High-Throughput Antigen Microarray Identifies Longitudinal Prognostic Autoantibody for Chemoimmunotherapy in Advanced Non-Small Cell Lung Cancer.

Chemoimmunotherapy has evolved as a standard treatment for advanced non-small cell lung cancer (aNSCLC). However, inevitable drug resistance has limited its efficacy, highlighting the urgent need for biomarkers of chemoimmunotherapy. A three-phase strategy to discover, verify, and validate longitudinal predictive autoantibodies (AAbs) for aNSCLC before and after chemoimmunotherapy was employed. A total of 528 plasma samples from 267 aNSCLC patients before and after anti-PD1 immunotherapy were collected, plus 30 independent formalin-fixed paraffin-embedded samples. Candidate AAbs were firstly selected using a HuProt high-density microarray containing 21,000 proteins in the discovery phase, followed by validation using an aNSCLC-focused microarray. Longitudinal predictive AAbs were chosen for ELISA based on responders versus non-responders comparison and progression-free survival (PFS) survival analysis. Prognostic markers were also validated using immunohistochemistry and publicly available immunotherapy datasets. We identified and validated a panel of two AAbs (MAX and DHX29) as pre-treatment biomarkers and another panel of two AAbs (MAX and TAPBP) as on-treatment predictive markers in aNSCLC patients undergoing chemoimmunotherapy. All three AAbs exhibited a positive correlation with early responses and PFS (p < 0.05). The kinetics of MAX AAb showed an increasing trend in responders (p < 0.05) and a tendency to initially increase and then decrease in non-responders (p < 0.05). Importantly, MAX protein and mRNA levels effectively discriminated PFS (p < 0.05) in aNSCLC patients treated with immunotherapy. Our results present a longitudinal analysis of changes in prognostic AAbs in aNSCLC patients undergoing chemoimmunotherapy.

The co-location of MARCO+ tumor-associated macrophages and CTSE+ tumor cells determined the poor prognosis in intrahepatic cholangiocarcinoma.

Intra-tumor immune infiltration is a crucial element interacting with tumor cells in intrahepatic cholangiocarcinoma (ICC). However, its phenotype and related spatial structure remained elusive. To address these limitations, we undertook a comprehensive study combining spatial data (29,632 spots from six samples) and single-cell data (21,158 cells from 35 samples). We identified two distinct infiltration patterns: macrophage+ (characterized by CD68 and MARCO) and plasma cell+ (characterized by IGHG1 and JCHAIN). The macrophage+ and plasma cell+ signatures showed adverse and favorable roles in ICC patients' survival, respectively. Notably, MARCO+ tumor-associated macrophage (TAM) was recognized as the main cell type in macrophage+ samples, indicating an immune-resistant microenvironment. Increased epithelial-mesenchymal transition activities, angiogenesis, and hypoxia were observed in MARCO+ TAM. The co-location of MARCO+ TAM and CTSE+ tumor cells was observed in spatial transcriptomics and bulk transcriptomics data, validated by multiplex immunofluorescence performed on twenty ICC samples. The co-location area exhibited similar protumorigenic pathways and suppressed immune response. CTSE exhibited associations with intrahepatic metastasis and vascular invasion. Both MARCO+ TAM and CTSE+ tumor cells were associated with worse survival and patients with high infiltration of two cell types displayed the worst survival. Within the co-location area, the galectin signaling pathway was most active in cell-cell communication, with LGALS9-CD44 identified as the main ligand-receptor pair. This study identified macrophage+ and plasma cell+ intra-tumor immune infiltration patterns and the co-location of MARCO+ TAM and CTSE+ tumor cells as contributors to immune resistance.

Identification of novel prognostic autoantibodies in diffuse large B-cell lymphoma treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone via a high-throughput antigen microarray.

