Genome-wide identification and investigation of monosaccharide transporter gene family based on their evolution and expression analysis under abiotic stress and hormone treatments in maize (Zea mays L.).

BACKGROUND: Monosaccharide transporter (MST) family, as a carrier for monosaccharide transport, plays an important role in carbon partitioning and widely involves in plant growth and development, stress response, and signaling transduction. However, little information on the MST family genes is reported in maize (Zea mays), especially in response to abiotic stresses. In this study, the genome-wide identification of MST family genes was performed in maize. RESULT: A total of sixty-six putative members of MST gene family were identified and divided into seven subfamilies (including SPT, PMT, VGT, INT, pGlcT, TMT, and ERD) using bioinformatics approaches, and gene information, phylogenetic tree, chromosomal location, gene structure, motif composition, and cis-acting elements were investigated. Eight tandem and twelve segmental duplication events were identified, which played an important role in the expansion of the ZmMST family. Synteny analysis revealed the evolutionary features of MST genes in three gramineous crop species. The expression analysis indicated that most of the PMT, VGT, and ERD subfamilies members responded to osmotic and cadmium stresses, and some of them were regulated by ABA signaling, while only a few members of other subfamilies responded to stresses. In addition, only five genes were induced by NaCl stress in MST family. CONCLUSION: These results serve to understand the evolutionary relationships of the ZmMST family genes and supply some insight into the processes of monosaccharide transport and carbon partitioning on the balance between plant growth and development and stress response in maize.

[Gene-gene/gene-environment interaction of transforming growth factor-ß signaling pathway and the risk of non-syndromic oral clefts].

OBJECTIVE: To explore the association between polymorphisms of transforming growth factor-ß (TGF-ß) signaling pathway and non-syndromic cleft lip with or without cleft palate (NSCL/P) among Asian populations, while considering gene-gene interaction and gene-environment interaction. METHODS: A total of 1 038 Asian NSCL/P case-parent trios were ascertained from an international consortium, which conducted a genome-wide association study using a case-parent trio design to investigate the genes affec-ting risk to NSCL/P. After stringent quality control measures, 343 single nucleotide polymorphism (SNP) spanning across 10 pivotal genes in the TGF-ß signaling pathway were selected from the original genome-wide association study(GWAS) dataset for further analysis. The transmission disequilibrium test (TDT) was used to test for SNP effects. The conditional Logistic regression models were used to test for gene-gene interaction and gene-environment interaction. Environmental factors collected for the study included smoking during pregnancy, passive smoking during pregnancy, alcohol intake during pregnancy, and vitamin use during pregnancy. Due to the low rates of exposure to smoking during pregnancy and alcohol consumption during pregnancy (<3%), only the interaction between maternal smoking during pregnancy and multivitamin supplementation during pregnancy was analyzed. The threshold for statistical significance was rigorously set at P =1.46×10-4, applying Bonferroni correction to account for multiple testing. RESULTS: A total of 23 SNPs in 4 genes yielded nominal association with NSCL/P (P<0.05), but none of these associations was statistically significant after Bonferroni' s multiple test correction. However, there were 6 pairs of SNPs rs4939874 (SMAD2) and rs1864615 (TGFBR2), rs2796813 (TGFB2) and rs2132298 (TGFBR2), rs4147358 (SMAD3) and rs1346907 (TGFBR2), rs4939874 (SMAD2) and rs1019855 (TGFBR2), rs4939874 (SMAD2) and rs12490466 (TGFBR2), rs2009112 (TGFB2) and rs4075748 (TGFBR2) showed statistically significant SNP-SNP interaction (P<1.46×10-4). In contrast, the analysis of gene-environment interactions did not yield any significant results after being corrected by multiple testing. CONCLUSION: The comprehensive evaluation of SNP associations and interactions within the TGF-ß signaling pathway did not yield any direct associations with NSCL/P risk in Asian populations. However, the significant gene-gene interactions identified suggest that the genetic architecture influencing NSCL/P risk may involve interactions between genes within the TGF-ß signaling pathway. These findings underscore the necessity for further investigations to unravel these results and further explore the underlying biological mechanisms.

