Diagnostic performance of machine learning in systemic infection following percutaneous nephrolithotomy and identification of associated risk factors.

Objective: This study aims to investigate the predictive performance of machine learning in predicting the occurrence of systemic inflammatory response syndrome (SIRS) and urosepsis after percutaneous nephrolithotomy (PCNL). Methods: A retrospective analysis was conducted on patients who underwent PCNL treatment between January 2016 and July 2022. Machine learning techniques were employed to establish and select the best predictive model for postoperative systemic infection. The feasibility of using relevant risk factors as predictive markers was explored through interpretability with Machine Learning. Results: A total of 1067 PCNL patients were included in this study, with 111 (10.4 %) patients developing SIRS and 49 (4.5 %) patients developing urosepsis. In the validation set, the risk model based on the GBM protocol demonstrated a predictive power of 0.871 for SIRS and 0.854 for urosepsis. Preoperative and postoperative platelet changes were identified as the most significant predictors. Both thrombocytopenia and thrombocytosis were found to be risk factors for SIRS or urosepsis after PCNL. Furthermore, it was observed that when the change in platelet count before and after PCNL surgery exceeded 30*109/L (whether an increase or decrease), the risk of developing SIRS or urosepsis significantly increased. Conclusion: Machine learning can be effectively utilized for predicting the occurrence of SIRS or urosepsis after PCNL. The changes in platelet count before and after PCNL surgery serve as important predictors.

Elucidating the reversible and irreversible self-assembly mechanisms of low-complexity aromatic-rich kinked peptides and steric zipper peptides.

Many RNA-binding proteins such as fused-in sarcoma (FUS) can self-assemble into reversible liquid droplets and fibrils through the self-association of their low-complexity (LC) domains. Recent experiments have revealed that SYG-rich segments in the FUS LC domains play critical roles in the reversible self-assembly behaviors of FUS. These FUS LC segments alone can self-assemble into reversible kinked fibrils, which are markedly different from the canonical irreversible steric zipper ß-sheet fibrils. However, the molecular determinants underlying the reversible and irreversible self-assembly are poorly understood. Herein we conducted extensive all-atom and coarse-grained molecular dynamics simulations of four representative hexapeptides: two low-complexity aromatic-rich kinked peptides from the amyotrophic lateral sclerosis-related FUS protein, FUS37-42 (SYSGYS) and FUS54-59 (SYSSYG); and two steric zipper peptides from Alzheimer's-associated Aß and Tau proteins, Aß16-21 (KLVFFA) and Tau306-311 (VQIVYK). We dissected their reversible and irreversible self-assembly dynamics, predicted their phase separation behaviors, and elucidated the underpinning molecular interactions. Our simulations showed that alternating stickers (Tyr) and spacers (Gly and Ser) in FUS37-42 and FUS54-59 facilitate the formation of highly dynamic coil-rich oligomers and lead to reversible self-assembly, while consecutive hydrophobic residues of LVFF in Aß16-21 and IVY in Tau306-311 act as hydrophobic patches, favoring the formation of stable ß-sheet-rich oligomers and driving the irreversible self-assembly. Intriguingly, we found that FUS37-42 and FUS54-59 peptides, possessing the same amino acid composition and the same number of sticker and spacer residues, display differential self-assembly propensities. This finding suggests that the self-assembly behaviors of FUS peptides are fine-tuned by the site-specific patterning of spacer residues (Ser and Gly). This study provides significant mechanistic insights into reversible and irreversible peptide self-assembly, which would be helpful for understanding the molecular mechanisms underlying the formation of biological liquid condensates and pathological solid amyloid fibrils.

The effects of iron-based nanomaterials (Fe NMs) on plants under stressful environments: Machine learning-assisted meta-analysis.

