Unbiasing Enhanced Sampling on a High-Dimensional Free Energy Surface with a Deep Generative Model.

Biased enhanced sampling methods that utilize collective variables (CVs) are powerful tools for sampling conformational ensembles. Due to their large intrinsic dimensions, efficiently generating conformational ensembles for complex systems requires enhanced sampling on high-dimensional free energy surfaces. While temperature-accelerated molecular dynamics (TAMD) can trivially adopt many CVs in a simulation, unbiasing the simulation to generate unbiased conformational ensembles requires accurate modeling of a high-dimensional CV probability distribution, which is challenging for traditional density estimation techniques. Here we propose an unbiasing method based on the score-based diffusion model, a deep generative learning method that excels in density estimation across complex data landscapes. We demonstrate that this unbiasing approach, tested on multiple TAMD simulations, significantly outperforms traditional unbiasing methods and can generate accurate unbiased conformational ensembles. With the proposed approach, TAMD can adopt CVs that focus on improving sampling efficiency and the proposed unbiasing method enables accurate evaluation of ensemble averages of important chemical features.

Volatile communication in plants relies on a KAI2-mediated signaling pathway.

Plants are constantly exposed to volatile organic compounds (VOCs) that are released during plant-plant communication, within-plant self-signaling, and plant-microbe interactions. Therefore, understanding VOC perception and downstream signaling is vital for unraveling the mechanisms behind information exchange in plants, which remain largely unexplored. Using the hormone-like function of volatile terpenoids in reproductive organ development as a system with a visual marker for communication, we demonstrate that a petunia karrikin-insensitive receptor, PhKAI2ia, stereospecifically perceives the (-)-germacrene D signal, triggering a KAI2-mediated signaling cascade and affecting plant fitness. This study uncovers the role(s) of the intermediate clade of KAI2 receptors, illuminates the involvement of a KAI2ia-dependent signaling pathway in volatile communication, and provides new insights into plant olfaction and the long-standing question about the nature of potential endogenous KAI2 ligand(s).

Industrial by-products-derived binders for in-situ remediation of high Pb content pyrite ash: Synergistic use of ground granulated blast furnace slag and steel slag to achieve efficient Pb retention and CO2 mitigation.

Ordinary Portland cement (OPC) is a cost-effective and conventional binder that is widely adopted in brownfield site remediation and redevelopment. However, the substantial carbon dioxide emission during OPC production and the concerns about its undesirable retention capacity for potentially toxic elements strain this strategy. To tackle this objective, we herein tailored four alternative binders (calcium aluminate cement, OPC-activated ground-granulated blast-furnace slag (GGBFS), white-steel-slag activated GGBFS, and alkaline-activated GGBFS) for facilitating immobilization of high Pb content pyrite ash, with the perspectives of enhancing Pb retention and mitigating anthropogenic carbon dioxide emissions. The characterizations revealed that the incorporation of white steel slag efficiently benefits the activity of GGBFS, herein facilitating the hydration products (mainly ettringite and calcium silicate hydrates) precipitation and Pb immobilization. Further, we quantified the cradle-to-gate carbon footprint and cost analysis attributed to each binder-Pb contaminants system, finding that the application of these alternative binders could be pivotal in the envisaged carbon-neutral world if the growth of the OPC-free roadmap continues. The findings suggest that the synergistic use of recycled white steel slag and GGBFS can be proposed as a profitable and sustainable OPC-free candidate to facilitate the management of lead-contaminated brownfield sites. The overall results underscore the potential immobilization mechanisms of Pb in multiple OPC-free/substitution binder systems and highlight the urgent need to bridge the zero-emission insights to sustainable in-situ solidification/stabilization technologies.

Monitoring drug metabolic pathways through extracellular vesicles in mouse plasma.