[A ssociations of short-term ambient particulate matter exposure and MTNR1B gene with triglyceride-glucose index: A family-based study].

OBJECTIVE: To explore the effects of short-term particulate matter (PM) exposure and the melatonin receptor 1B (MTNR1B) gene on triglyceride-glucose (TyG) index utilizing data from Fang-shan Family-based Ischemic Stroke Study in China (FISSIC). METHODS: Probands and their relatives from 9 rural areas in Fangshan District, Beijing, were included in the study. PM data were obtained from fixed monitoring stations of the National Air Pollution Monitoring System. TyG index was calculated by fasting triglyceride and glucose concentrations. The associations of short-term PM exposure and rs10830963 polymorphism of the MTNR1B gene with the TyG index were assessed using mixed linear models, in which covariates such as age, sex, and lifestyles were adjusted for. Gene-environment inter-action analysis was furtherly performed using the maximum likelihood methods to explore the potential effect modifier role of rs10830963 polymorphism in the association of PM with TyG index. RESULTS: A total of 4 395 participants from 2 084 families were included in the study, and the mean age of the study participants was (58.98±8.68) years, with 53. 90% females. The results of association analyses showed that for every 10 µg/m3 increase in PM2.5 concentration, TyG index increased by 0.017 (95%CI: 0.007-0.027), while for per 10 µg/m3 increment in PM10, TyG index increased by 0.010 (95%CI: 0.003-0.017). And the associations all had lagged effects. In addition, there was a positive association between the rs10830963 polymorphism and the TyG index. For per increase in risk allele G, TyG index was elevated by 0.040 (95%CI: 0.004-0.076). The TyG index was 0.079 (95%CI: 0.005-0.152) higher in carriers of the GG genotype compared with carriers of the CC genotype. The interaction of rs10830963 polymorphism with PM exposure had not been found to be statistically significant in the present study. CONCLUSION: Short-term exposure to PM2.5 and PM10 were associated with higher TyG index. The G allele of rs10830963 polymorphism in the MTNR1B gene was associated with the elevated TyG index.

Rehmmannia glutinosa polysaccharide exerts antiviral activity against pseudorabies virus and antioxidant activity.

Pseudorabies virus (PRV) is an important pathogen harming the global pig industry. Vaccines available for swine cannot protect against PRV completely. Furthermore, no antiviral drugs are available to treat PRV infections. Rehmmannia glutinosa polysaccharide (RGP) possesses several medicinal properties. However, its antiviral activity is not reported. In the present study, we found that RGP can inhibit PRV/XJ5 infection by western blotting, immunofluorescent assay (IFA), and TCID50 assay quantitative polymerase chain reaction (qPCR). We revealed RGP can inhibit virus adsorption and invasion into PK-15 cells in a dose-dependent manner via western blotting, IFA, TCID50 assay, and quantitative polymerase chain reaction (qPCR), and suppressed PRV/XJ5 replication through western blotting, and qPCR. Additionally, it also reduced PRV/XJ5-induced ROS, lipid oxidation, and improved SOD levels in PK-15 cells, which was observed by using corresponding test kits. To conclude, our findings suggest that RGP might be a novel therapeutic agent for preventing and controlling PRV infection and antioxidant agent.

Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress.

Control of cellular identity requires coordination of developmental programs with environmental factors such as nutrient availability, suggesting that perturbing metabolism can alter cell state. Here, we find that nucleotide depletion and DNA replication stress drive differentiation in human and murine normal and transformed hematopoietic systems, including patient-derived acute myeloid leukemia (AML) xenografts. These cell state transitions begin during S phase and are independent of ATR/ATM checkpoint signaling, double-stranded DNA break formation, and changes in cell cycle length. In systems where differentiation is blocked by oncogenic transcription factor expression, replication stress activates primed regulatory loci and induces lineage-appropriate maturation genes despite the persistence of progenitor programs. Altering the baseline cell state by manipulating transcription factor expression causes replication stress to induce genes specific for alternative lineages. The ability of replication stress to selectively activate primed maturation programs across different contexts suggests a general mechanism by which changes in metabolism can promote lineage-appropriate cell state transitions.

