes, respectively; 202,884 nonredundant structural variants were also detected. The characterization of pan-genomic variants suggests their importance during foxtail millet domestication and improvement, as exemplified by the identification of the yield gene SiGW3, where a 366-bp presence/absence promoter variant accompanies gene expression variation. We developed a graph-based genome and performed large-scale genetic studies for 68 traits across 13 environments, identifying potential genes for millet improvement at different geographic sites. These can be used in marker-assisted breeding, genomic selection and genome editing to accelerate crop improvement under different climatic conditions.

[Identification of immune-related prognostic signature for colon adenocarcinoma based on weighted gene co-expression network analysis]

Objective To identify immune-related molecular markers in an attempt to predict prognosis of colon adenocarcinoma (COAD). Methods Immune related genes (IREGs) was analyzed based on the TCGA database. Weighted gene co-expression network analysis (WGCNA) and Cox regression analysis were used to establish risk models. According to the median risk score, COAD patients were divided into high risk and low risk groups. The prognostic difference were compared between the two groups. The function of the model was validated using GEO. Results A total of 1015 IREGs was obtained. The established model consisted of three genes: RAR related orphan receptor C (RORC), leucine-rich repeat Fli-I-interacting protein 2 (LRRFIP2) and lectin galactoside-binding soluble galectin 4 (LGALS4). The high-risk group had significantly poorer prognosis than low-risk group in the GEO database, and it was validated using a GEO database. Further analysis via univariate and multivariate Cox regression analyses revealed that risk model could function as independent prognostic factor for COAD patients. Conclusion The risk model based on IREGs can predict the prognosis of patients with COAD.

A comparative study of tea polyphenols and its palmitic acid-modified derivatives: their effects on the microbial ecosystem and biogenic amines in Chinese sausage

Control of biogenic amines (BAs) is important to guarantee the safety of sausage-like fermented meat products. This study investigated the influences of tea polyphenols (TP) and its lipophilic palmitic acid-modified derivatives, palmitoyl-TP (pTP) and palmitoyl-epigallocatechin gallate (pEGCG), on BAs and microbial ecosystem in Chinese sausages. TP, epigallocatechin gallate (EGCG), pTP, and pEGCG all reduced the formation of BAs and N-nitrosodimethylamine at 0.05% (g/g); yet, compared with TP and EGCG, the modified derivatives exhibited stronger action on BAs decreasing (P < 0.05), and pEGCG showed the highest effect (a reduction of total BAs from 376.22 to 168.98 mg/kg compared to control). The improved inhibitory effect of pTP and pEGCG should be attributed to their stronger dual-directional regulation of the bacterial and fungal communities during the natural fermentation of sausage. The modified pTP and pEGCG highly suppressed the growth of Staphylococcus, Candida, and Kurtzmaniella, all of which were positively correlated with BAs formation (all P < 0.05). However, pTP and pEGCG worked more effectively than the unmodified ones to promote Lactobacillus, Lactococcus, and Debaryomyces (all P < 0.05). The results above are significant for the application of palmitoyl-TP and similar TP derivatives in meat products in consideration of food safety.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05717-z.

Human-computer interaction based on background knowledge and emotion certainty

Aiming at the problems of lack of background knowledge and the inconsistent response of robots in the current human-computer interaction system, we proposed a human-computer interaction model based on a knowledge graph ripple network. The model simulated the natural human communication process to realize a more natural and intelligent human-computer interaction system. This study had three contributions: first, the affective friendliness of human-computer interaction was obtained by calculating the affective evaluation value and the emotional measurement of human-computer interaction. Then, the external knowledge graph was introduced as the background knowledge of the robot, and the conversation entity was embedded into the ripple network of the knowledge graph to obtain the potential entity content of interest of the participant. Finally, the robot replies based on emotional friendliness and content friendliness. The experimental results showed that, compared with the comparison models, the emotional friendliness and coherence of robots with background knowledge and emotional measurement effectively improve the response accuracy by 5.5% at least during human-computer interaction.

