A nomogram predicting pneumonia after cardiac surgery: a retrospective modeling study.

BACKGROUND: Postoperative pneumonia (POP) is the most prevalent of all nosocomial infections in patients who underwent cardiac surgery. The aim of this study was to identify independent risk factors for pneumonia after cardiac surgery, from which we constructed a nomogram for prediction. METHODS: The clinical data of patients admitted to the Department of Cardiothoracic Surgery of Nanjing Drum Tower Hospital from October 2020 to September 2021 who underwent cardiac surgery were retrospectively analyzed, and the patients were divided into two groups according to whether they had POP: POP group (n=105) and non-POP group (n=1083). Preoperative, intraoperative, and postoperative indicators were collected and analyzed. Logistic regression was used to identify independent risk factors for POP in patients who underwent cardiac surgery. We constructed a nomogram based on these independent risk factors. Model discrimination was assessed via area under the receiver operating characteristic curve (AUC), and calibration was assessed via calibration plot. RESULTS: A total of 105 events occurred in the 1188 cases. Age (>55 years) (OR: 1.83, P=0.0225), preoperative malnutrition (OR: 3.71, P<0.0001), diabetes mellitus(OR: 2.33, P=0.0036), CPB time (Cardiopulmonary Bypass Time) > 135 min (OR: 2.80, P<0.0001), moderate to severe ARDS (Acute Respiratory Distress Syndrome )(OR: 1.79, P=0.0148), use of ECMO or IABP or CRRT (ECMO: Extra Corporeal Membrane Oxygenation; IABP: Intra-Aortic Balloon Pump; CRRT: Continuous Renal Replacement Therapy )(OR: 2.60, P=0.0057) and MV( Mechanical Ventilation )> 20 hours (OR: 3.11, P<0.0001) were independent risk factors for POP. Based on those independent risk factors, we constructed a simple nomogram with an AUC of 0.82. Calibration plots showed good agreement between predicted probabilities and actual probabilities. CONCLUSION: We constructed a facile nomogram for predicting pneumonia after cardiac surgery with good discrimination and calibration. The model has excellent clinical applicability and can be used to identify and adjust modifiable risk factors to reduce the incidence of POP as well as patient mortality.

Stem Cell-Derived Nanovesicles Embedded in Dual-Layered Hydrogel for Programmed ROS Regulation and Comprehensive Tissue Regeneration in Burn Wound Healing.

Burn wounds often bring high risks of delayed healing process and even death. Reactive oxygen species (ROS) play a crucial role in burn wound repair. However, the dynamic process in wound healing requires both the generation of ROS to inhibit bacteria and the subsequent reduction of ROS levels to initiate and promote tissue regeneration, which calls for a more intelligent ROS regulation dressing system. Hence, a dual-layered hydrogel (Dual-Gel) tailored to the process of burn wound repair is designed: the inner layer hydrogel (Gel 2) first responds to bacterial hyaluronidase (Hyal) to deliver aggregation-induced emission (AIE) photosensitizer (PS) functionalized adipose-derived stem cell nanovesicles, which generate ROS upon light irradiation to eliminate bacteria; then the outer layer hydrogel (Gel 1) continuously starts a long-lasting consumption of excess ROS at the wound site to accelerate tissue regeneration. Simultaneously, the stem cell nanovesicles trapped in the burns wound also provide nutrients and mobilize neighboring tissues to thoroughly assist in inflammation regulation, cell proliferation, migration and angiogenesis. In summary, this study develops an intelligent treatment approach on burn wounds by programmatically regulating ROS and facilitating comprehensive wound tissue repair. This article is protected by copyright. All rights reserved.

Heterointerfaces: Unlocking Superior Capacity and Rapid Mass Transfer Dynamics in Energy Storage Electrodes.