BACKGROUND: R-CHOP (rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone) is a standard first-line treatment for diffuse large B-cell lymphoma (DLBCL). However, 20%-40% of patients survive less than 5 years. Novel prognostic biomarkers remain in demand. METHODS: Baseline plasma autoantibodies (AAbs) were assessed in 336 DLBCLs. In the discovery phase (n = 20), a high-density antigen microarray (∼21,000 proteins) was used to expound AAb profiles. In the verification phase (n = 181), with a DLBCL-focused microarray, comparative results based on event-free survival at 24 months (EFS24) and lasso Cox regression models of progression-free survival (PFS) and overall survival (OS) were integrated to identify potential biomarkers. They were further validated by enzyme-linked immunosorbent assay in validation phase 1 (n = 135) and a dynamic cohort (n = 12). In validation phase 2, a two-AAb-based risk score was established. They were further validated in an immunohistochemistry cohort (n = 55) and four independent Gene Expression Omnibus datasets (n = 1598). RESULTS: Four AAbs (CREB1, N4BP1, UBAP2, and DEAF1) were identified that showed associations with EFS24 status (p < .05) and superior PFS and OS (p < .05). A novel risk score model based on CREB1 and N4BP1 AAbs was developed to predict PFS with areas under the curve of 0.72, 0.71, 0.76, and 0.82 at 1, 3, 5, and 7 years, respectively, in DLBCL treated with R-CHOP independent of the International Prognostic Index (IPI) and provided significant additional recurrence risk discrimination (p < .05) for the IPI. CREB1 and N4BP1 proteins and messenger RNAs were also associated with better PFS and OS (p < .05). CONCLUSIONS: This study identified a novel prognostic panel of CREB1, N4BP1, DEAF1, and UBAP2 AAbs that is independent of the IPI in DLBCL.

Spatial analyses revealed S100P + TFF1 + tumor cells in spread through air spaces samples correlated with undesirable therapy response in non-small cell lung cancer.

Spread through air spaces (STAS) is a recognized aggressive pattern in lung cancer, serving as a crucial risk factor for postoperative recurrence. However, its phenotype and related spatial structure have remained elusive. To address these limitations, we conducted a comprehensive study based on spatial data, analyzing over 30,000 spots from 14 non-STAS samples and one STAS sample. We observed increased proliferation activities and angiogenesis in STAS, identifying S100P as a potential biomarker for STAS. Furthermore, our investigation into the heterogeneity of STAS tumor cells revealed a subset identified as S100P + TFF1 +, exhibiting a negative impact on patients' survival in public datasets. This subtype exhibited the highest activities in the TGFb and hypoxia, suggesting its potential pro-tumor role within the tumor microenvironment. To assess the role of S100P + TFF1 + tumor cells in therapy response, we included data from two clinical trial cohorts (BPI-7711 for EGFR-TKI therapy and ORIENT-3 for immunotherapy). The presence of S100P + TFF1 + tumor cells correlated with worse responses to both EGFR-TKI therapy and immunotherapy. Notably, TFF1 emerged as a serum marker for predicting EGFR-TKI response. Cell-cell communication analysis revealed that the TGFb signaling pathway was the most activated in S100P + TFF1 + tumor cells, with TGFB2-TGFBR2 identified as the main ligand-receptor pair. This was further validated by multiplex immunofluorescence performed on twenty NSCLC samples. In summary, our study identified S100P as the biomarker for STAS and highlighted the adverse role of S100P + TFF1 + tumor cells in survival outcomes.

Integrative analyses of bulk and single-cell RNA-seq identified cancer-associated fibroblasts-related signature as a prognostic factor for immunotherapy in NSCLC.

An emerging view regarding cancer-associated fibroblast (CAF) is that it plays a critical role in tumorigenesis and immunosuppression in the tumor microenvironment (TME), but the clinical significance and biological functions of CAFs in non-small cell lung cancer (NSCLC) are still poorly explored. Here, we aimed to identify the CAF-related signature for NSCLC through integrative analyses of bulk and single-cell genomics, transcriptomics, and proteomics profiling. Using CAF marker genes identified in weighted gene co-expression network analysis (WGCNA), we constructed and validated a CAF-based risk model that stratifies patients into two prognostic groups from four independent NSCLC cohorts. The high-score group exhibits a higher abundance of CAFs, decreased immune cell infiltration, increased epithelial-mesenchymal transition (EMT), activated transforming growth factor beta (TGFß) signaling, and a limited survival rate compared with the low-score group. Considering the immunosuppressive feature in the high-score group, we speculated an inferior clinical response for immunotherapy in these patients, and this association was successfully verified in two NSCLC cohorts treated with immune checkpoint blockades (ICBs). Furthermore, single-cell RNA sequence datasets were used to clarify the molecular mechanisms underlying the aggressive and immunosuppressive phenotype in the high-score group. We found that one of the genes in the risk model, filamin binding LIM protein 1 (FBLIM1), is mainly expressed in fibroblasts and upregulated in CAFs compared to fibroblasts from normal tissue. FBLIM1-positive CAF subtype was correlated with increased TGFß expression, higher mesenchymal marker level, and immunosuppressive tumor microenvironment. Finally, we demonstrated that FBLIM1 might serve as a poor prognostic marker for immunotherapy in clinical samples. In conclusion, we identified a novel CAF-based classifier with prognostic value in NSCLC patients and those treated with ICBs. Single-cell transcriptome profiling uncovered FBLIM1-positive CAFs as an aggressive subtype with a high abundance of TGFß, EMT, and an immunosuppressive phenotype in NSCLC.