An E2-E3 pair contributes to seed size control in grain crops

Understanding the molecular mechanisms that regulate grain yield is important for improving agricultural productivity. Protein ubiquitination controls various aspects of plant growth but lacks understanding on how E2-E3 enzyme pairs impact grain yield in major crops. Here, we identified a RING-type E3 ligase SGD1 and its E2 partner SiUBC32 responsible for grain yield control in Setaria italica. The conserved role of SGD1 was observed in wheat, maize, and rice. Furthermore, SGD1 ubiquitinates the brassinosteroid receptor BRI1, stabilizing it and promoting plant growth. Overexpression of an elite SGD1 haplotype improved grain yield by about 12.8% per plant, and promote complex biological processes such as protein processing in endoplasmic reticulum, stress responses, photosystem stabilization, and nitrogen metabolism. Our research not only identifies the SiUBC32-SGD1-BRI1 genetic module that contributes to grain yield improvement but also provides a strategy for exploring key genes controlling important traits in Poaceae crops using the Setaria model system.

Prognostic and recurrent significance of SII in patients with pancreatic head cancer undergoing pancreaticoduodenectomy

Background

To investigate the clinical significance of preoperative inflammatory status in patients with pancreatic head carcinoma (PHC), we performed a single-center study to assess it.

Method

We studied a total of 164 patients with PHC undergoing PD surgery (with or without allogeneic venous replacement) from January 2018 to April 2022. Systemic immune-inflammation index (SII) was the most important peripheral immune index in predicting the prognosis according to XGBoost analysis. The optimal cutoff value of SII for OS was calculated according to Youden index based on the receiver operating characteristic (ROC) curve and the cohort was divided into Low SII group and High SII group. Demographic, clinical data, laboratory data, follow-up data variables were obtained and compared between the two groups. Kaplan-Meier curves, univariable and multivariable Cox regression models were used to determine the association between preoperative inflammation index, nutritional index and TNM staging system with OS and DFS respectively.

Results

The median follow-up time was 16 months (IQR 23), and 41.4% of recurrences occurred within 1 year. The cutoff value of SII was 563, with a sensitivity of 70.3%, and a specificity of 60.7%. Peripheral immune status was different between the two groups. Patients in High SII group had higher PAR, NLR than those in Low SII group (P <0.01, <0.01, respectively), and lower PNI (P <0.01). Kaplan-Meier analysis showed significantly poorer OS and DFS (P < 0.001, <0.001, respectively) in patients with high SII. By using the multivariable Cox regression model, high SII (HR, 2.056; 95% CI, 1.082-3.905, P=0.028) was significant predictor of OS. Of these 68 high-risk patients who recurrence within one year, patients with widespread metastasis had lower SII and worse prognosis (P <0.01).

Conclusion

High SII was significantly associated with poor prognosis in patients with PHC. However, in patients who recurrence within one year, SII was lower in patients at TNM stage III. Thus, care needs to be taken to differentiate those high-risk patients.

Integration of metabolomics and peptidomics reveals distinct molecular landscape of human diabetic kidney disease

Diabetic kidney disease (DKD) is the most common microvascular complication of diabetes, and there is an urgent need to discover reliable biomarkers for early diagnosis. Here, we established an effective urine multi-omics platform and integrated metabolomics and peptidomics to investigate the biological changes during DKD pathogenesis. Methods: Totally 766 volunteers (221 HC, 198 T2DM, 175 early DKD, 125 overt DKD, and 47 grey-zone T2DM patients with abnormal urinary mALB concentration) were included in this study. Non-targeted metabolic fingerprints of urine samples were acquired on matrix-free LDI-MS platform by the tip-contact extraction method using fluorinated ethylene propylene coated silicon nanowires chips (FEP@SiNWs), while peptide profiles hidden in urine samples were uncovered by MALDI-TOF MS after capturing urine peptides by porous silicon microparticles. Results: After multivariate analysis, ten metabolites and six peptides were verified to be stepwise regulated in different DKD stages. The altered metabolic pathways and biological processes associated with the DKD pathogenesis were concentrated in amino acid metabolism and cellular protein metabolic process, which were supported by renal transcriptomics. Interestingly, multi-omics significantly increased the diagnostic accuracy for both early DKD diagnosis and DKD status discrimination. Combined with machine learning, a stepwise prediction model was constructed and 89.9% of HC, 75.5% of T2DM, 69.6% of early DKD and 75.7% of overt DKD subjects in the external validation cohort were correctly classified. In addition, 87.5% of grey-zone patients were successfully distinguished from T2DM patients. Conclusion: This multi-omics platform displayed a satisfactory ability to explore molecular information and provided a new insight for establishing effective DKD management.