Mitigating the adverse effects of stressful environments on crops and promoting plant recovery in contaminated sites are critical to agricultural development and environmental remediation. Iron-based nanomaterials (Fe NMs) can be used as environmentally friendly nano-fertilizer and as a means of ecological remediation. A meta-analysis was conducted on 58 independent studies from around the world to evaluate the effects of Fe NMs on plant development and antioxidant defense systems in stressful environments. The application of Fe NMs significantly enhanced plant biomass (mean = 25%, CI = 20%-30%), while promoting antioxidant enzyme activity (mean = 14%, CI = 10%-18%) and increasing antioxidant metabolite content (mean = 10%, CI = 6%-14%), reducing plant oxidative stress (mean = -15%, CI = -20%∼-10%), and alleviating the toxic effects of stressful environments. The observed response was dependent on a number of factors, which were ranked in terms of a Random Forest Importance Analysis. Plant species was the most significant factor, followed by Fe NM particle size, duration of application, dose level, and Fe NM type. The meta-analysis has demonstrated the potential of Fe NMs in achieving sustainable agriculture and the future development of phytoremediation.

Boosted elimination of florfenicol by BiOClxBr1-x solid solutions via photocatalytic ozonation under visible light.

In this work, a series of BiOClxBr1-x (BCB) solid solutions are facilely designed for visible-light-driven photocatalytic ozonation (PCO) degradation of florfenicol (FF) in water environments, which could add to the library of efficient, cost-effective and robust nanocatalysts for water purification. BCB solid solutions in the structure of 2D nanosheets are achieved involving the etching of BiOBr "micro-flowers" with HCl at different concentrations, allowing a removal ratio of FF up to 97.3 % within 1 h, superior to bare BiOBr and bare BiOCl. A strengthened synergistic effect between photocatalysis and ozonation is substantiated, where the separation of photo-induced charge transfer is accelerated, the band gap is tuned and the utilization efficiency of ozone is enhanced. This facilitates the production of reactive oxygen species identified as •OH, •O2-, and 1O2 that will attack the FF molecule for degradation based on three pathways.

Enhancing water purification through F and Zn-modified Fe-MCM-41 catalytic ozonation.

Due to its low interfacial electron migration ability and highly hydrophilic, Fe-MCM-41 (FeM) had poor activity and stability during catalytic ozonation. To this end, the secondary metal Zn and Si-F group were introduced into the framework of FeM to create surface potential difference and hydrophobic sites. Comparative characterizations showed that there existed rich acid sites with great potential difference on F-Fe-Zn-MCM-41 (FFeZnM). Additionally, because of the existence of hydrophobic and electron-withdrawing Si-F unit, the electron migration ability, hydrophobicity and acidity of FFeZnM were enhanced. The greater O3 mass transfer was induced by Si-F group and O3 was directly activated at Fe and Zn Lewis acid sites into •OH, •O2- and 1O2. With •OH acting as main species, FFeZnM/O3 achieved the superior IBP removal (93.4%, 30 min) and TOC removal (46.6%, 120 min) over those of sole O3 and F-FeM/O3 processes, respectively. HCO3-, Cl-, NO3- and SO42- hindered IBP degradation by FFeZnM/O3, but high concentration humic acid (HA) exhibited promotion by forming HA-IBP complex. IBP degradation by FFeZnM/O3 was enhanced with tap water, river water, and effluent from the secondary sedimentation tank of the sewage plant acting as medium. This study proposed an innovative approach to catalyst design for catalytic ozonation.

Procoagulant genes may affect angiogenesis, epithelial-mesenchymal transition, survival prognosis and tumor immune microenvironment in patients with urothelial carcinoma.

Factors related to coagulation regulation are closely related to angiogenesis, epithelial-mesenchymal transition, tumor proliferation and metastasis, and tumor immune microenvironment remodeling in tumors. To date, there are no quantitative indicators of coagulation associated with urothelial cancer. We classified urothelial cancer into high coagulation and low coagulation subtypes by screening for procoagulant-related molecular features and screened out relevant genes representing the coagulation state of urothelial carcinoma. Tumors with increased procoagulant gene expression were consistently associated with higher T-staging (p < 0.001), lymph node metastasis (p < 0.001), stage (p < 0.001), and grade (p = 0.046). Furthermore, high expression of procoagulant genes predicts a worse prognosis, a higher tumor proliferation rate and increased angiogenesis within the tumor. In addition, according to cibersort algorithm, the increased expression of procoagulant gene was negatively correlated with the degree of T-lymphocyte infiltration and positively correlated with the degree of M2 macrophage infiltration. Increased expression of procoagulant genes in data sets treated with immune checkpoints also predicted worse response and worse prognosis. At the same time, the expression of procoagulant genes in bladder cancer promoted the activation of coagulation, EMT, TGF-ß and WNT pathways.

