Designing a synthetic moss genome using GenoDesigner.

The de novo synthesis of genomes has made unprecedented progress and achieved milestones, particularly in bacteria and yeast. However, the process of synthesizing a multicellular plant genome has not progressed at the same pace, due to the complexity of multicellular plant genomes, technical difficulties associated with large genome size and structure, and the intricacies of gene regulation and expression in plants. Here we outline the bottom-up design principles for the de novo synthesis of the Physcomitrium patens (that is, earthmoss) genome. To facilitate international collaboration and accessibility, we have developed and launched a public online design platform called GenoDesigner. This platform offers an intuitive graphical interface enabling users to efficiently manipulate extensive genome sequences, even up to the gigabase level. This tool is poised to greatly expedite the synthesis of the P. patens genome, offering an essential reference and roadmap for the synthesis of plant genomes.

Preparation of Polyimide/Ionic Liquid Hybrid Membrane for CO2/CH4 Separation.

Imidazole ionic liquids (ILs) have good affinity and good solubility for carbon dioxide (CO2). Such ionic liquids, combined with polyimide membrane materials, can solve the problem that, today, CO2 is difficult to separate and recover. In this study, the ionic liquid (IL) of 1-ethyl-3-methylimidazolium tetrafluoroborate (IL1), 1-pentyl-3-methylimidazolium tetrafluoroborate (IL2), 1-octyl-3-methylimidazolium tetrafluoroborate (IL3), and 1-dodecylimidazolium tetrafluoroborate (IL4) with different contents were added to a polyimide matrix, and a series of polyimide membranes blended with ionic liquid were prepared using a high-speed mixer. The mechanical properties and gas separation permeability of the membranes were investigated. Among them, the selectivity of the PI/IL3 membrane for CO2/CH4 was 180.55, which was 2.5 times higher than the PI membrane, and its CO2 permeability was 16.25 Barrer, which exceeded the Robeson curve in 2008; the separation performance of the membrane was the best in this work.

Updated overall survival and circulating tumor DNA analysis of ensartinib for crizotinib-refractory ALK-positive NSCLC from a phase II study.

BACKGROUND: The initial phase II stuty (NCT03215693) demonstrated that ensartinib has shown clinical activity in patients with advanced crizotinib-refractory, anaplastic lymphoma kinase (ALK)-positive non-small cell lung cancer (NSCLC). Herein, we reported the updated data on overall survival (OS) and molecular profiling from the initial phase II study. METHODS: In this study, 180 patients received 225 mg of ensartinib orally once daily until disease progression, death or withdrawal. OS was estimated by Kaplan‒Meier methods with two-sided 95% confidence intervals (CIs). Next-generation sequencing was employed to explore prognostic biomarkers based on plasma samples collected at baseline and after initiating ensartinib. Circulating tumor DNA (ctDNA) was detected to dynamically monitor the genomic alternations during treatment and indicate the existence of molecular residual disease, facilitating improvement of clinical management. RESULTS: At the data cut-off date (August 31, 2022), with a median follow-up time of 53.2 months, 97 of 180 (53.9%) patients had died. The median OS was 42.8 months (95% CI: 29.3-53.2 months). A total of 333 plasma samples from 168 patients were included for ctDNA analysis. An inferior OS correlated significantly with baseline ALK or tumor protein 53 (TP53) mutation. In addition, patients with concurrent TP53 mutations had shorter OS than those without concurrent TP53 mutations. High ctDNA levels evaluated by variant allele frequency (VAF) and haploid genome equivalents per milliliter of plasma (hGE/mL) at baseline were associated with poor OS. Additionally, patients with ctDNA clearance at 6 weeks and slow ascent growth had dramatically longer OS than those with ctDNA residual and fast ascent growth, respectively. Furthermore, patients who had a lower tumor burden, as evaluated by the diameter of target lesions, had a longer OS. Multivariate Cox regression analysis further uncovered the independent prognostic values of bone metastases, higher hGE, and elevated ALK mutation abundance at 6 weeks. CONCLUSION: Ensartinib led to a favorable OS in patients with advanced, crizotinib-resistant, and ALK-positive NSCLC. Quantification of ctDNA levels also provided valuable prognostic information for risk stratification.