Insights into simultaneous nitrogen and phosphorus removal in biofilm: The overlooked comammox Nitrospira and the positive role of glycogen-accumulating organisms

Simultaneous nitrogen and phosphorus removal (SNPR) biofilm system is an effective wastewater treatment process. However, the understanding on the mechanism of functional microorganisms driving SNPR is still limited, especially the role of complete ammonia oxidation (comammox) Nitrospira and glycogen-accumulating organisms (GAO). In this study, a sequencing batch biofilm reactor (SBBR) performing SNPR was operated for 249 d. Based on the 16S rRNA gene, comammox amoA amplicon sequencing, metagenomics and batch experiment, we found that comammox Nitrospira was the main ammonia-oxidizing microorganisms (AOM) and provided nitrite for anaerobic ammonia oxidation (anammox) bacteria (AnAOB). Besides, GAO was dominated by the bacteria of genus Defluviicoccus and played a primary role in reducing nitrate rather than nitrite. Fluorescent in situ hybridization (FISH) analysis confirmed that Nitrospira was enriched in the inner layer of the biofilm. Thus, we put forward a novel insight into the mechanism of SNPR biofilm system. Comammox Nitrospira was responsible for nitrite and nitrate production in the inner biofilm, and AnAOB consumed the produced nitrite during the anammox process. While GAO reduced nitrate to nitrite and polyphosphate-accumulating organisms (PAO) converted nitrite to dinitrogen via denitrifying phosphorus removal in the outer biofilm. These findings provide a new understanding in SNPR biofilm system.

The modified properties of sludge-based biochar with ferric sulfate and its effectiveness in promoting carbon release from particulate organic matter in rural household wastewater

The scarcity of carbon sources presents a significant challenge for the bio-treatment of rural domestic wastewater (RDW). This paper presented an innovative approach to address this issue by investigating the supplementary carbon source through in-situ degradation of particulate organic matter (POM) facilitated by ferric sulfate modified sludge-based biochar (SBC). To prepare SBC, five different contents of ferric sulfate (0%, 10%, 20%, 25%, and 33.3%) were added to sewage sludge. The results revealed that the pore and surface of SBC were enhanced, providing active sites and functional groups to accelerate the biodegradation of protein and polysaccharide. During the 8-day hydrolysis period, the concentration of soluble chemical oxidation demand (SCOD) increased and peaked (1087-1156 mg L^-1) on the fourth day. The C/N ratio increased from 3.50 (control) to 5.39 (25% ferric sulfate). POM was degraded the five dominant phyla, which were Actinobacteriota, Firmicutes, Synergistota, Proteobacteria, and Bacteroidetes. Although the relative abundance of dominant phyla changed, the metabolic pathway remained unchanged. The leachate of SBC (<20% ferric sulfate) was beneficial for microbes, but an excessive amount of ferric sulfate (33.3% ferric sulfate) could have inhibition effects on bacteria. In conclusion, ferric sulfate modified SBC holds the potential for the carbon degradation of POM in RDW, and further improvements should be made in future studies.

Nano t-Se Peninsulas Embedded in Natively Oxidized 2D TiSe2 Enable Uniform and Fast Memristive Switching

Memristive devices, regardless of their potential applications in memory and computing scenarios, still suffer from large cycle-to-cycle and device-to-device variations due to the stochastic growth of conductive filaments (CFs). In this work, we fabricated a crossbar memristor using the 2D TiSe₂ material and then oxidized it into TiO₂ in the atmosphere at a moderate temperature. Such a mild oxidation approach fails to evaporate all Se into the air, and after further annealing using thermal or electrical stimulations, the remnant Se atoms gather near the interfaces and grow into nanosized crystals with relatively high conductivity. The resulting peninsula-shaped nanocrystals distort the electric field, forcing CFs to grow on them, which could largely confine the location and length of CFs. As a result, this two-terminal TiSe₂/TiO₂/TiSe₂ device exhibits excellent resistive switching performance with a fairly low threshold voltage (V_set < 0.8 V, V_reset > 0.55 V) and high cycle-to-cycle consistency, enabling resistive switching at narrow operating variations, e.g., 500 ± 48 and 845 ± 39 mV. Our work offers a new approach to minimize the cycle-to-cycle stochasticity of the memristive device, paving the way for its applications in data storage and brain-inspired computing.

