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Purpose: Immunotherapy using PD-L1 blockade is effective in only a small group of cancer patients, and resistance is common. This emphasizes the importance of understanding the mechanisms of cancer immune evasion and resistance.A genome-scale CRISPR-Cas9 screen identified Bap1 as a regulator of PD-L1 expression. To measure tumor size and survival, tumor cells were subcutaneously injected into both syngeneic WT mice and immunocompromised mice. The phenotypic and transcriptional characteristics of Bap1-deleted tumors were examined using flow cytometry, RNA-seq, and CUT&Tag-seq analysis.We found that loss of histone deubiquitinase Bap1 in cancer cells activates a cDC1-CD8+ T cell-dependent anti-tumor immunity. The absence of Bap1 leads to an increase in genes associated with anti-tumor immune response and a decrease in genes related to immune evasion. As a result, the tumor microenvironment becomes inflamed, with more cDC1 cells and effector CD8+ T cells, but fewer neutrophils and regulatory T cells. We also found that the elimination of Bap1-deleted tumors depends on the tumor MHCI molecule and Fas-mediated CD8+ T cell cytotoxicity. Our analysis of TCGA data further supports these findings, showing a reverse correlation between BAP1 expression and mRNA signatures of activated DCs and T-cell cytotoxicity in various human cancers.The histone deubiquitinase Bap1 could be used as a biomarker for tumor stratification and as a potential therapeutic target for cancer immunotherapies.Methods: Immunotherapy using PD-L1 blockade is effective in only a small group of cancer patients, and resistance is common. This emphasizes the importance of understanding the mechanisms of cancer immune evasion and resistance.A genome-scale CRISPR-Cas9 screen identified Bap1 as a regulator of PD-L1 expression. To measure tumor size and survival, tumor cells were subcutaneously injected into both syngeneic WT mice and immunocompromised mice. The phenotypic and transcriptional characteristics of Bap1-deleted tumors were examined using flow cytometry, RNA-seq, and CUT&Tag-seq analysis.We found that loss of histone deubiquitinase Bap1 in cancer cells activates a cDC1-CD8+ T cell-dependent anti-tumor immunity. The absence of Bap1 leads to an increase in genes associated with anti-tumor immune response and a decrease in genes related to immune evasion. As a result, the tumor microenvironment becomes inflamed, with more cDC1 cells and effector CD8+ T cells, but fewer neutrophils and regulatory T cells. We also found that the elimination of Bap1-deleted tumors depends on the tumor MHCI molecule and Fas-mediated CD8+ T cell cytotoxicity. Our analysis of TCGA data further supports these findings, showing a reverse correlation between BAP1 expression and mRNA signatures of activated DCs and T-cell cytotoxicity in various human cancers.The histone deubiquitinase Bap1 could be used as a biomarker for tumor stratification and as a potential therapeutic target for cancer immunotherapies.Results: Immunotherapy using PD-L1 blockade is effective in only a small group of cancer patients, and resistance is common. This emphasizes the importance of understanding the mechanisms of cancer immune evasion and resistance.A genome-scale CRISPR-Cas9 screen identified Bap1 as a regulator of PD-L1 expression. To measure tumor size and survival, tumor cells were subcutaneously injected into both syngeneic WT mice and immunocompromised mice. The phenotypic and transcriptional characteristics of Bap1-deleted tumors were examined using flow cytometry, RNA-seq, and CUT&Tag-seq analysis.We found that loss of histone deubiquitinase Bap1 in cancer cells activates a cDC1-CD8+ T cell-dependent anti-tumor immunity. The absence of Bap1 leads to an increase in genes associated with anti-tumor immune response and a decrease in genes related to immune evasion. As a result, the tumor microenvironment becomes inflamed, with more cDC1 cells and effector CD8+ T cells, but fewer neutrophils and regulatory T cells. We also found that the elimination of Bap1-deleted tumors depends on the tumor MHCI molecule and Fas-mediated CD8+ T cell cytotoxicity. Our analysis of TCGA data further supports these findings, showing a reverse correlation between BAP1 expression and mRNA signatures of activated DCs and T-cell cytotoxicity in various human cancers.The histone deubiquitinase Bap1 could be used as a biomarker for tumor stratification and as a potential therapeutic target for cancer immunotherapies.Conclusion: Immunotherapy using PD-L1 blockade is effective in only a small group of cancer patients, and resistance is common. This emphasizes the importance of understanding the mechanisms of cancer immune evasion and resistance.A genome-scale CRISPR-Cas9 screen identified Bap1 as a regulator of PD-L1 expression. To measure tumor size and survival, tumor cells were subcutaneously injected into both syngeneic WT mice and immunocompromised mice. The phenotypic and transcriptional characteristics of Bap1-deleted tumors were examined using flow cytometry, RNA-seq, and CUT&Tag-seq analysis.We found that loss of histone deubiquitinase Bap1 in cancer cells activates a cDC1-CD8+ T cell-dependent anti-tumor immunity. The absence of Bap1 leads to an increase in genes associated with anti-tumor immune response and a decrease in genes related to immune evasion. As a result, the tumor microenvironment becomes inflamed, with more cDC1 cells and effector CD8+ T cells, but fewer neutrophils and regulatory T cells. We also found that the elimination of Bap1-deleted tumors depends on the tumor MHCI molecule and Fas-mediated CD8+ T cell cytotoxicity. Our analysis of TCGA data further supports these findings, showing a reverse correlation between BAP1 expression and mRNA signatures of activated DCs and T-cell cytotoxicity in various human cancers.The histone deubiquitinase Bap1 could be used as a biomarker for tumor stratification and as a potential therapeutic target for cancer immunotherapies. [ABSTRACT FROM AUTHOR]

Background: B1 cells are self-renewing innate-like B lymphocytes that provide the first line of defense against pathogens. B1 cells primarily reside in the peritoneal cavity and are known to originate from various fetal tissues, yet their developmental pathways and the mechanisms underlying maintenance of B1 cells throughout adulthood remain unclear. Results: We performed high-throughput single-cell analysis of the transcriptomes and B-cell receptor repertoires of peritoneal B cells of neonates, young adults, and elderly mice. Gene expression analysis of 31,718 peritoneal B cells showed that the neonate peritoneal cavity contained many B1 progenitors, and neonate B cell specific clustering revealed two trajectories of peritoneal B1 cell development, including pre-BCR dependent and pre-BCR independent pathways. We also detected profound age-related changes in B1 cell transcriptomes: clear difference in senescence genetic program was evident in differentially aged B1 cells, and we found an example that a B1 subset only present in the oldest mice was marked by expression of the fatty-acid receptor CD36. We also performed antibody gene sequencing of 15,967 peritoneal B cells from the three age groups and discovered that B1 cell aging was associated with clonal expansion and two B1 cell clones expanded in the aged mice had the same CDR-H3 sequence (AGDYDGYWYFDV) as a pathogenically linked cell type from a recent study of an atherosclerosis mouse model. Conclusions: Beyond offering an unprecedent data resource to explore the cell-to-cell variation in B cells, our study has revealed that B1 precursor subsets are present in the neonate peritoneal cavity and dissected the developmental pathway of the precursor cells. Besides, this study has found the expression of CD36 on the B1 cells in the aged mice. And the single-cell B-cell receptor sequencing reveals B1 cell aging is associated with clonal expansion. [ABSTRACT FROM AUTHOR]

Several single-cell RNA sequencing (scRNA-seq) studies analyzing immune response to COVID-19 infection have been recently published. Most of these studies have small sample sizes, which limits the conclusions that can be made with high confidence. By re-analyzing these data in a standardized manner, we validated 8 of the 20 published results across multiple datasets. In particular, we found a consistent decrease in T-cells with increasing COVID-19 infection severity, upregulation of type I Interferon signal pathways, presence of expanded B-cell clones in COVID-19 patients but no consistent trend in T-cell clonal expansion. Overall, our results show that the conclusions drawn from scRNA-seq data analysis of small cohorts of COVID-19 patients need to be treated with some caution. [ABSTRACT FROM AUTHOR]