High plasticity of ribosomal DNA organization in budding yeast.

In eukaryotic genomes, rDNA generally resides as a highly repetitive and dynamic structure, making it difficult to study. Here, a synthetic rDNA array on chromosome III in budding yeast was constructed to serve as the sole source of rRNA. Utilizing the loxPsym site within each rDNA repeat and the Cre recombinase, we were able to reduce the copy number to as few as eight copies. Additionally, we constructed strains with two or three rDNA arrays and found that the presence of multiple arrays did not affect the formation of a single nucleolus. Although alteration of the position and number of rDNA arrays did impact the three-dimensional genome structure, the additional rDNA arrays had no deleterious influence on cell growth or transcriptomes. Overall, this study sheds light on the high plasticity of rDNA organization and opens up opportunities for future rDNA engineering.

Opportunistic lung cancer screening with low-dose computed tomography in National Cancer Center of China: The first 14 years' experience.

BACKGROUND: In China, over 50% of lung cancer cases occur in nonsmokers. Thus, identifying high-risk individuals for targeted lung cancer screening is crucial. Beyond age and smoking, determining other risk factors for lung cancer in the Asian population has become a focal point of research. Using 30,000 participants in the prospectively enrolled cohort at China's National Cancer Center (NCC) over the past 14 years, we categorized participants by risk, with an emphasis on nonsmoking females. MATERIALS AND METHODS: Between November 2005 and December 2019, 31,431 individuals voluntarily underwent low-dose computed tomography (LDCT) scans for lung cancer screening at the NCC. We recorded details like smoking history, exposure to hazards, and family history of malignant tumors. Using the 2019 NCCN criteria, participants were categorized into high-, moderate-, and low-risk groups. Additionally, we separated non-high-risk groups into female never smokers (aged over 40) exposed to second-hand smoke (SHS) and others. Any positive results from initial scans were monitored per the I-ELCAP protocol (2006), and suspected malignancies were addressed through collaborative decisions between patients and physicians. We analyzed and compared the detection rates of positive results, confirmed lung cancers, and cancer stages across risk, age, and gender groups. RESULTS: Out of 31,431 participants (55.9% male, 44.1% female), 3695 (11.8%) showed positive baseline LDCT scans with 197 (0.6%; 106 females, 91 males) confirmed as lung cancer cases pathologically. Malignancy rate by age was 0.1% among those aged under 40 years, 0.4% among those aged 40-49 years, 0.8% among those aged 50-59 years, and 1.2% among those aged 60 years and older. From the 25,763 participants (56.9% male, 43.1% female) who completed questionnaires, 1877 (7.3%) were categorized as high risk, 6500 (25.2%) as moderate risk, and 17,386 (67.5%) as low risk. Of the 23,886 in the non-high-risk category, 8041 (33.7%) were females over 40 years old exposed to SHS. The high-risk group showed the highest lung cancer detection rate at 1.4%. However, females exposed to SHS had a notably higher detection rate than the rest of the non-high-risk group (1.1% vs. 0.5%; p < 0.0001). In this cohort, 84.8% of the detected lung cancers were at an early stage. CONCLUSIONS: In our study, using LDCT for lung cancer screening proved significant for high-risk individuals. For non-high-risk populations, LDCT screening could be considered for nonsmoking women with exposure to SHS.

Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae.

Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is a promising tool to study genomic rearrangements. However, the potential of SCRaMbLE to study genomic rearrangements is currently hindered, because a strain containing all 16 synthetic chromosomes is not yet available. Here, we construct SparLox83R, a yeast strain containing 83 loxPsym sites distributed across all 16 chromosomes. SCRaMbLE of SparLox83R produces versatile genome-wide genomic rearrangements, including inter-chromosomal events. Moreover, when combined with synthetic chromosomes, SCRaMbLE of hetero-diploids with SparLox83R leads to increased diversity of genomic rearrangements and relatively faster evolution of traits compared to hetero-diploids only with wild-type chromosomes. Analysis of the SCRaMbLEd strain with increased tolerance to nocodazole demonstrates that genomic rearrangements can perturb the transcriptome and 3D genome structure and consequently impact phenotypes. In summary, a genome with sparsely distributed loxPsym sites can serve as a powerful tool for studying the consequence of genomic rearrangements and accelerating strain engineering in Saccharomyces cerevisiae.