The ability to monitor the response of metabolic enzymes to drug exposure in individuals is highly appealing and critical to personalized medicine. Although pharmacogenomics assesses genotypic differences, it does not report changes in metabolic enzyme activities due to environmental factors such as drug interactions. Here, we report a quantitative proteomics strategy to monitor drug metabolic pathways by profiling metabolic enzymes in circulating extracellular vesicles (EVs) upon drug exposure. Mass spectrometry (MS)-based measurement revealed that changes in metabolic enzyme abundance in EVs paralleled those in hepatic cells isolated from liver tissue. Coupling with multiplexed isotopic labeling, we temporally quantified 34 proteins involved in drug absorption, distribution, metabolism, and excretion (ADME) pathways. Out of 44 known ADME proteins in plasma EVs, previously annotated mouse cytochrome P450 3A11 (Cyp3a11), homolog to human CYP3A4, and uridine 5'-diphospho (UDP) glucuronosyltransferase 2A3 (Ugt2a3), increased upon daily rifampicin dosage. Dasatinib, a tyrosine kinase inhibitor to treat leukemia, also elevated Cyp3a11 levels in plasma EVs, but to a lesser extent. Altogether, this study demonstrates that measuring drug enzymes in circulating EVs as an effective surrogate is highly feasible and may transform today's drug discovery and development for personalized medicine.

A compartment model for subcutaneous injection of monoclonal antibodies.

Despite the growing popularity of subcutaneous (SC) administration for monoclonal antibodies (mAbs), there remains a limited understanding of the significance of mAb transport rate constants within the interstitial space and the lymphatic system on their pharmacokinetics. To bridge this knowledge gap, we introduce a compartmental model for subcutaneously administered mAbs. Our model differentiates FcRn-expressing cells across various sites, and the model predictions agree with experimental data from both human and rat studies. Our findings indicate that the time to reach the maximum mAb concentration in the plasma, denoted by Tmax, displays a weak positive correlation with mAb half-life and a negligible correlation with bioavailability. In contrast, the half-life of mAbs exhibits a strong positive correlation with bioavailability. Moreover, the rate of mAb transport from lymph to plasma significantly affects the mAb half-life. Increasing the transport rates of mAbs from the injection site to the lymph or from lymph to plasma enhances bioavailability. These insights, combined with our compartmental model, contribute to a deeper understanding of the pharmacokinetics of subcutaneously administered mAbs.

Chemical Affinity-Based Isolation of Extracellular Vesicles from Biofluids for Proteomics and Phosphoproteomics Analysis.

Extracellular vesicles (EVs) from biofluids have recently gained significant attention in the field of liquid biopsy. Released by almost every type of cell, they provide a real-time snapshot of host cells and contain a wealth of molecular information, including proteins, in particular those with post-translational modifications (PTMs) such as phosphorylation, as the main player of cellular functions and disease onset and progression. However, the isolation of EVs from biofluids remains challenging due to low yields and impurities from current EV isolation methods, making the downstream analysis of EV cargo, such as EV phosphoproteins, difficult. Here, we describe a rapid and effective EV isolation method based on functionalized magnetic beads for EV isolation from biofluids such as human urine and downstream proteomics and phosphoproteomics analysis following EV isolation. The protocol enabled a high recovery yield of urinary EVs and sensitive profiles of EV proteome and phosphoproteome. Furthermore, the versatility of this protocol and relevant technical considerations are also addressed here.

Piezo1 transforms mechanical stress into pro senescence signals and promotes osteoarthritis severity.

Osteoarthritis (OA) is a prevalent disease among elderly people and is often characterized by chronic joint pain and dysfunction. Recently, growing evidence of chondrocyte senescence in the pathogenesis of OA has been found, and targeting senescence has started to be recognized as a therapeutic approach for OA. Piezo1, a mechanosensitive Ca2+ channel, has been reported to be harmful in sensing abnormal mechanical overloading and leading to chondrocyte apoptosis. However, whether Piezo1 can transform mechanical signals into senescence signals has rarely been reported. In this study, we found that severe OA cartilage expressed more Piezo1 and the senescence markers p16 and p21. 24 h of periodic mechanical stress induced chondrocyte senescence in vitro. In addition, we demonstrated the pivotal role of Piezo1 in OA chondrocyte senescence induced by mechanical stress. Piezo1 sensed mechanical stress and promoted chondrocyte senescence via its Ca2+ channel ability. Moreover, Piezo1 promoted SASP factors production under mechanical stress, particularly in IL-6 and IL-1ß. p38MAPK and NF-κB activation were two key pathways that responded to Piezo1 activation and promoted IL-6 and IL-1ß production, respectively. Collectively, our study revealed a connection between abnormal mechanical stress and chondrocyte senescence, which was mediated by Piezo1.