Combined modulation format identification and optical signal-to-noise ratio monitoring with high accuracy and generalizability based on a proposed fused module few-shot learning algorithm in dynamic coherent optical transmissions.

Modulation format identification (MFI) and optical signal-to-noise ratio (OSNR) monitoring are important portions of optical performance monitoring (OPM) for future dynamic optical networks. In this paper, we proposed a fusion module few-shot learning (FMFSL) algorithm as an improvement upon the ordinary few-shot learning algorithms for image recognition with the specialty in adopting a combination of a dilated convolutional group and an asymmetric convolutional group to advance the feature extraction. FMFSL algorithm is applied in MFI and OSNR monitoring in coherent optical communication systems with its performance investigated in both back-to-back and fiber transmission scenarios using small-scale constellation diagrams. The results show that FMFSL algorithm can achieve 100% accuracy in MFI and higher OSNR monitoring accuracy compared to the few-shot learning algorithms Deep Nearest Neighbor Neural Network (DN4) and Prototypical Nets (PN) with 2.14% and 4.28% for 64QAM and 3.38% and 8.06% for 128QAM, respectively, without much increase in time consumption. Furthermore, the trained FMFSL algorithm remains excellent in MFI and OSNR monitoring without retraining while employed in back-to-back transmission scenarios with smaller OSNR intervals and fiber transmission scenarios with different amounts of Kerr nonlinearity, demonstrating its high capabilities in generalization and robustness. FMFSL algorithm provides a potential solution for OPM in future dynamic optical networks as a novel machine learning tool.

The involvement of SigmaR1K142 degradation mediated by ERAD in neural senescence linked with CdCl2 exposure.

Alzheimer's disease (AD) is the most common cause of dementia worldwide. Due to its uncertain pathogenesis, there is currently no treatment available for AD. Increasing evidences have linked cellular senescence to AD, although the mechanism triggering cellular senescence in AD requires further exploration. To investigate the involvement of cellular senescence in AD, we explored the effects of cadmium chloride (CdCl2) exposure, one of the potential environmental risk factors for AD, on neuron senescence in vivo and in vitro. ß-amyloid (Aß) and tubulin-associated protein (tau) pathologies were found to be enhanced by CdCl2 exposure in the in vitro models, while p53/p21/Rb cascade-related neuronal senescence pathways were activated. Conversely, the use of melatonin, a cellular senescence inhibitor, or a cadmium ion chelator suppressed CdCl2-induced neuron senescence, along with the Aß and tau pathologies. Mechanistically, CdCl2 exposure activated the suppressor enhancer Lin-12/Notch 1-like (SEL1L)/HMG-CoA reductase degradation 1 (HRD1)-regulated endoplasmic reticulum-associated degradation (ERAD), which enhanced the ubiquitin degradation of sigma-1 receptor (SigmaR1) by specifically recognizing its K142 site, resulting in the activation of the p53/p21/Rb pathway via the induction of Ca2+ dyshomeostasis and mitochondrial dysfunction. In the in vivo models, the administration of the SigmaR1 agonist ANAVEX2-73 rescues neurobehavioral inhibition and alleviates cellular senescence and AD-like pathology in the brain tissue of CdCl2-exposed mice. Consequently, the present study revealed a novel senescence-associated regulatory route for the SEL1L/HRD1/SigmaR1 axis that affects the pathological progression of CdCl2 exposure-associated AD. CdCl2 exposure activated SEL1L/HRD1-mediated ERAD and promoted the ubiquitinated degradation of SigmaR1, activating p53/p21/Rb pathway-regulated neuronal senescence. The results of the present study suggest that SigmaR1 may function as a neuroprotective biomarker of neuronal senescence, and pharmacological activation of SigmaR1 could be a promising intervention strategy for AD therapy.

