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Abstract The ATR kinase, which coordinates cellular responses to DNA replication stress, is also essential for the proliferation of normal unstressed cells. Although its role in the replication stress response is well defined, the mechanisms by which ATR supports normal cell proliferation remain elusive. Here, we show that ATR is dispensable for the viability of G0-arrested naïve B cells. However, upon cytokine-induced proliferation, Atr-deficient B cells initiate DNA replication efficiently, but by mid-S phase they display dNTP depletion, fork stalling, and replication failure. Nonetheless, productive DNA replication and dNTP levels can be restored in Atr-deficient cells by suppressing origin firing, such as partial inhibition of CDC7 and CDK1 kinase activities. Together, these findings indicate that ATR supports the proliferation of normal unstressed cells by tempering the pace of origin firing during the early S phase to avoid exhaustion of dNTPs and importantly also other replication factors.

ATR kinase is a key regulator of chromosome integrity. Here the authors by analysing the phenotype of a mouse model expressing a kinase-dead ATR, reveal the effect of ATR inhibition compared to ATR loss and its consequences for meiosis, DNA replication, checkpoint activation and genome instability .

Non-homologous end-joining is the key pathway for repairing double-stranded DNA breaks in mammalian cells. Here the authors show that PAXX promotes the accumulation of KU at DNA breaks and is essential for end-joining in cells lacking XLF.

Abstract The current study was to explore the prevalence and risk factors elements of pre-frailty and frailty among patients undergoing hemodialysis (HD) in central China. A cross-sectional, multi-institutional investigation was conducted. From March to May 2024, using the convenience sampling method, a total of 408 HD patients from four hospitals in Xiangyang, China, were recruited for this study. The participants’ demographics, lifestyle factors, factors related to dialysis treatment, the FRAIL scale, psychological resilience, and medical coping modes were assessed using a questionnaire. Multi-categorical logistic regression was performed to examine factors associated with pre-frailty and frailty in this population. Furthermore, to evaluate the independent relationship between frailty and psychological resilience, multiple regression analysis was used to adjust potential confounders and obtain odds ratios (OR) and 95% confidence intervals (CI). Pearson correlation analysis was used for correlation analysis among various scales. Among the 408 participants, the prevalence of pre-frailty and frailty among participants for all ages was 26.2% and 38.5%. Multivariate logistic regression analysis showed that smoking status, falls, heart disease, and psychological resilience are all associated with pre-frailty and frailty. The Pearson correlation analysis showed that resignation was positively related to frailty and negatively related to psychological resilience in patients. Confrontation and avoidance were positively related to psychological resilience. Frailty was negatively related to psychological resilience. Psychological resilience was independently linearly associated with pre-frailty (OR 0.49, 95% CI 0.32–0.75, p

Abstract Sponges harbour complex microbiomes and as ancient metazoans and important ecosystem players are emerging as powerful models to understand the evolution and ecology of symbiotic interactions. Metagenomic studies have previously described the functional features of sponge symbionts, however, little is known about the metabolic interactions and processes that occur under different environmental conditions. To address this issue, we construct here constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp. Our models define the importance of sponge-derived nutrients for microbiome stability and discover how different organic inputs can result in net heterotrophy or autotrophy of the symbiont community. The analysis further reveals the key role that a newly discovered bacterial taxon has in cross-feeding activities and how it dynamically adjusts with nutrient inputs. Our study reveals insights into the functioning of a sponge microbiome and provides a framework to further explore and define metabolic interactions in holobionts.