Heterogeneous electrode materials possess abundant heterointerfaces with a localized "space charge effect", which enhances capacity output and accelerates mass/charge transfer dynamics in energy storage devices. These promising features open new possibilities for demanding applications such as electric vehicles, grid energy storage, and portable electronics. However, the fundamental principles and working mechanisms that govern heterointerfaces are not yet fully understood, impeding the rational design of electrode materials. In this study, we systematically discuss the heterointerface evolution during charging and discharging process as well as the intricate interaction between heterointerfaces and charge/mass transport phenomena. We also provide guidelines along with feasible strategies for engineering structural heterointerfaces to address specific challenges encountered in various application scenarios. This review offers innovative solutions for the development of heterogeneous electrode materials, enabling more efficient energy storage beyond conventional electrochemistry. Furthermore, it provides fresh insights into the advancement of clean energy conversion and storage technologies. This review contributes to the knowledge and understanding of heterointerfaces, paving the way for the design and optimization of next-generation energy storage materials for a sustainable future. This article is protected by copyright. All rights reserved.

Rapid P-TEFb-dependent transcriptional reorganization underpins the glioma adaptive response to radiotherapy.

Dynamic regulation of gene expression is fundamental for cellular adaptation to exogenous stressors. P-TEFb-mediated pause-release of RNA polymerase II (Pol II) is a conserved regulatory mechanism for synchronous transcriptional induction in response to heat shock, but this pro-survival role has not been examined in the applied context of cancer therapy. Using model systems of pediatric high-grade glioma, we show that rapid genome-wide reorganization of active chromatin facilitates P-TEFb-mediated nascent transcriptional induction within hours of exposure to therapeutic ionizing radiation. Concurrent inhibition of P-TEFb disrupts this chromatin reorganization and blunts transcriptional induction, abrogating key adaptive programs such as DNA damage repair and cell cycle regulation. This combination demonstrates a potent, synergistic therapeutic potential agnostic of glioma subtype, leading to a marked induction of tumor cell apoptosis and prolongation of xenograft survival. These studies reveal a central role for P-TEFb underpinning the early adaptive response to radiotherapy, opening avenues for combinatorial treatment in these lethal malignancies.

Multifunctional polyvinyl alcohol/poly-dopamine hydrogels loaded with bio-nano composites promote wound healing by repairing endogenous electric fields.

In this paper, a heart-shaped nanocomposite (MXenen@Cu-MOF, MC) has been prepared by hydrothermal method. This material can effectively prevent the accumulation of MXene, improve the material's electrical conductivity and antibacterial properties. In addition, it is loaded into Polyvinyl alcohol/Poly-dopamine hydrogel wound dressings (PPMC), which can effectively destroy bacterial biofilms and provide a new pathway for internal electrical currents, helping to repair internal electric fields and promote wound healing. Through the concentration gradient experiments of hydrogel such as antibacterial, conductive, hemolysis and cell migration, we believe that the addition of MC can improve the basic properties of hydrogel. Among them, PPMC0.2 is the hydrogel with the best performance under the premise of meeting bio-compatibility. Its resistance, between 500 and 1000 Ω, is lower than the skin resistance at the wound site and provides the basis for the passage of current through the body. In addition, the cell mobility (24 h) of PPMC0.2 reached 58 %, and the wound healing rate (6 day) was 81.84 %, which was much higher than that of other experimental groups. The experimental results proved that PPMC hydrogel can promote wound healing, and this study also provided a new therapeutic idea for chronic wound healing.

Tribological behaviors of an attapulgite-graphene nanocomposite as an additive for mineral lubricating oil.