Overexpressing S100A9 ameliorates NK cell dysfunction in estrogen receptor-positive breast cancer.

BACKGROUND: Estrogen receptor (ER) positive human epidermal growth factor receptor 2 (HER2) negative breast cancer (ER+/HER2-BC) and triple-negative breast cancer (TNBC) are two distinct breast cancer molecular subtypes, especially in tumor immune microenvironment (TIME). The TIME of TNBC is considered to be more inflammatory than that of ER+/HER2-BC. Natural killer (NK) cells are innate lymphocytes that play an important role of tumor eradication in TME. However, studies focusing on the different cell states of NK cells in breast cancer subtypes are still inadequate. METHODS: In this study, single-cell mRNA sequencing (scRNA-seq) and bulk mRNA sequencing data from ER+/HER2-BC and TNBC were analyzed. Key regulator of NK cell suppression in ER+/HER2-BC, S100A9, was quantified by qPCR and ELISA in MCF-7, T47D, MDA-MB-468 and MDA-MB-231 cell lines. The prognosis predictability of S100A9 and NK activation markers was evaluated by Kaplan-Meier analyses using TCGA-BRAC data. The phenotype changes of NK cells in ER+/HER2-BC after overexpressing S100A9 in cancer cells were evaluated by the production levels of IFN-gamma, perforin and granzyme B and cytotoxicity assay. RESULTS: By analyzing scRNA-seq data, we found that multiple genes involved in cellular stress response were upregulated in ER+/HER2-BC compared with TNBC. Moreover, TLR regulation pathway was significantly enriched using differentially expressed genes (DEGs) from comparing the transcriptome data of ER+/HER2-BC and TNBC cancer cells, and NK cell infiltration high/low groups. Among the DEGs, S100A9 was identified as a key regulator. Patients with higher expression levels of S100A9 and NK cell activation markers had better overall survival. Furthermore, we proved that overexpression of S100A9 in ER+/HER2-cells could improve cocultured NK cell function. CONCLUSION: In conclusion, the study we presented demonstrated that NK cells in ER+/HER2-BC were hypofunctional, and S100A9 was an important regulator of NK cell function in ER+BC. Our work contributes to elucidate the regulatory networks between cancer cells and NK cells and may provide theoretical basis for novel drug development.

Zixue Powder attenuates septic thrombosis via reducing neutrophil extracellular trap through blocking platelet STING activation.

ETHNOPHARMACOLOGICAL RELEVANCE: Microthrombosis is commonly seen in sepsis and COVID-19. Zixue Powder (ZXP) is a traditional Chinese herbal formula with the potential to treat microvascular and infectious diseases. However, the role and mechanism of ZXP in sepsis-associated thrombosis remain unclear. AIM OF THE STUDY: Investigating the therapeutic effectiveness and underlying mechanisms of ZXP in septic thrombosis. MATERIALS AND METHODS: ZXP's compositions were examined with UPLC-QTOF-MS. The efficacy of ZXP on sepsis-induced thrombosis was assessed through various methods: liver tissue pathology was examined using hematoxylin-eosin staining, platelet count was determined by a blood cell analyzer, and an enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of serum tissue factor (TF), thromboxane B2 (TXB2), D-Dimer, and plasminogen activator inhibitor-1 (PAI-1). Neutrophil extracellular traps (NETs) were localized and expressed in liver tissues by immunofluorescence, and the number of NETs in peripheral blood was evaluated by ELISA, which measured the quantity of cf-DNA and MPO-DNA in serum. Platelet P-selectin expression and platelet-neutrophil aggregation were measured by flow cytometry, and plasma P-selectin expression was measured by ELISA. Furthermore, the mechanism of the stimulator of interferon genes (STING) signaling pathway in ZXP's anti-sepsis thrombosis effect was investigated using the STING agonist, Western blot experiments, and immunoprecipitation experiments. RESULTS: UPLC-QTOF-MS identified 40 chemical compositions of ZXP. Administration of ZXP resulted in significant improvements in liver thrombosis, platelet counts, and levels of TXB2, TF, PAI-1, and D-Dimer in septic rats. Moreover, ZXP inhibited NETs formation in both liver tissue and peripheral blood. Additionally, ZXP decreased the levels of P-selectin in both platelets and plasma, as well as the formation of platelet-neutrophil aggregates, thereby suppressing P-selectin-mediated NETs release. Immunoprecipitation and immunofluorescence staining experiments revealed that ZXP attenuated P-selectin secretion by inhibiting STING-mediated assembly of platelet soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) complex, ultimately preventing inhibition of NETs formation. CONCLUSION: Our study showed that ZXP effectively mitigates platelet granule secretion primarily through modulation of the STING pathway, consequently impeding NET-associated thrombosis in sepsis. These findings offer valuable insights for future research on the development and application of ZXP.

