Strengthening gold with dispersed nanovoids.

Materials often fail prematurely or catastrophically under load while containing voids, posing a challenge to materials manufacturing. We found that a metal (gold) containing spherical voids with a fraction of up to 10% does not fracture prematurely in tension when the voids are shrunk to the submicron or nanometer scale. Instead, the dispersed nanovoids increase the strength and ductility of the material while simultaneously reducing its weight. Apart from the suppressed stress or strain concentration, such structure provides enormous surface area and promotes surface-dislocation interactions, which enable strengthening and additional strain hardening and thus toughening. Transforming voids from crack-like detrimental defects into a beneficial "ingredient" provides an inexpensive and environmentally friendly approach for the development of a new class of lightweight, high-performance materials.

Numerical modeling of ultrasound-triggered microneedle-mediated delivery of drug particles into bacterial biofilms.

Ultrasonic microneedle patches, a class of ultrasound-driven transdermal drug delivery systems, are promising in addressing bacterial biofilms. This device has been proven to be more effective in treating Staphylococcus aureus biofilms than drug in free solution. However, there exists a notable gap in understanding how various excitation conditions and material parameters affect drug delivery efficiency. This study aims to fill this void by conducting an comprehensive multi-physics numerical analysis of ultrasonic microneedle patches, with the ultimate goal of enhancing drug delivery. First, we investigate the impact of various ultrasound frequencies on drug penetration depths. The findings reveal that local resonance can accelerate drug release within a shorter time window (first 1.5 h), whereas non-resonant frequencies enable more profound and prolonged diffusion. This information is crucial for medical professionals in selecting the most effective frequency for optimal drug administration. Furthermore, our investigation extends to the effects of applied voltage on temperature distribution, a critical aspect for ensuring medical safety during the application of these patches. Additionally, we examine how particles of different sizes respond to acoustic pressure and streaming fields, providing valuable insights for tailoring drug delivery strategies to specific therapeutic needs. Overall, our findings offer comprehensive guidelines for the effective use of ultrasonic microneedle patches, potentially shifting the paradigm in patient care and enhancing the overall quality of life.

Deciphering carbon emissions in urban sewer networks: Bridging urban sewer networks with city-wide environmental dynamics.

As urbanization accelerates, understanding and managing carbon emissions from urban sewer networks have become crucial for sustainable urban water cycles. This review examines the factors influencing greenhouse gas (GHG) emissions within urban sewage systems, analyzing the complex effects between water quality, hydrodynamics, and sewer infrastructure on GHG production and emission processes. It reveals significant spatiotemporal heterogeneity in GHG emissions, particularly under long-term scenarios where flow rates and temperatures exhibit strong impacts and correlations. Given the presence of fugitive and dissolved potential GHGs, standardized monitoring and accounting methods are deemed essential. Advanced modeling techniques emerge as crucial tools for large-scale carbon emission prediction and management. The review identifies that traditional definitions and computational frameworks for carbon emission boundaries fail to fully consider the inherent heterogeneity of sewers and the dynamic changes and impacts of multi-source pollution within the sewer system during the urban water cycle. This includes irregular fugitive emissions, the influence of stormwater systems, climate change, geographical features, sewer design, and the impacts of food waste and antibiotics. Key strategies for emission management are discussed, focusing on the need for careful consideration of approaches that might inadvertently increase global emissions, such as ventilation, chemical treatments, and water management practices. The review advocates for an overarching strategy that encompasses a holistic view of carbon emissions, stressing the importance of refined emission boundary definitions, novel accounting practices, and comprehensive management schemes in line with the water treatment sector's move towards carbon neutrality. It champions the adoption of interdisciplinary, technologically advanced solutions to mitigate pollution and reduce carbon emissions, emphasizing the importance of integrating cross-scale issues and other environmentally friendly measures in future research directions.

Enhancing effluent quality prediction in wastewater treatment plants through the integration of factor analysis and machine learning.