Spatially homogeneous few-cycle compression of Yb lasers via all-solid-state free-space soliton management.

The high power and variable repetition-rate of Yb femtosecond lasers makes them very attractive for ultrafast science. However, for capturing sub-200 fs dynamics, efficient, high-fidelity and high-stability pulse compression techniques are essential. Spectral broadening using an all-solid-state free-space geometry is particularly attractive, as it is simple, robust and low-cost. However, spatial and temporal losses caused by spatio-spectral inhomogeneities have been a major challenge to date, due to coupled space-time dynamics associated with unguided nonlinear propagation. In this work, we use all-solid-state free-space compressors to demonstrate compression of 170 fs pulses at a wavelength of 1030nm from a Yb:KGW laser to ∼9.2 fs, with a highly spatially homogeneous mode. This is achieved by ensuring that the nonlinear beam propagation in periodic layered Kerr media occurs in spatial soliton modes, and by confining the nonlinear phase through each material layer to less than 1.0 rad. A remarkable spatio-spectral homogeneity of ∼0.87 can be realized, which yields a high efficiency of >50% for few-cycle compression. The universality of the method is demonstrated by implementing high-quality pulse compression under a wide range of laser conditions. The high spatiotemporal quality and the exceptional stability of the compressed pulses are further verified by high-harmonic generation. Our predictive method offers a compact and cost-effective solution for high-quality few-cycle-pulse generation from Yb femtosecond lasers, and will enable broad applications in ultrafast science and extreme nonlinear optics.

Construction of Cu(I)-Organic Frameworks with Effective Sorption Behavior for Iodine and Congo Red.

The assembly of a tetradentate pyridine-derived ligand with CuX has afforded two isostructural Cu(I)-organic frameworks [Cu2X2(TBD)·DMF]n (X = Cl for 1 and Br for 2) in this work. Structural analysis indicates that the compounds feature hybrid layered architectures, and the three-dimensional supramolecular frameworks are finally fabricated through the alternative stacking of adjacent layers wherein large open channels are simultaneously constructed. The chemical stability has been studied showing the excellent skeleton maintenance of the prepared solids in various solvents and even in water. Moreover, the iodine and dye sorption performance for compound 1 has been further tested. The Cu(I)-based metal-organic framework exhibits outstanding sorption and separation abilities on the targeted species, which could be considered as a promising adsorbent with high efficiency and selectivity.

Rapid identification of candidate genes controlling male-sterility in Foxtail millet (Setaria italica).

Photo-(thermo-) sensitive genic male-sterile line is the key component of two-line hybridization system in foxtail millet (Setaria italica), but the genetic basis of male sterility in most male-sterile lines is still unclear. In the present study, a large F2 population was developed derived from a cross between the photo-(thermo-) sensitive male-sterile line A2 and the fertile-line 1484-5. Thirty plants with extreme high and extreme low fertility were selected from the population to construct a sterile DNA pool and a fertile DNA pool, respectively. Sequencing both DNA pools and data analysis revealed that two QTLs conferred male-sterility, qSiMS6.1 with a major effect and qSiMS6.2 with a minor effect, on chromosome 6. Both QTLs exhibited complete dominance. The major QTL, qSiMS6.1, was delimited to a 186-kb interval between the markers SiM20 and SiM9 by the joint analysis of QTL-seq and QTL mapping with SSR and structure variation markers. Millet_GLEAN_10020454 in this region is the most likely candidate gene for qSiMS6.1 since it is predicted to encode a male-sterile 5 like protein. These results lay a solid foundation for qSiMS6.1 cloning and provided gene resources for breeding new male-sterile lines. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01269-2.

