DELFMUT: duplex sequencing-oriented depth estimation model for stable detection of low-frequency mutations.

Duplex sequencing technology has been widely used in the detection of low-frequency mutations in circulating tumor deoxyribonucleic acid (DNA), but how to determine the sequencing depth and other experimental parameters to ensure the stable detection of low-frequency mutations is still an urgent problem to be solved. The mutation detection rules of duplex sequencing constrain not only the number of mutated templates but also the number of mutation-supportive reads corresponding to each forward and reverse strand of the mutated templates. To tackle this problem, we proposed a Depth Estimation model for stable detection of Low-Frequency MUTations in duplex sequencing (DELFMUT), which models the identity correspondence and quantitative relationships between templates and reads using the zero-truncated negative binomial distribution without considering the sequences composed of bases. The results of DELFMUT were verified by real duplex sequencing data. In the case of known mutation frequency and mutation detection rule, DELFMUT can recommend the combinations of DNA input and sequencing depth to guarantee the stable detection of mutations, and it has a great application value in guiding the experimental parameter setting of duplex sequencing technology.

Dynamical Janus Interface Design for Reversible and Fast-Charging Zinc-Iodine Battery under Extreme Operating Conditions.

Aqueous zinc (Zn) iodine (I2) batteries have emerged as viable alternatives to conventional metal-ion batteries. However, undesirable Zn deposition and irreversible iodine conversion during cycling have impeded their progress. To overcome these concerns, we report a dynamical interface design by cation chemistry that improves the reversibility of Zn deposition and four-electron iodine conversion. Due to this design, we demonstrate an excellent Zn-plating/-stripping behavior in Zn||Cu asymmetric cells over 1000 cycles with an average Coulombic efficiency (CE) of 99.95%. Moreover, the Zn||I2 full cells achieve a high-rate capability (217.1 mA h g-1 at 40 A g-1; C rate of 189.5C) at room temperature and enable stable cycling with a CE of more than 99% at -50 °C at a current density of 0.05 A g-1. In situ spectroscopic investigations and simulations reveal that introducing tetraethylammonium cations as ion sieves can dynamically modulate the electrode-electrolyte interface environment, forming the unique water-deficient and chloride ion (Cl-)-rich interface. Such Janus interface accounts for the suppression of side reactions, the prevention of ICl decomposition, and the enrichment of reactants, enhancing the reversibility of Zn-stripping/-plating and four-electron iodine chemistry. This fundamental understanding of the intrinsic interplay between the electrode-electrolyte interface and cations offers a rational standpoint for tuning the reversibility of iodine conversion.

Stabilizing the Layer-Structured Oxide Cathode by Modulating the Oxygen Redox Activity for Sodium Ion Batteries.

The layer-structured oxide cathode for sodium-ion batteries has attracted a widespread attention due to the unique redox properties and the anionic redox activity providing additional capacity. Nevertheless, such excessive oxygen redox reactions will lead to irreversible oxygen release, resulting in a rapid deterioration of the cycling stability. Herein, sulfur ion is successfully introduced to the O3-NaNi0.3Mn0.5Cu0.1Ti0.05W0.05O2 material through high-temperature quenching, thereby developing a novel Na2S-modified O3/P2-NaNi0.3Mn0.5Cu0.1Ti0.05W0.05O2 composite with extended cycling life. The S2- is analyzed for the ability to enhance the reversibility of oxidation-reduction reactions under high voltage and suppress the loss of lattice oxygen during cycling. The stable S─O covalent bonds are found to inhibit the oxygen generation and release within the structure. Benefiting from these improvements, the Na2S-modified O3/P2-NaNi0.3Mn0.5Cu0.1Ti0.05W0.05O2 exhibited a high reversible capacity of 173.1 mA h g-1 over a wide voltage range of 1.5-4.3 V under test conditions at 0.1 C and 81.5% capacity retention after 120 cycles at 1 C. The Na2S-modified O3/P2-NaNi0.3Mn0.5Cu0.1Ti0.05W0.05O2 demonstrates the excellent rate capability with the reversible capacities of 173.1,137.0,114.7,96.7, and 80.1 mA h g-1 at 0.1, 0.2, 0.5, 1, and 2 C.

Synergistic Effect of Co-Mo Pinning in Lay-Structured Oxide Cathode for Enhancing Stability toward Potassium-Ion Batteries.