Effects of the application of nanoscale zero-valent iron on plants: Meta analysis, mechanism, and prospects.

In order to determine the ideal conditions for the application of nanoscale zero-valent iron (nZVI) in agricultural production, this review studies the effects of nZVI application on plant physiological parameters, presents its mechanism and prospective outcomes. In this research, it was observed that the application of nZVI had both favorable and unfavorable effects on plant growth, photosynthesis, oxidative stress, and nutrient absorption levels. Specifically, the application of nZVI significantly increased the biomass and length of plants, and greatly reduced the germination rate of seeds. In terms of photosynthesis, there was no significant effect for the application of nZVI on the synthesis of photosynthetic pigments (chlorophyll and carotenoids). In terms of oxidative stress, plants respond by increasing the activity of antioxidant enzyme under mild nZVI stress and trigger oxidative burst under severe stress. In addition, the application of nZVI significantly increased the absorption of nutrients (B, K, P, S, Mg, Zn, and Fe). In summary, the application of nZVI can affect the plant physiological parameters, and the degree of influence varies depending on the concentration, preparation method, application method, particle size, and action time of nZVI. These findings are important for evaluating nZVI-related risks and enhancing nZVI safety in agricultural production.

Knowledge-Induced Multiple Kernel Fuzzy Clustering.

The introduction of domain knowledge opens new horizons to fuzzy clustering. Then knowledge-driven and data-driven fuzzy clustering methods come into being. To address the challenges of inadequate extraction mechanism and imperfect fusion mode in such class of methods, we propose the Knowledge-induced Multiple Kernel Fuzzy Clustering (KMKFC) algorithm. First, to extract knowledge points better, the Relative Density-based Knowledge Extraction (RDKE) method is proposed to extract high-density knowledge points close to cluster centers of real data structure, and provide initialized cluster centers. Moreover, the multiple kernel mechanism is introduced to improve the adaptability of clustering algorithm and map data to high-dimensional space, so as to better discover the differences between the data and obtain superior clustering results. Second, knowledge points generated by RDKE are integrated into KMKFC through a knowledge-influence matrix to guide the iterative process of KMKFC. Third, we also provide a strategy of automatically obtaining knowledge points, and thus propose the RDKE with Automatic knowledge acquisition (RDKE-A) method and the corresponding KMKFC-A algorithm. Then we prove the convergence of KMKFC and KMKFC-A. Finally, experimental studies demonstrate that the KMKFC and KMKFC-A algorithms perform better than thirteen comparison algorithms with regard to four evaluation indexes and the convergence speed.

Single-cell and spatial transcriptomics reveal 5-methylcytosine RNA methylation regulators immunologically reprograms tumor microenvironment characterizations, immunotherapy response and precision treatment of clear cell renal cell carcinoma.

Clear cell Renal Cell Carcinoma (ccRCC) is a highly heterogeneous disease, making it challenging to predict prognosis and therapy efficacy. In this study, we aimed to explore the role of 5-methylcytosine (m5C) RNA modification in ccRCC and its potential as a predictor for therapy response and overall survival (OS). We established a novel 5-methylcytosine RNA modification-related gene index (M5CRMRGI) and studied its effect on the tumor microenvironment (TME) using single-cell sequencing data for in-depth analysis, and verified it using spatial sequencing data. Our results showed that M5CRMRGI is an independent predictor of OS in multiple datasets and exhibited outstanding performance in predicting the OS of ccRCC. Distinct mutation profiles, hallmark pathways, and infiltration of immune cells in TME were observed between high- and low-M5CRMRGI groups. Single-cell/spatial transcriptomics revealed that M5CRMRGI could reprogram the distribution of tumor-infiltrating immune cells. Moreover, significant differences in tumor immunogenicity and tumor immune dysfunction and exclusion (TIDE) were observed between the two risk groups, suggesting a better response to immune checkpoint blockade therapy of the high-risk group. We also predicted six potential drugs binding to the core target of the M5CRMRGI signature via molecular docking. Real-world treatment cohort data proved once again that high-risk patients were appropriate for immune checkpoint blockade therapy, while low-risk patients were appropriate for Everolimus. Our study shows that the m5C modification landscape plays a role in TME distribution. The proposed M5CRMRGI-guided strategy for predicting survival and immunotherapy efficacy, we reported here, might also be applied to more cancers other than ccRCC.

