Predictive model based on multiple immunofluorescence quantitative analysis for pathological complete response to neoadjuvant immunochemotherapy in lung squamous cell carcinoma.

Objective: This study aims to establish a prediction model for neoadjuvant immunochemotherapy (NICT) in lung squamous cell carcinoma to guide clinical treatment. Methods: This retrospective study included 50 patients diagnosed with lung squamous cell carcinoma who received NICT. The patients were divided into the pathological complete response (PCR) group and the non-PCR group. HE staining and multiple immunofluorescence (mIF) techniques were utilized to analyze the differences in the immune microenvironment between these groups. LASSO regression and optimal subset regression were employed to identify the most significant variables and construct a prediction model. Results: The PCR group showed higher densities of lymphocyte nuclei and karyorrhexis based on HE staining. Furthermore, based on mIF analysis, the PCR group showed higher cell densities of CD8+, PD-L1+, and CD8+PD-L1+ in the tumor region, while showing lower cell densities of CD3+Foxp3+, Foxp3+, and CD163+. Logistic univariate analysis revealed CD8+PD-L1+, PD-L1+, CD8+, CD4+LAG-3+, lymphocyte nuclei, and karyorrhexis as significant factors influencing PCR. By using diverse screening methods, the three most relevant variables (CD8+, PD-L1+, and CD8+PD-L1+ in the tumor region) were selected to establish the prediction model. The model exhibited excellent performance in both the training set (AUC=0.965) and the validation set (AUC=0.786). In the validation set, In comparison to the conventional TPS scoring criteria, the model attained superior accuracy (0.85), specificity(0.67), and sensitivity (0.92). Conclusion: NICT treatment might induce anti-tumor effects by enriching immune cells and reactivating exhausted T cells. CD8+, PD-L1+, and CD8+PD-L1+ cell abundances within the tumor region have been closely associated with therapeutic efficacy. Incorporating these three variables into a predictive model allows accurate forecasting of treatment outcomes and provides a reliable basis for selecting NICT treatment strategies.

GhWER controls fiber initiation and early elongation by regulating ethylene signaling pathway in cotton (Gossypium hirsutum).

Cotton fibers are specialized single-cell trichomes derived from epidermal cells, similar to root hairs and trichomes in Arabidopsis. While the MYB-bHLH-WD40 (MBW) complex has been shown to regulate initiation of both root hairs and trichomes in Arabidopsis, the role of their homologous gene in cotton fiber initiation remains unknown. In this study, we identified a R2R3 MYB transcription factor (TF), GhWER, which exhibited a significant increase in expression within the outer integument of ovule at -1.5 DPA (days post anthesis). Its expression peaked at -1 DPA and then gradually decreased. Knockout of GhWER using CRISPR technology inhibited the initiation and early elongation of fiber initials, resulting in the shorter mature fiber length. Additionally, GhWER interacted with two bHLH TF, GhDEL65 and GhbHLH121, suggesting a potential regulatory complex for fiber development. RNA-seq analysis of the outer integument of the ovule at -1.5 DPA revealed that the signal transduction pathways of ethylene, auxin and gibberellin were affected in the GhWER knockout lines. Further examination demonstrated that GhWER directly activated ethylene signaling genes, including ACS1 and ETR2. These findings highlighted the biological function of GhWER in regulating cotton fiber initiation and early elongation, which has practical significance for improving fiber quality and yield. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01477-6.

Predictive value of fluid balance before extubation on its outcome in mechanically ventilated adults in the intensive care unit.