Fluorides immobilization through calcium aluminate cement-based backfill: Accessing the detailed leaching characterization under torrential rainfall.

Urbanization and economic development have increased the demand for fertilizers to sustain food crop yields. Huge amounts of by-products, especially phosphogypsum (PG), are generated during the wet processing of rock phosphate to produce fertilizers. Chronic exposure to fluoride in phosphogypsum in groundwater as a result of the weathering of fluoride-containing waste poses a significant health risk to millions of people. We propose a method for using calcium aluminate cement (CAC) to remediate high fluoride contents in solid waste. Column leaching tests under harsh rainfall conditions confirmed the efficient fluoride immobilization capacity of a CAC binder. Although the fluoride concentrations in leachates during the first 1-2 days (1.25 mg/L) slightly exceeded the threshold of 1.00 mg/L, the concentrations over 3-28 days (ranging from 0.98 to 0.83 mg/L) consistently remained well within the acceptable range. Furthermore, our characterization and geochemical modeling revealed the fluoride retention mechanisms of CAC-stabilized PG under laboratory-simulated conditions of torrential rainfall. During leaching, physical encapsulation prevents fluoride from contacting leachate. However, an unfavorable pH value can cause the release of fluoride from the cement matrix, which is subsequently captured by aluminate hydrate through adsorption or co-precipitation. We quantified the carbon footprint of CAC for immobilizing 1 mg of fluoride in PG, obtaining a remarkably low value of 4.4 kg of CO2, in contrast to the emissions associated with the use of ordinary Portland cement (OPC). The findings suggest a unique opportunity for extensive PG remediation. This opportunity extends the horizons of achieving zero-waste emissions in the phosphorus industry and has practical significance in the context of reducing carbon emissions.

Artificial intelligence planning and 3D printing augmented modules in the treatment of a complicated hip joint revision: a case report.

Total hip revision with osseous defects can be very difficult. Artificial intelligence offers preoperative planning, real-time measurement, and intraoperative judgment, which can guide prothesis placement more accurately. Three-dimensional printed metel augment modules which are made according to the individualized osseous anatomy, can fit the osseous defects well and provide mechanical support. In this case, we used AI to plan the size and position of the acetabular cup and 3D-printed augmented modules in a complicated hip revision with an acetabular bone defects, which achieved stable fixation and relieved hip pain postoperatively.

Ochronotic arthropathy effectively treated with total hip and total knee arthroplasty: a case report.

Ochronosis is a rare autosomal recessive disorder of tyrosine metabolism characterized by multilevel spinal degeneration and arthritis of large weight-bearing joints, which is referred to as ochronotic arthropathy. In this case report, we describe diagnosis and treatment of ochronotic arthropathy in a patient who underwent total hip arthroplasty (THA) and total knee arthroplasty (TKA). The Harris hip score was 26 preoperatively and 45, 68, 76, 90, 92, and 94 at 1, 3, 6, 9, 11, and 14 months, respectively, postoperatively. The forgotten joint score (FJS) of the hip was 27.8, 52.8, 81.1, 89.0, 90.6, and 92.4 at 1, 3, 6, 9, 11, and 14 months, respectively, postoperatively. TKA was performed 8 months after THA. The Knee Society Score was 36 before TKA and 74, 82, and 90 at 1, 3, and 6 months, respectively, after TKA. The FJS of the knee was 36.6, 63.9, and 84.5 at 1, 3, and 6 months, respectively, after TKA. The patient's knee range of motion returned to normal, with significant reduction in pain and improved satisfaction levels after TKA. THA and TKA can achieve good clinical outcomes in patients with ochronosis accompanied by severe joint pain.

One-Pot Analytical Pipeline for Efficient and Sensitive Proteomic Analysis of Extracellular Vesicles.