Raman effect in the spectral broadening of ultrashort laser pulses in saturated versus unsaturated hydrocarbon molecules.

A conventional hollow core fiber (HCF) scheme is implemented to investigate spectral broadening of Titanium:Sapphire (Ti-Sa) femtosecond laser pulses in saturated hydrocarbon molecules compared to unsaturated ones. While the saturated molecules exhibit a spectral broadening similar to noble gases, for the unsaturated ones with π bonds, broadening towards blue is restrained. Numerical simulations underpin that it is a combination of group velocity dispersion (GVD) and Raman scattering which limits the spectral broadening for the unsaturated molecules. Compression of low energy ∼40fs pulses to ∼8fs using saturated hydrocarbons is demonstrated, suggesting the feasibility of this media for high repetition rate laser pulse compression.

Near- and Extended-Edge X-Ray-Absorption Fine-Structure Spectroscopy Using Ultrafast Coherent High-Order Harmonic Supercontinua.

Recent advances in high-order harmonic generation have made it possible to use a tabletop-scale setup to produce spatially and temporally coherent beams of light with bandwidth spanning 12 octaves, from the ultraviolet up to x-ray photon energies >1.6 keV. Here we demonstrate the use of this light for x-ray-absorption spectroscopy at the K- and L-absorption edges of solids at photon energies near 1 keV. We also report x-ray-absorption spectroscopy in the water window spectral region (284-543 eV) using a high flux high-order harmonic generation x-ray supercontinuum with 10^{9} photons/s in 1% bandwidth, 3 orders of magnitude larger than has previously been possible using tabletop sources. Since this x-ray radiation emerges as a single attosecond-to-femtosecond pulse with peak brightness exceeding 10^{26} photons/s/mrad^{2}/mm^{2}/1% bandwidth, these novel coherent x-ray sources are ideal for probing the fastest molecular and materials processes on femtosecond-to-attosecond time scales and picometer length scales.

Helicity-Selective Enhancement and Polarization Control of Attosecond High Harmonic Waveforms Driven by Bichromatic Circularly Polarized Laser Fields.

High harmonics driven by two-color counterrotating circularly polarized laser fields are a unique source of bright, circularly polarized, extreme ultraviolet, and soft x-ray beams, where the individual harmonics themselves are completely circularly polarized. Here, we demonstrate the ability to preferentially select either the right or left circularly polarized harmonics simply by adjusting the relative intensity ratio of the bichromatic circularly polarized driving laser field. In the frequency domain, this significantly enhances the harmonic orders that rotate in the same direction as the higher-intensity driving laser. In the time domain, this helicity-dependent enhancement corresponds to control over the polarization of the resulting attosecond waveforms. This helicity control enables the generation of circularly polarized high harmonics with a user-defined polarization of the underlying attosecond bursts. In the future, this technique should allow for the production of bright highly elliptical harmonic supercontinua as well as the generation of isolated elliptically polarized attosecond pulses.

Ultrafast multi-wavelength switch based on dynamics of spectrally-shifted solitons in a dual­core photonic crystal fiber.

Nonlinear propagation of ultrafast near infrared pulses in anomalous dispersion region of dual-core photonic crystal fiber was studied. Polarization tunable soliton-based nonlinear switching at multiple non-excitation wavelengths was demonstrated experimentally for fiber excitation by 100 fs pulses at 1650 nm. The highest-contrast switching was obtained with the fiber length of just 14 mm, which is significantly shorter compared to the conventional non-solitonic in-fiber switching based on nonlinear optical loop mirror. Advanced numerical simulations show good agreement with the experimental results, suggesting that the underlying dual-core soliton fission process supports nonlinear optical switching and simultaneous pulse compression to few-cycle durations at the level of 20 fs.

The co-location of CD14+APOE+ cells and MMP7+ tumour cells contributed to worse immunotherapy response in non-small cell lung cancer.