Precisely predicting the concentration of nitrogen-based pollutants from the wastewater treatment plants (WWTPs) remains a challenging yet crucial task for optimizing operational adjustments in WWTPs. In this study, an integrated approach using factor analysis (FA) and machine learning (ML) models was employed to accurately predict effluent total nitrogen (Ntoteff) and nitrate nitrogen (NO3-Neff) concentrations of the WWTP. The input values for the ML models were honed through FA to optimize factors, thereby significantly enhancing the ML prediction accuracy. The prediction model achieved a highest coefficient of determination (R2) of 97.43 % (Ntoteff) and 99.38 % (NO3-Neff), demonstrating satisfactory generalization ability for predictions up to three days ahead (R2 >80 %). Moreover, the interpretability analysis identified that the denitrification factor, the pollutant load factor, and the meteorological factor were significant. The model framework proposed in this study provides a valuable reference for optimizing the operation and management of wastewater treatment.

Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem.

Emerging spatial omics technologies continue to advance the molecular mapping of tissue architecture and the investigation of gene regulation and cellular crosstalk, which in turn provide new mechanistic insights into a wide range of biological processes and diseases. Such technologies provide an increasingly large amount of information content at multiple spatial scales. However, representing and harmonizing diverse spatial datasets efficiently, including combining multiple modalities or spatial scales in a scalable and flexible manner, remains a substantial challenge. Here, we present Giotto Suite, a suite of open-source software packages that underlies a fully modular and integrated spatial data analysis toolbox. At its core, Giotto Suite is centered around an innovative and technology-agnostic data framework embedded in the R software environment, which allows the representation and integration of virtually any type of spatial omics data at any spatial resolution. In addition, Giotto Suite provides both scalable and extensible end-to-end solutions for data analysis, integration, and visualization. Giotto Suite integrates molecular, morphology, spatial, and annotated feature information to create a responsive and flexible workflow for multi-scale, multi-omic data analyses, as demonstrated here by applications to several state-of-the-art spatial technologies. Furthermore, Giotto Suite builds upon interoperable interfaces and data structures that bridge the established fields of genomics and spatial data science, thereby enabling independent developers to create custom-engineered pipelines. As such, Giotto Suite creates an immersive ecosystem for spatial multi-omic data analysis.

A Novel Polysaccharide from Sargassum weizhouense: Extraction Optimization, Structural Characterization, Antiviral and Antioxidant Effects.

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically important pathogens in the global swine industry over the past three decades. There is no licensed antiviral medication that can effectively control this infection. In the present study, the structure of SP-1 isolated and purified from Sargassum weizhouense was analyzed, and its antioxidant capacity and antiviral effect in MARC-145 cells against PRRSV were investigated. The results showed that SP-1 is a novel polysaccharide which mainly is composed of →4)-ß-D-ManpA-(1→, →4)-α-L-GulpA-(1→ and a small amount of →4)-ß-D-GalpA-(1→. PRRSV adsorption, replication, and release were all suppressed by SP-1. SP-1 therapy down-regulated mRNA expression of the CD163 receptor while increasing the antioxidant gene expression of Nrf2, TXNIP, and HO-1; increasing the protein expression of NQO1 and HO-1; and drastically reducing the protein expression of p-p65. The findings indicated that SP-1 reduces PRRSV adsorption, replication, and release through blocking the expression of the crucial CD163 receptor during infection. Meanwhile, SP-1 exerts antioxidant effects in PRRSV-infected cells through the activation of the Nrf2-HO1 signaling pathway.

Lactobacillus co-fermentation of Cerasus humilis juice alters chemical properties, enhances antioxidant activity, and improves gut microbiota.

Fermentation with Lactobacillus has been shown to improve the nutritional value of juice. In this study, Cerasus humilis juice was fermented using two commercial probiotics, namely, Lactobacillus acidophilus and Lactobacillus plantarum. The total antioxidant capacity (TAOC), viable count, chemical properties, antioxidant activity after in vitro digestion, and alterations in the gut microbiota composition of the fermented juice were investigated. After fermentation, the TAOC increased from 107.66 U mL-1 to 126.72 U mL-1; viable count increased from 5.85 lg (CFU mL-1) to 8.17 lg (CFU mL-1); and the contents of total phenols, total flavonoids, proanthocyanins, four organic acids, and 29 amino acids had changed. Overall, 47 compounds were identified in the juice, 20 of which were enriched after fermentation. Furthermore, Lactobacillus co-fermentation improved the antioxidant properties of the juice after in vitro digestion and increased the abundance of probiotics to regulate the gut microbiota. These findings illustrate the potential use of Lactobacillus acidophilus and Lactobacillus plantarum in the co-fermentation of C. humilis juice to enhance its nutritional and functional properties.