Extracellular vesicle (EV) proteomics emerges as an effective tool for discovering potential biomarkers for disease diagnosis, monitoring, and therapeutics. However, the current workflow of mass spectrometry-based EV proteome analysis is not fully compatible in a clinical setting due to inefficient EV isolation methods and a tedious sample preparation process. To streamline and improve the efficiency of EV proteome analysis, here we introduce a one-pot analytical pipeline integrating a robust EV isolation approach, EV total recovery and purification (EVtrap), with in situ protein sample preparation, to detect urinary EV proteome. By incorporating solvent-driven protein capture and fast on-bead digestion, the one-pot pipeline enabled the whole EV proteome analysis to be completed within one day. In comparison with the existing workflow, the one-pot pipeline was able to obtain better peptide yield and identify the equivalent number of unique EV proteins from 1 mL of urine. Finally, we applied the one-pot pipeline to profile proteomes in urinary EVs of bladder cancer patients. A total of 2774 unique proteins were identified in 53 urine samples using a 15 min gradient library-free data-independent acquisition method. Taken altogether, our novel one-pot analytical pipeline demonstrated its potential for routine and robust EV proteomics in biomedical applications.

Mechanistic insights into Pb and sulfates retention in ordinary Portland cement and aluminous cement: Assessing the contributions from binders and solid waste.

Identifying immobilization mechanisms of potentially toxic elements (PTEs) is of paramount importance in the field application of solidification/stabilization. Traditionally, demanding and extensive experiments are required to better access the underlying retention mechanisms, which are usually challenging to quantify and clarify precisely. Herein, we present a geochemical model with parametric fitting techniques to reveal the solidification/stabilization of Pb-rich pyrite ash through conventional (ordinary Portland cement) and alternative (calcium aluminate cement) binders. We found that ettringite and calcium silicate hydrates exhibit strong affinities for Pb at alkaline conditions. When the hydration products are unable to stabilize all the soluble Pb in the system, part of the soluble Pb may be immobilized as Pb(OH)2. At acidic and neutral conditions, hematite from pyrite ash and newly-formed ferrihydrite are the main controlling factors of Pb, coupled with anglesite and cerussite precipitation. Thus, this work provides a much-needed complement to this widely-applied solid waste remediation technique for the development of more sustainable mixture formulations.

Enhanced cadmium phytoextraction efficiency of ryegrass (Lolium perenne L.) by porous media immobilized Enterobacter sp. TY-1.

Although studies on immobilized microorganisms have been conducted, their performance remains unclear for enhancing plants to remediate cadmium (Cd)-contaminated soil. In this study, a Cd-resistant strain TY-1 with good plant growth promotion traits was immobilized by biochar (BC) or oyster shell (OS) power to strengthen ryegrass to remediate Cd-contaminated soil. SEM-EDS combined with FTIR showed that TY-1 could tolerate Cd toxicity by surface precipitation, and functional groups such as hydroxyl and carbonyl groups might be involved. In the biocomposite treatments, soil pH increased, and the activity of fertility-related enzymes such as dehydrogenase increased by 109.01%-128.01%. The relative abundance of genus Saccharimonadales decreased from 7.97% to 3.35% in BS-TY and 2.61% in OS-TY, respectively. Thus, a suitable environment for ryegrass growth was created. The fresh weight, dry weight, plant height and Cd accumulation of ryegrass in TY treatment increased by 122.92%, 114.81%, 42.08% and 8.05%, respectively, compared to the control. Cd concentration in ryegrass was further increased in BC-TY and OS-TY by 24.14% and 40.23%, respectively. The improvement in soil microcosm and plant biomass forms an ongoing virtuous cycle, demonstrating that using carrier materials to improve the efficiency of microbial-assisted phytoremediation is realistic and feasible.

The influence of prosthetic positioning and proximal femoral morphology on leg length discrepancy and early clinical outcomes of cementless total hip arthroplasty.