In this work, an attapulgite-graphene nanocomposite was prepared. The tribological properties of the prepared attapulgite-graphene nanocomposite as an additive for 200SN mineral lubricating oil were investigated using an SRV-IV tribometer through ball-on-disk contact mode for the first time. The characterization of the prepared nanocomposite indicated that attapulgite nanofibers are enveloped by the graphene nanosheets and present fine combination. The tribological test results show that the friction-reducing and antiwear properties of 200SN were obviously improved by adding the attapulgite-graphene nanocomposite. Through the characterization and analysis of the worn surface and cross-section, it was found that a tribofilm composed of Fe, Fe3O4, FeO, Fe2O3, FeOOH, graphite, graphene, SiO2 and organic compounds was formed on the worn surface. Furthermore, the bonding between the tribofilm and steel matrix is tight. The tribofilm and lubricating oil achieve a solid-liquid coupling lubrication effect, which is responsible for the improvement of the friction-reducing and antiwear properties.

Pericytes in Alzheimer's disease: Key players and therapeutic targets.

Alzheimer's disease (AD) is a devastating neurodegenerative disorder that leads to progressive cognitive decline and neuropathological changes. Pericytes, which are vessel mural cells on the basement membrane of capillaries, play a crucial role in regulating cerebrovascular functions and maintaining neurovascular unit integrity. Emerging research substantiates the involvement of pericytes in AD. This review provides a comprehensive overview of pericytes, including their structure, origin, and markers and various functions within the central nervous system. Emphatically, the review explores the intricate mechanisms through which pericytes contribute to AD, including their interactions with amyloid beta and apolipoprotein E, as well as various signaling pathways. The review also highlights potential for targeted pericyte therapy for AD, with a focus on stem cell therapy and drug treatments. Future research directions include the classification of pericyte subtypes, studies related to aging, and the role of pericytes in exosome-related mechanisms in AD pathology. In conclusion, this review consolidates current knowledge on the pivotal roles of pericytes in AD and their potential as therapeutic targets, providing valuable insights for future research and clinical interventions aimed at addressing the impact of AD on patients' lives.

The potential advantages of 18F sodium fluoride positron emission tomography-computed tomography for clinical staging and management planning in patients with nasopharyngeal carcinoma.

Background: The staging and treatment planning of nasopharyngeal carcinoma (NPC) face challenges due to limited sensitivity of conventional imaging. 18F-sodium fluoride (18F-NaF) positron emission tomography-computed tomography (PET/CT) offers potential advantages in detecting early bone involvement. This retrospective cohort study aimed to assess the potential advantage of 18F-NaF PET/CT for clinical staging and management planning in patients with NPC and to compare 18F-NaF PET/CT findings with those of conventional imaging modalities. Methods: We enrolled a cohort of patients with NPC who underwent 18F-NaF PET/CT at our PET/CT center between July 1, 2017, and June 30, 2021, and analyzed the findings of 18F-NaF PET/CT and conventional imaging modalities. Data from multidisciplinary team discussions on clinical staging and management planning both before and after 18F-NaF PET/CT were recorded. Additionally, any changes in clinical staging and management planning following 18F-NaF PET/CT were documented. Results: A total of 58 patients were included in this study. After 18F-NaF PET/CT imaging, clinical tumor-node-metastasis (TNM) staging was observed to have changed in seven cases (12.1%). Among these, four cases had changes in T stage and three cases in the M stage. Additionally, changes in clinical management plans were observed in eight patients (13.8%). Changes due the results of 18F-NaF PET/CT included three cases with major modification (two cases switched from curative treatment to palliative treatment, and one case switched from palliative treatment to curative treatment) and five cases with minor changes. The minor changes involved alteration to the radiotherapy target volume (three cases with an increased target volume and one case with a reduced target area). Furthermore, one case required an alteration to the radiotherapy strategy for local bone involvement. Conclusions: The use of 18F-NaF PET/CT in patients newly diagnosed with NPC may offer potential advantages for clinical staging and treatment planning, enabling physicians to select a more individualized treatment approach.

Association of sleep duration and prevalence of sarcopenia: A large cross-sectional study.