Effects of Quercitrin on PRV-Induced Secretion of Reactive Oxygen Species and Prediction of lncRNA Regulatory Targets in 3D4/2 Cells.

Quercitrin is a kind of flavonoid that is found in many plants; it has good antioxidant activity, and can regulate oxidative stress induced by Pseudorabies virus (PRV)-infected cells. In this study, the secretion of reactive oxygen species (ROS) induced by PRV infection was detected by flow cytometry, and RNA expression profiles of the 3D4/2 cells were produced and analyzed by sequenced GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes); the sequencing results were verified by RT-qCR. The results showed that the secretion of ROS induced by PRV infection in 3D4/2 cells could be significantly decreased by quercitrin. The differentially expressed 1055 mRNA, 867 lncRNA, 99 miRNA, and 69 circRNA were detected between the control group and the PRV infection group. The differentially expressed 1202 mRNA, 785 lncRNA, 115 miRNA, and 79 circRNA were found between the PRV+ quercitrin group and the control group. The differentially expressed 357 mRNA, 69 lncRNA, 111 miRNA, and 81 circRNA were obtained between the PRV+ quercitrin group and the PRV group. The significantly differentially expressed mRNAs were mainly involved in cell metabolism, regulatory protein phosphorylation, protein phosphorylation, antioxidation, regulatory phosphorylation, and so on. Among them, the mRNAs related to antioxidant response and oxidative stress were thioredoxin-interacting protein (TXNIP) and nitric oxide synthase 2 (NOS2). According to the network diagram of lncRNA-miRNA-mRNA, two targeted miRNA (ssc-miR-450c-3p and novel-m0400-3p) relationships with TXNIP and NOS2 were screened. This study provides a scientific foundation for further research for the function of quercitrin in anti-virus-induced oxidative stress.

Analyzing Spatial Transcriptomics Data Using Giotto.

Spatial transcriptomic technologies have been developed rapidly in recent years. The addition of spatial context to expression data holds the potential to revolutionize many fields in biology. However, the lack of computational tools remains a bottleneck that is preventing the broader utilization of these technologies. Recently, we have developed Giotto as a comprehensive, generally applicable, and user-friendly toolbox for spatial transcriptomic data analysis and visualization. Giotto implements a rich set of algorithms to enable robust spatial data analysis. To help users get familiar with the Giotto environment and apply it effectively in analyzing new datasets, we will describe the detailed protocols for applying Giotto without any advanced programming skills. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Getting Giotto set up for use Basic Protocol 2: Pre-processing Basic Protocol 3: Clustering and cell-type identification Basic Protocol 4: Cell-type enrichment and deconvolution analyses Basic Protocol 5: Spatial structure analysis tools Basic Protocol 6: Spatial domain detection by using a hidden Markov random field model Support Protocol 1: Spatial proximity-associated cell-cell interactions Support Protocol 2: Assembly of a registered 3D Giotto object from 2D slices.

Advances in spatial transcriptomic data analysis.

Spatial transcriptomics is a rapidly growing field that promises to comprehensively characterize tissue organization and architecture at the single-cell or subcellular resolution. Such information provides a solid foundation for mechanistic understanding of many biological processes in both health and disease that cannot be obtained by using traditional technologies. The development of computational methods plays important roles in extracting biological signals from raw data. Various approaches have been developed to overcome technology-specific limitations such as spatial resolution, gene coverage, sensitivity, and technical biases. Downstream analysis tools formulate spatial organization and cell-cell communications as quantifiable properties, and provide algorithms to derive such properties. Integrative pipelines further assemble multiple tools in one package, allowing biologists to conveniently analyze data from beginning to end. In this review, we summarize the state of the art of spatial transcriptomic data analysis methods and pipelines, and discuss how they operate on different technological platforms.