Dynamic retention of thallium(I) on humic acid: Novel insights into the heterogeneous complexation ability and responsiveness

Widely distributed soil humic acid (HA) would significantly affect the environmental migration behavior of Tl(I), but a quantitative and mechanistic understanding of the dynamic Tl(I) retention process on HA is limited. A unified kinetic model was established by coupling the humic ion-binding model with a stirred-flow kinetic model, which quantified the complexation constants and responsiveness coefficients during dynamic Tl(I)-HA complexation. Furthermore, the heterogeneous complexation mechanism of HA and Tl(I) was revealed by batch adsorption experiments, stirred-flow migration experiments, and 2D-FTIR-COS analysis. An increase in pH significantly improved the responsiveness of HA organic binding sites, promoting Tl(I) dynamic retention. Monodentate carboxyl groups induced rapid Tl(I) complexation (k_d = 1.9 min^-1) in strongly acidic environments. Under weakly acidic conditions, Tl(I) retention on HA was mainly attributed to the synergistic complexation effect of carboxyl and amide groups. Among the groups, multidentate carboxyl-phenolic hydroxyl sites could achieve sustained Tl(I) retention due to their stable complexing properties (logK = 4.48∼7.46) and slow response (k_d = 1.1 × 10^-3 min^-1). These findings are crucial for a comprehensive understanding of the environmental interactions of Tl(I) with humic substances in swamp environments.

Application of cholecystic duct plasty in the prevention of biliary complications following orthotopic liver transplantation

Background

The purpose was aimed to evaluate the safety and effectiveness of cholecystic duct plasty (CDP) and biliary reconstruction techniques preventing biliary complications following orthotopic liver transplantation (OLT) first proposed by our center.

Methods

127 enrolled patients who underwent LT in our center from January 2015 to December 2019 were analyzed retrospectively. According to the mode of biliary tract reconstruction, patients were divided into CDP group (Group 1, n = 53) and control group (Group 2, n = 74). The differences of perioperative general data, biliary complications and long-term prognosis between two groups were compared and analyzed.

Results

All patients completed the operation successfully, the incidence of perioperative complications was 22.8%. There was no significant difference in perioperative general data and complications between the two groups. Follow-up ended in June 2020, with a median follow-up period of 31 months. During the follow-up period, biliary complications occurred in 26 patients, with an overall incidence of 20.5%. The overall incidence of biliary complications and anastomotic stenosis in Group 1 was lower than that in Group 2 (P < 0.05). There was no significant difference in overall prognosis between the two groups (P = 0.274), however, the cumulative incidence of biliary complications in Group 1 was lower than that in Group 2 (P = 0.035).

Conclusion

Reconstruction of common bile duct by CDP represents considerable safety and practicability, particularly for patients with small diameter of common bile duct or wide discrepancy of bile duct size between donor and recipient.

Self-organized mud cracking amplifies the resilience of an iconic "Red Beach" salt marsh

Self-organized patterning, resulting from the interplay of biological and physical processes, is widespread in nature. Studies have suggested that biologically triggered self-organization can amplify ecosystem resilience. However, if purely physical forms of self-organization play a similar role remains unknown. Desiccation soil cracking is a typical physical form of self-organization in coastal salt marshes and other ecosystems. Here, we show that physically self-organized mud cracking was an important facilitating process for the establishment of seepweeds in a "Red Beach" salt marsh in China. Transient mud cracks can promote plant survivorship by trapping seeds, and enhance germination and growth by increasing water infiltration in the soil, thus facilitating the formation of a persistent salt marsh landscape. Cracks can help the salt marsh withstand more intense droughts, leading to postponed collapse and faster recovery. These are indications of enhanced resilience. Our work highlights that self-organized landscapes sculpted by physical agents can play a critical role in ecosystem dynamics and resilience to climate change.