• A series of MoO 3 -ZrO 2 solid acid catalysts were obtained for acetalization of glycerol. • The Mo species existed as highly dispersed state in MoO 3 -ZrO 2 materials. • The formation of Brønsted and Lewis acid sites was confirmed by the DFT calculations. • The 20 %-MoO 3 -ZrO 2 catalyst exhibited the optimal catalytic performance. • The MoO 3 -ZrO 2 catalyst showed excellent universality and reusability in acetalization reaction. Glycerol acetalization to solketal is a promising method of increasing the additional value of glycerol, which is a by-product in biodiesel industry. In this work, a series of mesoporous x-MoO 3 -ZrO 2 (x = Mo/Zr) solid acid catalysts with controllable Mo contents were designed and synthesized for the acetalization of glycerol. As important influence factors of solid acid catalysts, the mesoporous structure and existential state of Mo species were systematically investigated. Results show that Mo species were introduced as planned and existed in a homogeneously dispersed state in MoO 3 -ZrO 2 materials. The acidic properties of MoO 3 -ZrO 2 were explored through NH 3 -TPD and pyridine-chemisorbed FT-IR spectroscopy, and the formation of Brønsted and Lewis acid sites was confirmed by density functional theory calculations. Given their excellent acidity, MoO 3 -ZrO 2 catalysts were employed for the acetal reaction of glycerol. Among the tested catalysts, the 20 %-MoO 3 -ZrO 2 catalyst exhibited the optimal catalytic performance and reusability, achieving a conversion of 89 % for glycerol and a selectivity of 97 % for solketal. Consequently, MoO 3 -ZrO 2 is a green solid acid catalyst with promising applications in solvent-free solketal production from glycerol. [Display omitted] [ABSTRACT FROM AUTHOR]

Three-Dimensional graphene (3D-G) material is regarded as an excellent carbon material, which reveals cross-linked porous structure, high specific surface area, strong mechanical strength and high conductivity inheriting from the graphene. In this work, we fabricate the novel 3D-G based materials by decoration of sodium citrate (SC) for supercapacitor and lithium ion batteries (LIBs) applications. SC with abundant functional groups and short carbon chain can ensure the interface between graphene sheets or between graphene and other composite materials, lead to shorter diffusion path for ions transportation. Owing to the large surface area and pore volume, 3D-G (SC) shows outstanding specific capacitance (301 F g −1 ) when it is applied in supercapacitors. Besides that, 3D-G (SC) compounds with Fe 3 O 4 particles and 3D-G@Fe 3 O 4 (SC) are applied in LIBs. The 3D-G@Fe 3 O 4 (SC) has a higher discharge capacity (1310.6 mAh g −1 ) than 3D-G@Fe 3 O 4 (1270 mAh g −1 ) at 0.1 C, and it even increase to an excellent capacity (1550 mAh g −1 ) after 100 cycles. Moreover, 3D-G@Fe 3 O 4 (SC) shows excellent cycling stability that specific capacity retains 1031 mAh g −1 after 1000 cycles. This work may extend a novel approach to prepare 3D-G electrode material for efficient storage devices. [ABSTRACT FROM AUTHOR]

[Display omitted] • The Ni@NCNT-C catalysts with controlled Ni content and annealing temperature are obtained. • The 0.1Ni@NCNT-C-800 exhibits high activity and stability in CO 2 reduction. • The catalyst owns a low overpotential (−0.27 V vs. RHE) and high FE CO % (∼100%). • The CO partial current density can reach 230 mA cm−2 and the activity can be maintained over 40 h. • A broad potential range of 900 mV is obtained under high FE CO % (∼100%). The electrochemical CO 2 reduction reaction (CO 2 RR) to CO is regarded as a potential way to relieve CO 2 level and produce value-added chemicals. However, most reported catalysts only possess high Faraday efficiency of CO (FE CO %) under a narrow potential range, and this shortage largely limits its ultimate practical viability. Herein, we develop a facile method to synthesize nickel encased by nitrogen-doped carbon nanotubes on carbon support (Ni@NCNT-C) catalyst for CO 2 RR. As for the important influence factors, the Ni content and treatment temperature are carefully controlled, and their influence on textural property and catalytic performance is investigated. The 0.1Ni@NCNT-C-800 catalyst provides a low overpotential (−0.27 V vs. RHE) and high FE CO % (∼100%). The CO partial current density can reach 230 mA cm−2 and the activity can be maintained over 40 h. More importantly, a wide potential range of 900 mV (−0.27 V to − 1.17 V vs. RHE) can be obtained when FE CO % is continuously maintained at nearly 100%. This work may provide a route to seek a robust catalyst for high-efficiency CO 2 RR over a wide potential range. [ABSTRACT FROM AUTHOR]

A series of functional ionic liquid supported silica nanoparticles with different acidity (ILs/SiO 2 ) have been prepared by covalent bonds using novel, non-toxic ethanol as solvent. Compared with using toluene or acetonitrile as solvent in traditional prepared method, the process represents a green, environmental friendly route to synthesize supported functional ionic liquid catalysts (SFILCs). These SFILCs, with the benefits of ionic liquid and the advantages of immobilization, were first systematically utilized in biomass dehydration reactions and proved to be efficient heterogeneous catalysts for the preparation of furan derivatives from various carbohydrates. However, the supported dual acidic functional ionic liquid catalyst (3-sulfobutyl-1-(3-propyltriethoxysilane) imidazolium hydrogen sulfate) was found to be more active and selective than other ILs/SiO 2 and the conversion of fructose, glucose, xylose, sucrose, cellobiose was up to 99, 96, 94, 76 and 99%. Moreover, the reducing sugar (TRS) yield of microcrystalline cellulose dehydration was up to 77%. [ABSTRACT FROM AUTHOR]

The electrochemical CO 2 reduction reaction (CO 2 RR) that transforms CO 2 to CO has attracted great interest. Transition metal nanoparticles encapsulated in nitrogen-doped carbon (M@NC) catalysts exhibit outstanding catalytic performance. However, the role of metal and N species in M@NC catalysts remains unclear. In this work, Co@C, Co@NC, Ni@C, and Ni@NC catalysts were achieved and employed in CO 2 RR. The Ni@NC catalyst exhibits an industry level current density of 220 mA cm−2 and a high Faradaic efficiency of 98% for CO production at − 0.87 V vs. RHE for 100 h. In addition, the N species, especially the pyrrolic-N in the shell of Ni@NC material provide active sites for adsorbing and activating CO 2 molecules, and metal nanoparticles improve the electronic structure of N species, thereby decreasing their ability for radical attack (*COOH, *CO, and *H). Consequently, this work can guide the design of M@NC catalyst for CO 2 RR to CO. [Display omitted] • Different kinds of metal nanoparticles encapsulated within carbon shells are achieved. • The Ni@NC catalyst exhibits a large current density of 220 mA cm–2 and a high FE CO % of 98%. • The Ni@NC catalyst has excellent stability in CO 2 RR. • The pyrrolic-N in the shell of Ni@NC material provides active sites for CO 2 molecules. • The decrease of adsorption for radical attack (*COOH, *CO, and *H) improves the catalytic performance of CO 2 RR. [ABSTRACT FROM AUTHOR]

• MCr–LDH/BiOBr nanocomposites were prepared via a rapid crystallization method at room temperature. • BiOBr nanoparticles combined with MCr–LDH flakes to fabricate heterojunctions. • Electrons transfer from LDHs to BiOBr. • The adsorption properties for pollutants, separation and transition of photogenerated carriers are improved effectively. • The composites showed enhanced photocatalytic degradation efficiencies of all RhB, MO, and BPA. [Display omitted] The removal of low concentration pollutants in water is very important for environmental remediation. Herein, MCr–LDHs/BiOBr (M = Zn, Ni, Cu) heterojunction nanocomposites were fabricated by a facile rapid crystallization method. Visible-light responsive heterojunctions could be formed efficiently at the intimately contacted interface between BiOBr nano-crystallites and LDHs nano-flakes, which showed higher photocatalytic degradation activities of cationic, anionic, and electrically neutral organic pollutants than pristine LDHs and BiOBr. Degradation of 99.5% Rhodamine B, 80% methyl orange, and 97% bisphenol A could be achieved by the composite catalysts under visible-light irradiation in 15 min, 60 min, and 40 min, respectively, and cycling test proved the good reusability of composite catalysts as well. Benefitting from superior adsorption properties for ionic organic pollutants, and effective separation and transition of photogenerated holes and electrons, the MCr–LDH/BiOBr composite catalysts exhibit wide applicability for removal of various organic pollutants in water and have potential application prospects in the future. [ABSTRACT FROM AUTHOR]