Near telomere-to-telomere genome of the model plant Physcomitrium patens.

The model plant Physcomitrium patens has played a pivotal role in enhancing our comprehension of plant evolution and development. However, the current genome harbours numerous regions that remain unfinished and erroneous. To address these issues, we generated an assembly using Oxford Nanopore reads and Hi-C mapping. The assembly incorporates telomeric and centromeric regions, thereby establishing it as a near telomere-to-telomere genome except a region in chromosome 1 that is not fully assembled due to its highly repetitive nature. This near telomere-to-telomere genome resolves the chromosome number at 26 and provides a gap-free genome assembly as well as updated gene models to aid future studies using this model organism.

Predictive value of 18 F-FDG PET/CT and serum tumor markers for tumor mutational burden in patients with non-small cell lung cancer.

PURPOSE: To investigate the correlations between metabolic parameters (MPs) of 18 F-fluorodeoxyglucose (FDG) uptake on positron emission tomography/computed tomography (PET/CT), serum tumor markers (STMs), and tumor mutational burden (TMB) in patients with non-small cell lung cancer (NSCLC). MATERIALS AND METHODS: In this retrospective study, we enrolled 129 patients with NSCLC (males, 78; females, 51) who underwent baseline TMB and STM tests and 18 F-FDG PET/CT scans before treatment between March 2018 and September 2022. Patients were categorized into TMB-high (TMB ≥10 mutations/Mb; n = 27 [20.9%]) and non-TMB-high (TMB <10 mutations/Mb; n = 102 [79.1%]) groups. Binary logistic regression analyses were performed to determine independent predictors of TMB-high. Univariate and multivariate linear regression analyses were performed to determine independent predictors of TMB level on a log scale. Subgroup analyses for adenocarcinoma (ADC), ADC with EGFR+, ADC with EGFR-, and squamous cell carcinoma (SCC) were performed. RESULTS: For ADC, all MPs (SULpeak , SULmax , SULmean , MTV, and TLG) were significantly higher in the TMB-high group than the non-TMB-high group; smoker (odds ratio [OR] = 27.08, p = 0.018), EGFR+ (OR = 0.03, p = 0.033), KRAS+ (OR = 7.98, p = 0.083), high CEA (OR = 33.56, p = 0.029), and high CA125 (OR = 13.68, p = 0.030) were independent predictors of TMB-high; and all MPs showed significant positive linear correlations with TMB on a log scale, with SULpeak as an independent predictor. However, no significant correlation was observed for SCC. CONCLUSION: MPs and STMs can predict the TMB level for patients with ADC, and may serve as potential substitutes for TMB with increased value and easy implementation in guiding immunotherapy through noninvasive methods.

Building a eukaryotic chromosome arm by de novo design and synthesis.

The genome of an organism is inherited from its ancestor and continues to evolve over time, however, the extent to which the current version could be altered remains unknown. To probe the genome plasticity of Saccharomyces cerevisiae, here we replace the native left arm of chromosome XII (chrXIIL) with a linear artificial chromosome harboring small sets of reconstructed genes. We find that as few as 12 genes are sufficient for cell viability, whereas 25 genes are required to recover the partial fitness defects observed in the 12-gene strain. Next, we demonstrate that these genes can be reconstructed individually using synthetic regulatory sequences and recoded open-reading frames with a "one-amino-acid-one-codon" strategy to remain functional. Finally, a synthetic neochromsome with the reconstructed genes is assembled which could substitute chrXIIL for viability. Together, our work not only highlights the high plasticity of yeast genome, but also illustrates the possibility of making functional eukaryotic chromosomes from entirely artificial sequences.

[Effectiveness of Kirschner wire fixation and coracoclavicular ligament reconstruction with suture anchor in treatment of Cho type â ¡C distal clavicle fractures].