Intra-tumour immune infiltration is a crucial determinant affecting immunotherapy response in non-small cell lung cancer (NSCLC). However, its phenotype and related spatial structure have remained elusive. To overcome these restrictions, we undertook a comprehensive study comprising spatial transcriptomic (ST) data (28 712 spots from six samples). We identified two distinct intra-tumour infiltration patterns: immune exclusion (characterised by myeloid cells) and immune activation (characterised by plasma cells). The immune exclusion and immune activation signatures showed adverse and favourable roles in NSCLC patients' survival, respectively. Notably, CD14+APOE+ cells were recognised as the main cell type in immune exclusion samples, with increased epithelial‒mesenchymal transition and decreased immune activities. The co-location of CD14+APOE+ cells and MMP7+ tumour cells was observed in both ST and bulk transcriptomics data, validated by multiplex immunofluorescence performed on 20 NSCLC samples. The co-location area exhibited the upregulation of proliferation-related pathways and hypoxia activities. This co-localisation inhibited T-cell infiltration and the formation of tertiary lymphoid structures. Both CD14+APOE+ cells and MMP7+ tumour cells were associated with worse survival. In an immunotherapy cohort from the ORIENT-3 clinical trial, NSCLC patients who responded unfavourably exhibited higher infiltration of CD14+APOE+ cells and MMP7+ tumour cells. Within the co-location area, the MK, SEMA3 and Macrophage migration inhibitory factor (MIF) signalling pathway was most active in cell‒cell communication. This study identified immune exclusion and activation patterns in NSCLC and the co-location of CD14+APOE+ cells and MMP7+ tumour cells as contributors to immune resistance.

Single-cell and spatial analyses revealed the co-location of cancer stem cells and SPP1+ macrophage in hypoxic region that determines the poor prognosis in hepatocellular carcinoma.

In hepatocellular carcinoma (HCC), classical cancer stem cells (CSC) markers were shared by normal stem cells, targeting which may hinder hepatic regeneration and cause liver failure. Additionally, the spatial structure of CSC still remained elusive. To address these limitations, we undertook a comprehensive study combining single-cell data (56,022 cells from 20 samples) and spatial data (38,191 spots from eight samples) to obtain CSC signature and uncover its spatial structure. Utilizing the CytoTRACE algorithm, we discretely identified CSC, which displayed upregulated proliferation pathways regulated by HIF1A. A CSC signature of 107 genes was then developed using Weighted Gene Co-expression Network Analysis (WGCNA). Notably, HCC patients with high CSC levels exhibited an accumulation of SPP1+ macrophages (Macro_SPP1) expressing metalloproteinases (MMP9, MMP12, and MMP7) regulated by HIF1A, suggesting a hypoxic tumor region connecting Macro_SPP1 and CSC. Both CSC and Macro_SPP1 correlated with worse prognosis and undesirable immunotherapy response. Spatial analysis revealed the co-location of CSC and Macro_SPP1, with CD8 T cells excluded from the tumor region. The co-location area and non-tumor area of boundary exhibited a high level of hypoxia, with the HAVRC2 checkpoint highly expressed. Within the co-location area, the SPP1 signaling pathway was most active in cell-cell communication, with SPP1-CD44 and SPP1-ITGA/ITGB identified as the main ligand-receptor pairs. This study successfully constructed a CSC signature and demonstrated the co-location of CSC and Macro_SPP1 in a hypoxic region that exacerbates the tumor microenvironment in HCC.

Single-cell and spatial transcriptomics reveal a high glycolysis B cell and tumor-associated macrophages cluster correlated with poor prognosis and exhausted immune microenvironment in diffuse large B-cell lymphoma.