[Display omitted] • A series of Ni/SiO 2 catalysts were prepared with different nickel salt precursors. • The intermediates of calcination process studied by in-situ DRIFTS and online TG-MS. • The catalyst with nickel acetylacetonate precursor performed the highest activity. • The precursor influenced the Ni dispersion and strength of metal-support interaction. • The precursor determined the reaction pathway and apparent activation energy. In this work, a series of Ni-based CO 2 methanation catalysts were prepared with different nickel salt precursors. The Ni-AA catalyst with nickel acetylacetonate precursor displayed the highest activity among these catalysts. The in-situ diffused reflectance infrared Fourier transform spectroscopy (in-situ DRIFTS) and the online-tandem thermogravimetric mass spectrometry (TG-MS) were performed to investigate the intermediates of the catalyst calcination process. The superior performance of the Ni-AA catalyst could be derived from its special coordinating anion. Furthermore, the rapid deactivation of the Ni-S catalyst with nickel sulfate precursor was attributed to the generation of the Ni 3 S 2 after reduction pretreatment. As for the Ni-Cl catalyst with nickel chloride precursor, its negligible activity could be owing to poisoning effect of the Cl− by the coverage of the catalyst surface. Therefore, the significant role of the metal salt precursor should be preferentially considered when designing the Ni-based catalysts and even other metal based heterogeneous catalysts. [ABSTRACT FROM AUTHOR]

[Display omitted] • Novel 3D hierarchical P2-Na 0.8 Mn 0.6 Ni 0.2 Cu 0.1 Mg 0.1 O 2 is designed and prepared. • P2-Na 0.8 Mn 0.6 Ni 0.2 Cu 0.1 Mg 0.1 O 2 exhibits water/air stability. • Na-storage reaction mechanisms of P2-Na 0.8 Mn 0.6 Ni 0.2 Cu 0.1 Mg 0.1 O 2 are explored. • P2–O2 phase transition is postponed up to 4.2 V in P2-Na 0.8 Mn 0.6 Ni 0.2 Cu 0.1 Mg 0.1 O 2. • P2-Na 0.8 Mn 0.6 Ni 0.2 Cu 0.1 Mg 0.1 O 2 exhibits cycling stability under high voltage. P2-Na x MnO 2 are promising cathodes for sodium-ion batteries (SIBs) owing to their high specific capacities and fast 2D Na+ diffusion path. However, the poor storage stability, irreversible phase transition, and ultrahigh initial Coulombic efficiency (ICE) hinder their full-cells application. Herein, composition designing and structure engineering is combined to tackle these handicaps. A novel Ni2+/Cu2+/Mg2+ co-doped P2-Na 0.8 Mn 0.6 Ni 0.2 Cu 0.1 Mg 0.1 O 2 (P2-NaMNCuMg) with 3D hierarchical structure is designed and synthesized. The divalent Ni2+/Cu2+/Mg2+ co-doping could postpone P2-O2 phase transition up to 4.2 V and restrain the Jahn-Teller effect of Mn3+, and the Ni2+ and Cu2+ can participate in the redox reaction process for charge compensation. The 3D hierarchical structure is conducive to enhancing structural stability and Na+ transfer rate. Benefiting from the co-doping elements and well-designed 3D hierarchical structure, the P2-NaMNCuMg exhibits good water/air stability and delivers a reversible capacity of 160.8 mAh g−1 with ICE of 113.8% at 20 mA g−1 and prolonged cycling stability of 82.9% capacity retention over 500 cycles at 500 mA g−1. Moreover, the full-cells based on P2-NaMNCuMg cathode achieve a power density of 1221.5 W kg−1 at 500 mA g−1 in 1.5–4.2 V, demonstrating the potential of P2-NaMNCuMg as high-performance cathode for high-voltage SIBs. [ABSTRACT FROM AUTHOR]

A hierarchically porous carbon (HPC) is prepared via a facile hard-templating method using silica as a template, which is thoroughly removed by an in-situ polytetrafluoroethylene (PTFE) pyrolytic process without further post treatment. The Brunauer-Emmett-Teller specific surface area for HPC can reach up to 664 m2 g−1. The usage of PTFE and carbon precursor (glucosamine) lead to F, N co-doping on HPC. Electrochemical measurements show that HPC possesses a much higher specific capacitance (1161 F g−1) in a KI-additive electrolyte (H 2 SO 4 + KI) than that (183 F g−1) in H 2 SO 4 electrolyte due to the presence of oxidation states of I species such as IO 3 ˉ and I 3 ˉ, as confirmed by X-ray photoelectron spectroscopy (XPS), which can bring about superior pseudocapacitance by redox reaction. Furthermore, the operation voltage for the symmetric supercapacitor assembled by the as-prepared HPC can reach up to a much higher value of 1.7 V in KI-additive electrolyte compared with that in H 2 SO 4 electrolyte. Marrying high operation voltage and high specific capacitance, the assembled supercapacitor can deliver a high energy density of 78.8 Wh kg−1 under a high-power output of 680 W kg−1. Image, graphical abstract [ABSTRACT FROM AUTHOR]

Three-dimensional graphene-wrapped Co 0.85 Se@C hybrids with high volumetric capacities are prepared as anode materials for lithium-ion batteries. • A novel three-dimensional graphene-wrapped Co 0.85 Se@C composite is synthesized. • C-O-Co is formed from reactions between the Co 0.85 Se@C and oxygen-containing groups. • The specific capacity of GCS reaches to 1022.5 mAh g−1 after 200 cycles at 0.1 A g−1. • The anode electrode exhibits good long-cycling durability and rate performance. To overcome the drawbacks of poor long-term cyclic and large volume expansion for selenides, which have high theoretical specific capacity and are promising candidates to fulfill the requirement of high volumetric energy density for lithium-ion batteries, we prepared a novel three-dimensional graphene-wrapped Co 0.85 Se@C composite (3D-G@Co 0.85 Se@C) through a capillary evaporation-induced drying method. This process leads to a shrinkage of graphene assembly, generating an ideal configuration compact composite material. XPS analysis confirms that the C-O-Co is formed from reactions between the Co 0.85 Se@C and oxygen-containing groups on graphene oxide during the preparation process. Such a strong covalent interaction between the Co 0.85 Se@C and graphene, together with its compact structure are favorable to high volumetric capacity. The electrochemical measurements show that the specific capacity of the GCS is about 1022.5 mAh g−1 after 200 cycles at 0.1 A g−1, corresponding to a remarkably reversible volumetric capacity of 2096.1 mAh cm−3. Moreover, good long-cycling durability and rate performance are also achieved. Consequently, this composite is a promising electrode material with high volumetric capacity in lithium-ion batteries. [ABSTRACT FROM AUTHOR]