Owing to the high economic efficiency and energy density potential, manganese-based layer-structured oxides have attracted great interests as cathode materials for potassium ion batteries. In order to alleviate the continuous phase transition and K+ re-embedding from Jahn-Teller distortion, the [Mn-Co-Mo]O6 octahedra are introduced into P3-K0.45MnO2 herein to optimize the local electron structure. Based on the experimental and computational results, the octahedral center metal molybdenum in [MoO6] octahedra proposes a smaller ionic radius and higher oxidation state to induce second-order JTE (pseudo-JTE) distortion in the adjacent [MnO6] octahedra. This distortion compresses the [MnO6] octahedra along the c-axis, leading to an increased interlayer spacing in the K+ layer. Meanwhile, the Mn3+/Mn4+ is balanced by [CoO6] octahedra and the K+ diffusion pathway is optimized as well. The proposed P3-K0.45Mn0.9Co0.05Mo0.05O2 cathode material shows an enhanced cycling stability and rate performance. It demonstrates a high capacity of 80.2 mAh g-1 at 100 mAh g-1 and 77.3 mAh g-1 at 500 mAh g-1. Furthermore, it showcases a 2000 cycles stability with a 59.6% capacity retention. This work presents a promising solution to the challenges faced by manganese-based layered oxide cathodes and offers a deep mechanism understanding and improved electrochemical performance.

Genomic and transcriptomic profiling of combined small-cell lung cancer through microdissection: unveiling the transformational pathway of mixed subtype.

BACKGROUND: Combined small-cell lung carcinoma (cSCLC) represents a rare subtype of SCLC, the mechanisms governing the evolution of cancer genomes and their impact on the tumor immune microenvironment (TIME) within distinct components of cSCLC remain elusive. METHODS: Here, we conducted whole-exome and RNA sequencing on 32 samples from 16 cSCLC cases. RESULTS: We found striking similarities between two components of cSCLC-LCC/LCNEC (SCLC combined with large-cell carcinoma/neuroendocrine) in terms of tumor mutation burden (TMB), tumor neoantigen burden (TNB), clonality structure, chromosomal instability (CIN), and low levels of immune cell infiltration. In contrast, the two components of cSCLC-ADC/SCC (SCLC combined with adenocarcinoma/squamous-cell carcinoma) exhibited a high level of tumor heterogeneity. Our investigation revealed that cSCLC originated from a monoclonal source, with two potential transformation modes: from SCLC to SCC (mode 1) and from ADC to SCLC (mode 2). Therefore, cSCLC might represent an intermediate state, potentially evolving into another histological tumor morphology through interactions between tumor and TIME surrounding it. Intriguingly, RB1 inactivation emerged as a factor influencing TIME heterogeneity in cSCLC, possibly through neoantigen depletion. CONCLUSIONS: Together, these findings delved into the clonal origin and TIME heterogeneity of different components in cSCLC, shedding new light on the evolutionary processes underlying this enigmatic subtype.

Interference-induced generation of a chirp-free short isolated attosecond pulse in the water window region with multicolor laser fields.

Compensating for the intrinsic attosecond chirp (atto-chirp) of wideband high-order harmonics in the water window region is a significant challenge, in order to obtain isolated attosecond pulses (IAPs) with a width of tens of attoseconds (as). Here, we propose to realize the generation of IAP with duration as short as 20 as, central energy of 365 eV, and bandwidth exceeding 150 eV from chirp-free high harmonics generated by a four-color driving laser, without the necessity for atto-chirp compensation with natural materials. Unlike any other gating methods that an IAP arises from only one electron ionization event, we take advantage of the interference between harmonic radiation produced by multiple ionizing events. We further demonstrate that such chirp-free short IAP survives after taking account of macroscopic propagation effects. Given that the synthesized multicolor laser field can also effectively increase the harmonic flux, this work provides a practical way for experiments to generate the broad bandwidth chirp-free IAPs in the water window region.

Constructing Cyclic Hydrogen Bonding to Suppress Side Reactions and Dendrite Formation on Zinc Anodes.

The high electrochemical reactivity of H2O molecules and zinc metal results in severe side reactions and dendrite formation on zinc anodes. Here we demonstrate that these issues can be addressed by using N-hydroxymethylacetamide (NHA) as additives in 2 M ZnSO4 electrolytes. The addition of NHA molecules, acting as both a hydrogen bond donor and acceptor, enables the formation of cyclic hydrogen bonding with H2O molecules. This interaction disrupts the existing hydrogen bonding networks between H2O molecules, hindering proton transport, and containing H2O molecules within the cyclic hydrogen bonding structure to prevent deprotonation. Additionally, NHA molecules show a preference for adsorption on the (101) crystal surface of zinc metal. This preferential adsorption reduces the surface energy of the (101) plane, facilitating the homogeneous Zn deposition along the (101) direction. Thus, the NHA enables Zn||Zn symmetric cell with a cycle lifespan of 1100 hours at 5 mA cm-2 and Zn||Cu asymmetric cell with a high Coulombic efficiency over 99.5%. Moreover, the NHA-modified Zn||AC zinc ion hybrid capacitor is capable of sustaining 15000 cycles at 2 A g-1. This electrolyte additive engineering presents a promising strategy to enhance the performance and broaden the application potential of zinc metal-based energy storage devices.

ARID1A deficiency promotes progression and potentiates therapeutic antitumour immunity in hepatitis B virus-related hepatocellular carcinoma.