Abstract Low-light image enhancement aims to enhance the visibility and contrast of low-light images while eliminating complex degradation issues such as noise, artifacts, and color distortions. Most existing low-light image enhancement methods either focus on quality while neglecting computational efficiency or have limited learning and generalization capabilities. To address these issues, we propose a Bilateral Enhancement Network with signal-to-noise ratio fusion, called BiEnNet, for lightweight and generalizable low-light image enhancement. Specifically, we design a lightweight Bilateral enhancement module with SNR (Signal-to-Noise Ratio) Fusion (BSF), which serves the SNR map of the input low-light image as the interpolation weights to dynamically fuse global brightness features and local detail features extracted from a bilateral network and achieve differentiated enhancement across different regions. To improve the network’s generalization ability, we propose a Luminance Normalization (LNM) module for preprocessing and a Dual-Exposure Processing (DEP) module for post-processing. LNM divides the channels of input features into luminance-related channels and luminance independent channels, and reduces the inconsistency of the degradation distribution of input low-light images by only normalizing the luminance-related channels. DEP learns overexposure and underexposure corrections simultaneously by employing the ReLU activation function, inverting operation, and residual network, which can improve the robustness of enhancement effects under different exposure conditions while reducing network parameters. Experiments on the LOL-V1 dataset shows BiEnNet significantly increased PSNR by 8.6 $$\%$$ and SSIM by 3.6 $$\%$$ compared to FLW-Net, reduced parameters by 98.78 $$\%$$ , and improved computational speed by 52.64 $$\%$$ compared to the classical KIND.

Abstract Wazwaz Kaur Boussinesq (WKB) equation can effectively simulate the behavior of water waves in shallow water, including the nonlinear effect and dispersion phenomenon of waves, which is of great significance for understanding the dynamic process of ocean, river and other water bodies. To enrich the wave equation theory, the (3+1)-dimensional integer order derivative of WKB equation is changed to the fractional one with beta derivative. The current work deals with the fractional (3+1)-dimensional WKB equation for discussing its chaotic behavior and establishing some new analytic solutions. The chaotic properties of the equation are verified by the trend of evolution along with time, Lyapunov exponents and initial sensitivity analysis. And then complete discrimination system for polynomial method is applied to derive some trigonometric, hyperbolic, Jacobi elliptic and other solutions. The graphical demonstrations are provided for part of these solutions. From these visualized graphs, the solitary, periodic and quasi-periodic wave are shown and the effect of fractional derivatives on the equation can be seen intuitively.

Abstract This study aims to investigate the potential relationships between the systemic immune-inflammation index (SII) and body mass index (BMI), waist circumference, and the prevalence of obesity. A cross-sectional analysis was conducted on 7,645 individuals aged 20 and above from the NHANES 2017–2020. Multivariate linear regression analyses were conducted to evaluate the association of the logarithmically transformed SII (lgSII) with BMI and waist circumference. Additionally, multivariable logistic regression was utilized to explore the relationship between lgSII and the prevalence of obesity. Fitted smoothing curves and threshold-effect analysis were applied to elucidate nonlinear relationships. In the fully adjusted model, a positive relationship was observed between lgSII and BMI, waist circumference, and obesity prevalence (β = 3.13, 95% CI 2.10–4.16; β = 7.81, 95% CI 5.50–10.13; OR = 1.44, 95% CI 1.12–1.86). The variables of gender, age, race, education, marital status, poverty income ratio (PIR), energy intake, sleep disorder, smoking status, and alcohol use did not significantly modify the positive association between lgSII and obesity. However, physical activity appeared to influence the positive correlation between lgSII and obesity. Using a two-segment linear regression model, an inverted U-shaped relationship was observed between lgSII and both BMI and waist circumference. Furthermore, lgSII demonstrated a linear positive correlation with obesity prevalence. When stratified by physical activity, lgSII showed a non-significant negative correlation with obesity in the physically active group. Our findings underscore a robust association between the logarithmically transformed SII and BMI, waist circumference, and the prevalence of obesity.