BACKGROUND: Leg length discrepancy (LLD) is a common complication of total hip arthroplasty (THA). However, the relationship between femoral prosthesis filling, proximal femoral morphology, and acetabular prosthesis positioning with postoperative LLD and clinical outcomes is unclear. The aims of this study were to investigate the influence of canal flare index (CFI), canal fill ratio (CFR), center of rotation (COR), and femoral offset (FO) on (1) postoperative LLD; and (2) clinical outcomes in the two stem designs with different coating distribution. METHODS: The study cohort included 161 patients who underwent primary cementless THA between January 2021 and March 2022 with either proximal coating or full coating stems. Multivariate logistic regression was used to assess the effect of CFI, CFR, COR, and FO on postoperative LLD, and linear regression to assess their effect on clinical outcomes. RESULTS: No statistical difference was found in clinical outcomes or postoperative LLD between the two groups. High CFI (p = 0.014), low ΔVCOR (p = 0.012), and Gender (p = 0.028) were found independent risk factors for LLD one day postoperative. High CFI was also an independent risk factor for postoperative subjectively perceived LLD (p = 0.013). CFR at the level of 2 cm below the LT (p = 0.017) was an independent risk factor for Harris Hip Score. CONCLUSIONS: Proximal femoral morphology and acetabular prosthesis positioning but not femoral prosthesis filling affected the LLD. High CFI was an independent risk factor for postoperative LLD and subjectively perceived LLD, and low ΔVCOR was also an independent risk factor for postoperative LLD. Women were susceptible to postoperative LLD.

Senescence-responsive miR-33-5p promotes chondrocyte senescence and osteoarthritis progression by targeting SIRT6.

Osteoarthritis (OA) is a prevalent disease among elderly individuals that is caused by cartilage degeneration. Chondrocyte senescence involved in the development of OA, and antisenescence therapies have been proposed for OA treatment. In our study, we identified the role of a microRNA, miR-33-5p, in promoting chondrocyte senescence and OA progression. miR-33-5p expression was upregulated under senescence conditions. miR-33-5p-mimic transfection can induce cellular senescence, while transfection of a miR-33-5p-inhibitor in chondrocytes alleviated senescence induced by IL-1ß. Moreover, SIRT6 expression was downregulated under IL-1ß treatment, and could be restored by miR-33-5p-inhibitor transfection. Luciferase assays revealed that miR-33-5p targeted the SIRT6 mRNA 3' UTR. In addition, SIRT6 mRNA expression showed negative correlations with senescence and OA degree in human cartilage. Bioinformatic analysis also confirmed the pro-senescence effect of miR-33-5p. Furthermore, periodic intraarticular injection of agomiR-33-5p induced cartilage loss and OA-like cartilage changes. To conclude, we revealed the pro-senescence and cartilage-destructive effect of miR-33-5p, whose expression was elevated under various senescence conditions, and showed that SIRT6 was one of its targets. Therefore, miR-33-5p is a potential therapeutic target for treating OA.

Sirtuins in osteoarthritis: current understanding.

Osteoarthritis (OA) is a common disease characterized by severe chronic joint pain, that imposes a large burden on elderly people. OA is a highly heterogeneous disease, and multiple etiologies contribute to its progression. Sirtuins (SIRTs) are Class III histone deacetylases (HDACs) that regulate a comprehensive range of biological processes such as gene expression, cell differentiation, and organism development, and lifespan. Over the past three decades, increasing evidence has revealed that SIRTs are not only important energy sensors but also protectors against metabolic stresses and aging, and an increasing number of studies have focused on the functions of SIRTs in OA pathogenesis. In this review, we illustrate the biological functions of SIRTs in OA pathogenesis from the perspectives of energy metabolism, inflammation, autophagy and cellular senescence. Moreover, we offer insights into the role played by SIRTs in regulating circadian rhythm, which has recently been recognized to be crucial in OA development. Here, we provide the current understanding of SIRTs in OA to guide a new direction for OA treatment exploration.

Mass spectrometry-based phosphoproteomics in clinical applications.

Protein phosphorylation is an essential post-translational modification that regulates many aspects of cellular physiology, and dysregulation of pivotal phosphorylation events is often responsible for disease onset and progression. Clinical analysis on disease-relevant phosphoproteins, while quite challenging, provides unique information for precision medicine and targeted therapy. Among various approaches, mass spectrometry (MS)-centered characterization features discovery-driven, high-throughput and in-depth identification of phosphorylation events. This review highlights advances in sample preparation and instrument in MS-based phosphoproteomics and recent clinical applications. We emphasize the preeminent data-independent acquisition method in MS as one of the most promising future directions and biofluid-derived extracellular vesicles as an intriguing source of the phosphoproteome for liquid biopsy.