Objective: To evaluate the effectiveness of Kirschner wire fixation and coracoclavicular ligament reconstruction with suture anchor in the treatment of Cho type ⅡC distal clavicle fractures. Methods: The data of 17 patients with Cho type ⅡC distal clavicular fractures, who were treated with Kirschner wire fixation and coracoclavicular ligament reconstruction with suture anchor between June 2019 and June 2021, was retrospectively analyzed. There were 11 males and 6 females with an average age of 38.7 years (range, 19-72 years). The fractures were caused by falling in 12 cases and traffic accident in 5 cases. All patients had fresh closed fractures. The interval from injury to operation was 1-5 days (mean, 2.6 days). The preoperative injury severity score (ISS) was 6-27 (mean, 10.2). The operation time, intraoperative blood loss, hospital stay, fracture healing, and postoperative complications were analyzed. The shoulder joint function was evaluated by disabilities of the arm, shoulder, and hand (DASH) score and Constant score at last follow-up. Results: All operations were completed successfully. The operation time was 20-50 minutes (mean, 31.6 minutes). The intraoperative blood loss was 30-100 mL (mean, 50.6 mL). The hospital stay was 4-9 days (mean, 5.3 days). All incisions healed by first intention. All patients were followed up 12-16 months (mean, 13 months). All clavicle fractures healed, and the healing time was 8-15 weeks (mean, 11 weeks). No complications such as fracture displacement or nonunion caused by internal fixation failure occurred. During the follow-up, skin irritation caused by the Kirschner wire withdrawal occurred in 3 cases. The Kirschner wires were removed after fracture healing in 17 patients. At last follow-up, the Constant score of shoulder joint was 90-100 (mean, 98.2). The DASH score was 0-10 (mean, 1.5). Conclusion: Kirschner wire fixation combined with coracoclavicular ligament reconstruction with suture anchor in the treatment of Cho type ⅡC distal clavicle fractures has less postoperative complications and slight complications. It is convenient to remove the internal fixator. The Kirschner wire does not fix the distal clavicle fracture through the acromion, which has little effect on shoulder joint function and can obtain good effectiveness.

Modulating Metal-Nitrogen Coupling in Anti-Perovskite Nitride via Cation Doping for Efficient Reduction of Nitrate to Ammonia.

The complexes of metal center and nitrogen ligands are the most representative systems for catalyzing hydrogenation reactions in small molecule conversion. Developing heterogeneous catalysts with similar active metal-nitrogen functional centers, nevertheless, still remains challenging. In this work, we demonstrate that the metal-nitrogen coupling in anti-perovskite Co4 N can be effective modulated by Cu doping to form Co3 CuN, leading to strongly promoted hydrogenation process during electrochemical reduction of nitrate (NO3 - RR) to ammonia. The combination of advanced spectroscopic techniques and density functional theory calculations reveal that Cu dopants strengthen the Co-N bond and upshifted the metal d-band towards the Fermi level, promoting the adsorption of NO3 - and *H and facilitating the transition from *NO2 /*NO to *NO2 H/*NOH. Consequently, the Co3 CuN delivers noticeably better NO3 - RR activity than the pristine Co4 N, with optimal Faradaic efficiency of 97 % and ammonia yield of 455.3 mmol h-1 cm-2 at -0.3 V vs. RHE. This work provides an effective strategy for developing high-performance heterogeneous catalyst for electrochemical synthesis.

Multislip-enabled morphing of all-inorganic perovskites.

All-inorganic lead halide perovskites (CsPbX3, X = Cl, Br or I) are becoming increasingly important for energy conversion and optoelectronics because of their outstanding performance and enhanced environmental stability. Morphing perovskites into specific shapes and geometries without damaging their intrinsic functional properties is attractive for designing devices and manufacturing. However, inorganic semiconductors are often intrinsically brittle at room temperature, except for some recently reported layered or van der Waals semiconductors. Here, by in situ compression, we demonstrate that single-crystal CsPbX3 micropillars can be substantially morphed into distinct shapes (cubic, L and Z shapes, rectangular arches and so on) without localized cleavage or cracks. Such exceptional plasticity is enabled by successive slips of partial dislocations on multiple [Formula: see text] systems, as evidenced by atomic-resolution transmission electron microscopy and first-principles and atomistic simulations. The optoelectronic performance and bandgap of the devices were unchanged. Thus, our results suggest that CsPbX3 perovskites, as potential deformable inorganic semiconductors, may have profound implications for the manufacture of advanced optoelectronics and energy systems.