BACKGROUND: Exploring predictive biomarkers and therapeutic strategies of ICBs has become an urgent need in clinical practice. Increasing evidence has shown that ARID1A deficiency might play a critical role in sculpting tumor environments in various tumors and might be used as pan-cancer biomarkers for immunotherapy outcomes. The current study aims to explored the immune-modulating role of ARID1A deficiency in Hepatitis B virus (HBV) related hepatocellular carcinoma (HBV-HCC) and its potential immunotherapeutic implications. METHODS: In the current study, we performed a comprehensive analysis using bioinformatics approaches and pre-clinical experiments to evaluate the ARID1A regulatory role on the biological behavior, and immune landscape of Hepatitis B virus (HBV) related hepatocellular carcinoma (HBV-HCC). A total of 425 HBV-related hepatocellular carcinoma patients from TCGA-LIHC, AMC and CHCC-HBV cohort were enrolled in bioinformatics analysis. Immunohistochemical staining of HBV-HCC specimens and ARID1A deficiency cellular models were used to validate the results of the analysis. RESULTS: Our results have shown that ARID1A deficiency promoted tumor proliferation and metastasis. More importantly, ARID1A deficiency in HBV-HCC was associated with the higher TMB, elevated immune activity, and up-regulated expression of immune checkpoint proteins, especially TIM-3 in HBV-HCC. Further, the expression of Galectin-9, which is the ligand of TIM-3, was elevated in the ARID1A knockout HBV positive cell line. CONCLUSION: To conclude, we have shown that the ARID1A deficiency was correlated with more active immune signatures and higher expression of immune checkpoints in HBV-HCC. Additionally, the present study provides insights to explore the possibility of the predictive role of ARID1A in HBV-HCC patients responsive to immunotherapy.

Genome-Wide Identification, Expression, and Interaction Analysis of the Auxin Response Factor and AUX/IAA Gene Families in Vaccinium bracteatum.

BACKGROUND: Auxin, a plant hormone, plays diverse roles in the modulation of plant growth and development. The transport and signal transduction of auxin are regulated by various factors involved in shaping plant morphology and responding to external environmental conditions. The auxin signal transduction is primarily governed by the following two gene families: the auxin response factor (ARF) and auxin/indole-3-acetic acid (AUX/IAA). However, a comprehensive genomic analysis involving the expression profiles, structures, and functional features of the ARF and AUX/IAA gene families in Vaccinium bracteatum has not been carried out to date. RESULTS: Through the acquisition of genomic and expression data, coupled with an analysis using online tools, two gene family members were identified. This groundwork provides a distinguishing characterization of the chosen gene families in terms of expression, interaction, and response in the growth and development of plant fruits. In our genome-wide search of the VaARF and VaIAA genes in Vaccinium bracteatum, we identified 26 VaARF and 17 VaIAA genes. We analyzed the sequence and structural characteristics of these VaARF and VaIAA genes. We found that 26 VaARF and 17 VaIAA genes were divided into six subfamilies. Based on protein interaction predictions, VaIAA1 and VaIAA20 were designated core members of VaIAA gene families. Moreover, an analysis of expression patterns showed that 14 ARF genes and 12 IAA genes exhibited significantly varied expressions during fruit development. CONCLUSION: Two key genes, namely, VaIAA1 and VaIAA20, belonging to a gene family, play a potentially crucial role in fruit development through 26 VaARF-IAAs. This study provides a valuable reference for investigating the molecular mechanism of fruit development and lays the foundation for further research on Vaccinium bracteatum.

Rational Design of an In-Situ Polymer-Inorganic Hybrid Solid Electrolyte Interphase for Realising Stable Zn Metal Anode under Harsh Conditions.

The in-depth understanding of the composition-property-performance relationship of solid electrolyte interphase (SEI) is the basis of developing a reliable SEI to stablize the Zn anode-electrolyte interface, but it remains unclear in rechargeable aqueous zinc ion batteries. Herein, a well-designed electrolyte based on 2 M Zn(CF3SO3)2-0.2 M acrylamide-0.2 M ZnSO4 is proposed. A robust polymer (polyacrylamide)-inorganic (Zn4SO4(OH)6.xH2O) hybrid SEI is in situ constructed on Zn anodes through controllable polymerization of acrylamide and coprecipitation of SO4 2- with Zn2+ and OH-. For the first time, the underlying SEI composition-property-performance relationship is systematically investigated and correlated. The results showed that the polymer-inorganic hybrid SEI, which integrates the high modulus of the inorganic component with the high toughness of the polymer ingredient, can realize high reversibility and long-term interfacial stability, even under ultrahigh areal current density and capacity (30 mA cm-2~30 mAh cm-2). The resultant Zn||NH4V4O10 cell also exhibits excellent cycling stability. This work will provide a guidance for the rational design of SEI layers in rechargeable aqueous zinc ion batteries.