Iron clusters regulate local charge distribution in Fe-N4 sites to boost oxygen electroreduction.

The atomically-dispersed and nitrogen-coordinated iron (FeNC) on a carbon catalyst is a potential non-noble metal catalyst that can replace precious metal electrocatalysts. However, its activity is often unsatisfactory owing to the symmetric charge distribution around the iron matrix. In this study, atomically- dispersed Fe-N4 and Fe nanoclusters loaded with N-doped porous carbon (FeNCs/FeSAs-NC-Z8@34) were rationally fabricated by introducing homologous metal clusters and increasing the N content of the support. FeNCs/FeSAs-NC-Z8@34 exhibited a half-wave potential of 0.918 V, which exceeded that of the commercial benchmark Pt/C catalyst. Theoretical calculations verified that introducing Fe nanoclusters can break the symmetric electronic structure of Fe-N4, thus inducing charge redistribution. Furthermore, it can optimize a part of Fe 3d occupancy orbitals and accelerate OO fracture in OOH* (rate-determining step), thus significantly improving oxygen reduction reaction activity. This work provides a reasonably advanced pathway to modulate the electronic structure of the single-atom center and optimize the catalytic activity of single-atom catalysts.

Accuracy of intravascular ultrasound-derived virtual fractional flow reserve (FFR) and FFR derived from computed tomography for functional assessment of coronary artery disease.

BACKGROUND: Coronary computed tomography-derived fractional flow reserve (CT-FFR) and intravascular ultrasound-derived fractional flow reserve (IVUS-FFR) are two functional assessment methods for coronary stenoses. However, the calculation algorithms for these methods differ significantly. This study aimed to compare the diagnostic performance of CT-FFR and IVUS-FFR using invasive fractional flow reserve (FFR) as the reference standard. METHODS: Six hundred and seventy patients (698 lesions) with known or suspected coronary artery disease were screened for this retrospective analysis between January 2020 and July 2021. A total of 40 patients (41 lesions) underwent intravascular ultrasound (IVUS) and FFR evaluations within six months after completing coronary CT angiography were included. Two novel CFD-based models (AccuFFRct and AccuFFRivus) were used to compute the CT-FFR and IVUS-FFR values, respectively. The invasive FFR ≤ 0.80 was used as the reference standard for evaluating the diagnostic performance of CT-FFR and IVUS-FFR. RESULTS: Both AccuFFRivus and AccuFFRct demonstrated a strong correlation with invasive FFR (R = 0.7913, P < 0.0001; and R = 0.6296, P < 0.0001), and both methods showed good agreement with FFR. The area under the receiver operating characteristic curve was 0.960 (P < 0.001) for AccuFFRivus and 0.897 (P < 0.001) for AccuFFRct in predicting FFR ≤ 0.80. FFR ≤ 0.80 were predicted with high sensitivity (96.6%), specificity (85.7%), and the Youden index (0.823) using the same cutoff value of 0.80 for AccuFFRivus. A good diagnostic performance (sensitivity 89.7%, specificity 85.7%, and Youden index 0.754) was also demonstrated by AccuFFRct. CONCLUSIONS: AccuFFRivus, computed from IVUS images, exhibited a high diagnostic performance for detecting myocardial ischemia. It demonstrated better diagnostic power than AccuFFRct, and could serve as an accurate computational tool for ischemia diagnosis and assist in clinical decision-making.

Robot-assisted partial nephrectomy for large complex renal cancer: step-by-step segmental artery unclamping