Background: The purpose of this study was to examine the relationship between sleep duration and risk of sarcopenia in in general U.S. population. Methods: Utilizing publicly available data from the National Health and Nutrition Examination Survey spanning from 2011 to 2014, we explored the association between sleep duration and prevalence of sarcopenia. To investigate their relationship, we conducted weighted multivariate logistic regression analysis, restricted cubic splines (RCS) curve, and subgroup analysis. Results: The study included 8,200 individuals, among whom 99 (0.9 %) had sarcopenia. The RCS curve revealed a U-shaped association of sarcopenia with sleep duration (P for nonlinearity = 0.020), showing that the risk of sarcopenia decreases with increasing sleep duration, reaching the lowest risk around 6.67 h. After controlling for underlying cofounders, compared to individuals with sleep duration < 5 h, the odds ratios with 95 % confidence intervals of sarcopenia were 0.64 (0.27, 1.49), 0.50 (0.20, 1.26), 0.65 (0.27, 1.60), and 2.31 (0.73, 7.30) for < 5-6, 6.5-7.5, 8-9, and > 9 h group. The U-shaped association between sleep time and prevalence of sarcopenia also was observed in the subjects who aged < 40 or ≥ 40 years, were male or female, with or without hypertension, and diabetes mellitus. Conclusions: In summary, both short and long sleep durations increased prevalence of sarcopenia. Further studies are needed to explore the underlying mechanisms.

High-Entropy Polymer Electrolytes Derived from Multivalent Polymeric Ligands for Solid-State Lithium Metal Batteries with Accelerated Li+ Transport.

Solid-state polymer-based electrolytes (SSPEs) exhibit great possibilities in realizing high-energy-density solid-state lithium metal batteries (SSLMBs). However, current SSPEs suffer from low ionic conductivity and unsatisfactory interfacial compatibility with metallic Li because of the high crystallinity of polymers and sluggish Li+ movement in SSPEs. Herein, differing from common strategies of copolymerization, a new strategy of constructing a high-entropy SSPE from multivariant polymeric ligands is proposed. As a protocol, poly(vinylidene fluoride-co-hexafluoropropylene) (PH) chains are grafted to the demoed polyethylene imine (PEI) with abundant -NH2 groups via a click-like reaction (HE-PEIgPHE). Compared to a PH-based SSPE, our HE-PEIgPHE shows a higher modulus (6.75 vs 5.18 MPa), a higher ionic conductivity (2.14 × 10-4 vs 1.03 × 10-4 S cm-1), and a higher Li+ transference number (0.55 vs 0.42). A Li|HE-PEIgPHE|Li cell exhibits a long lifetime (1500 h), and a Li|HE-PEIgPHE|LiFePO4 cell delivers an initial capacity of 160 mAh g-1 and a capacity retention of 98.7%, demonstrating the potential of our HE-PEIgPHE for the SSLMBs.

Exploring the immune characteristions of CRKP pneumonia at single-cell level.

The immune dysregulation associated with carbapenem-resistant Klebsiella pneumoniae (CRKP) severity was investigated through single-cell RNA sequencing (scRNA-seq) of 5 peripheral blood samples from 3 patients with moderate and severe CRKP pneumonia. Additionally, scRNA-seq datasets from two individuals with COVID-19 were included for comparative analysis. The dynamic characterization and functional properties of each immune cell type were examined by delineating the transcriptional profiles of immune cells throughout the transition from moderate to severe conditions. Overall, most immune cells in CRKP patients exhibited a robust interferon-α response and inflammatory reaction compared to healthy controls, mirroring observations in COVID-19 patients. Furthermore, cell signatures associated with NK cells, macrophages, and monocytes were identified in CRKP progression including PTPRCAP for NK cells, C1QB for macrophages, and S100A12 for both macrophages and monocytes. In summary, this study offers a comprehensive scRNA-seq resource for illustrating the dynamic immune response patterns during CRKP progression, thereby shedding light on the associations between CRKP and COVID-19.

Pressureless Welding of Temperature-Invariant Multifunctionality Body Based on Hydroxyl-Functionalized Boron Nitride Nanosheets and Bifunctional Monoethanolamine Cross-linker.