• Mesoporous Ce-Zr solid solution supported Ni based catalysts for CO 2 methanation. • The molar ratio of Ce/Zr greatly affected the low-temperature catalytic activity. • The redox property of the support promoted the low-temperature catalytic activity. • The redox property of the support changed the reaction routes by tuning intermediates. • Apparent activation energy could be decreased by employing redox catalytic support. We facilely fabricated the mesoporous Ce-Zr solid solutions (Ce/Zr molar ratio = 0–100%) with excellent textural properties and employed them as the supports of the Ni-based catalysts for CO 2 methanation. These supported catalysts were systematically measured by various techniques, such as X-ray diffraction (XRD), N 2 physisorption, transmission electron microscope (TEM), selective area electron diffraction (SAED), X-ray photoelectron spectroscopy (XPS), H 2 temperature-programmed reduction (H 2 -TPR), CO 2 temperature-programmed desorption (CO 2 -TPD), etc. In this catalytic system, the influencing factors of the supports on the promotion of the low-temperature catalytic performances toward CO 2 methanation were carefully investigated. Besides, temperature-programmed surface reaction (TPSR) and in-situ diffused reflectance infrared Fourier transform spectroscopy (DRIFTS) of the CO 2 methanation were also carried out to investigate the reaction mechanism and the possible reaction intermediates. The kinetic study were also conducted to investigate the apparent activation energies of the CO 2 methanation over these Ni-based catalysts with different supports. The influencing factors on the stabilization of the metallic Ni active sites were also investigated by conducting the 40 h stability test over the 15Ni/M-Ce80Zr20 and 15Ni/SiO 2 catalysts. It was found that the Ni-based catalysts supported on the mesoporous Ce-Zr solid solutions were provided with advanced low-temperature activity owing to the redox property of the support, which could tune the reaction intermediates and decrease the apparent activation energy during the CO 2 methanation. [ABSTRACT FROM AUTHOR]

With the further expansion of the fossil crisis and the increasing demand for biodiesel, it is imperative to develop highly reusable catalysts. Therefore, in this study, the completed synthesis of MgO/ZSM-5 catalysts via impregnation and ultrasonic dispersion methods were achieved to be applied in the clean production from Spirulina platensis- derived biodiesel. Physiochemical analyses including thermogravimetry (TG), temperature programmed desorption of CO 2 (CO 2 -TPD), X-ray diffraction (XRD), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS), Fourier transform infrared spectroscopy (FTIR) and Brunauer–Emmett–Teller surface area (BET) were used to define the basicity, structure, composition and morphology of synthesized catalysts. The optimum process conditions obtained by Taguchi method were as follows, the molar ratio of ethanol to oil was 15/1, the catalyst concentration was 3 wt%, and the yield of biodiesel reached 92.1% after 1 h reaction at 75 °C. The optimal catalyst had strong stability and catalytic activity in the repeated cycle test, even after five cycles, the yield of biodiesel was still above 85%. The transesterification of Spirulina oil catalyzed by MgO/ZSM-5 catalyst accorded with the pseudo-first-order kinetics, and the activation energy was 49.67 kJ/mol. Finally, the economic feasibility analysis of biodiesel illustrated that the new supported catalyst can effectively reduce the cost of production and provide favorable support for the future continuously industrial production. Image 1 • The cavitation of ultrasonic enhanced the dispersion of MgO over ZSM-5 zeolite. • The S–MgO/ZSM-5-650 catalyst was used to produce Spirulina -derived biodiesel. • The optimized catalyst had superior stability and catalytic activity. • High yield of 92.1% was achieved under optimum reaction conditions. • The results approved the kinetics of the reaction fit a pseudo-first-order model. [ABSTRACT FROM AUTHOR]

[Display omitted] • A strategy for low-temperature fabrication of K 2 O supported mesoporous ZrO 2 was developed. • The carbon species was preserved in the synthesis process of mesoporous zirconia. • The carbon species greatly reduced conversion temperature of KNO 3 to K 2 O on mesoporous ZrO 2. • The mesoporous and phase structure of the zirconia support was well stabilized by carbon species. • K 2 O supported mesoporous ZrO 2 exhibited good activity in transesterification reaction. In the present work, a new strategy was developed to fabricate strong basicity on mesoporous zirconia by in-situ preservation of carbon species originated from organic template during the thermal treatment of mesoporous ZrO 2. The carbon species was maintained on mesoporous zirconia by calcination in N 2 prior to the introduction of base precursor KNO 3. The decomposition temperature of KNO 3 to strongly basic site K 2 O was significantly reduced from higher than 650℃ to about 400℃ in the presence of carbon species, which fascinatingly converted the endothermic decomposition reaction to exothermic process. More importantly, the tetragonal ZrO 2 support with excellent mesostructure was well stabilized by the carbon species after introduction of K species. Therefore, K 2 O supported on mesoporous tetragonal zirconia (K 2 O/M-ZrO 2 -C) were successfully fabricated. The resultant mesoporous basic material presented good activity in the synthesis of dimethyl carbonate (DMC) and the DMC yield was 60.0 %, apparently higher than that (18.1 %) of the catalyst prepared without preserving carbon species (K 2 O/M-ZrO 2). The strong basicity and the uniform mesopores of the catalyst were suggested to be contributed to the high activity. The obtained results will provide some fundamental understanding and guidance for rational catalyst design. [ABSTRACT FROM AUTHOR]

• Fibrous silica nanosphere (KCC-1) is prepared by improved microemulsion strategy. • KCC-1 has large surface area and multi-dimensional dendrimeric mesoporous channel. • Highly dispersed Ni obtained over KCC-1 due to good accessibility of surface area. • Ni/KCC-1 performs excellent low-temperature catalytic activity of CO 2 methanation. • TPSR and in-situ DRIFTS of CO 2 methanation reveal reaction kinetics and mechanism. In this work, we reported that the fibrous silica nanosphere, also called as KCC-1, was facilely synthesized by the improved microemulsion hydrothermal fabrication strategy. The obtained KCC-1 was investigated as the support of the Ni based catalysts toward CO 2 methanation. The obtained catalysts with unique dendrimeric mesopore structure and outstanding structural properties could provide easily accessible as well as highly dispersed Ni nanoparticles to the gaseous reactants. Besides, the Ni based catalysts with commercial SiO 2 and MCM-41 as supports were also prepared as the reference catalysts to demonstrate the advantages of the dendrimeric mesoporous channels. Various techniques, such as X-ray powder diffraction (XRD), N 2 physisorption, transmission electron microscopy (TEM), H 2 temperature programmed reduction (H 2 -TPR), CO 2 temperature programmed desorption (CO 2 -TPD), X-ray photoelectron spectroscopy (XPS), etc., were used to characterize the catalytic supports and corresponding catalysts. It was found that the metallic Ni nanoparticles could be highly dispersed over the catalysts supported on fibrous KCC-1 with dendrimeric mesoporous channels. Furthermore, the catalytic performances toward CO 2 methanation had been further evaluated over these catalysts at different temperatures. It was found that the KCC-1 supported catalyst performed much higher low-temperature catalytic activities than the reference catalysts supported on commercial SiO 2 and MCM-41, suggesting that the fibrous and dendrimeric mesoporous channels displayed distinctive advantages by accommodating enough metallic Ni active sites. The kinetic study also revealed that the topology of the mesoporous channel could obviously influence the apparent activation energy in the CO 2 methanation reaction. Besides, the temperature programmed surface reaction (TPSR) and in-situ Diffused Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) of the CO 2 methanation were also carried out to reveal the possible reaction pathway and mechanism. We also found that the fibrous silica nanosphere (KCC-1) supported catalyst demonstrated much better sintering-proof property of the metallic Ni nanoparticles than the reference catalysts during the 40 h stability tests at 400 °C. Therefore, the present fibrous silica nanosphere (KCC-1) could be considered as the promising support for Ni based catalysts toward CO 2 methanation. [ABSTRACT FROM AUTHOR]

Engineering graphene with efficient ion and electron transport properties is vital for development of high performance, next generation energy storage devices. The protocols generally involve pore generation and doping of graphene with the heteroatoms. Herein we report the realization of pore generation, control, and N-doping of graphene in one single process using reduced metal salt as etching agent and environment friendly N 2 gas as doping agent. Furthermore, we found the porous structure (pore size and density), the dopant bonding configuration and doping amount can be controlled by change the metal salt and nitrogen source, which allows us to investigate the influence of pore and N-doping structure of porous graphene (PG) in their supercapacitor performance. Specifically, the N-doping, PG prepared by Ni salt (PG-Ni) shows the smaller pore size (average pore size of ~20–30 nm) and larger pore density. PG-Ni exhibits high specific capacitance of 575 F/g along with the energy density of 51.2 Wh/kg at 0.5 A/g current density and also shows good rate, cycling performances. Considering the excellent performance, ease of the process, and pore structure controllability, we believe the method provides a new route for developing graphene based high performance supercapacitors. Unlabelled Image • Pore generation, control, and N-doping of graphene in one single process • N atom doped by using N 2 as doping agent • N-doping configuration and porous structure can be controlled • Remarkable enhancement of supercapacitor permeance of N-doping porous graphene [ABSTRACT FROM AUTHOR]