Abstract In 2015, we launched the mesoSPIM initiative, an open-source project for making light-sheet microscopy of large cleared tissues more accessible. Meanwhile, the demand for imaging larger samples at higher speed and resolution has increased, requiring major improvements in the capabilities of such microscopes. Here, we introduce the next-generation mesoSPIM (“Benchtop”) with a significantly increased field of view, improved resolution, higher throughput, more affordable cost, and simpler assembly compared to the original version. We develop an optical method for testing detection objectives that enables us to select objectives optimal for light-sheet imaging with large-sensor cameras. The improved mesoSPIM achieves high spatial resolution (1.5 µm laterally, 3.3 µm axially) across the entire field of view, magnification up to 20×, and supports sample sizes ranging from sub-mm up to several centimeters while being compatible with multiple clearing techniques. The microscope serves a broad range of applications in neuroscience, developmental biology, pathology, and even physics.

Abstract The tumour microenvironment is infiltrated by immunosuppressive cells, such as regulatory T cells (Tregs), which contribute to tumour escape and impede immunotherapy outcomes. Soluble fibrinogen-like protein 2 (sFGL2), a Treg effector protein, inhibits immune cell populations, via receptors FcγRIIB and FcγRIII, leading to downregulation of CD86 in antigen presenting cells and limiting T cell activation. Increased FGL2 expression is associated with tumour progression and poor survival in several different cancers, such as glioblastoma multiforme, lung, renal, liver, colorectal, and prostate cancer. Querying scRNA-seq human cancer data shows FGL2 is produced by cells in the tumour microenvironment (TME), particularly monocytes and macrophages as well as T cells and dendritic cells (DCs), while cancer cells have minimal expression of FGL2. We studied the role of FGL2 exclusively produced by cells in the TME, by leveraging Fgl2 knockout mice. We tested two murine models of cancer in which the role of FGL2 has not been previously studied: epithelial ovarian cancer and melanoma. We show that absence of FGL2 leads to a more activated TME, including activated DCs (CD86+, CD40+) and T cells (CD25+, TIGIT+), as well as demonstrating for the first time that the absence of FGL2 leads to more activated natural killer cells (DNAM-1+, NKG2D+) in the TME. Furthermore, the absence of FGL2 leads to prolonged survival in the B16F10 melanoma model, while the absence of FGL2 synergizes with oncolytic virus to prolong survival in the ID8-p53 −/− Brca2 −/− ovarian cancer model. In conclusion, targeting FGL2 is a promising cancer treatment strategy alone and in combination immunotherapies.

Abstract Telomere length (TL) shortening is a pivotal indicator of biological aging and is associated with many human diseases. The genetic determinates of human TL have been widely investigated, however, most existing studies were conducted based on adult tissues which are heavily influenced by lifetime exposure. Based on the analyses of terminal restriction fragment (TRF) length of telomere, individual genotypes, and gene expressions on 166 healthy placental tissues, we systematically interrogate TL-modulated genes and their potential functions. We discover that the TL in the placenta is comparatively longer than in other adult tissues, but exhibiting an intra-tissue homogeneity. Trans-ancestral TL genome-wide association studies (GWASs) on 644,553 individuals identify 20 newly discovered genetic associations and provide increased polygenic determination of human TL. Next, we integrate the powerful TL GWAS with placental expression quantitative trait locus (eQTL) mapping to prioritize 23 likely causal genes, among which 4 are functionally validated, including MMUT, RRM1, KIAA1429, and YWHAZ. Finally, modeling transcriptomic signatures and TRF-based TL improve the prediction performance of human TL. This study deepens our understanding of causal genes and transcriptomic determinants of human TL, promoting the mechanistic research on fine-grained TL regulation.

