Sampled-Data Model-Free Adaptive Control for Nonlinear Continuous-Time Systems.

This work aims at presenting a new sampled-data model-free adaptive control (SDMFAC) for continuous-time systems with the explicit use of sampling period and past input and output (I/O) data to enhance control performance. A sampled-data-based dynamical linearization model (SDDLM) is established to address the unknown nonlinearities and nonaffine structure of the continuous-time system, which all the complex uncertainties are compressed into a parameter gradient vector that is further estimated by designing a parameter updating law. By virtue of the SDDLM, we propose a new SDMFAC that not only can use both additional control information and sampling period information to improve control performance but also can restrain uncertainties by including a parameter adaptation mechanism. The proposed SDMFAC is data-driven and thus overcomes the problems caused by model-dependence as in the traditional control design methods. The simulation study is performed to demonstrate the validity of the results.

Biochar Decreases Cr Toxicity and Accumulation in Sunflower Grown in Cr(VI)-Polluted Soil.

Biochar is preferentially recommended for the remediation of heavy metal-polluted soils. Sunflower is an important high-biomass oil crop with a promising potential for phytoremediation of Cr(VI)-polluted soil. However, how biochar affects sunflower growth and Cr accumulation in Cr(VI)-polluted soil needs to be elucidated. Here, a pot culture experiment was conducted to study whether soil amendment with biochar (0, 0.1%, 1%, and 5%, w/w) can mitigate Cr toxicity and accumulation in sunflower seedlings grown in soils artificially polluted with different levels of Cr(VI) (0, 50, and 250 mg Cr(VI)/kg soil). The addition of Cr(VI) exhibited significant phytotoxicity, as evidenced by inhibited plant growth and even the death of seedlings at 250 mg/kg Cr(VI). Overall, biochar amendment showed positive effects on plant growth and Cr immobilization, dependent on both the biochar dose and Cr addition level. When 50 mg/kg Cr(VI) was added, 1% biochar showed positive effects similar to 5% biochar on improving plant growth and mineral nutrition (particularly K), reducing Cr content in shoots and roots, and decreasing Cr availability and Cr(VI) content in the soil. In comparison with non-amendment, 1% and 5% biochar caused 85% and 100% increase in shoot dry weights, and 75% and 86% reduction in shoot Cr concentrations, respectively. When 250 mg/kg Cr(VI) was added, a 5% dose produced much better benefits than 1%, while a 0.1% dose did not help plants to survive. Overall, an appropriate dose of biochar enhanced Cr(VI) immobilization and subsequently decreased its toxicity and accumulation in sunflower seedlings. Our findings confirm that biochar can be used as an efficient amendment for the remediation of Cr(VI)-polluted soils and cleaner production of sunflower oil and biomass.

Response of peanut plant and soil N-fixing bacterial communities to conventional and biodegradable microplastics.

Microplastics (MPs) occur and distribute widely in agroecosystems, posing a potential threat to soil-plant systems. However, little is known about their effects on legumes and N-fixing microbes. Here, we explored the effects of high-density polyethylene (HDPE), polystyrene (PS), and polylactic acid (PLA) on the growth of peanuts and soil N-fixing bacterial communities. All MPs treatments showed no phytotoxic effects on plant biomass, and PS and PLA even increased plant height, especially at the high dose. All MPs changed soil NO3--N and NH4+-N contents and the activities of urease and FDAse. Particularly, high-dose PLA decreased soil NO3--N content by 97% and increased soil urease activity by 104%. In most cases, MPs negatively affected plant N content, and high-dose PLA had the most pronounced effects. All MPs especially PLA changed soil N-fixing bacterial community structure. Symbiotic N-fixer Rhizoboales were greatly enriched by high-dose PLA, accompanied by the emergence of root nodulation, which may represent an adaptive strategy for peanuts to overcome N deficiency caused by PLA MPs pollution. Our findings indicate that MPs can change peanut-N fixing bacteria systems in a type- and dose-dependent manner, and biodegradable MPs may have more profound consequences for N biogeochemical cycling than traditional MPs.

Remediation Agents Drive Bacterial Community in a Cd-Contaminated Soil.