BACKGROUND: Although there are many reasons for extubation failure, maintaining negative or lower positive fluid balances 24 hours before extubation may be a key measure for successful extubation. AIM: To assess the predictive value of fluid balance before extubation and its outcome in mechanically ventilated cases in the intensive care unit (ICU). STUDY DESIGN: This retrospective cohort study involved collecting clinical data from patients undergoing mechanical ventilation in Lanzhou general adult ICU from January 2022 to December 2022. Based on extubation outcomes, the patients were divided into a successful extubation group and a failed extubation group. Their fluid balance levels 24 h before extubation were compared with analyse the predictive value of fluid balance on extubation outcomes in patients undergoing mechanical ventilation. RESULTS: In this study, clinical data from 545 patients admitted to a general adult ICU were collected. According to the inclusion and exclusion criteria, 265 (48.6%) patients were included, of which 197 (74.3%) were successfully extubated; extubation was unsuccessful in 68 (25.7%) patients. The total intake and fluid balance levels in patients in the failed extubation group 24 h before extubation were significantly higher than those in the successful extubation group, with a median of 2679.00 (2410.44-3193.50) mL versus 2435.40 (1805.04-2957.00) mL, 831.50 (26.25-1407.94) mL versus 346.00 (-163.00-941.50) mL. Receiver operating characteristic (ROC) curve analysis showed that the optimal cut-off value for predicting extubation outcomes was 497.5 mL (sensitivity 64.7%, specificity 59.4%) for fluid balance 24 h before extubation. The area under the ROC curve was 0.627 (95% confidence interval [CI] 0.547-0.707). Based on the logistic regression model, cumulative fluid balance >497.5 mL 24 h before extubation could predict its outcomes in mechanically ventilated patients in the ICU (OR = 5.591, 95% CI [2.402-13.015], p < .05). CONCLUSIONS: The fluid balance level 24 h before extubation was correlated with the outcome of extubation in mechanically ventilated patients in the ICU. The risk of extubation failure was higher when the fluid balance level was >497.5 mL. RELEVANCE TO CLINICAL PRACTICE: Tracheal intubation is a crucial life support technique for many critically ill patients, and determining the appropriate time for extubation remains a challenge for clinicians. Although there are many reasons for extubation failure, acute pulmonary oedema caused by continuous positive fluid balance and volume overload is one of the main reasons for extubation failure. Therefore, it is very important to study the relationship between fluid balance and extubation outcome to improve the prognosis of patients with invasive mechanical ventilation in ICU.

A dominant negative mutation of GhMYB25-like alters cotton fiber initiation, reducing lint and fuzz.

Cotton (Gossypium hirsutum) fibers, vital natural textile materials, are single-cell trichomes that differentiate from the ovule epidermis. These fibers are categorized as lint (longer fibers useful for spinning) or fuzz (shorter, less useful fibers). Currently, developing cotton varieties with high lint yield but without fuzz remains challenging due to our limited knowledge of the molecular mechanisms underlying fiber initiation. This study presents the identification and characterization of a naturally occurring dominant negative mutation GhMYB25-like_AthapT, which results in a reduced lint and fuzzless phenotype. The GhMYB25-like_AthapT protein exerts its dominant negative effect by suppressing the activity of GhMYB25-like during lint and fuzz initiation. Intriguingly, the negative effect of GhMYB25-like_AthapT could be alleviated by high expression levels of GhMYB25-like. We also uncovered the role of GhMYB25-like in regulating the expression of key genes such as GhPDF2 (PROTODERMAL FACTOR 2), CYCD3; 1 (CYCLIN D3; 1), and PLD (Phospholipase D), establishing its significance as a pivotal transcription factor in fiber initiation. We identified other genes within this regulatory network, expanding our understanding of the determinants of fiber cell fate. These findings offer valuable insights for cotton breeding and contribute to our fundamental understanding of fiber development.

Synergistic interplay of redox homeostasis and polysaccharide synthesis promotes cotton fiber elongation.