Degradation of tetracycline under a wide pH range in a heterogeneous photo bio-electro-fenton system using FeMn-LDH/g-C3N4 cathode: Performance and mechanism.

The widespread use of antibiotics and the inefficiency of traditional degradation treatments pose threats to the environment and human health. Previous studies have reported the potential of bio-electro-Fenton (BEF) processes for antibiotic removal. However, some drawbacks, such as a strict pH range of 2-3 and iron sludge generation, limit their large-scale application. Thus, to overcome the narrow pH range of traditional BEF processes, a photo-BEF (PBEF) system was established using a novel FeMn-layered double hydroxide (LDH)/graphitic carbon nitride (g-C3N4) (FM/CN) composite cathode. The performance of the PBEF system was investigated by degrading tetracycline (TC) under low-power LED lamp irradiation. The results indicated that the pH range of the PBEF system could be expanded to 3-11 using an FM/CN cathode, which exhibited a TC removal efficiency of 63.0%-75.9%. The highest TC removal efficiency was achieved at pH 7. The efficient mineralization of TC by the PBEF system can be high, up to 67.6%. In addition, the TC removal mechanism was discussed in terms of reactive oxygen species, TC degradation intermediate analyses, and density functional theory (DFT) calculations. Strong oxidative hydroxyl radicals (·OH) were the dominant reactive oxidizing species in the PBEF system, followed by ·O2- and h+. Three pathways of TC degradation were proposed based on the analysis of intermediates, and the reactive sites attacked by electrophilic reagents were explored using DFT modeling. In addition, the overall toxicity of TC degradation intermediates effectively decreased in the PBEF system. This work offers deep insights into the TC removal mechanisms and performance of the PBEF system over a wide pH range of 3-11.

Comparing survival outcomes between neoadjuvant and adjuvant chemotherapy within T2N1M0 stage hormone receptor-positive, HER2-negative breast cancer: a retrospective cohort study based on SEER database.

BACKGROUND: Guideline recommendations for the application of neoadjuvant chemotherapy (NACT) in T2N1M0 stage hormone receptor-positive, HER2-negative (HR + /HER2-) breast cancer are ambiguous. The debate continues regarding whether NACT or adjuvant chemotherapy (ACT) offers superior survival outcomes for these patients. MATERIALS AND METHODS: Female patients diagnosed with HR + /HER2- breast cancer at T2N1M0 stage between 2010 and 2020, were identified from the Surveillance, Epidemiology, and End Results database and divided into two groups, the NACT group and the ACT group. Propensity score matching (PSM) was utilized to establish balanced cohorts between groups, considering baseline features. Kaplan-Meier (K-M) analysis and the Cox proportional hazards model were executed to assess the efficacy of both NACT and ACT in terms of overall survival (OS) and breast cancer-specific survival (BCSS). A logistic regression model was employed to examine the association between predictive variables and response to NACT. RESULTS: After PSM, 4,682 patients were finally included. K-M curves showed that patients receiving NACT exhibited significantly worse OS and BCSS when compared with patients undergoing ACT. Multivariable Cox analysis indicated that not achieving pathologic complete response (non-pCR) after NACT (versus ACT), was identified as an adverse prognostic factor for OS (HR 1.58, 95% CI 1.36-1.83) and BCSS (HR 1.70, 95% CI 1.44-2. 02). The logistic regression model revealed that low tumor grade independently predicted non-pCR. CONCLUSION: Among T2N1M0 stage HR + /HER2- patients, OS and BCSS of NACT were inferior to ACT. Patients who attained non-pCR after NACT demonstrated significantly worse survival outcomes compared with those who received ACT.