The HCK/BTK inhibitor KIN-8194 is active in MYD88-driven lymphomas and overcomes mutated BTKCys481 ibrutinib resistance.

Activating mutations in MYD88 promote malignant cell growth and survival through hematopoietic cell kinase (HCK)-mediated activation of Bruton tyrosine kinase (BTK). Ibrutinib binds to BTKCys481 and is active in B-cell malignancies driven by mutated MYD88. Mutations in BTKCys481, particularly BTKCys481Ser, are common in patients with acquired ibrutinib resistance. We therefore performed an extensive medicinal chemistry campaign and identified KIN-8194 as a novel dual inhibitor of HCK and BTK. KIN-8194 showed potent and selective in vitro killing of MYD88-mutated lymphoma cells, including ibrutinib-resistant BTKCys481Ser-expressing cells. KIN-8194 demonstrated excellent bioavailability and pharmacokinetic parameters, with good tolerance in rodent models at pharmacologically achievable and active doses. Pharmacodynamic studies showed sustained inhibition of HCK and BTK for 24 hours after single oral administration of KIN-8194 in an MYD88-mutated TMD-8 activated B-cell diffuse large B-cell lymphoma (ABC DLBCL) and BCWM.1 Waldenström macroglobulinemia (WM) xenografted mice with wild-type BTK (BTKWT)- or BTKCys481Ser-expressing tumors. KIN-8194 showed superior survival benefit over ibrutinib in both BTKWT- and BTKCys481Ser-expressing TMD-8 DLBCL xenografted mice, including sustained complete responses of >12 weeks off treatment in mice with BTKWT-expressing TMD-8 tumors. The BCL_2 inhibitor venetoclax enhanced the antitumor activity of KIN-8194 in BTKWT- and BTKCys481Ser-expressing MYD88-mutated lymphoma cells and markedly reduced tumor growth and prolonged survival in mice with BTKCys481Ser-expressing TMD-8 tumors treated with both drugs. The findings highlight the feasibility of targeting HCK, a key driver of mutated MYD88 pro-survival signaling, and provide a framework for the advancement of KIN-8194 for human studies in B-cell malignancies driven by HCK and BTK.

Multimodal Metabolic Imaging Reveals Pigment Reduction and Lipid Accumulation in Metastatic Melanoma.

Objective and Impact Statement. Molecular signatures are needed for early diagnosis and improved treatment of metastatic melanoma. By high-resolution multimodal chemical imaging of human melanoma samples, we identify a metabolic reprogramming from pigmentation to lipid droplet (LD) accumulation in metastatic melanoma. Introduction. Metabolic plasticity promotes cancer survival and metastasis, which promises to serve as a prognostic marker and/or therapeutic target. However, identifying metabolic alterations has been challenged by difficulties in mapping localized metabolites with high spatial resolution. Methods. We developed a multimodal stimulated Raman scattering and pump-probe imaging platform. By time-domain measurement and phasor analysis, our platform allows simultaneous mapping of lipids and pigments at a subcellular level. Furthermore, we identify the sources of these metabolic signatures by tracking deuterium metabolites at a subcellular level. By validation with mass spectrometry, a specific fatty acid desaturase pathway was identified. Results. We identified metabolic reprogramming from a pigment-containing phenotype in low-grade melanoma to an LD-rich phenotype in metastatic melanoma. The LDs contain high levels of cholesteryl ester and unsaturated fatty acids. Elevated fatty acid uptake, but not de novo lipogenesis, contributes to the LD-rich phenotype. Monounsaturated sapienate, mediated by FADS2, is identified as an essential fatty acid that promotes cancer migration. Blocking such metabolic signatures effectively suppresses the migration capacity both in vitro and in vivo. Conclusion. By multimodal spectroscopic imaging and lipidomic analysis, the current study reveals lipid accumulation, mediated by fatty acid uptake, as a metabolic signature that can be harnessed for early diagnosis and improved treatment of metastatic melanoma.

Ixazomib, dexamethasone, and rituximab in treatment-naive patients with Waldenström macroglobulinemia: long-term follow-up.