Cell polarity is the foundation of cell development and tissue morphogenesis. The investigation of polarized growth provides opportunities to gain profound insights into morphogenesis and tissue functionality in organisms. Currently, there are still many mysteries surrounding the mechanisms that regulate polarized cell growth. Cotton fiber cells serve as an excellent model for studying polarized growth, and provide important clues for unraveling the molecular mechanisms, signaling pathways, and regulatory networks of polarized growth. In this study, we characterized two functional genes, GhMDHAR1AT/DT and GhDHAR2AT/DT with predominant expression during fiber elongation. Loss of function of both genes contributed to a significant increase in fiber length. Transcriptomic data revealed up-regulated expression of antioxidant genes in CRISPR mutant lines, along with delayed expression of secondary wall-related genes and temporally prolonged expression of primary wall-related genes. Experimental evidence demonstrated that the increase in GSH content and glutathione peroxidase (GPX) enzyme activity led to enhanced total antioxidant capacity (T-AOC), resulting in reduced H2O2 levels, which contributed to the extension of fiber elongation stage in CRISPR mutant lines. Moreover, the increased polysaccharide synthesis in CRISPR mutant lines was found to provide an abundant supply of raw materials for fiber cell wall elongation, suggesting that synergistic interplay between redox homeostasis and polysaccharide synthesis in fiber cells may facilitate cell wall remodeling and fiber elongation. This study provides valuable insights for deciphering the mechanisms of cell polarized growth and improving cotton fiber quality.

Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton.

Polyploidy complicates transcriptional regulation and increases phenotypic diversity in organisms. The dynamics of genetic regulation of gene expression between coresident subgenomes in polyploids remains to be understood. Here we document the genetic regulation of fiber development in allotetraploid cotton Gossypium hirsutum by sequencing 376 genomes and 2,215 time-series transcriptomes. We characterize 1,258 genes comprising 36 genetic modules that control staged fiber development and uncover genetic components governing their partitioned expression relative to subgenomic duplicated genes (homoeologs). Only about 30% of fiber quality-related homoeologs show phenotypically favorable allele aggregation in cultivars, highlighting the potential for subgenome additivity in fiber improvement. We envision a genome-enabled breeding strategy, with particular attention to 48 favorable alleles related to fiber phenotypes that have been subjected to purifying selection during domestication. Our work delineates the dynamics of gene regulation during fiber development and highlights the potential of subgenomic coordination underpinning phenotypes in polyploid plants.

Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem.

BACKGROUND: Somatic embryogenesis is a major process for plant regeneration. However, cell communication and the gene regulatory network responsible for cell reprogramming during somatic embryogenesis are still largely unclear. Recent advances in single-cell technologies enable us to explore the mechanism of plant regeneration at single-cell resolution. RESULTS: We generate a high-resolution single-cell transcriptomic landscape of hypocotyl tissue from the highly regenerable cotton genotype Jin668 and the recalcitrant TM-1. We identify nine putative cell clusters and 23 cluster-specific marker genes for both cultivars. We find that the primary vascular cell is the major cell type that undergoes cell fate transition in response to external stimulation. Further developmental trajectory and gene regulatory network analysis of these cell clusters reveals that a total of 41 hormone response-related genes, including LAX2, LAX1, and LOX3, exhibit different expression patterns in the primary xylem and cambium region of Jin668 and TM-1. We also identify novel genes, including CSEF, PIS1, AFB2, ATHB2, PLC2, and PLT3, that are involved in regeneration. We demonstrate that LAX2, LAX1 and LOX3 play important roles in callus proliferation and plant regeneration by CRISPR/Cas9 editing and overexpression assay. CONCLUSIONS: This study provides novel insights on the role of the regulatory network in cell fate transition and reprogramming during plant regeneration driven by somatic embryogenesis.

A Quantitative Study of a Directional Heat Island in Hefei, China Based on Multi-Source Data.

Surface urban heat islands (SUHIs) are essential for evaluating urban thermal environments. However, current quantitative studies of SUHIs ignore the thermal radiation directionality (TRD), which directly affects study precision; furthermore, they fail to assess the effects of TRD characteristics at different land-use intensities, on the quantitative studies of SUHIs. To bridge this research gap, this study eliminates the interference of atmospheric attenuation and daily temperature variation factors, in quantifying the TRD based on land surface temperature (LST), from MODIS data and station air temperature data for Hefei (China) from 2010-2020. The influence of TRD on SUHI intensity quantification was evaluated by comparing the TRD under different land-use intensities in Hefei. The results show that: (1) daytime and nighttime directionality can reach up to 4.7 K and 2.6 K, and occur in areas with the highest and medium urban land-use intensity, respectively. (2) There are two significant TRD hotspots for daytime urban surfaces, where the sensor zenith angle is approximately the same as the forenoon solar zenith angle, and where the sensor zenith angle is near its nadir in the afternoon. (3) The TRD can contribute up to 2.0 K to the results of assessing the SUHI intensity based on satellite data, which is approximately 31-44% of the total SUHI in Hefei.

Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium.

Phenotypic diversity and evolutionary innovation ultimately trace to variation in genomic sequence and rewiring of regulatory networks. Here, we constructed a pan-genome of the Gossypium genus using ten representative diploid genomes. We document the genomic evolutionary history and the impact of lineage-specific transposon amplification on differential genome composition. The pan-3D genome reveals evolutionary connections between transposon-driven genome size variation and both higher-order chromatin structure reorganization and the rewiring of chromatin interactome. We linked changes in chromatin structures to phenotypic differences in cotton fiber and identified regulatory variations that decode the genetic basis of fiber length, the latter enabled by sequencing 1,005 transcriptomes during fiber development. We showcase how pan-genomic, pan-3D genomic and genetic regulatory data serve as a resource for delineating the evolutionary basis of spinnable cotton fiber. Our work provides insights into the evolution of genome organization and regulation and will inform cotton improvement by enabling regulome-based approaches.

Single-cell RNA-seq reveals fate determination control of an individual fibre cell initiation in cotton (Gossypium hirsutum).

Cotton fibre is a unicellular seed trichome, and lint fibre initials per seed as a factor determines fibre yield. However, the mechanisms controlling fibre initiation from ovule epidermis are not understood well enough. Here, with single-cell RNA sequencing (scRNA-seq), a total of 14 535 cells were identified from cotton ovule outer integument of Xu142_LF line at four developmental stages (1.5, 1, 0.5 days before anthesis and the day of anthesis). Three major cell types, fibre, non-fibre epidermis and outer pigment layer were identified and then verified by RNA in situ hybridization. A comparative analysis on scRNA-seq data between Xu142 and its fibreless mutant Xu142 fl further confirmed fibre cluster definition. The developmental trajectory of fibre cell was reconstructed, and fibre cell was identified differentiated at 1 day before anthesis. Gene regulatory networks at four stages revealed the spatiotemporal pattern of core transcription factors, and MYB25-like and HOX3 were demonstrated played key roles as commanders in fibre differentiation and tip-biased diffuse growth respectively. A model for early development of a single fibre cell was proposed here, which sheds light on further deciphering mechanism of plant trichome and the improvement of cotton fibre yield.

Inhibition of CD146 lessens uveal melanoma progression through reducing angiogenesis and vasculogenic mimicry.

PURPOSE: Anti-angiogenesis drug therapy is ineffective in treating uveal melanoma since it only targets angiogenesis leaving vasculogenic mimicry aside. There is no effective clinical strategy targeting vasculogenic mimicry, yet. We show here that CD146 is a novel target to inhibit uveal melanoma progression since it regulates both uveal melanoma angiogenesis and vasculogenic mimicry activity. METHODS: CD146 inhibition was achieved with its specific siRNAs or antibody AA98. Tube formation and migration of primary human retinal microvascular endothelial cells and tube-like structure formation, migration, invasion of uveal melanoma cells were evaluated after CD146 inhibition. The underlying mechanisms were investigated by Western blot and immunofluorescence. Finally, uveal melanoma cells were injected subretinally into the eyes of nude mice and AA98 was administrated. Tumor size was revealed by H&E staining, and angiogenesis and vasculogenic mimicry were evaluated with CD31-PAS staining. RESULTS: CD146 inhibition induced declines in tube formation and migration of primary human retinal microvascular endothelial cells and tube-like structure formation of uveal melanoma cells. CD146 mediated VEGFR/AKT/p38/NF-κB and FAK/VE-cadherin signal cascades were partially responsible for these biological effects. CD146 blockade by siRNA or AA98 also resulted in inhibition of migration and invasion as well as EMT process of uveal melanoma cells. The physiological relevance of such declines was confirmed by showing that AA98 treatment markedly suppressed the tumor growth, angiogenesis and vasculogenic mimicry induced by implantation of uveal melanoma cells into the eyes of nude mice. CONCLUSIONS: CD146 is a novel mediator of both angiogenesis and vasculogenic mimicry in uveal melanoma. Its antibody AA98 has the potency to be developed as a new antibody drug for treating uveal melanoma. Our results warrant further assessment of CD146 as a potential target to improve therapeutic management of uveal melanoma in a clinical setting.