Molecular Dynamics Simulation Research on Fe Atom Precipitation Behaviour of Cu-Fe Alloys during the Rapid Solidification Processes.

To explore the crystalline arrangement of the alloy and the processes involving iron (Fe) precipitation, we employed molecular dynamics simulation with a cooling rate of 2 × 1010 for Cu100-XFeX (where X represents 1%, 3%, 5%, and 10%) alloy. The results reveal that when the Fe content was 1%, Fe atoms consistently remained uniformly distributed as the temperature of the alloy decreased. Further, there was no Fe atom aggregation phenomenon. The crystal structure was identified as an FCC-based Cu crystal, and Fe atoms existed in the matrix in solid solution form. When the Fe content was 3%, Fe atoms tended to aggregate with the decreasing temperature of the alloy. Moreover, the proportion of BCC crystal structure exhibited no obvious changes, and the crystal structure remained FCC-based Cu crystal. When the Fe content was between 5% and 10%, the Fe atoms exhibited obvious aggregation with the decreasing temperature of the alloy. At the same time, the aggregation phenomenon was found to be more significant with a higher Fe content. Fe atom precipitation behaviour can be delineated into three distinct stages. The initial stage involves the gradual accumulation of Fe clusters, characterised by a progressively stable cluster size. This phenomenon arises due to the interplay between atomic attraction and the thermal motion of Fe-Fe atoms. In the second stage, small Fe clusters undergo amalgamation and growth. This growth is facilitated by non-diffusive local structural rearrangements of atoms within the alloy. The third and final stage represents a phase of equilibrium where both the size and quantity of Fe clusters remain essentially constant following the crystallisation of the alloy.

Comparison of Different Endovascular Treatments of Femoropopliteal Artery In-Stent Restenosis: A Systematic Review and Bayesian Network Meta-Analysis.

BACKGROUND: This Bayesian network meta-analysis (NMA) sought to evaluate the efficacy of different endovascular treatments for femoropopliteal artery in-stent restenosis (FP-ISR). METHODS: PubMed, Embase, Cochrane Central Register of Controlled Trials, and Web of science for clinical trials from database inception to March 31, 2023, with no language restrictions to retrieve randomized controlled trials or cohort studies evaluating the impact of any kind of endovascular treatments for FP-ISR. Pair-wise meta-analysis and Bayesian NMA were performed to pool the outcome estimates different endovascular treatments. The primary end points under consideration were primary patency rates at both 6-month and 12-month follow-up. RESULTS: A total of 15 studies with 1,424 patients were ultimately enrolled to be analyzed, 7 types of endovascular treatment were identified for comparison. In terms of primary patency and freedom from target lesion revascularization (TLR) at 6-month and12-month follow-up, the direct meta-analysis findings showed that drug-coated balloons (DCB) and covered stent (CS) are considerably superior to plain old balloon angioplasty (POBA), Excimer laser atherectomy (ELA) + DCB is significantly better than DCB. According to the meta-analysis based on Bayesian theory, during the 6-month and 12-months follow-up, we could not find significant difference between the different treatments in terms of the primary patency and the freedom from TLR, based on the surface values under the cumulative ranking curve (SUCRA), CS was considered the best treatment in terms of primary patency (6 months SUCRA = 85.2; 12 months SUCRA = 78.9) and freedom from TLR (6 months SUCRA = 84.9; 12 months SUCRA = 70.9); directional atherectomy + POBA may lead to higher survival rate at 12 months (SUCRA = 89.1) than others treatments; in addition, both ELA + POBA and ELA + DCB have higher limb salvage than POBA. CONCLUSIONS: The findings of this NMA suggest that CS showed positive encouraging results in primary patency and TLR in FP-ISR at 6 and 12 months. However, due to the potential influence of certain confounding factors, the long-term results necessitate validation through numerous randomized controlled trials.