Association of Clinical and Radiological Features with Disease Severity of Symptomatic Immune Checkpoint Inhibitor-Related Pneumonitis.

OBJECTIVES: To investigate the predictive ability of clinical and chest computed tomography (CT) features to predict the severity of symptomatic immune checkpoint inhibitor-related pneumonitis (CIP). METHODS: This study included 34 patients diagnosed with symptomatic CIP (grades 2-5) and divided into mild (grade 2) and severe CIP (grades 3-5) groups. The groups' clinical and chest CT features were analyzed. Three manual scores (extent, image finding, and clinical symptom scores) were conducted to evaluate the diagnostic performance alone and in combination. RESULTS: There were 20 cases of mild CIP and 14 cases of severe CIP. More severe CIP occurred within 3 months than after 3 months (11 vs. 3 cases, p = 0.038). Severe CIP was significantly associated with fever (p < 0.001) and the acute interstitial pneumonia/acute respiratory distress syndrome pattern (p = 0.001). The diagnostic performance of chest CT scores (extent score and image finding score) was better than that of clinical symptom score. The combination of the three scores demonstrated the best diagnostic value, with an area under the receiver operating characteristic curve of 0.948. CONCLUSIONS: The clinical and chest CT features have important application value in assessing the disease severity of symptomatic CIP. We recommend the routine use of chest CT in a comprehensive clinical evaluation.

Mechanism of Resveratrol Improving Ischemia-Reperfusion Injury by Regulating Microglial Function Through microRNA-450b-5p/KEAP1/Nrf2 Pathway.

Alterations in the M1/M2 polarization phenotype significantly affect disease progression. Antioxidant and anti-inflammatory protective effects of resveratrol (Res) have been demonstrated. This paper tested the hypothesis that Res could protect against cerebral ischemia-reperfusion injury (CI/RI) by modulating microglial polarization via the miR-450b-5p/KEAP1/Nrf2 pathway. Rats were first treated with Res and adenovirus that interfered with miR-450b-5p or KEAP1, and then established a middle cerebral artery occlusion-reperfusion model using modified nylon sutures. Rats were then evaluated for neurological and behavioral functions, and markers of M2 microglia were detected by immunofluorescence staining. Additionally, the signature patterns of miR-450b-5p, KEAP1, and Nrf2 were determined. The collected data demonstrated that Res exerted neuroprotective effects in CI/RI by promoting microglial M2 polarization. Additionally, Res could regulate the Nrf2 pathway by targeting KEAP1 by up-regulating miR-450b-5p. Up-regulating miR-450b-5p or down-regulating KEAP1 could further promote the protective effect of Res, while down-regulating miR-450b-5p or up-regulating KEAP1 worked oppositely. Our study demonstrates that Res exerts neuroprotective effects on microglial M2 polarization through the miR-450b-5p/KEAP1/Nrf2 pathway during CI/RI.

Radiomic-signature changes after early treatment improve the prediction of progression-free survival in patients with advanced anaplastic lymphoma kinase-positive non-small cell lung cancer.

BACKGROUND: The prognosis of lung cancer varies widely, even in cases wherein the tumor stage, genetic mutation, and treatment regimens are the same. Thus, an effective means for risk stratification of patients with lung cancer is needed. PURPOSE: To develop and validate a combined model for predicting progression-free survival and risk stratification in patients with advanced anaplastic lymphoma kinase (ALK)-positive non-small cell lung cancer (NSCLC) treated with ensartinib. MATERIAL AND METHODS: We analyzed 203 tumor lesions in 114 patients and evaluated average radiomic feature measures from all lesions at baseline and changes in these features after early treatment (Δradiomic features). Combined models were developed by integrating clinical with radiomic features. The prediction performance and clinical value of the proposed models were evaluated using receiver operating characteristic analysis, calibration curve, decision curve analysis (DCA), and Kaplan-Meier survival analysis. RESULTS: Both the baseline and delta combined models achieved predictive efficacy with a high area under the curve. The calibration curve and DCA indicated the high accuracy and clinical usefulness of the combined models for tumor progression prediction. In the Kaplan-Meier analysis, the delta and baseline combined models, Δradiomic signature, and two selected clinical features could distinguish patients with a higher progression risk within 42 weeks. The delta combined model had the best performance. CONCLUSION: The combination of clinical and radiomic features provided a prognostic value for survival and progression in patients with NSCLC receiving ensartinib. Radiomic-signature changes after early treatment could be more valuable than those at baseline alone.