BACKGROUND: Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous malignancy characterized by varied responses to treatment and prognoses. Understanding the metabolic characteristics driving DLBCL progression is crucial for developing personalized therapies. METHODS: This study utilized multiple omics technologies including single-cell transcriptomics (n = 5), bulk transcriptomics (n = 966), spatial transcriptomics (n = 10), immunohistochemistry (n = 34), multiple immunofluorescence (n = 20) and to elucidate the metabolic features of highly malignant DLBCL cells and tumor-associated macrophages (TAMs), along with their associated tumor microenvironment. Metabolic pathway analysis facilitated by scMetabolism, and integrated analysis via hdWGCNA, identified glycolysis genes correlating with malignancy, and the prognostic value of glycolysis genes (STMN1, ENO1, PKM, and CDK1) and TAMs were verified. RESULTS: High-glycolysis malignant DLBCL tissues exhibited an immunosuppressive microenvironment characterized by abundant IFN_TAMs (CD68+CXCL10+PD-L1+) and diminished CD8+ T cell infiltration. Glycolysis genes were positively correlated with malignancy degree. IFN_TAMs exhibited high glycolysis activity and closely communicating with high-malignancy DLBCL cells identified within datasets. The glycolysis score, evaluated by seven genes, emerged as an independent prognostic factor (HR = 1.796, 95% CI: 1.077-2.995, p = 0.025 and HR = 2.631, 95% CI: 1.207-5.735, p = 0.015) along with IFN_TAMs were positively correlated with poor survival (p < 0.05) in DLBCL. Immunohistochemical validation of glycolysis markers (STMN1, ENO1, PKM, and CDK1) and multiple immunofluorescence validation of IFN_TAMs underscored their prognostic value (p < 0.05) in DLBCL. CONCLUSIONS: This study underscores the significance of glycolysis in tumor progression and modulation of the immune microenvironment. The identified glycolysis genes and IFN_TAMs represent potential prognostic markers and therapeutic targets in DLBCL.

SASEGAN-TCN: Speech enhancement algorithm based on self-attention generative adversarial network and temporal convolutional network.

Traditional unsupervised speech enhancement models often have problems such as non-aggregation of input feature information, which will introduce additional noise during training, thereby reducing the quality of the speech signal. In order to solve the above problems, this paper analyzed the impact of problems such as non-aggregation of input speech feature information on its performance. Moreover, this article introduced a temporal convolutional neural network and proposed a SASEGAN-TCN speech enhancement model, which captured local features information and aggregated global feature information to improve model effect and training stability. The simulation experiment results showed that the model can achieve 2.1636 and 92.78% in perceptual evaluation of speech quality (PESQ) score and short-time objective intelligibility (STOI) on the Valentini dataset, and can accordingly reach 1.8077 and 83.54% on the THCHS30 dataset. In addition, this article used the enhanced speech data for the acoustic model to verify the recognition accuracy. The speech recognition error rate was reduced by 17.4%, which was a significant improvement compared to the baseline model experimental results.

Longitudinal plasma proteomic profiling of EML4-ALK positive lung cancer receiving ALK-TKIs therapy.

BACKGROUND: Anaplastic lymphoma kinase-tyrosine kinase inhibitors (ALK-TKIs) has demonstrated remarkable therapeutic effects in ALK-positive non-small cell lung cancer (NSCLC) patients. Identifying prognostic biomarkers can enhance the clinical efficacy of relapsed or refractory patients. METHODS: We profiled 737 plasma proteins from 159 pre-treatment and on-treatment plasma samples of 63 ALK-positive NSCLC patients using data-independent acquisition-mass spectrometry (DIA-MS). The consensus clustering algorithm was used to identify subtypes with distinct biological features. A plasma-based prognostic model was constructed using the LASSO-Cox method. We performed the Mfuzz analysis to classify the patterns of longitudinal changes in plasma proteins during treatment. 52 baseline plasma samples from another independent ALK-TKI treatment cohort were collected to validate the potential prognostic markers using ELISA. RESULTS: We identified three subtypes of ALK-positive NSCLC with distinct biological features and clinical efficacy. Patients in subgroup 1 exhibited activated humoral immunity and inflammatory responses, increased expression of positive acute-phase response proteins, and the worst prognosis. Then we constructed and verified a prognostic model that predicts the efficacy of ALK-TKI therapy using the expression levels of five plasma proteins (SERPINA4, ATRN, APOA4, TF, and MYOC) at baseline. Next, we explored the longitudinal changes in plasma protein expression during treatment and identified four distinct change patterns (Clusters 1-4). The longitudinal changes of acute-phase proteins during treatment can reflect the treatment status and tumor progression of patients. Finally, we validated the prognostic efficacy of baseline plasma CRP, SAA1, AHSG, SERPINA4, and TF in another independent NSCLC cohort undergoing ALK-TKI treatment. CONCLUSIONS: This study contributes to the search for prognostic and drug-resistance biomarkers in plasma samples for ALK-TKI therapy and provides new insights into the mechanism of drug resistance and the selection of follow-up treatment.

A hybrid path-oriented code assignment CDMA-based MAC protocol for underwater acoustic sensor networks.