ABSTRACT Introduction Main renal artery clamping and selective arterial clamping are two conventional devascularization methods for robot-assisted partial nephrectomy (RAPN) (1, 2). Decreasing warm ischemic (WI) time (3, 4) and improving clear surgical visualization (5) are the main surgically modifiable factors for RAPN, especially in large complex renal cancer (6). In this study, we described our surgical technique, focusing on gradual segmental artery unclamping on patients with large renal tumors. Material and methods Two patients (R.E.N.A.L score 10 and 11) underwent RAPN with gradual segmental artery unclamping (Figures 1 and 2). The unclamping included five key steps. First, all renal segmental arteries were identified as tumor feeding vessel(s) and the vessels for normal kidney parenchyma under the guidance of CT angiography (CTA) 3-division (3D) reconstruction. Second, all segmental arteries were isolated, and the feeding one(s) should be blocked before other arteries were blocked. Third, the tumor was resected outside the pseudocapsule, and the deep resection bed was sutured for initial hemostasis. Fourth, the segmental arteries were reopened except for the tumor feeding one(s), and normal kidney parenchyma restored blood supply. And fifth, the resection bed was completely sutured, and the feeding vessel supplying the tumor was opened after the suture. Warm ischemia time (WIT) was defined as the time measured between clamping and unclamping of the renal artery. WIT1 was the time for normal kidney parenchyma and WIT2 was the time for resection area. Patient demographics, perioperative variables, and warm ischemic time were included in our study. And we presented the details of gradual segmental artery unclamping in the video. Results In both cases, the total operation times were 215 and 130 mins for patient 1 and patient 2, respectively. WIT1 and WIT2 for patient 1 were 15 min and 33 min., and WIT1 and WIT2 for patient 2 were 21 min and 32 min, respectivelly. The maximum diameters of the masses resected were 10.8 and 7.3 cm, and surgical margins were negative. No patient had complications after operation. Preoperative and postoperative eGFR did not change significantly. Pre- and postoperative eGFR were 111 and 108 mL/min for patient 1, 91 and 83 mL/min for patient 2, respectively. Key hints for outcomes optimization during RAPN on patients with large complex renal tumors: 1) Each segmental renal artery is precised clamped before we excise the tumor, and an excellent surgical vision is essential for precising excision and shortening clamping time, 2) Other segmental renal arteries are unclamped except tumor feeding branch after suturing deep layer of parenchyma, and most normal parenchyma restores blood supply, 3) Preoperative high-resolution computed tomography angiography (CTA) and 3D reconstructive renal structure serve as a guide to clear the approach to find the tumor and segmental arteries (7, 8). Conclusions Gradual segmental artery unclamping is feasible and efficient to excise large complex renal cancer. Compared with main renal artery clamping, it can shorten the warm ischemic time of normal parenchyma; On the other hand, compared with selective segmental arterial clamping, the technique can reduce bleeding from the deep resection bed, keep a clear surgical vision, and decrease the incidence of positive margin.

Naphthoquinone-dopamine hybrids disrupt α-synuclein fibrils by their intramolecular synergistic interactions with fibrils and display a better effect on fibril disruption.

α-Synuclein (αSyn) is an intrinsically disordered protein and its abnormal aggregation into amyloid fibrils is the main hallmark of Parkinson's disease (PD). The disruption of preformed αSyn fibrils using small molecules is considered as a potential strategy for PD treatment. Recent experiments have reported that naphthoquinone-dopamine hybrids (NQDA), synthesized by naphthoquinone (NQ) and dopamine (DA) molecules, can significantly disrupt αSyn fibrils and cross the blood-brain barrier. To unravel the fibril-disruptive mechanisms at the atomic level, we performed microsecond molecular dynamics simulations of αSyn fibrils in the absence and presence of NQDA, NQ, DA, or NQ+DA molecules. Our simulations showed that NQDA reduces the ß-sheet content, disrupts K45-E57 and E46-K80 salt-bridges, weakens the inter-protofibril interaction, and thus destabilizes the αSyn fibril structure. NQDA has the ability to form cation-π and H-bonding interactions with K45/K80, and form π-π stacking interactions with Y39/F94. Those interactions between NQDA and αSyn fibrils play a crucial role in disaggregating αSyn fibrils. Moreover, we found that NQDA has a better fibril destabilization effect than that of NQ, DA, and NQ+DA molecules. This is attributed to the synergistic fibril-binding effect between NQ and DA groups in NQDA molecules. The DA group can form strong π-π stacking interactions with aromatic residues Y39/F94 of the αSyn fibril, while the DA molecule cannot. In addition, NQDA can form stronger cation-π interactions with residues K45/K80 than those of both NQ and DA molecules. Our results provide the molecular mechanism underlying the disaggregation of the αSyn fibril by NQDA and its better performance in fibril disruption than NQ, DA, and NQ+DA molecules, which offers new clues for the screening and development of promising drug candidates to treat PD.