Unravelling the Interfacial Dynamics of Bandgap Funneling in Bismuth-Based Halide Perovskites.

An environmentally friendly mixed-halide perovskite MA3 Bi2 Cl9- x Ix with a bandgap funnel structure has been developed. However, the dynamic interfacial interactions of bandgap funneling in MA3 Bi2 Cl9- x Ix perovskites in the photoelectrochemical (PEC) system remain ambiguous. In light of this, single- and mixed-halide lead-free bismuth-based hybrid perovskites-MA3 Bi2 Cl9- y Iy and MA3 Bi2 I9 (named MBCl-I and MBI)-in the presence and absence of the bandgap funnel structure, respectively, are prepared. Using temperature-dependent transient photoluminescence and electrochemical voltammetric techniques, the photophysical and (photo)electrochemical phenomena of solid-solid and solid-liquid interfaces for MBCl-I and MBI halide perovskites are therefore confirmed. Concerning the mixed-halide hybrid perovskites MBCl-I with a bandgap funnel structure, stronger electronic coupling arising from an enhanced overlap of electronic wavefunctions results in more efficient exciton transport. Besides, MBCl-I's effective diffusion coefficient and electron-transfer rate demonstrate efficient heterogeneous charge transfer at the solid-liquid interface, generating improved photoelectrochemical hydrogen production. Consequently, this combination of photophysical and electrochemical techniques opens up an avenue to explore the intrinsic and interfacial properties of semiconductor materials for elucidating the correlation between material characterization and device performance.

Creating two-dimensional solid helium via diamond lattice confinement.

The universe abounds with solid helium in polymorphic forms. Therefore, exploring the allotropes of helium remains vital to our understanding of nature. However, it is challenging to produce, observe and utilize solid helium on the earth because high-pressure techniques are required to solidify helium. Here we report the discovery of room-temperature two-dimensional solid helium through the diamond lattice confinement effect. Controllable ion implantation enables the self-assembly of monolayer helium atoms between {100} diamond lattice planes. Using state-of-the-art integrated differential phase contrast microscopy, we decipher the buckled tetragonal arrangement of solid helium monolayers with an anisotropic nature compressed by the robust diamond lattice. These distinctive helium monolayers, in turn, produce substantial compressive strains to the surrounded diamond lattice, resulting in a large-scale bandgap narrowing up to ~2.2 electron volts. This approach opens up new avenues for steerable manipulation of solid helium for achieving intrinsic strain doping with profound applications.

Corrigendum to "Long-term L-3-n-butylphthalide pretreatment attenuates ischemic brain injury in mice with permanent distal middle cerebral artery occlusion through the Nrf2 pathway" [Heliyon 8 (7), (July 2022), Article e09909].

[This corrects the article DOI: 10.1016/j.heliyon.2022.e09909.].

Achieving thermally stable nanoparticles in chemically complex alloys via controllable sluggish lattice diffusion.

Nanoparticle strengthening provides a crucial basis for developing high-performance structural materials with potentially superb mechanical properties for structural applications. However, the general wisdom often fails to work well due to the poor thermal stability of nanoparticles, and the rapid coarsening of these particles will lead to the accelerated failures of these materials especially at elevated temperatures. Here, we demonstrate a strategy to achieve ultra-stable nanoparticles at 800~1000 °C in a Ni59.9-xCoxFe13Cr15Al6Ti6B0.1 (at.%) chemically complex alloy, resulting from the controllable sluggish lattice diffusion (SLD) effect. Our diffusion kinetic simulations reveal that the Co element leads to a significant reduction in the interdiffusion coefficients of all the main elements, especially for the Al element, with a maximum of up to 5 orders of magnitude. Utilizing first-principles calculations, we further unveil the incompressibility of Al induced by the increased concentration of Co plays a critical role in controlling the SLD effect. These findings are useful for providing advances in the design of novel structural alloys with extraordinary property-microstructure stability combinations for structural applications.