Soil remediation agents (SRAs) such as biochar and hydroxyapatite (HAP) have shown a promising prospect in in situ soil remediation programs and safe crop production. However, the effects of SRAs on soil microbial communities still remain unclear, particularly under field conditions. Here, a field case study was conducted to compare the effects of biochar and HAP on soil bacterial communities in a slightly Cd-contaminated farmland grown with sweet sorghum of different planting densities. We found that both biochar and HAP decreased the diversity and richness of soil bacteria, but they differently altered bacterial community structure. Biochar decreased Chao1 (-7.3%), Observed_species (-8.6%), and Shannon indexes (-1.3%), and HAP caused Shannon (-2.0%) and Simpson indexes (-0.1%) to decline. The relative abundance (RA) of some specific taxa and marker species was differently changed by biochar and HAP. Overall, sweet sorghum cultivation did not significantly alter soil bacterial diversity and richness but caused changes in the RA of some taxa. Some significant correlations were observed between soil properties and bacterial abundance. In conclusion, soil remediation with biochar and HAP caused alterations in soil bacterial communities. Our findings help to understand the ecological impacts of SRAs in soil remediation programs.

Recurrence risk assessment for stage III colorectal cancer based on five methylation biomarkers in plasma cell-free DNA.

For stage III colorectal cancer (CRC) patients with a high risk of recurrence, intensified adjuvant chemotherapy can improve overall survival. We aimed to develop a circulating tumor DNA (ctDNA) methylation marker model for predicting the relapse risk of stage III CRC patients. Differentially methylated markers identified between 53 normal mucosa samples and 165 CRC tissue samples, as well as between plasma samples from 75 stage I/II (early-stage) CRC patients and 55 stage IV (late-stage) CRC patients, were analyzed using Student's t-tests. The overlapping methylation markers shared by plasma and tissue samples were used to establish a methylation marker model to evaluate the tumor burden in the peripheral blood of CRC patients using the random forest method. This model was verified in the validation cohort (n = 44) and then applied to predict recurrence risk in 50 stage III CRC patients and monitor the clinical disease course in serial samples from four CRC patients. We built a five-marker-based ctDNA methylation model that had high sensitivity (84.21%) and specificity (84%) in identifying late-stage CRC in a validation cohort containing 24 stage I/II CRC patients and 20 stage IV CRC patients. The model achieved high sensitivity (87.5%) and specificity (94.12%) in predicting tumor relapse in an independent cohort of 50 stage III CRC patients and could be an independent recurrence risk factor for stage III patients [Hazard ratio (HR), 60.4; 95% confidence interval (CI): 7.68-397; p = 9.73e-5]. Analysis of serial blood samples of CRC showed that the model could monitor disease relapse earlier than imaging examination and serum carcinoembryonic antigen (CEA) and so may provide an opportunity for the early adjustment of therapeutic strategies. Moreover, the model could potentially monitor the clinical course and treatment response dynamically. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Effects of microplastics on cadmium accumulation by rice and arbuscular mycorrhizal fungal communities in cadmium-contaminated soil.

Both microplastics (MPs) and cadmium (Cd) are common contaminants in soil-rice systems, but their combined effects remain unknown. Thereby, we explored the effects of three MPs, i.e., polyethylene terephthalate (PET), polylactic acid (PLA), and polyester (PES), on Cd accumulation in rice and the community diversity and structure of arbuscular mycorrhizal fungi (AMF) in soil spiked with or without Cd. Results showed that 2% PLA decreased shoot biomass (-28%), but PET had a weaker inhibitive effect. Overall, Cd alone did not significantly change shoot and root biomass and increased root biomass in combination with 0.2% PES. MPs generally increased soil Cd availability but decreased Cd accumulation in rice tissues. Both MPs and Cd improved the bioavailability and uptake of Fe and Mn in rice roots. MPs altered the diversity and community composition of AMF, depending on their type and dose and co-existing Cd. Overall, 2% PLA caused the most distinct changes in soil properties, plant growth and Cd accumulation, and AMF communities, but showed no synergistic interactions with Cd. In conclusion, MPs can mediate rice performance and Cd accumulation via altering soil properties, nutrient uptake, and root mycorrhizal communities, and biodegradable PLA MPs thought environment-friendly can exhibit higher phytotoxicity than conventional MPs.