Dissecting the Effect of ALS Mutation G335D on the Early Aggregation of the TDP-43 Amyloidogenic Core Peptide: Helix-to-ß-Sheet Transition and Conformational Shift.

The aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) into fibrillary deposits is associated with amyotrophic lateral sclerosis (ALS). The 311-360 fragment of TDP-43 (TDP-43311-360), the amyloidogenic core region, can spontaneously aggregate into fibrils, and the ALS-associated mutation G335D has an enhanced effect on TDP-43311-360 fibrillization. However, the molecular mechanism underlying G335D-enhanced aggregation at atomic level remains largely unknown. By utilizing all-atom molecular dynamics (MD) and replica exchange with solute tempering 2 (REST2) simulations, we investigated influences of G335D on the dimerization (the first step of aggregation) and conformational ensemble of the TDP-43311-360 peptide. Our simulations show that G335D mutation increases inter-peptide interactions, especially inter-peptide hydrogen-bonding interactions in which the mutant site has a relatively large contribution, and enhances the dimerization of TDP-43311-360 peptides. The α-helix regions in the NMR-resolved conformation of the TDP-43311-360 monomer (321-330 and 335-343) play an essential role in the formation of the dimer. G335D mutation induces helix unfolding and promotes α-to-ß conversion. G335D mutation alters the conformational distribution of TDP-43311-360 dimers and causes population shift from helix-rich to ß-sheet-rich conformations, which facilitates the fibrillization of the TDP-43311-360 peptide. Our MD and REST2 simulation results suggest that the 321-330 region is of paramount importance to α-to-ß transition and could be the initiation site for TDP-43311-360 fibrillization. Our work reveals the mechanism underlying the enhanced aggregation propensity of the G335D TDP-43311-360 peptide, which provides atomistic insights into the G335D mutation-caused pathogenicity of TDP-43 protein.

A Fuzzy Clustering Validity Index Induced by Triple Center Relation.

The existing clustering validity indexes (CVIs) show some difficulties to produce the correct cluster number when some cluster centers are close to each other, and the separation processing mechanism appears simple. The results are imperfect in case of noisy data sets. For this reason, in this study, we come up with a novel CVI for fuzzy clustering, referred to as the triple center relation (TCR) index. The originality of this index is twofold. On the one hand, a new fuzzy cardinality is built on the strength of the maximum membership degree, and a novel compactness formula is constructed by combining it with the within-class weighted squared error sum. On the other hand, starting from the minimum distance between different cluster centers, the mean distance as well as the sample variance of cluster centers in the statistical sense are further integrated. These three factors are combined by means of product to form a triple characterization of the relationship between cluster centers, and hence a 3-D expression pattern of separability is formed. Subsequently, the TCR index is put forward by combining the compactness formula with the separability expression pattern. By virtue of the degenerate structure of hard clustering, we show an important property of the TCR index. Finally, based on the fuzzy C -means (FCMs) clustering algorithm, experimental studies were conducted on 36 data sets (incorporating artificial and UCI data sets, images, the Olivetti face database). For comparative purposes, 10 CVIs were also considered. It has been found that the proposed TCR index performs best in finding the correct cluster number, and has excellent stability.

Dissecting how ALS-associated D290V mutation enhances pathogenic aggregation of hnRNPA2286-291 peptides: Dynamics and conformational ensembles.

The aggregation of RNA binding proteins, including hnRNPA1/2, TDP-43 and FUS, is heavily implicated in causing or increasing disease risk for a series of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). A recent experimental study demonstrated that an ALS-related D290V mutation in the low complexity domain (LCD) of hnRNPA2 can enhance the aggregation propensity of wild type (WT) hnRNPA2286-291 peptide. However, the underlying molecular mechanisms remain elusive. Herein, we investigated effects of D290V mutation on aggregation dynamics of hnRNPA2286-291 peptide and the conformational ensemble of hnRNPA2286-291 oligomers by performing all-atom molecular dynamic and replica-exchange molecular dynamic simulations. Our simulations demonstrate that D290V mutation greatly reduces the dynamics of hnRNPA2286-291 peptide and that D290V oligomers possess higher compactness and ß-sheet content than WT, indicative of mutation-enhanced aggregation capability. Specifically, D290V mutation strengthens inter-peptide hydrophobic, main-chain hydrogen bonding and side-chain aromatic stacking interactions. Those interactions collectively lead to the enhancement of aggregation capability of hnRNPA2286-291 peptides. Overall, our study provides insights into the dynamics and thermodynamic mechanisms underlying D290V-induced disease-causing aggregation of hnRNPA2286-291, which could contribute to better understanding of the transitions from reversible condensates to irreversible pathogenic aggregates of hnRNPA2 LCD in ALS-related diseases.