Bulk hexagonal boron nitride (h-BN) ceramics with structural integrity, high-temperature resistance and low expansion rate are expected for multifunctional applications in extreme conditions. However, due to its sluggish self-diffusion and intrinsic inertness, it remains a great challenge to overcome high-energy barrier for h-BN powder sintering. Herein, a cross-linking and pressureless-welding strategy is reported to produce bulk boron nitride nanosheets (BNNSs) ceramics with well-crystalized and dense B-N covalent-welding frameworks. The essence of this synthesis strategy lies in the construction of >B─O─H2C─H2C─H2N:→B< bond bridge connection structure among hydroxyl functionalized BNNSs (BNNSs-OH) using bifunctional monoethanolamine (MEA) as cross-linker through esterification and intermolecular-coordination reactions. The prepared BNNSs-interlaced ceramics have densities not less than 1.2 g cm-3, and exhibit exceptional mechanical robustness and resiliency, excellent thermomechanical stability, ultra-low linear thermal expansion coefficient of 0.06 ppm °C-1, and high thermal diffusion coefficient of 4.76 mm2 s-1 at 25 °C and 3.72 mm2 s-1 at 450 °C. This research not only reduces the free energy barrier from h-BN particles to bulk ceramics through facile multi-step physicochemical reaction, but also stimulates further exploration of multifunctional applications for bulk h-BN ceramics over a wide temperature range.

Mental health problems of front-line medical staff in the early stage of public health emergencies.

In the face of the unprecedented public health crisis caused by the novel coronavirus pneumonia epidemic, front-line health workers are under enormous mental pressure. This paper aims to explore the mental health challenges faced by front-line health workers in the early stages of a public health emergency, such as stress, anxiety, and depression. At the same time, the factors that increase their mental stress are analyzed, and practical measures are put forward to prevent and manage mental health problems, aiming at improving the quality of medical treatment during public health emergencies. This paper has some reference value for people engaged in mental health prevention.

Construction of a TP53 mutation-associated ceRNA network as prognostic biomarkers in hepatocellular carcinoma.

Background: Hepatocellular carcinoma (HCC) continues to endanger human health worldwide. Regulatory networks of competing endogenous RNAs (ceRNAs) play important roles in HCC. TP53 is the second most often altered gene in HCC and has a significant role in regulating target genes such as miRNAs and lncRNAs. Methods: Data from patients with TP53 mutation were collected through the cBioPortal database and differential analysis was performed to screen RNAs related to TP53 mutation. The lncRNA-miRNA-mRNA relationship was predicted by the miRcode, miRDB, and TargetScan databases. The ceRNA networks were screened and visualized by Cytoscape. Core ceRNA networks were generated by differential analysis, coexpression analysis, prognostic analysis and subcellular localization. Finally, methylation, mutation, PPI, GSEA, immunity and drug sensitivity analyses of MEX3A were performed to determine the role of MEX3A in HCC. Results: We identified 1508 DEmRNAs, 85 DEmiRNAs and 931 DElncRNAs and obtained a ceRNA network including 28 lncRNAs, 4 miRNAs and 31 mRNAs. Twenty hub DERNAs in the TP53-altered-related ceRNA network were screened out by Cytoscape and the core ceRNA network (LINC00491/TCL6-hsa-miR-139-5p-MEX3A) was obtained by multiple analyses. In addition, we discovered that the methylation level of MEX3A was decreased and the mutation frequency was raised in HCC. Furthermore, elevated MEX3A expression was associated with alterations in the HCC immunological microenvironment. Conclusion: We successfully constructed a reciprocal ceRNA network, which could provide new ideas for exploring HCC mechanisms and therapeutic approaches.

Voxel Design of Grayscale DLP 3D-Printed Soft Robots.