Lower Bounds on Quantum Annealing Times.

The adiabatic theorem provides sufficient conditions for the time needed to prepare a target ground state. While it is possible to prepare a target state much faster with more general quantum annealing protocols, rigorous results beyond the adiabatic regime are rare. Here, we provide such a result, deriving lower bounds on the time needed to successfully perform quantum annealing. The bounds are asymptotically saturated by three toy models where fast annealing schedules are known: the Roland and Cerf unstructured search model, the Hamming spike problem, and the ferromagnetic p-spin model. Our bounds demonstrate that these schedules have optimal scaling. Our results also show that rapid annealing requires coherent superpositions of energy eigenstates, singling out quantum coherence as a computational resource.

Integrated biochemical and transcriptomic analysis reveals the effects of Burkholderia sp. SRB-1 on cadmium accumulating in Chrysopogon zizanioides L. under Cd stress.

Application of plant growth-promoting rhizobacteria plays a vital role in enhancing phytoremediation efficiency. In this study, multiple approaches were employed to investigate the underlying mechanisms of Burkholderia sp. SRB-1 (SRB-1) on elevating Cd uptake and accumulation. Inoculation experiment indicated that SRB-1 could facilitate plant growth and Cd tolerance, as evidenced by the enhanced plant biomass and antioxidative enzymes activities. Cd content in plant shoots and roots increased about 36.56%-39.66% and 25.97%-130.47% assisted with SRB-1 when compared with control. Transcriptomics analysis revealed that SRB-1 upregulated expression of amiE, AAO1-2 and GA2-ox related to auxin and gibberellin biosynthesis in roots. Auxin and gibberellin, as hormone signals, regulated plant Cd tolerance and growth through activating hormone signal transduction pathways, which might also contribute to 67.94% increase of dry weight. The higher expression levels of ATP-binding cassette transporter subfamilies (ABCB, ABCC, ABCD and ABCG) in Chrysopogon zizanioides roots contributed to higher Cd uptake in Cd15 B (323.83 mg kg-1) than Cd15 (136.28 mg kg-1). Further, SRB-1 facilitated Cd migration from roots to shoots via upregulating the expression of Nramp, ZIP and HMA families. Our integrative analysis provided a molecular-scale perspective on Burkholderia sp. SRB-1 contributing to C. zizanioides performance.

In-situ remediation of phosphogypsum in a cement-free pathway: Utilization of ground granulated blast furnace slag and NaOH pretreatment.

In-situ remediating phosphogypsum (PG) for cemented paste backfill (CPB) in the contaminated site is economic management for promoting sustainable developments in the phosphate industry. This study concerns the combined use of NaOH pretreatment and ground-granulated blast furnace slag (GGBFS) additives to promote the solidification/stabilization of PG with a lower carbon footprint pathway. According to physico-chemical analyses, the NaOH pretreatment effectively removed approximately 95% of F within the PG, which may originally be present as sparingly soluble fluorides or coexisting with silicates. The micro mineralogical characterization illustrates that the pretreatment can accelerate the early age hydration, with more hydration products observed, including calcium silicate hydrates and ettringite, effective F and P retention candidates. Whereas the incorporation of GGBFS plays an essential role in promoting the generation of additional cement hydrates at the following stages. The macro mechanical performance analysis indicates that the mixtures of pretreated-PG-OPC-GGBFS exhibit an excellent mechanical performance satisfying the design criteria. Subsequent elemental mapping and toxicity characteristic leaching procedures demonstrate that this combined approach has a competitive F and P immobilization ability compared to the typical OPC binder and individual GGBFS addition. The newly formed phases effectively controlled the concentration of F and P through adsorption, incorporation, or encapsulation. Objectively, the proposed methodology can be a promising candidate pathway for extrapolating the in-situ immobilization of PG. This study opens up new perspectives for synergetically recycling PG and GGBFS in a profitable and low carbon footprint way.