The Ni-based catalysts were widely investigated as the catalysts toward CO 2 methanation reaction because of their availabilities. However, compared with the noble metal based catalysts, the design and exploitation of Ni-based catalysts with outstanding low-temperature catalytic activities is still a big challenge. In order to solve this problem, the highly dispersed Ni catalysts had been facilely prepared by employing the basic amine functionalized mesoporous MFI nanosponge zeolite as the support. The functionalized amine group could induce the precisely regioselective precipitation of the Ni precursor in the mesoporous channels and the highly dispersed Ni nanoparticles were obtained. Besides, the La 2 O 3 and MgO had been used to modify the surface basicity to further promote the low-temperature catalytic activities of the Ni-based catalysts. These catalysts were systematically measured by XRD, N 2 physisorption, STEM, XPS, H 2 -TPR, and CO 2 -TPD. It was observed that the metallic Ni nanoparticles were homogenously distributed among the mesoporous channels. Furthermore, the La 2 O 3 and MgO modification could obviously promote the surface basicity of the catalysts, which intensified the CO 2 adsorption and activation. Thus, their apparent activation energies of CO 2 methanation evidently decreased and their low-temperature activities were greatly promoted. Besides, it was also found that the thermal agglomeration of the Ni nanoparticles could be successfully inhibited via the confinement effect of the amine functionalized mesoporous channels, interpreting their excellent catalytic stabilities toward CO 2 methanation. The highly dispersed Ni catalysts could be facilely prepared by employing the basic amine functionalized mesoporous zeolite as the catalytic support, which could precisely control the regioselective precipitation of the Ni precursor. The La 2 O 3 and MgO could promote the low-temperature catalytic activities of the Ni based catalysts by modifying the surface basicity. Image 1 • Highly dispersed Ni catalysts prepared by employing the amine functionalized support. • The basic amine group induced the regioselective precipitation of the Ni precursor. • The high Ni dispersion and basic modification promoted the low-temperature activity. • The apparent activation energy of CO 2 methanation were greatly decreased. • Thermal sintering of the Ni inhibited by the confinement effect of the mesopore. [ABSTRACT FROM AUTHOR]

RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches. We describe automatic assessment protocols for comparisons between prediction and experiment. Our analyses reveal some critical steps to be overcome to achieve good accuracy in modeling RNA structures: identification of helix-forming pairs and of non-Watson-Crick modules, correct coaxial stacking between helices and avoidance of entanglements. Three of the top four modeling groups in this round also ranked among the top four in the CASP15 contest., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Introduction: This study aimed to investigate the virome diversity of the SLE disease and the association between viral infections and the disease., Methods: SLE-related RNA-Seq data were retrieved from public databases. A rigorous computational workflow was employed to identify the human viruses. Differential expression analysis and functional enrichment analysis were conducted in R., Results: We identified ten human virus species from 826 RNA-Seq samples of human blood, comprising 688 SLE patients and 138 healthy controls. Eight of the ten virus species exhibited higher positive rates in SLE patients compared to healthy controls, with Human betaherpesvirus 5 (HHV5) having the highest positive rate (4.1%) and being exclusively detected in SLE samples. The virus abundances were low and comparable in both SLE patients and healthy controls. Analysis of the antiviral interferon-stimulated genes (ISGs) in samples showed higher ISG expression levels in HHV4 and HHV5-positive samples compared to virus-negative samples. Several genes that were up-regulated in SLE patients were further up-regulated after HHV5 infection, and they were mainly enriched in immune response-related biological processes. Additionally, the expression levels of several marker genes of SLE severity were compared between HHV5-positive and virus-negative SLE patients, suggesting that HHV5 infection may be associated with aggravated SLE disease., Discussion: We found that SLE patients are more susceptible to viral infections than healthy individuals. Viral infections, such as HHV5, may be associated with aggravated SLE disease. This study deepens our understanding of the association between viruses and SLE and provides new insights into prevention and control of the disease., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The authors declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Wu, Zhang, Wang, Liu, Qiu, Ge, Miao, Meng and Peng.)

Inositol 1,4,5-trisphosphate (IP3) receptor type 1 ( ITPR1 ), 2 ( ITPR2 ), and 3 ( ITPR3 ) encode the IP3 receptor (IP3R), a key player in intracellular calcium release. In four unrelated patients, we report that an identical ITPR3 de novo variant-NM_002224.3:c.7570C>T, p.Arg2524Cys-causes, through a dominant-negative effect, a complex multisystemic disorder with immunodeficiency. This leads to defective calcium homeostasis, mitochondrial malfunction, CD4 + lymphopenia, a quasi-absence of naïve CD4 + and CD8 + cells, an increase in memory cells, and a distinct TCR repertoire. The calcium defect was recapitulated in Jurkat knock-in. Site-directed mutagenesis displayed the exquisite sensitivity of Arg 2524 to any amino acid change. Despite the fact that all patients had severe immunodeficiency, they also displayed variable multisystemic involvements, including ectodermal dysplasia, Charcot-Marie-Tooth disease, short stature, and bone marrow failure. In conclusion, unlike previously reported ITPR1-3 deficiencies leading to narrow, mainly neurological phenotypes, a recurrent dominant ITPR3 variant leads to a multisystemic disease, defining a unique role for IP3R3 in the tetrameric IP3R complex.

While single-cell technologies have greatly advanced our comprehension of human brain cell types and functions, studies including large numbers of donors and multiple brain regions are needed to extend our understanding of brain cell heterogeneity. Integrating atlas-level single-cell data presents a chance to reveal rare cell types and cellular heterogeneity across brain regions. Here we present the Brain Cell Atlas, a comprehensive reference atlas of brain cells, by assembling single-cell data from 70 human and 103 mouse studies of the brain throughout major developmental stages across brain regions, covering over 26.3 million cells or nuclei from both healthy and diseased tissues. Using machine-learning based algorithms, the Brain Cell Atlas provides a consensus cell type annotation, and it showcases the identification of putative neural progenitor cells and a cell subpopulation of PCDH9 high microglia in the human brain. We demonstrate the gene regulatory difference of PCDH9 high microglia between hippocampus and prefrontal cortex and elucidate the cell-cell communication network. The Brain Cell Atlas presents an atlas-level integrative resource for comparing brain cells in different environments and conditions within the Human Cell Atlas., (© 2024. The Author(s).)

The three-dimensional genome structure organized by CTCF is required for development. Clinically identified mutations in CTCF have been linked to adverse developmental outcomes. Nevertheless, the underlying mechanism remains elusive. In this investigation, we explore the regulatory roles of a clinically relevant R567W point mutation, located within the 11 th zinc finger of CTCF, by introducing this mutation into both murine models and human embryonic stem cell-derived cortical organoid models. Mice with homozygous CTCF R567W mutation exhibit growth impediments, resulting in postnatal mortality, and deviations in brain, heart, and lung development at the pathological and single-cell transcriptome levels. This mutation induces premature stem-like cell exhaustion, accelerates the maturation of GABAergic neurons, and disrupts neurodevelopmental and synaptic pathways. Additionally, it specifically hinders CTCF binding to peripheral motifs upstream to the core consensus site, causing alterations in local chromatin structure and gene expression, particularly at the clustered protocadherin locus. Comparative analysis using human cortical organoids mirrors the consequences induced by this mutation. In summary, this study elucidates the influence of the CTCF R567W mutation on human neurodevelopmental disorders, paving the way for potential therapeutic interventions., (© 2024. The Author(s).)