Deep Learning-Based Emergency Care Process Reengineering of Interventional Data for Patients with Emergency Time-Series Events of Myocardial Infarction.

This paper proposes a representation learning framework HE-LSTM model for heterogeneous temporal events, which can automatically adapt to the multiscale sampling frequency of multisource heterogeneous data. The proposed model also demonstrates its superiority over other typical approaches on real data sets. A controlled study is performed according to computerized randomization, with 38 patients in each of the two groups. The study group has a higher resuscitation success rate and patient satisfaction than the conventional group (P < 0.05), and the time from the first consultation to the completion of the first ECG, the time from the completion of the ECG to the activation of the path lab, and the time from the emergency admission to the balloon dilation were significantly shorter in the study group than in the conventional group (P < 0.05). The emergency care process reengineering intervention helps patients with acute myocardial infarction to be treated quickly and effectively, thus improving their resuscitation success rate and satisfaction rate, and is worthy to be caused in the clinic and widely applied.

Histone ubiquitination controls organ size in cotton (Gossypium hirsutum).

Ubiquitination plays a vital role in modifying protein activity and destiny. Ub-conjugating enzyme E2 is one of the enzymes that participates in this precise process. There are at least 169 E2 proteins in the allotetraploid cotton (Gossypium hirsutum), but their function remains unknown. Here we identify an E2 gene GhUBC2L and show its positive role in cell proliferation and expansion. Complete knock-down of GhUBC2L in cotton resulted in retarded growth and reduced organ size. Conversely, overexpression of GhUBC2L promoted cotton growth, generating enlarged organs in size. Monoubiquitination of H2A and H2B was strongly impaired in GhUBC2L-suppressed cotton but slightly enhanced in GhUBC2L-overexpressed plant. GhUbox8, a U-box type E3 ligase protein, was found to interact with GhUBC2L both in vivo and in vitro, indicating their synergistical function in protein ubiquitination. Furthermore, GhUbox8 was shown to interact with a series of histone proteins, including histone H2A and H2B, indicating its potential monoubiquitination on H2A and H2B. Expression of genes relating to cell cycle and organ development were altered when the expression of GhUBC2L was changed. Our results show that GhUBC2L modulates histone monoubiquitination synergistically with GhUbox8 to regulate the expression of genes involved in organ development and cell cycle, thus controlling organ size in cotton. This research provides new insights into the role of protein ubiquitination in organ size control. Histone monoubiquitination plays an important role in plant development. Here, we identified an E2 enzyme GhUBC2L that modulates histone monoubiquitination synergistically with an E3 ligase GhUbox8 to mediate organ size control in cotton.

A systematic review and meta-analysis: value of ultrasound-guided vacuum-assisted biopsy in the diagnosis and treatment of breast lesions.