Mitigating soil salinity stress with titanium gypsum and biochar composite materials: Improvement effects and mechanism.

Titanium gypsum and biochar are considered effective amendments for mitigating soil salinity stress. However, the knowledge is inadequate regarding their efficiency and application as an improvement. In this study, TG-B composite was prepared by using industrial by-products titanium gypsum and biochar as raw materials and then modified by ball milling method, to characterize its microscopic characteristics and explore the improvement effect on saline-alkali soil and plant growth. Besides, we explored the mechanism of TG-B in improving saline-alkali soil and the dynamic balance of the solution reaction process. Our results showed that the CaSO4·2H2O particles in TG-B were finer, dispersed evenly, and contacted fully with soil gelatinous particles, which was more conducive to the improvement of saline-alkali soil. The results of TG-B with different ball milling ratios and different materials dosages indicated that the application rate of TG-B was 5%, and the optimum ratio of TG-B was TG: B (mass ratio) = 10:1, with the best soil improvement effect. The pot experiment proved that the indicators of indicating soil salinity such as pH, EC, SAR, and soluble Na+ decreased by 20.74%, 77.24%, 68.77%, and 44.70%, respectively, thus playing a good role in improving saline-alkali soil. In addition, pot experiments demonstrated that compared with the control group, the soil porosity and soil moisture content in the TG-B group increased by 15.95% and 38.71%, respectively, and further improve the structure and diversity of soil bacterial community when compared with titanium gypsum and biochar alone. Finally, the application of TG-B promoted the germination and growth of rice significantly through the synergistic effects of composite material components. These results all suggested that the application of TG-B was an effective strategy to improve soil salinity and promote plant growth. Therefore, it might provide new insights into the utilization of solid waste resources to improve saline-alkali lands.

Influence of ALS-linked M337V mutation on the conformational ensembles of TDP-43321-340 peptide monomer and dimer.

The transactive response (TAR) DNA/RNA-binding protein 43 (TDP-43) can self-assemble into both functional stress granules via liquid-liquid phase separation (LLPS) and pathogenic amyloid fibrillary aggregates that are closely linked to amyotrophic lateral sclerosis. Previous experimental studies reported that the low complexity domain (LCD) of TDP-43 plays an essential role in the LLPS and aggregation of the full-length protein, and it alone can also undergo LLPS to form liquid droplets mainly via intermolecular interactions in the 321-340 region. And the ALS-associated M337V mutation impairs LCD's LLPS and facilitates liquid-solid phase transition. However, the underlying atomistic mechanism is not well understood. Herein, as a first step to understand the M337V-caused LLPS disruption of TDP-43 LCD mediated by the 321-340 region and the fibrillization enhancement, we investigated the conformational properties of monomer/dimer of TDP-43321-340 peptide and its M337V mutant by performing extensive all-atom explicit-solvent replica exchange molecular dynamic simulations. Our simulations demonstrate that M337V mutation alters the residue regions with high helix/ß-structure propensities and thus affects the conformational ensembles of both monomer and dimer. M337V mutation inhibits helix formation in the N-terminal Ala-rich region and the C-terminal mutation site region, while facilitating their long ß-sheet formation, albeit with a minor impact on the average probability of both helix structure and ß-structure. Further analysis of dimer system shows that M337V mutation disrupts inter-molecular helix-helix interactions and W334-W334 π-π stacking interactions which were reported to be important for the LLPS of TDP-43 LCD, whereas enhances the overall peptide residue-residue interactions and weakens peptide-water interactions, which is conducive to peptide fibrillization. This study provides mechanistic insights into the M337V-mutation-induced impairment of phase separation and facilitation of fibril formation of TDP-43 LCD.

Robot-assisted partial nephrectomy for large complex renal cancer: step-by-step segmental artery unclamping.