Primary microcephaly is a rare neurogenic and genetically heterogeneous disorder characterized by significant brain size reduction that results in numerous neurodevelopmental disorders (NDD) problems, including mild to severe intellectual disability (ID), global developmental delay (GDD), seizures and other congenital malformations. This disorder can arise from a mutation in genes involved in various biological pathways, including those within the brain. We characterized a recessive neurological disorder observed in nine young adults from five independent consanguineous Pakistani families. The disorder is characterized by microcephaly, ID, developmental delay (DD), early-onset epilepsy, recurrent infection, hearing loss, growth retardation, skeletal and limb defects. Through exome sequencing, we identified novel homozygous variants in five genes that were previously associated with brain diseases, namely CENPJ (NM_018451.5: c.1856A > G; p.Lys619Arg), STIL (NM_001048166.1: c.1235C > A; p.(Pro412Gln), CDK5RAP2 (NM_018249.6 c.3935 T > G; p.Leu1312Trp), RBBP8 (NM_203291.2 c.1843C > T; p.Gln615*) and CEP135 (NM_025009.5 c.1469A > G; p.Glu490Gly). These variants were validated by Sanger sequencing across all family members, and in silico structural analysis. Protein 3D homology modeling of wild-type and mutated proteins revealed substantial changes in the structure, suggesting a potential impact on function. Importantly, all identified genes play crucial roles in maintaining genomic integrity during cell division, with CENPJ, STIL, CDK5RAP2, and CEP135 being involved in centrosomal function. Collectively, our findings underscore the link between erroneous cell division, particularly centrosomal function, primary microcephaly and ID., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Motivation: Cell-type deconvolution methods aim to infer cell composition from bulk transcriptomic data. The proliferation of developed methods coupled with inconsistent results obtained in many cases, highlights the pressing need for guidance in the selection of appropriate methods. Additionally, the growing accessibility of single-cell RNA sequencing datasets, often accompanied by bulk expression from related samples enable the benchmark of existing methods., Results: In this study, we conduct a comprehensive assessment of 31 methods, utilizing single-cell RNA-sequencing data from diverse human and mouse tissues. Employing various simulation scenarios, we reveal the efficacy of regression-based deconvolution methods, highlighting their sensitivity to reference choices. We investigate the impact of bulk-reference differences, incorporating variables such as sample, study and technology. We provide validation using a gold standard dataset from mononuclear cells and suggest a consensus prediction of proportions when ground truth is not available. We validated the consensus method on data from the stomach and studied its spillover effect. Importantly, we propose the use of the critical assessment of transcriptomic deconvolution (CATD) pipeline which encompasses functionalities for generating references and pseudo-bulks and running implemented deconvolution methods. CATD streamlines simultaneous deconvolution of numerous bulk samples, providing a practical solution for speeding up the evaluation of newly developed methods., Availability and Implementation: https://github.com/Papatheodorou-Group/CATD_snakemake., Competing Interests: The authors declare no competing interests., (© The Author(s) 2024. Published by Oxford University Press.)

A novel In 2 O 3 @NC catalyst has been prepared and employed in CO 2 electroreduction to HCOOH. The C and N species successfully improve the electronic structure of In 2 O 3 and enhance the adsorption ability of CO 2 . The In 2 O 3 @NC catalyst exhibits a remarkably high FE HCOOH of 97.1%, j total of 190 mA cm -2 , and stability for 60 h.

Riboswitches are regulatory elements found in the untranslated regions (UTRs) of certain mRNA molecules. They typically comprise two distinct domains: an aptamer domain that can bind to specific small molecules, and an expression platform that controls gene expression. Riboswitches work by undergoing a conformational change upon binding to their specific ligand, thus activating or repressing the genes downstream. This mechanism allows gene expression regulation in response to metabolites or small molecules. To systematically summarise riboswitch structures and their related ligand binding functions, we present Ribocentre-switch, a comprehensive database of riboswitches, including the information as follows: sequences, structures, functions, ligand binding pockets and biological applications. It encompasses 56 riboswitches and 26 orphan riboswitches from over 430 references, with a total of 89 591 sequences. It serves as a good resource for comparing different riboswitches and facilitating the identification of potential riboswitch candidates. Therefore, it may facilitate the understanding of RNA structural conformational changes in response to ligand signaling. The database is publicly available at https://riboswitch.ribocentre.org., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The prediction of RNA three-dimensional structures remains an unsolved problem. Here, we report assessments of RNA structure predictions in CASP15, the first CASP exercise that involved RNA structure modeling. Forty-two predictor groups submitted models for at least one of twelve RNA-containing targets. These models were evaluated by the RNA-Puzzles organizers and, separately, by a CASP-recruited team using metrics (GDT, lDDT) and approaches (Z-score rankings) initially developed for assessment of proteins and generalized here for RNA assessment. The two assessments independently ranked the same predictor groups as first (AIchemy_RNA2), second (Chen), and third (RNAPolis and GeneSilico, tied); predictions from deep learning approaches were significantly worse than these top ranked groups, which did not use deep learning. Further analyses based on direct comparison of predicted models to cryogenic electron microscopy (cryo-EM) maps and x-ray diffraction data support these rankings. With the exception of two RNA-protein complexes, models submitted by CASP15 groups correctly predicted the global fold of the RNA targets. Comparisons of CASP15 submissions to designed RNA nanostructures as well as molecular replacement trials highlight the potential utility of current RNA modeling approaches for RNA nanotechnology and structural biology, respectively. Nevertheless, challenges remain in modeling fine details such as noncanonical pairs, in ranking among submitted models, and in prediction of multiple structures resolved by cryo-EM or crystallography., (© 2023 The Authors. Proteins: Structure, Function, and Bioinformatics published by Wiley Periodicals LLC.)

The growing number of available single-cell gene expression datasets from different species creates opportunities to explore evolutionary relationships between cell types across species. Cross-species integration of single-cell RNA-sequencing data has been particularly informative in this context. However, in order to do so robustly it is essential to have rigorous benchmarking and appropriate guidelines to ensure that integration results truly reflect biology. Here, we benchmark 28 combinations of gene homology mapping methods and data integration algorithms in a variety of biological settings. We examine the capability of each strategy to perform species-mixing of known homologous cell types and to preserve biological heterogeneity using 9 established metrics. We also develop a new biology conservation metric to address the maintenance of cell type distinguishability. Overall, scANVI, scVI and SeuratV4 methods achieve a balance between species-mixing and biology conservation. For evolutionarily distant species, including in-paralogs is beneficial. SAMap outperforms when integrating whole-body atlases between species with challenging gene homology annotation. We provide our freely available cross-species integration and assessment pipeline to help analyse new data and develop new algorithms., (© 2023. Springer Nature Limited.)

Tick-borne encephalitis virus (TBEV) is the causative agent of a potentially fatal neurological infection in humans. Investigating virus-host interaction is important for understanding the pathogenesis of TBEV and developing effective antiviral drugs against this virus. Here, we report that mammalian ste20-like kinase 3 (MST3) is involved in the regulation of TBEV infection. The knockdown or knockout of MST3, but not other mammalian ste20-like kinase family members, inhibited TBEV replication. The knockdown of MST3 also significantly reduced TBEV replication in mouse primary astrocytes. Life cycle analysis indicated that MST3 remarkably impaired virion assembly efficiency and specific infectivity by respectively 59% and 95% in MST3-knockout cells. We further found that MST3 interacts with the viral proteins NS2A and prM; and MST3 enhances the interaction of NS2A-NS4A. Thus, MST3-NS2A complex plays a major role in recruiting prM-E heterodimers and NS4A and mediates the virion assembly. Additionally, we found that MST3 was biotinylated and combined with other proteins (e.g., ATG5, Sec24A, and SNX4) that are associated with the cellular membrane required for TBEV infection. Overall, our study revealed a novel function for MST3 in TBEV infection and identified as a novel host factor supporting TBEV assembly., (© 2023 Wiley Periodicals LLC.)