BACKGROUND: In recent years, according to global statistics, breast cancer is the main disease affecting women. Ultrasound-guided vacuum-assisted biopsy (VAB) has become a frequently used method for breast cancer detection because of its accuracy, simplicity, and fewer complications. METHODS: In PubMed, Medline, EMbase and Cochrane central register of controlled trials, the retrieval time was from the establishment of the database to March 2021, and the keywords included breast tumor, breast cancer-related diseases, breast lesions, vacuum-assisted breast biopsy, sensitivity and specificity. Meta-analysis was performed using RevMan5.3 software provided by the Cochrane Collaboration. RESULTS: A total of 10 articles were included using a random-effects model that pooled the sensitivity, specificity, and other accuracy measures of VAB. The summary receiver operating characteristic (SROC) characteristic curve was used to summarize the overall accuracy. The sensitivity range was 0.94 to 1.00 (mean, 0.981; 95% CI, 0.972-0.987) with a specificity range of 0.87-1.00 (mean, 0.999; 95% CI, 0.997-0.999). The preoperative platelet-lymphocyte ratio (PLR) was 93.84 (95% CI, 41.55-211.95), the neutrophil to lymphocyte ratio (NLR) was 0.05 (95% CI, 0.03-0.09), the sensitivity and specificity of χ2 were 37.10 (P=0.011) and 32.00 (P=0.043), respectively, while those of PLR, NLR, and duration of response (DOR) were 46.98 (P=0.001), 54.92 (P=0.001), and 43.49 (P=0.002), respectively. Differences were considerable. DISCUSSION: In this meta-analysis, a total of 10 articles were included. VAB is an accurate type of biopsy to detect female breast cancer. The results of the meta-analysis were stable, and VAB had high sensitivity (98%) and specificity (nearly 100%).

Cotton pan-genome retrieves the lost sequences and genes during domestication and selection.

BACKGROUND: Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components. RESULTS: We construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost from Gossypium hirsutum and Gossypium barbadense reference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV). We document the landscape of PAV selection accompanied by asymmetric gene gain and loss and identify 124 PAVs linked to favorable fiber quality and yield loci. CONCLUSIONS: This variation repertoire points to genomic divergence during cotton domestication and improvement, which informs the characterization of favorable gene alleles for improved breeding practice using a pan-genome-based approach.

A Modified Actin (Gly65Val Substitution) Expressed in Cotton Disrupts Polymerization of Actin Filaments Leading to the Phenotype of Ligon Lintless-1 (Li1) Mutant.

Dynamic remodeling of the actin cytoskeleton plays a central role in the elongation of cotton fibers, which are the most important natural fibers in the global textile industry. Here, a high-resolution mapping approach combined with comparative sequencing and a transgenic method revealed that a G65V substitution in the cotton actin Gh_D04G0865 (GhACT17D in the wild-type) is responsible for the Gossypium hirsutum Ligon lintless-1 (Li1) mutant (GhACT17DM). In the mutant GhACT17DM from Li1 plant, Gly65 is substituted with valine on the lip of the nucleotide-binding domain of GhACT17D, which probably affects the polymerization of F-actin. Over-expression of GhACT17DM, but not GhACT17D, driven by either a CaMV35 promoter or a fiber-specific promoter in cotton produced a Li1-like phenotype. Compared with the wild-type control, actin filaments in Li1 fibers showed higher growth and shrinkage rates, decreased filament skewness and parallelness, and increased filament density. Taken together, our results indicate that the incorporation of GhACT17DM during actin polymerization disrupts the establishment and dynamics of the actin cytoskeleton, resulting in defective fiber elongation and the overall dwarf and twisted phenotype of the Li1 mutant.

Structural insights into homotrimeric assembly of cellulose synthase CesA7 from Gossypium hirsutum.

Cellulose is one of the most abundant organic polymers in nature. It contains multiple ß-1,4-glucan chains synthesized by cellulose synthases (CesAs) on the plasma membrane of higher plants. CesA subunits assemble into a pseudo-sixfold symmetric cellulose synthase complex (CSC), known as a 'rosette complex'. The structure of CesA remains enigmatic. Here, we report the cryo-EM structure of the homotrimeric CesA7 from Gossypium hirsutum at 3.5-angstrom resolution. The GhCesA7 homotrimer shows a C3 symmetrical assembly. Each protomer contains seven transmembrane helices (TMs) which form a channel potentially facilitating the release of newly synthesized glucans. The cytoplasmic glycosyltransferase domain (GT domain) of GhCesA7 protrudes from the membrane, and its catalytic pocket is directed towards the TM pore. The homotrimer GhCesA7 is stabilized by the transmembrane helix 7 (TM7) and the plant-conserved region (PCR) domains. It represents the building block of CSCs and facilitates microfibril formation. This structure provides insight into how eukaryotic cellulose synthase assembles and provides a mechanistic basis for the improvement of cotton fibre quality in the future.