INTRODUCTION: Main renal artery clamping and selective arterial clamping are two conventional devascularization methods for robot-assisted partial nephrectomy (RAPN) (1, 2). Decreasing warm ischemic (WI) time (3, 4) and improving clear surgical visualization (5) are the main surgically modifiable factors for RAPN, especially in large complex renal cancer (6). In this study, we described our surgical technique, focusing on gradual segmental artery unclamping on patients with large renal tumors. MATERIAL AND METHODS: Two patients (R.E.N.A.L score 10 and 11) underwent RAPN with gradual segmental artery unclamping (Figures 1 and 2). The unclamping included five key steps. First, all renal segmental arteries were identified as tumor feeding vessel(s) and the vessels for normal kidney parenchyma under the guidance of CT angiography (CTA) 3-division (3D) reconstruction. Second, all segmental arteries were isolated, and the feeding one(s) should be blocked before other arteries were blocked. Third, the tumor was resected outside the pseudocapsule, and the deep resection bed was sutured for initial hemostasis. Fourth, the segmental arteries were reopened except for the tumor feeding one(s), and normal kidney parenchyma restored blood supply. And fifth, the resection bed was completely sutured, and the feeding vessel supplying the tumor was opened after the suture. Warm ischemia time (WIT) was defined as the time measured between clamping and unclamping of the renal artery. WIT1 was the time for normal kidney parenchyma and WIT2 was the time for resection area. Patient demographics, perioperative variables, and warm ischemic time were included in our study. And we presented the details of gradual segmental artery unclamping in the video. RESULTS: In both cases, the total operation times were 215 and 130 mins for patient 1 and patient 2, respectively. WIT1 and WIT2 for patient 1 were 15 min and 33 min., and WIT1 and WIT2 for patient 2 were 21 min and 32 min, respectivelly. The maximum diameters of the masses resected were 10.8 and 7.3 cm, and surgical margins were negative. No patient had complications after operation. Preoperative and postoperative eGFR did not change significantly. Pre- and postoperative eGFR were 111 and 108 mL/min for patient 1, 91 and 83 mL/min for patient 2, respectively. Key hints for outcomes optimization during RAPN on patients with large complex renal tumors: 1) Each segmental renal artery is precised clamped before we excise the tumor, and an excellent surgical vision is essential for precising excision and shortening clamping time, 2) Other segmental renal arteries are unclamped except tumor feeding branch after suturing deep layer of parenchyma, and most normal parenchyma restores blood supply, 3) Preoperative high-resolution computed tomography angiography (CTA) and 3D reconstructive renal structure serve as a guide to clear the approach to find the tumor and segmental arteries (7, 8). CONCLUSIONS: Gradual segmental artery unclamping is feasible and efficient to excise large complex renal cancer. Compared with main renal artery clamping, it can shorten the warm ischemic time of normal parenchyma; On the other hand, compared with selective segmental arterial clamping, the technique can reduce bleeding from the deep resection bed, keep a clear surgical vision, and decrease the incidence of positive margin.

EGCG attenuates α-synuclein protofibril-membrane interactions and disrupts the protofibril.

The fibrillary aggregates of α-synuclein (α-syn) are closely associated with the etiology of Parkinson's disease (PD). Mounting evidence shows that the interaction of α-syn with biological membranes is a culprit for its aggregation and cytotoxicity. While some small molecules can effectively inhibit α-syn fibrillization in solution, their potential roles in the presence of membrane are rarely studied. Among them, green tea extract epigallocatechin gallate (EGCG) is currently under active investigation. Herein, we investigated the effects of EGCG on α-syn protofibril (an intermediate of α-syn fibril formation) in the presence of a model membrane and on the interactions between α-syn protofibril and the membrane, as well as the underlying mechanisms, by performing microsecond all-atom molecular dynamics simulations. The results show that EGCG has destabilization effects on α-syn protofibril, albeit to a lesser extent than that in solution. Intriguingly, we find that EGCG forms overwhelming H-bonding and cation-π interactions with membrane and thus attenuates protofibril-membrane interactions. Moreover, the decreased protofibril-membrane interactions impede the membrane damage by α-syn protofibril and enable the membrane integrity. These findings provide atomistic understanding towards the attenuation of α-syn protofibril-induced cytotoxicity by EGCG in cellular environment, which is helpful for the development of EGCG-based therapeutic strategies against PD.