Tailoring Titanium Carbide Clusters for New Materials: from Met-Cars to Carbon-Doped Superatoms.

Tailoring materials with prescribed properties and regular structures is a critical and challenging research topic. Early transition metals were found to form supermagic M8C12 metallocarbohedrenes (Met-Cars); however, stable metal carbides are not limited to this common stoichiometry. Utilizing self-developed deep-ultraviolet laser ionization mass spectrometry, here, we report a strategy to generate new titanium carbides by reacting pure Tin clusters with acetylene. Interestingly, two products corresponding to Ti17C2 and Ti19C10 exhibit superior abundances in addition to the Ti8C12 Met-Cars. Using global-minimum search, the structures of Ti17C2 and Ti19C10 are determined to be an ellipsoidal D4d and a rod-shaped D5h geometry, respectively, both with carbon-capped Ti4C moieties and superatomic features. We illustrate the electronic structures and bonding nature in these carbon-doped superatoms concerning their enhanced stability and local aromaticity, shedding light on a new class of metal-carbide nanomaterials with atomic precision.

Tuning the dimensional order in self-assembled magnetic nanostructures: theory, simulations, and experiments.

A major obstacle to building nanoscale magnetic devices or even experimentally studying novel nanomagnetic spin textures is the present lack of a simple and robust method to fabricate various nano-structured alloys. Here, theoretical and experimental investigations were conducted to understand the underlying physical mechanisms of magnetic particle self-assembly in zero applied magnetic field. By changing the amount of NaOH added during the synthesis, we demonstrate that the resulting morphology of the assembled FeCo structure can be tuned from zero-dimensional (0D) nanoparticles to one-dimensional (1D) chains, and even three-dimensional (3D) networks. Two numerical simulations were developed to predict aspects of nanostructure formation by accounting for the magnetic interactions between individual magnetic nanoparticles. The first utilized the Boltzmann distribution to determine the equilibrium structure of a nanochain, iteratively predicting the local deviation angle θ of each particle as it attaches to a forming chain. The second simulation illustrates the differences in nanostructure arrangement and dimensionality (0D, 1D, or 3D) that arise from random interactions at various nanoparticle densities. The simulation results closely match the experimental findings, as seen from SEM images, demonstrating their ability to capture the system's structural properties. In addition, magnetic hysteresis measurements of the samples were performed along two orthogonal directions to show the influence of dimensional order on the magnetic behavior. The normalized remanence (MR/MS||) of the FeCo alloys increases as the dimensions of nanostructures are increased. Of the three cases, the FeCo 3D network structures exhibit the highest normalized nanostructure remanence of 0.33 and an increased coercivity to above 200 Oe at 300 K. This combined numerical and experimental investigation aims to shed light on the preparation of FeCo nanostructures with tailorable dimensional order and it opens new avenues for exploring the complex spin textures and coercive behavior of these multi-dimensional nanomagnetic structures.

Actuating Liquid Crystals Rapidly and Reversibly by Using Chemical Catalysis.