Computational modeling of RNA three-dimensional (3D) structure may help in unrevealing the molecular mechanisms of RNA molecules and in designing molecules with novel functions. An unbiased blind assessment to benchmark the computational modeling is required to understand the achievements and bottlenecks of the prediction, while a standard structure comparison protocol is necessary. RNA-Puzzles is a community-wide effort on the assessment of blind prediction of RNA tertiary structures. And RNA-Puzzles toolkit is a computational resource derived from RNA-Puzzles, which includes (i) decoy sets generated by different RNA 3D structure prediction methods; (ii) 3D structure normalization, analysis, manipulation, and visualization tools; and (iii) 3D structure comparison metric tools. In this chapter, we illustrate a standard RNA 3D structure prediction assessment protocol using the selected tools from RNA-Puzzles toolkit: rna-tools and RNA_assessment., (© 2023. Springer Science+Business Media, LLC, part of Springer Nature.)

The primate neocortex exerts high cognitive ability and strong information processing capacity. Here, we establish a single-cell RNA sequencing dataset of 133,454 macaque visual cortical cells. It covers major cortical cell classes including 25 excitatory neuron types, 37 inhibitory neuron types and all glial cell types. We identified layer-specific markers including HPCAL1 and NXPH4, and also identified two cell types, an NPY-expressing excitatory neuron type that expresses the dopamine receptor D3 gene; and a primate specific activity-dependent OSTN + sensory neuron type. Comparisons of our dataset with humans and mice show that the gene expression profiles differ between species in relation to genes that are implicated in the synaptic plasticity and neuromodulation of excitatory neurons. The comparisons also revealed that glutamatergic neurons may be more diverse across species than GABAergic neurons and non-neuronal cells. These findings pave the way for understanding how the primary cortex fulfills the high-cognitive functions., (© 2022. The Author(s).)

The liver has been studied extensively due to the broad number of diseases affecting its vital functions. However, therapeutic advances have been hampered by the lack of knowledge concerning human hepatic development. Here, we addressed this limitation by describing the developmental trajectories of different cell types that make up the human liver at single-cell resolution. These transcriptomic analyses revealed that sequential cell-to-cell interactions direct functional maturation of hepatocytes, with non-parenchymal cells playing essential roles during organogenesis. We utilized this information to derive bipotential hepatoblast organoids and then exploited this model system to validate the importance of signalling pathways in hepatocyte and cholangiocyte specification. Further insights into hepatic maturation also enabled the identification of stage-specific transcription factors to improve the functionality of hepatocyte-like cells generated from human pluripotent stem cells. Thus, our study establishes a platform to investigate the basic mechanisms directing human liver development and to produce cell types for clinical applications., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)

Retinal ganglion cells (RGCs) are the brain's gateway to the visual world. They can be classified into different types on the basis of their electrophysiological, transcriptomic, or morphological characteristics. Here, we characterize the transcriptomic, morphological, and functional features of 472 high-quality RGCs using Patch sequencing (Patch-seq), providing functional and morphological annotation of many transcriptomic-defined cell types of a previously established RGC atlas. We show a convergence of different modalities in defining the RGC identity and reveal the degree of correspondence for well-characterized cell types across multimodal data. Moreover, we complement some RGC types with detailed morphological and functional properties. We also identify differentially expressed genes among ON, OFF, and ON-OFF RGCs such as Vat1l, Slitrk6, and Lmo7, providing candidate marker genes for functional studies. Our research suggests that the molecularly distinct clusters may also differ in their roles of encoding visual information., Competing Interests: Declaration of interests The authors declare no competing financial interests., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

The extent to which neurogenesis occurs in adult primates remains controversial. In this study, using an optimized single-cell RNA sequencing pipeline, we profiled 207,785 cells from the adult macaque hippocampus and identified 34 cell populations comprising all major hippocampal cell types. Analysis of their gene expression, specification trajectories and gene regulatory networks revealed the presence of all key neurogenic precursor cell populations, including a heterogeneous pool of radial glia-like cells (RGLs), intermediate progenitor cells (IPCs) and neuroblasts. We identified HMGB2 as a novel IPC marker. Comparison with mouse single-cell transcriptomic data revealed differences in neurogenic processes between species. We confirmed that neurogenesis is recapitulated in ex vivo neurosphere cultures from adult primates, further supporting the existence of neural precursor cells (NPCs) that are able to proliferate and differentiate. Our large-scale dataset provides a comprehensive adult neurogenesis atlas for primates., (© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Existing protocols for full-length single-cell RNA sequencing produce libraries of high complexity (thousands of distinct genes) with outstanding sensitivity and specificity of transcript quantification. These full-length libraries have the advantage of allowing probing of transcript isoforms, are informative regarding single-nucleotide polymorphisms and allow assembly of the VDJ region of the T- and B-cell-receptor sequences. Since full-length protocols are mostly plate-based at present, they are also suited to profiling cell types where cell numbers are limiting, such as rare cell types during development. A disadvantage of these methods has been the scalability and cost of the experiments, which has limited their popularity as compared with droplet-based and nanowell approaches. Here, we describe an automated protocol for full-length single-cell RNA sequencing, including both an in-house automated Smart-seq2 protocol and a commercial kit-based workflow. The protocols take 3-5 d to complete, depending on the number of plates processed in a batch. We discuss these two protocols in terms of ease of use, equipment requirements, running time, cost per sample and sequencing quality. By benchmarking the lysis buffers, reverse transcription enzymes and their combinations, we have optimized the in-house automated protocol to dramatically reduce its cost. An automated setup can be adopted easily by a competent researcher with basic laboratory skills and no prior automation experience. These pipelines have been employed successfully for several research projects allied with the Human Cell Atlas initiative ( www.humancellatlas.org ).

CO 2 reforming of methane (CRM) can effectively convert two greenhouse gases (CO 2 and CH 4 ) into syngas (CO + H 2 ). This process can achieve the efficient resource utilization of CO 2 and CH 4 and reduce greenhouse gases. Therefore, CRM has been considered as a significantly promising route to solve environmental problems caused by greenhouse effect. Ni-based catalysts have been widely investigated in CRM reactions due to their various advantages, such as high catalytic activity, low price, and abundant reserves. However, Ni-based catalysts usually suffer from rapid deactivation because of thermal sintering of metallic Ni active sites and surface coke deposition, which restricted the industrialization of Ni-based catalysts toward the CRM process. In order to address these challenges, scientists all around the world have devoted great efforts to investigating various influencing factors, such as the option of appropriate supports and promoters and the construction of strong metal-support interaction. Therefore, we carefully summarized recent development in the design and preparation of Ni-based catalysts with advanced catalytic activity and enhanced anti-coke performance toward CRM reactions in this review. Specifically, recent progresses of Ni-based catalysts with different supports, additives, preparation methods, and so on, have been summarized in detail. Furthermore, recent development of reaction mechanism studies over Ni-based catalysts was also covered by this review. Finally, it is prospected that the Ni-based catalyst supported by an ordered mesoporous framework and the combined reforming of methane will become the future development trend., (Copyright © 2020 Wu, Xu, Chen, Lv, Wen, Cui, Wu, Yang, Miao and Hu.)

We present the Single-Cell Clustering Assessment Framework, a method for the automated identification of putative cell types from single-cell RNA sequencing (scRNA-seq) data. By iteratively applying a machine learning approach to a given set of cells, we simultaneously identify distinct cell groups and a weighted list of feature genes for each group. The differentially expressed feature genes discriminate the given cell group from other cells. Each such group of cells corresponds to a putative cell type or state, characterized by the feature genes as markers. Benchmarking using expert-annotated scRNA-seq datasets shows that our method automatically identifies the 'ground truth' cell assignments with high accuracy.