Grayscale digital light processing (DLP) printing is a simple yet effective way to realize the variation of material properties by tuning the grayscale value. However, there is a lack of available design methods for grayscale DLP 3D-printed structures due to the complexities arising from the voxel-level grayscale distribution, nonlinear material properties, and intricate structures. Inspired by the dexterous motions of natural organisms, a design and fabrication framework for grayscale DLP-printed soft robots is developed by combining a grayscale-dependent hyperelastic constitutive model and a voxel-based finite-element model. The constitutive model establishes the relationship between the projected grayscale value and the nonlinear mechanical properties, while the voxel-based finite-element model enables fast and efficient calculation of the mechanical performances with arbitrarily distributed material properties. A multiphysics modeling and experimental method is developed to validate the homogenization assumption of the degree of conversion (DoC) variation in a single voxel. The design framework is used to design structures with reduced stress concentration and programmable multimodal motions. This work paves the way for integrated design and fabrication of functional structures using grayscale DLP 3D printing.

Clinical relevance of somatic mutations in Chinese lung adenocarcinoma and their prognostic implications for survival.

BACKGROUND: To comprehensively elucidate the genomic and mutational features of lung cancer cases, and lung adenocarcinoma (LUAD), it is imperative to conduct ongoing investigations into the genomic landscape. In this study, we aim to analyze the somatic mutation profile and assessed the significance of these informative genes utilizing a retrospective LUAD cohort. METHODS: A total of 247 Chinese samples were analyzed to exhibit the tumor somatic genomic alterations in patients with LUAD. The Cox regression analysis was employed to identify prognosis-related genes and establish a predictive model for stratifying patients with LUAD. RESULTS: In the Dianjiang People's Hospital (DPH) cohort, the top five frequent mutated genes were (Epidermal growth factor receptor) EGFR (68%), TP53 (30%), RBM10 (13%), LRP1B (9%), and KRAS (9%). Of which, EGFR is a mostly altered driver gene, and most mutation sites are located in tyrosine kinase regions. Oncogene pathway alteration and mutation signature analysis demonstrated the RTK-RAS pathway alteration, and smoking was the main carcinogenic factor of the DPH cohort. Furthermore, we identified 34 driver genes in the DPH cohort, including EGFR (68%), TP53 (30.4%), RBM10 (12.6%), KRAS (8.5%), LRP1B (8.5%), and so on, and 45 Clinical Characteristic-Related Genes (CCRGs) were found to closely related to the clinical high-risk factors. We developed a Multiple Parameter Gene Mutation (MPGM) risk model by integrating critical genes and oncogenic pathway alterations in LUAD patients from the DPH cohort. Based on publicly available LUAD datasets, we identified five genes, including BRCA2, Anaplastic lymphoma kinase (ALK), BRAF, EGFR, and Platelet-Derived Growth Factor Receptor Alpha (PDGFRA), according to the multivariable Cox regression analysis. The MPGM-low group showed significantly better overall survival (OS) compared to the MPGM-high group (p < 0.0001, area under the curve (AUC) = 0.754). The robust performance was validated in 55 LUAD patients from the DPH cohort and another LUAD dataset. Immune characteristics analysis revealed a higher proportion of primarily DCs and mononuclear cells in the MPGM-low risk group, while the MPGM-high risk group showed lower immune cells and higher tumor cell infiltration. CONCLUSION: This study provides a comprehensive genomic landscape of Chinese LUAD patients and develops an MPGM risk model for LUAD prognosis stratification. Further follow-up will be performed for the patients in the DPH cohort consistently to explore the resistance and prognosis genetic features.

Dearomative [2 + 1] Spiroannulation of Bromophenols with Electron-Deficient Alkenes.