Proteasome inhibition is a standard of care for the primary treatment of patients with Waldenström macroglobulinemia (WM). We present the long-term follow-up of a prospective, phase II clinical trial that evaluated the combination of ixazomib, dexamethasone, and rituximab (IDR) in 26 treatment-naive patients with WM. IDR was administered as 6 monthly induction cycles followed by 6 every-2-month maintenance cycles. The MYD88 L265P mutation was detected in all patients, and CXCR4 mutations were detected in 15 patients (58%). The median time to response (TTR) and time to major response (TTMR) were 2 and 6 months, respectively. Patients with and without CXCR4 mutations had median TTR of 3 months and 1 month, respectively (P = .003), and median TTMR of 10 months and 3 months, respectively (P = .31). The overall, major, and very good partial response (VGPR) rates were 96%, 77%, and 19%, respectively. The rate of VGPR in patients with and without CXCR4 mutations were 7% and 36%, respectively (P = .06). The median progression-free survival (PFS) was 40 months, the median duration of response (DOR) was 38 months, and the median time to next treatment (TTNT) was 40 months. PFS, DOR, and TTNT were not affected by CXCR4 mutational status. The safety profile was excellent with no grade 4 adverse events or deaths to date. IDR provides a safe and effective frontline treatment option for symptomatic patients with WM. This study was registered at www.clinicaltrials.gov as #NCT02400437.

SYK is activated by mutated MYD88 and drives pro-survival signaling in MYD88 driven B-cell lymphomas.

Activating MYD88 mutations promote pro-survival signaling through BTK and HCK, both targets of ibrutinib. Despite high response rates, complete responses to ibrutinib are lacking, and other MYD88 triggered pro-survival pathways may contribute to primary drug resistance. B-cell receptor (BCR) signaling has been observed in lymphomas driven by mutated MYD88, even without activating the BCR pathway mutations. We identified activated SYK (p-SYK), a component of BCR in complex with MYD88 in MYD88-mutated WM and ABC DLBCL lymphoma cells. Confocal microscopy confirmed co-localization of MYD88 with SYK in MYD88-mutated cells. Knockdown of MYD88 or use of a MYD88 signaling inhibitor abrogated SYK activation, while expression of mutated but not wild-type MYD88 amplified p-SYK in MYD88-mutated and wild-type lymphoma cells. Knockdown of SYK or use of inhibitors targeting SYK blocked p-STAT3 and p-AKT signaling in MYD88-mutated cells. Cell viability analysis showed that combining ibrutinib and SYK inhibitors triggered synthetic killing of MYD88-mutated lymphoma cells. Our findings extend the spectrum of mutated MYD88 pro-survival signaling to include SYK directed BCR cross talk in MYD88-mutated lymphomas. Targeting SYK in combination with ibrutinib produces synthetic lethality, providing a framework for the clinical investigation of ibrutinib with SYK inhibitors in MYD88-mutated lymphomas.

Genomic evolution of ibrutinib-resistant clones in Waldenström macroglobulinaemia.

Ibrutinib is highly active in Waldenström macroglobulinaemia (WM) patients, but disease progression can occur due to acquired mutations in BTK, the target of ibrutinib, or PLCG2, the protein downstream of BTK. However, not all resistant patients harbour these alterations. We have performed a whole-exome sequencing study to identify alternative molecular mechanisms that can drive ibrutinib resistance. Our findings include deletions on chromosomes 6q, including homozygous deletions, and 8p, which encompass key regulators of BTK, MYD88/NF-κB, and apoptotic signalling. Moreover, we have identified recurring mutations in ubiquitin ligases, innate immune signalling, and TLR/MYD88 pathway regulators in ibrutinib-resistant WM patients.

Genomic Landscape of Waldenström Macroglobulinemia and Its Impact on Treatment Strategies.