Seven DNA Methylation Biomarker Prediction Models for Monitoring the Malignant Progression From Advanced Adenoma to Colorectal Cancer.

Advanced adenoma (AA) holds a significantly increased risk for progression to colorectal cancer (CRC), and we developed a noninvasive DNA methylation prediction model to monitor the risk of AA progression to CRC. We analyzed the differential methylation markers between 53 normal mucosa and 138 CRC tissues, as well as those in cfDNA (cell-free DNA) between 59 AA and 68 early-stage CRC patients. We screened the overlapping markers between tissue DNA and cfDNA for model variables and optimized the selected variables. Then, we established a cfDNA methylation prediction model (SDMBP model) containing seven methylation markers that can effectively discriminate early-stage CRC and AA in the training and validation cohorts, and the AUC (area under the curve) reached 0.979 and 0.918, respectively. Our model also reached high precision (AUC=0.938) in detecting advanced CRC (stage III/IV) and presented better performance than serum CEA and CA199 in screening CRC. The cd-score of the SDMBP model could also robustly predict the TNM stage of CRC. Overall, our SDMBP model can monitor the malignant progression from AA to CRC, and may provide a noninvasive monitoring method for high-risk populations with AA.

Effects of microplastics and carbon nanotubes on soil geochemical properties and bacterial communities.

A 100-day soil incubation experiment was conducted to explore the effects of conventional (high-density polyethylene, HDPE) and biodegradable (polylactic acid, PLA) microplastics (MPs) and multiwall carbon nanotubes (MWCNTs) on soil geochemical properties and bacterial communities. Generally, soil pH was increased by 10% HDPE and 10% PLA, but decreased by increasing MWCNTs. Soil dissolved organic carbon content was only increased by 10% PLA. NO3--N content was significantly decreased by MPs, with a decrement of 99% by 10% PLA. Similarly, available P content was reduced by 10% MPs. The activities of urease and alkaline phosphatase were stimulated by 10% PLA, but generally inhibited by HDPE. Conversely, FDAse activity was stimulated by HDPE, but inhibited by 10% PLA, whereas invertase activity decreased with increasing MWCNTs. Overall, both MPs and MWCNTs changed soil bacterial diversity. Co-exposure to 10% MPs and MWCNTs of 1 and 10 mg/kg caused the lowest species richness and Shannon indexes. MPs especially at the 10% dose changed bacterial community composition and the associated metabolic pathways, causing the enrichment of specific taxa and functional genes. Our findings show that conventional and biodegradable MPs differently change soil geochemical properties and microbial community structure and functions, which can be further modified by co-existing MWCNTs.

Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function.

BACKGROUND: Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results. RESULTS: Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS. CONCLUSIONS: This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub ( https://github.com/qibebt-bioinfo/meta-apo ) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.

Identification of Different Form Tim-3 Proteins by a Unique Set of Tim-3 Monoclonal Antibodies.

T-cell immunoglobulin and mucin domain-3 (Tim-3) has been suggested to be a critical immune checkpoint target for cancer immunotherapy. However, limited progress with Tim-3 immunotherapy has been achieved over the last decade due to the lack of specific Tim-3 monoclonal antibodies. In this study, we have successfully developed a unique set of Tim-3 antibodies that are able to detect different molecular weights (by Western blot mobility) of Tim-3 proteins ectopically expressed in the same CHO cells. Some of the antibody clones detect only 33 or 55 kDa bands, the rest can recognize both 33 and 55 kDa bands on polyacrylamide gel electrophoresis gel. Antibody clones with 55 kDa specificity uniquely bind to the membrane form of Tim-3 on macrophage, which colocalizes with the CD68, and could be used as a specific marker for tumor-associated macrophage, whereas other clones showed cytoplasmic staining in tumor cells. The membrane form of Tim-3 on tumor-associated macrophages may bear significant roles for clinical application of Tim-3, but less likely for cytoplasmic one. The availability of this unique set of antibodies will be critical for an ultimate understanding of Tim-3 function in tumor microenvironment and potential clinical applications.