A base-assisted dearomative [2 + 1] spiroannulation of p/o-bromophenols with activated olefins (methylenemalonates) to construct various cyclopropyl spirocyclohexadienone skeletons is reported. Furthermore, several other halophenols (X = Cl, I) were also tolerated in this process. Control experiments reveal a dearomative Michael addition of phenols at their halogenated positions to methylenemalonates, followed by intramolecular radical-based SRN1 dehalogenative cyclopropanation. However, according to the density functional theory (DFT) calculations, an SN2 dehalogenative cyclopropanation with the same low activation energy barrier should not be excluded. The utility of this method is showcased by gram-scale syntheses and transformations of the dearomatized products.

Genetic Landscape and Its Prognostic Impact in Children With Langerhans Cell Histiocytosis.

CONTEXT.­: Langerhans cell histiocytosis (LCH) is a rare myeloid neoplasm that predominantly affects young children. OBJECTIVE.­: To investigate genetic alterations and their correlation with clinical characteristics and prognosis in pediatric LCH. DESIGN.­: We performed targeted sequencing to detect mutations in LCH lesions from pediatric patients. RESULTS.­: A total of 30 genomic alterations in 5 genes of the MAPK pathway were identified in 187 of 223 patients (83.9%). BRAF V600E (B-Raf proto-oncogene, serine/threonine kinase) was the most common mutation (51.6%), followed by MAP2K1 (mitogen-activated protein kinase kinase 1) alterations (17.0%) and other BRAF mutations (13.0%). ARAF (A-Raf proto-oncogene, serine/threonine kinase) and KRAS (KRAS proto-oncogene, GTPase) mutations were relatively rare (2.2% and 0.9%, respectively). Additionally, FNBP1 (formin-binding protein 1)::BRAF fusion and MAP3K10 (mitogen-activated protein kinase kinase 10) mutations A17T and R823C were identified in 1 case each, with possible constitutive activation of ERK1/2 phosphorylation. BRAF V600E was more frequent in patients with risk organ involvement, while MAP2K1 mutation was more prevalent in patients with single-system LCH (P = .001). BRAF V600E was associated with craniofacial bone, skin, liver, spleen, and ear involvement (all P < .05). Patients with other BRAF mutations had a higher proportion of spinal column involvement (P = .006). Univariate analysis showed a significant difference in progression-free survival among the 4 molecular subgroups for patients treated with first-line therapy (P = .02). According to multivariate analysis, risk organ involvement was the strongest independent adverse prognostic factor (hazard ratio, 8.854; P < .001); BRAF or MAP2K1 mutation was not an independent prognostic factor. CONCLUSIONS.­: Most pediatric patients with LCH carry somatic mutations involving the MAPK pathway, correlating with clinical characteristics and outcomes for first-line chemotherapy.

The Rapid Evolution of De Novo Proteins in Structure and Complex.

Recent studies in the rice genome-wide have established that de novo genes, evolving from non-coding sequences, enhance protein diversity through a stepwise process. However, the pattern and rate of their evolution in protein structure over time remain unclear. Here, we addressed these issues within a surprisingly short evolutionary timescale (<1 million years for 97% of Oryza de novo genes) with comparative approaches to gene duplicates. We found that de novo genes evolve faster than gene duplicates in the intrinsic disordered regions (IDRs, such as random coils), secondary structure elements (such as α-helix and ß-strand), hydrophobicity, and molecular recognition features (MoRFs). In de novo proteins, specifically, we observed an 8-14% decay in random coils and IDR lengths and a 2.3-6.5% increase in structured elements, hydrophobicity, and MoRFs, per million years on average. These patterns of structural evolution align with changes in amino acid composition over time as well. We also revealed higher positive charges but smaller molecular weights for de novo proteins than duplicates. Tertiary structure predictions showed that most de novo proteins, though not typically well-folded on their own, readily form low-energy and compact complexes with other proteins facilitated by extensive residue contacts and conformational flexibility, suggesting a faster-binding scenario in de novo proteins to promote interaction. These analyses illuminate a rapid evolution of protein structure in de novo genes in rice genomes, originating from non-coding sequences, highlighting their quick transformation into active, protein complex-forming components within a remarkably short evolutionary timeframe.