Abstract E-cadherin is an essential cell‒cell adhesion protein that mediates canonical cadherin-catenin complex formation in epithelial lateral membranes. Ankyrin-G (AnkG), a scaffold protein linking membrane proteins to the spectrin-based cytoskeleton, coordinates with E-cadherin to maintain epithelial cell polarity. However, the molecular mechanisms governing this complex formation and its relationships with the cadherin-catenin complex remain elusive. Here, we report that AnkG employs a promiscuous manner to encapsulate three discrete sites of E-cadherin by the same region, a dynamic mechanism that is distinct from the canonical 1:1 molar ratio previously described for other AnkG or E-cadherin-mediated complexes. Moreover, we demonstrate that AnkG-binding-deficient E-cadherin exhibited defective accumulation at the lateral membranes and show that disruption of interactions resulted in cell polarity malfunction. Finally, we demonstrate that E-cadherin is capable of simultaneously anchoring to AnkG and β-catenin, providing mechanistic insights into the functional orchestration of the ankyrin-spectrin complex with the cadherin-catenin complex. Collectively, our results show that complex formation between E-cadherin and AnkG is dynamic, which enables the maintenance of epithelial cell polarity by ensuring faithful targeting of the adhesion molecule-scaffold protein complex, thus providing molecular mechanisms for essential E-cadherin-mediated complex assembly at cell‒cell junctions.

Abstract Giardia duodenalis is a gastrointestinal protozoan ubiquitous in nature. It is a confirmed zoonotic pathogen, and cattle are considered a source of giardiasis outbreaks in humans. This study aimed to evaluate the prevalence and multilocus genotype (MLG) of G. duodenalis in dairy cattle in Central Inner Mongolia. This study was based on the small subunit ribosomal RNA (SSU rRNA), glutamate dehydrogenase (gdh), triosephosphate isomerase (tpi), and beta-giardin (bg) genes of G. duodenalis. DNA extraction, polymerase chain reaction (PCR), and sequence analysis were performed on 505 dairy cattle fecal samples collected in 2021 from six sampling sites and four age groups in Central Inner Mongolia to determine the prevalence and MLG distribution of G. duodenalis. The PCR results of SSU rRNA revealed that the overall prevalence of G. duodenalis was 29.5% (149/505) and that the overall prevalence of the diarrhea and nondiarrhea samples was 31.5% (46/146) and 28.5% (103/359), respectively; the difference was not significant (p > 0.05). SSU rRNA sequence analysis revealed that G. duodenalis assemblage E (91.1%, 133/146) was primarily detected and that assemblage A (8.9%, 13/146) was detected in 13 samples. The G. duodenalis—positive samples were PCR amplified and sequenced for gdh, tpi, and bg, from which 38, 47, and 70 amplified sequences were obtained, respectively. A combination of G. duodenalis assemblages A and E were detected in seven samples. Multilocus genotyping yielded 25 different assemblage E MLGs, which formed six subgroups. To the best of our knowledge, this is the first report regarding G. duodenalis infection in dairy cattle in Inner Mongolia, China. This study revealed that Inner Mongolian cattle pose a risk of giardiasis transmission to humans and that the distribution of local cattle G. duodenalis assemblage E MLGs is diverse. The findings of this study can bridge the knowledge gap in the molecular epidemiological investigation of giardiasis in Central Inner Mongolia.

Abstract Background Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Methods Using measurements of ~4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N = 437), we identified 413 higher plasma abundances of protein targets and 30 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p

S-methyl methionine (SMM) is a key molecule in production of dimethylsulfoniopropionate (DMSP), an important marine anti-stress compound, with roles in global nutrient cycling. Here, the authors determine the mechanism of SMM synthesis and uncover unexpected roles for SMM in archaea, CPR bacteria and animals.

Abstract Due to the huge toxicity of co-contaminated soil with PAHs and heavy metals and the complexity of their remediation, it is thus critical to take effective remediation actions to remove heavy metals and PAHs simultaneously from the co-contaminated soil. Biosurfactant-enhanced soil washing (BESW) were investigated in this study for remediation of soil co-contaminated with phenanthrene (PHE) and cadmium (Cd). The co-existence of PHE and Cd caused the change of the structure of soil and rhamnolipid micelle, which lead to different removal rate of PHE and Cd from co-contaminated soil compared with single contaminated soil. The results of FT-IR and NMR showed that PHE entered micelles of rhamnolipid and Cd formed the complexation with the external carboxyl groups of rhamnolipid micelle. We also found that pH, concentration of rhamnolipid solution, temperature and ionic strength had influence on co-contaminated soil remediation. The effects of above mentioned four factors on co-contaminated soil remediation in BESW processes were analyzed by using Taguchi design of experiment method. Taguchi based Grey Relational Analysis was conducted to identify the optimal remediation conditions, which included pH = 9, concentration of rhamnolipid = 5 g/L, temperature = 15 °C and ionic strength = 0.01 M. Under the optimal conditions for BESW, removal rates of cadmium and phenanthrene reached 72.4% and 87.8%, respectively in co-contaminated soil.