Dissecting the genetic basis of heterosis in elite super-hybrid rice

Y900 is one of the top hybrid rice (Oryza sativa) varieties, with its yield exceeding 15 t·hm-2. To dissect the mechanism of heterosis, we sequenced the male parent line R900 and female parent line Y58S using long-read and Hi-C technology. High-quality reference genomes of 396.41 Mb and 398.24 Mb were obtained for R900 and Y58S, respectively. Genome-wide variations between the parents were systematically identified, including 1,367,758 single-nucleotide polymorphisms, 299,149 insertions/deletions, and 4,757 structural variations. The level of variation between Y58S and R900 was the lowest among the comparisons of Y58S with other rice genomes. More than 75% of genes exhibited variation between the two parents. Compared with other two-line hybrids sharing the same female parent, the portion of Geng/japonica (GJ)-type genetic components from different male parents increased with yield increasing in their corresponding hybrids. Transcriptome analysis revealed that the partial dominance effect was the main genetic effect that constituted the heterosis of Y900. In the hybrid, both alleles from the two parents were expressed, and their expression patterns were dynamically regulated in different tissues. The cis-regulation was dominant for young panicle tissues, while trans-regulation was more common in leaf tissues. Overdominance was surprisingly prevalent in stems and more likely regulated by the trans-regulation mechanism. Additionally, R900 contained many excellent GJ haplotypes, such as NARROW LEAF1, Oryza sativa SQUAMOSA PROMOTER BINDING PROTEIN-LIKE13, and Grain number, plant height, and heading date8, making it a good complement to Y58S. The fine-tuned mechanism of heterosis involves genome-wide variation, GJ introgression, key functional genes, and dynamic gene/allele expression and regulation pattern changes in different tissues and growth stages.

Microbial Niche Differentiation during Nitrite-Dependent Anaerobic Methane Oxidation

Nitrite-dependent anaerobic methane oxidation (n-DAMO) has been demonstrated to play important roles in the global methane and nitrogen cycle. However, despite diverse n-DAMO bacteria widely detected in environments, little is known about their physiology for microbial niche differentiation. Here, we show the microbial niche differentiation of n-DAMO bacteria through long-term reactor operations combining genome-centered omics and kinetic analysis. With the same inoculum dominated by both species "Candidatus Methylomirabilis oxyfera" and "Candidatus Methylomirabilis sinica", n-DAMO bacterial population was shifted to "Ca. M. oxyfera" in a reactor fed with low-strength nitrite, but shifted to "Ca. M. sinica" with high-strength nitrite. Metatranscriptomic analysis showed that "Ca. M. oxyfera" harbored more complete function in cell chemotaxis, flagellar assembly, and two-component system for better uptake of nitrite, while "Ca. M. sinica" had a more active ion transport and stress response system, and more redundant function in nitrite reduction to mitigate nitrite inhibition. Importantly, the half-saturation constant of nitrite (0.057 mM vs 0.334 mM NO₂^-) and inhibition thresholds (0.932 mM vs 2.450 mM NO₂^-) for "Ca. M. oxyfera" vs "Ca. M. sinica", respectively, were highly consistent with genomic results. Integrating these findings demonstrated biochemical characteristics, especially the kinetics of nitrite affinity and inhibition determine niche differentiation of n-DAMO bacteria.

Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species

Effective utilization of wild relatives is key to overcoming challenges in genetic improvement of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher high-quality genomes for tomato wild species are insufficient. Here, we report chromosome-scale tomato genomes from nine wild species and two cultivated accessions, representative of Solanum section Lycopersicon, the tomato clade. Together with two previously released genomes, we elucidate the phylogeny of Lycopersicon and construct a section-wide gene repertoire. We reveal the landscape of structural variants and provide entry to the genomic diversity among tomato wild relatives, enabling the discovery of a wild tomato gene with the potential to increase yields of modern cultivated tomatoes. Construction of a graph-based genome enables structural-variant-based genome-wide association studies, identifying numerous signals associated with tomato flavor-related traits and fruit metabolites. The tomato super-pangenome resources will expedite biological studies and breeding of this globally important crop.

Effect of KMnO4/pH adjustment of extracellular polymeric substances under waste activated sludge on sludge dewatering

In this study, we examine the dewaterability of sludge after treatment by KMnO4 at various pH levels, with the goal of understanding the dewaterability of strong oxidizers to waste activated sludge. Good dewatering performance is observed, with capillary suction times (CST) reduced from 263.4 to 30.1 s, and specific resistance to filtration (SRF) falling by 19.6%. Proteins and polysaccharides in tightly bound extracellular polymeric substances (EPS) were also significantly reduced. Based on spectroscopic and electrochemical analysis, we propose mechanisms for the improved dewatering in terms of changes to the sludge's physicochemical properties and EPS. Under strong oxidation, the structure surrounding the bound water is oxidized and bound water is released, so the dewaterability of the sludge is improved.Weiliang Pan and Jiaoni Li contributed equally to this work.