With the development and prosperity of the global economy, the emission of carbon dioxide (CO 2 ) has become an increasing concern. Its greenhouse effect will cause serious environmental problems, such as the global warming and climate change. Therefore, the worldwide scientists have devoted great efforts to control CO 2 emissions through various strategies, such as capture, resource utilization, sequestration, etc. Among these, the catalytic conversion of CO 2 to methane is considered as one of the most efficient routes for resource utilization of CO 2 owing to the mild reaction conditions and simple reaction device. Pioneer thermodynamic studies have revealed that low reaction temperature is beneficial to the high catalytic activity and CH 4 selectivity. However, the low temperature will be adverse to the enhancement of the reaction rate due to kinetic barrier for the activation of CO 2 . Therefore, the invention of highly efficient catalysts with promising low temperature activities toward CO 2 methanation reaction is the key solution. The Ni based catalysts have been widely investigated as the catalysts toward CO 2 methanation due to their low cost and excellent catalytic performances. However, the Ni based catalysts usually perform poor low-temperature activities and stabilities. Therefore, the development of highly efficient Ni based catalysts with excellent low-temperature catalytic performances has become the research focus as well as challenge in this field. Therefore, we summarized the recent research progresses of constructing highly efficient Ni based catalysts toward CO 2 methanation in this review. Specifically, the strategies on how to enhance the catalytic performances of the Ni based catalysts have been carefully reviewed, which include various influencing factors, such as catalytic supports, catalytic auxiliaries and dopants, the fabrication methods, reaction conditions, etc. Finally, the future development trend of the Ni based catalysts is also prospected, which will be helpful to the design and fabrication of the Ni catalysts with high efficiency toward CO 2 methanation process., (Copyright © 2020 Lv, Xu, Chen, Cui, Wen, Li, Wu, Yang, Miao, Hu and Shou.)

Plutonium mononitride is one of the main fuels for Generation IV reactors and can be prepared from nitrogenation of plutonium hydride. We investigated the adsorption and dissociation of nitrogen on PuH 2 (111) surface to elaborate the initial stage of nitrogenation. The adsorption energies varied greatly with respect to the adsorption sites and orientations of the adsorbed molecule. The nitrogen exhibited preferential adsorption above the ccp site, where the molecular nitrogen was nearly parallel to the PuH 2 surface and pointed to the nearest Pu atom. The orbital hybridization and the electrostatic attraction between the Pu and N weakened the N-N bond in the adsorbed molecule. The mechanism of the dissociation process was investigated within transition state theory, and the analysis of the activation barrier indicated that dissociation of nitrogen is not the rate-determining step of nitrogenation. These findings can contribute to a better understanding of the nuclear fuel cycle.

Definitive haematopoiesis in the fetal liver supports self-renewal and differentiation of haematopoietic stem cells and multipotent progenitors (HSC/MPPs) but remains poorly defined in humans. Here, using single-cell transcriptome profiling of approximately 140,000 liver and 74,000 skin, kidney and yolk sac cells, we identify the repertoire of human blood and immune cells during development. We infer differentiation trajectories from HSC/MPPs and evaluate the influence of the tissue microenvironment on blood and immune cell development. We reveal physiological erythropoiesis in fetal skin and the presence of mast cells, natural killer and innate lymphoid cell precursors in the yolk sac. We demonstrate a shift in the haemopoietic composition of fetal liver during gestation away from being predominantly erythroid, accompanied by a parallel change in differentiation potential of HSC/MPPs, which we functionally validate. Our integrated map of fetal liver haematopoiesis provides a blueprint for the study of paediatric blood and immune disorders, and a reference for harnessing the therapeutic potential of HSC/MPPs.

Cathepsin C (CatC) is a cysteine protease involved in a variety of immune and inflammatory pathways such as activation of cytotoxicity of various immune cells. Homozygous or compound heterozygous variants in the CatC coding gene CTSC cause different conditions that have in common severe periodontitis. Periodontitis may occur as part of Papillon-Lefèvre syndrome (PLS; OMIM#245000) or Haim-Munk syndrome (HMS; OMIM#245010), or may present as an isolated finding named aggressive periodontitis (AP1; OMIM#170650). AP1 generally affects young children and results in destruction of the periodontal support of the primary dentition. In the present study we report exome sequencing of a three generation consanguineous Turkish family with a recessive form of early-onset AP1. We identified a novel homozygous missense variant in exon 2 of CTSC (NM_148170, c.G302C, p.Trp101Ser) predicted to disrupt protein structure and to be disease causing. This is the first described CTSC variant specific to the nonsyndromic AP1 form. Given the broad phenotypic spectrum associated with CTSC variants, reporting this novel variant gives new insights on genotype/phenotype correlations and might improve diagnosis of patients with early-onset AP1.

Single-cell transcriptomics is a versatile tool for exploring heterogeneous cell populations, but as with all genomics experiments, batch effects can hamper data integration and interpretation. The success of batch-effect correction is often evaluated by visual inspection of low-dimensional embeddings, which are inherently imprecise. Here we present a user-friendly, robust and sensitive k-nearest-neighbor batch-effect test (kBET; https://github.com/theislab/kBET ) for quantification of batch effects. We used kBET to assess commonly used batch-regression and normalization approaches, and to quantify the extent to which they remove batch effects while preserving biological variability. We also demonstrate the application of kBET to data from peripheral blood mononuclear cells (PBMCs) from healthy donors to distinguish cell-type-specific inter-individual variability from changes in relative proportions of cell populations. This has important implications for future data-integration efforts, central to projects such as the Human Cell Atlas.

Ordered mesoporous molybdate-zirconium oxophosphate (M-ZrPMo) solid acid catalysts with controllable molybdenum contents (0-20%) are designed and synthesized through a one-pot evaporation-induced self-assembly strategy. Afterwards, ordered mesostructure and molybdenum species in the materials are systematically researched by a variety of means. The results show that M-ZrPMo has highly ordered mesoporous structure with large specific surface area (∼200 m 2 ·g -1 ), big pore volume (∼0.30 cm 3 ·g -1 ) and pore size (∼6.5 nm). Additionally, ordered mesoporous structure of M-ZrPMo can be efficiently preserved even treated at 700 °C, presenting an outstanding thermal stability. Meanwhile, the molybdenum species are introduced as designed and homogeneously dispersed in mesoporous framework even at molybdenum content up to 20%. More importantly, the Brønsted and Lewis acidic properties of these materials are successfully enhanced with the introduction of molybdenum species. Meantime, the M-ZrPMo is employed as a solid acid catalyst for alkylation of aromatic compounds and esterification of levulinic acid with 1-butanol. The effect of molybdenum contents and calcination temperature on catalytic performance is thoroughly discussed. The excellent activity and reusability suggested that M-ZrPMo is a promising solid acid catalyst., (Copyright © 2018. Published by Elsevier Inc.)

Protein-ligand docking is a powerful method in drug discovery. The reliability of docking can be quantified by RMSD between a docking structure and an experimentally determined one. However, most experimentally determined structures are not available in practice. Evaluation by scoring functions is an alternative for assessing protein-ligand docking results. This chapter first provides a brief introduction to scoring methods used in docking. Then details are provided on how to use Cyscore programs. Finally it describes a case study for evaluation of protein-ligand docking.

We describe a general binding score for predicting the nucleic acid binding probability in proteins. The score is directly derived from physicochemical and evolutionary features and integrates a residue neighboring network approach. Our process achieves stable and high accuracies on both DNA- and RNA-binding proteins and illustrates how the main driving forces for nucleic acid binding are common. Because of the effective integration of the synergetic effects of the network of neighboring residues and the fact that the prediction yields a hierarchical scoring on the protein surface, energy funnels for nucleic acid binding appear on protein surfaces, pointing to the dynamic process occurring in the binding of nucleic acids to proteins., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Modeling of side-chain conformations on a fixed protein backbone, also called side-chain packing, plays an important role in protein structure prediction, protein design, molecular docking, and functional analysis. RASP, or RApid Side-chain Predictor, is a recently developed program that can model protein side-chain conformations with both high accuracy and high speed. Moreover, it can generate structures with few atomic clashes. This chapter first provides a brief introduction to the principle and performances of the RASP package. Then details on how to use RASP programs to predict protein side-chain conformations are elaborated. Finally, it describes case studies for structure refinement in homology modeling and residue substitution.