Next-generation sequencing has revealed recurring somatic mutations in Waldenström macroglobulinemia (WM), including MYD88 (95%-97%), CXCR4 (30%-40%), ARID1A (17%), and CD79B (8%-15%). Deletions involving chromosome 6q are common in patients with mutated MYD88 and include genes that modulate NFKB, BCL2, Bruton tyrosine kinase (BTK), and apoptosis. Patients with wild-type MYD88 WM show an increased risk of transformation and death and exhibit many mutations found in diffuse large B-cell lymphoma. The discovery of MYD88 and CXCR4 mutations in WM has facilitated rational drug development, including the development of BTK and CXCR4 inhibitors. Responses to many agents commonly used to treat WM, including the BTK inhibitor ibrutinib, are affected by MYD88 and/or CXCR4 mutation status. The mutation status of both MYD88 and CXCR4 can be used for a precision-guided treatment approach to WM.

Expression of the prosurvival kinase HCK requires PAX5 and mutated MYD88 signaling in MYD88-driven B-cell lymphomas.

Hematopoietic cell kinase (HCK) is an SRC family member that is aberrantly upregulated in B-cell neoplasms dependent on MYD88-activating mutations and supports their growth and survival. We showed herein that activation of Toll-like receptor (TLR) signaling in MYD88 wild-type B cells also triggered HCK expression, denoting on path regulatory function for HCK by MYD88. To clarify the signaling cascades responsible for aberrant HCK expression in MYD88-mutated B-cell lymphomas, we performed promoter-binding transcription factor (TF) profiling, PROMO weighted TF consensus binding motif analysis, and chromatin immunoprecipitation studies. We identified PAX5, and the mutated MYD88 downstream signaling mediators STAT3, NF-κB, and AP-1, as important drivers of HCK transcription. Knockdown of PAX5, a crucial regulatory factor required for B-cell commitment and identity, abrogated HCK transcription in MYD88-mutated lymphoma cells. Among AP-1 complex components, JunB showed greatest relevance to TLR/MYD88 signaling and HCK transcription regulation. In MYD88-mutated Waldenström macroglobulinemia and activated B-cell-diffuse large B-cell lymphoma cells, knockdown of MYD88 reduced phosphorylation of JunB but not c-Jun, and knockdown of JunB reduced HCK protein levels. Deletion of STAT3, NF-κB, and AP-1 binding sites reduced corresponding TFs binding and HCK promoter activity. Moreover, inhibitors to STAT3, NF-κB, and AP-1 reduced HCK promoter activity and messenger RNA levels, particularly in combination, in MYD88-mutated lymphoma cells. The findings provide new insights into the transcriptional regulation of HCK prosurvival signaling by mutated MYD88, and the importance of JunB as a downstream mediator of the MYD88-directed signaling apparatus.

Deepening of response after completing rituximab-containing therapy in patients with Waldenstrom macroglobulinemia.

Rituximab-containing regimens are commonly used for frontline therapy in patients with symptomatic Waldenström macroglobulinemia (WM). We had observed that a portion of WM patients experienced deepening of response months to years after therapy completion. We carried a retrospective study aimed at describing this phenomenon. We gathered baseline data, and responses at end of induction, end of maintenance and best response. Deepening of response was defined as ≥25% decrease in serum IgM achieved at a later time from therapy completion. Of 178 patients included, 116 (65%) received maintenance therapy and 62 (35%) were observed. In patients who received maintenance, 44 (38%) had ≥25% decrease in serum IgM level after the end of maintenance with a median time from end of maintenance to lowest IgM level of 1.6 years (range 0.1-7.9 years). In patients who were observed, 19 (31%) had ≥25% decrease in serum IgM level after the end of induction with a median time from end of induction to lowest IgM level of 1.6 years (range 0.2-5.1 years). Baseline hemoglobin <11.5 g/dL, bone marrow involvement ≥50%, CXCR4 mutations and serum IgM ≥4000 mg/dL were associated with lower odds of deepening of response after therapy completion. Deepening of response was associated with better progression-free survival (PFS; HR 0.46, 95% CI 0.26-0.80; P = .006) and better survival after frontline treatment initiation (SAFTI; HR 0.21, 95% CI 0.06-0.73; P = .01). In conclusion, deepening of response occurs in one third of WM patients after completing rituximab-containing regimens and was associated with better PFS and SAFTI.