Microtubules and catalytic motor proteins underlie the microscale actuation of living materials, and they have been used in reconstituted systems to harness chemical energy to drive new states of organization of soft matter (e.g., liquid crystals (LCs)). Such materials, however, are fragile and challenging to translate to technological contexts. Rapid (sub-second) and reversible changes in the orientations of LCs at room temperature using reactions between gaseous hydrogen and oxygen that are catalyzed by Pd/Au surfaces are reported. Surface chemical analysis and computational chemistry studies confirm that dissociative adsorption of H2 on the Pd/Au films reduces preadsorbed O and generates 1 ML of adsorbed H, driving nitrile-containing LCs from a perpendicular to a planar orientation. Subsequent exposure to O2 leads to oxidation of the adsorbed H, reformation of adsorbed O on the Pd/Au surface, and a return of the LC to its initial orientation. The roles of surface composition and reaction kinetics in determining the LC dynamics are described along with a proof-of-concept demonstration of microactuation of beads. These results provide fresh ideas for utilizing chemical energy and catalysis to reversibly actuate functional LCs on the microscale.

AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding.

Protein function annotation has been one of the longstanding issues in biological sciences, and various computational methods have been developed. However, the existing methods suffer from a serious long-tail problem, with a large number of GO families containing few annotated proteins. Herein, an innovative strategy named AnnoPRO was therefore constructed by enabling sequence-based multi-scale protein representation, dual-path protein encoding using pre-training, and function annotation by long short-term memory-based decoding. A variety of case studies based on different benchmarks were conducted, which confirmed the superior performance of AnnoPRO among available methods. Source code and models have been made freely available at: https://github.com/idrblab/AnnoPRO and https://zenodo.org/records/10012272.

MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery.

In the context of precision medicine, multiomics data integration provides a comprehensive understanding of underlying biological processes and is critical for disease diagnosis and biomarker discovery. One commonly used integration method is early integration through concatenation of multiple dimensionally reduced omics matrices due to its simplicity and ease of implementation. However, this approach is seriously limited by information loss and lack of latent feature interaction. Herein, a novel multiomics early integration framework (MOINER) based on information enhancement and image representation learning is thus presented to address the challenges. MOINER employs the self-attention mechanism to capture the intrinsic correlations of omics-features, which make it significantly outperform the existing state-of-the-art methods for multiomics data integration. Moreover, visualizing the attention embedding and identifying potential biomarkers offer interpretable insights into the prediction results. All source codes and model for MOINER are freely available https://github.com/idrblab/MOINER.

Single-cell analysis of immune and stroma cell remodeling in clear cell renal cell carcinoma primary tumors and bone metastatic lesions.

BACKGROUND: Despite therapeutic advances, once a cancer has metastasized to the bone, it represents a highly morbid and lethal disease. One third of patients with advanced clear cell renal cell carcinoma (ccRCC) present with bone metastasis at the time of diagnosis. However, the bone metastatic niche in humans, including the immune and stromal microenvironments, has not been well-defined, hindering progress towards identification of therapeutic targets. METHODS: We collected fresh patient samples and performed single-cell transcriptomic profiling of solid metastatic tissue (Bone Met), liquid bone marrow at the vertebral level of spinal cord compression (Involved), and liquid bone marrow from a different vertebral body distant from the tumor site but within the surgical field (Distal), as well as bone marrow from patients undergoing hip replacement surgery (Benign). In addition, we incorporated single-cell data from primary ccRCC tumors (ccRCC Primary) for comparative analysis. RESULTS: The bone marrow of metastatic patients is immune-suppressive, featuring increased, exhausted CD8 + cytotoxic T cells, T regulatory cells, and tumor-associated macrophages (TAM) with distinct transcriptional states in metastatic lesions. Bone marrow stroma from tumor samples demonstrated a tumor-associated mesenchymal stromal cell population (TA-MSC) that appears to be supportive of epithelial-to mesenchymal transition (EMT), bone remodeling, and a cancer-associated fibroblast (CAFs) phenotype. This stromal subset is associated with poor progression-free and overall survival and also markedly upregulates bone remodeling through the dysregulation of RANK/RANKL/OPG signaling activity in bone cells, ultimately leading to bone resorption. CONCLUSIONS: These results provide a comprehensive analysis of the bone marrow niche in the setting of human metastatic cancer and highlight potential therapeutic targets for both cell populations and communication channels.