Abstract In aerial multi-view photogrammetry, whether there is a special positional distribution pattern among candidate homologous pixels of a matching pixel in the multi-view images? If so, can this positional pattern be used to precisely confirm the real homologous pixels? These problems have not been studied at present. Therefore, the study of the positional distribution pattern among candidate homologous pixels based on the adjustment theory in surveying is investigated in this paper. Firstly, the definition and computing method of pixel’s pseudo object-space coordinates are given, which can transform the problem of multi-view matching for confirming real homologous pixels into the problem of surveying adjustment for computing the pseudo object-space coordinates of the matching pixel. Secondly, according to the surveying adjustment theory, the standardized residual of each candidate homologous pixel of the matching pixel is figured out, and the positional distribution pattern among these candidate pixels is theoretically inferred utilizing the quantitative index of standardized residual. Lastly, actual aerial images acquired by different sensors are used to carry out experimental verification of the theoretical inference. Experimental results prove not only that there is a specific positional distribution pattern among candidate homologous pixels, but also that this positional distribution pattern can be used to develop a new object-side multi-view image matching method. The proposed study has an important reference value on resolving the defects of existing image-side multi-view matching methods at the mechanism level.

Abstract Real-time seizure detection is a resource intensive process as it requires continuous monitoring of patients on stereoelectroencephalography. This study improves real-time seizure detection in drug resistant epilepsy (DRE) patients by developing patient-specific deep learning models that utilize a novel self-supervised dynamic thresholding approach. Deep neural networks were constructed on over 2000 h of high-resolution, multichannel SEEG and video recordings from 14 DRE patients. Consensus labels from a panel of epileptologists were used to evaluate model efficacy. Self-supervised dynamic thresholding exhibited improvements in positive predictive value (PPV; difference: 39.0%; 95% CI 4.5–73.5%; Wilcoxon–Mann–Whitney test; N = 14; p = 0.03) with similar sensitivity (difference: 14.3%; 95% CI − 21.7 to 50.3%; Wilcoxon–Mann–Whitney test; N = 14; p = 0.42) compared to static thresholds. In some models, training on as little as 10 min of SEEG data yielded robust detection. Cross-testing experiments reduced PPV (difference: 56.5%; 95% CI 25.8–87.3%; Wilcoxon–Mann–Whitney test; N = 14; p = 0.002), while multimodal detection significantly improved sensitivity (difference: 25.0%; 95% CI 0.2–49.9%; Wilcoxon–Mann–Whitney test; N = 14; p

Mito-SEPs are small peptides that can modulate oxidative metabolism in mitochondria. Here the authors show that C15ORF48 encodes a mito-SEP, MOCCI, capable of altering mitochondria respiration to suppress inflammation, while C15ORF48 3’ untranslated region also contains a miRNA, miR-147b, that synergizes with MOCCI to modulate host anti-viral responses.

Small open reading frame-encoded peptides (SEPs), shorter than 100 amino acids, are involved in many cell biological processes. Here the authors identify 16 nuclear-encoded mitochondrial SEPs, including BRAWNIN, an essential regulator of respiratory chain complex III assembly and ATP production.