Due to the characteristics of underwater acoustic channel, media access control (MAC) protocols designed for underwater acoustic sensor networks (UWASNs) are quite different from those for terrestrial wireless sensor networks. Moreover, in a sink-oriented network with event information generation in a sensor field and message forwarding to the sink hop-by-hop, the sensors near the sink have to transmit more packets than those far from the sink, and then a funneling effect occurs, which leads to packet congestion, collisions and losses, especially in UWASNs with long propagation delays. An improved CDMA-based MAC protocol, named path-oriented code assignment (POCA) CDMA MAC (POCA-CDMA-MAC), is proposed for UWASNs in this paper. In the proposed MAC protocol, both the round-robin method and CDMA technology are adopted to make the sink receive packets from multiple paths simultaneously. Since the number of paths for information gathering is much less than that of nodes, the length of the spreading code used in the POCA-CDMA-MAC protocol is shorter greatly than that used in the CDMA-based protocols with transmitter-oriented code assignment (TOCA) or receiver-oriented code assignment (ROCA). Simulation results show that the proposed POCA-CDMA-MAC protocol achieves a higher network throughput and a lower end-to-end delay compared to other CDMA-based MAC protocols.

An immunosuppressive subtype of senescent tumor cells predicted worse immunotherapy response in lung adenocarcinoma.

Senescent tumor cells (STCs) can induce immunosuppression, promoting tumor progression and therapy resistance. However, the specific characteristics of immunosuppressive STC have not been thoroughly investigated. This study aimed to characterize and elucidate the immunosuppressive phenotype of STC in lung adenocarcinoma by employing single-cell and bulk transcriptomics, as well as serum proteomics profiling. We identified senescence-related genes specific to tumors and identified Cluster10 of STC as the immunomodulatory subtype. Cluster10 exhibited a distinct secretome dominated by cytokines such as CXCL1, CXCL2, and CXCL8 and showed activation of transcription factors associated with cytokine secretion, including NFKB1, RELA, and STAT3. Notably, Cluster10 demonstrated the highest degree of intercellular communication among all cell types, with interactions as LGALS9-TIM3 and MIF-CD74. Furthermore, Cluster10 showed significant associations with poor prognosis and diminished response to immunotherapy. Analysis of serum proteomics data from our in-house cohort identified CXCL8 as a potential marker for predicting immunotherapeutic outcomes.

Distinctive physiological and molecular responses of foxtail millet and maize to nicosulfuron.

Introduction: Nicosulfuron is the leading acetolactate synthase inhibitor herbicide product, and widely used to control gramineous weeds. Here, we investigated the metabolic process of nicosulfuron into foxtail millet and maize, in order to clarify the mechanism of the difference in sensitivity of foxtail millet and maize to nicosulfuron from the perspective of physiological metabolism and provide a theoretical basis for the breeding of nicosulfuron-resistant foxtail millet varieties. Methods: We treated foxtail millet (Zhangzagu 10, Jingu 21) and maize (Nongda 108, Ditian 8) with various doses of nicosulfuron in both pot and field experiments. The malonaldehyde (MDA) content, target enzymes, detoxification enzymes, and antioxidant enzymes, as well as related gene expression levels in the leaf tissues of foxtail millet and maize were measured, and the yield was determined after maturity. Results: The results showed that the recommended dose of nicosulfuron caused Zhangzagu 10 and Jingu 21 to fail to harvest; the yield of the sensitive maize variety (Ditian 8) decreased by 37.09%, whereas that of the resistant maize variety (Nongda 108) did not decrease. Nicosulfuron stress increased the CYP450 enzyme activity, MDA content, and antioxidant enzyme activity of foxtail millet and maize, reduced the acetolactate synthase (ALS) activity and ALS gene expression of foxtail millet and Ditian 8, and reduced the glutathione S-transferase (GST) activity and GST gene expression of foxtail millet. In conclusion, target enzymes, detoxification enzymes, and antioxidant enzymes were involved in the detoxification metabolism of nicosulfuron in plants. ALS and GST are the main factors responsible for the metabolic differences among foxtail millet, sensitive maize varieties, and resistant maize varieties. Discussion: These findings offer valuable insights for exploring the target resistance (TSR) and non-target resistance (NTSR) mechanisms in foxtail millet under herbicide stress and provides theoretical basis for future research of develop foxtail millet germplasm with diverse herbicide resistance traits.