Abstract Adipogenesis plays an important role in the regulation of whole-body energy homeostasis and is inextricably related to obesity. Several studies have highlighted the relevance of microRNAs in adipocyte differentiation, but the contributions of long non-coding RNAs (lncRNAs) are still largely uncharacterized. Here, we determined that lncRNA MIR31HG is related to adipocyte lineage commitment. We demonstrated that knockdown of MIR31HG inhibited adipocyte differentiation, whereas overexpression of MIR31HG promoted adipogenesis in vitro and in vivo. Furthermore, inhibition of MIR31HG reduced the enrichment of active histone markers, histone H3 lysine 4 trimethylation (H3K4me3) and acetylation (AcH3), in the promoter of the adipogenic-related gene, fatty acid binding protein 4 (FABP4), leading to suppression of its expression and adipogenesis. These results provide new insights into the molecular mechanisms of MIR31HG in terms of adipogenesis and may have implications for obesity and associated disorders.

Abstract Several recent clinical studies have suggested that the levels of circulating 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF) are significantly higher in patients with gestational diabetes mellitus (GDM), impaired glucose tolerance (IGT), and type 2 diabetes mellitus (T2DM). This study recruited a total of 516 participants. The following patient populations were enrolled: 99 newly diagnosed cases with T2DM, 219 cases with prediabetes [82 with isolated impaired glucose tolerance (I − IGT), 66 with isolated impaired fasting glucose (I − IFG) and 71 with impaired glucose tolerance and impaired fasting glucose (IGT + IFG)], and 198 cases with normal glucose tolerance [NGT, including 99 first-degree relatives of type 2 diabetes patients (FDRs) and 99 non-FDRs]. We investigated the circulating CMPF levels in subjects with different glucose metabolism statuses and examined the potential link between CMPF and β cell function. Our results indicate that the serum CMPF levels were elevated in the prediabetes, T2DM, and FDRs groups compared to the NGT group. Additionally, the serum CMPF concentrations were independently and negatively associated with the triglyceride levels and Stumvoll first-phase insulin secretion index. Cumulatively, our findings suggest that the circulating CMPF levels can predict glycolipid metabolism disorders. Furthermore, elevated serum CMPF concentrations may determine hyperglycemia and β cell dysfunction.

Abstract To select metabolic biomarkers and differentially expressed genes (DEGs) associated with resistant-ascites syndrome (resistant-AS), we used innovative techniques such as metabolomics and transcriptomics to comparatively examine resistant-AS chickens and AS controls. Metabolomic evaluation of chicken serum using ultra-performance liquid chromatography-quadruple time-of-flight high-sensitivity mass spectrometry (UPLC-QTOF/HSMS) showed significantly altered lysoPC(18:1), PE(18:3/16:0), PC(20:1/18:3), DG(24:1/22:6/0:0), PS(18:2/18:0), PI(16:0/16:0), PS(18:0/18:1), PS(14:1/14:0), dihydroxyacetone, ursodeoxycholic acid, tryptophan, L-valine, cycloserine, hypoxanthine, and 4-O-Methylmelleolide concentrations on day 21 and LysoPC(18:0), LysoPE(20:1/0:0), LysoPC(16:0), LysoPE(16:0/0:0), hypoxanthine, dihydroxyacetone, 4-O-Methylmelleolide, LysoPC(18:2), and PC(14:1/22:1) concentrations on day 35, between the susceptible and resistant groups. Compared to the susceptible group, transcriptomic analysis of liver samples using RNA-seq revealed 413 DEGs on day 21 and 214 DEGs on day 35 in the resistant group. Additional evaluations using gene ontology (GO) indicate that significant enrichment occurred in the oxygen transportation, defensive reactions, and protein modifications of the decreased DEGs as well as in the cell morphological formation, neural development, and transforming growth factor (TGF)-beta signalling of the increased DEGs on day 21. Oxygen transportation was also significantly enriched for downregulated DEGs on day 35. The combinatory evaluation of the metabolome and the transcriptome suggests the possible involvement of glycerophospholipid metabolism in the development of resistant-AS in broilers.