SpaNCMG: improving spatial domains identification of spatial transcriptomics using neighborhood-complementary mixed-view graph convolutional network.

The advancement of spatial transcriptomics (ST) technology contributes to a more profound comprehension of the spatial properties of gene expression within tissues. However, due to challenges of high dimensionality, pronounced noise and dynamic limitations in ST data, the integration of gene expression and spatial information to accurately identify spatial domains remains challenging. This paper proposes a SpaNCMG algorithm for the purpose of achieving precise spatial domain description and localization based on a neighborhood-complementary mixed-view graph convolutional network. The algorithm enables better adaptation to ST data at different resolutions by integrating the local information from KNN and the global structure from r-radius into a complementary neighborhood graph. It also introduces an attention mechanism to achieve adaptive fusion of different reconstructed expressions, and utilizes KPCA method for dimensionality reduction. The application of SpaNCMG on five datasets from four sequencing platforms demonstrates superior performance to eight existing advanced methods. Specifically, the algorithm achieved highest ARI accuracies of 0.63 and 0.52 on the datasets of the human dorsolateral prefrontal cortex and mouse somatosensory cortex, respectively. It accurately identified the spatial locations of marker genes in the mouse olfactory bulb tissue and inferred the biological functions of different regions. When handling larger datasets such as mouse embryos, the SpaNCMG not only identified the main tissue structures but also explored unlabeled domains. Overall, the good generalization ability and scalability of SpaNCMG make it an outstanding tool for understanding tissue structure and disease mechanisms. Our codes are available at https://github.com/ZhihaoSi/SpaNCMG.

Precursor-mediated in situ growth of hierarchical N-doped graphene nanofibers confining nickel single atoms for CO2 electroreduction.

Despite the various strategies for achieving metal-nitrogen-carbon (M-N-C) single-atom catalysts (SACs) with different microenvironments for electrochemical carbon dioxide reduction reaction (CO2RR), the synthesis-structure-performance correlation remains elusive due to the lack of well-controlled synthetic approaches. Here, we employed Ni nanoparticles as starting materials for the direct synthesis of nickel (Ni) SACs in one spot through harvesting the interaction between metallic Ni and N atoms in the precursor during the chemical vapor deposition growth of hierarchical N-doped graphene fibers. By combining with first-principle calculations, we found that the Ni-N configuration is closely correlated to the N contents in the precursor, in which the acetonitrile with a high N/C ratio favors the formation of Ni-N3, while the pyridine with a low N/C ratio is more likely to promote the evolution of Ni-N2. Moreover, we revealed that the presence of N favors the formation of H-terminated edge of sp2 carbon and consequently leads to the formation of graphene fibers consisting of vertically stacked graphene flakes, instead of the traditional growth of carbon nanotubes on Ni nanoparticles. With a high capability in balancing the *COOH formation and *CO desorption, the as-prepared hierarchical N-doped graphene nanofibers with Ni-N3 sites exhibit a superior CO2RR performance compared to that with Ni-N2 and Ni-N4 ones.

NiFe Nanoparticle Nest Supported on Graphene as Electrocatalyst for Highly Efficient Oxygen Evolution Reaction.

Designing cost-efffective electrocatalysts for the oxygen evolution reaction (OER) holds significant importance in the progression of clean energy generation and efficient energy storage technologies, such as water splitting and rechargeable metal-air batteries. In this work, an OER electrocatalyst is developed using Ni and Fe precursors in combination with different proportions of graphene oxide. The catalyst synthesis involved a rapid reduction process, facilitated by adding sodium borohydride, which successfully formed NiFe nanoparticle nests on graphene support (NiFe NNG). The incorporation of graphene support enhances the catalytic activity, electron transferability, and electrical conductivity of the NiFe-based catalyst. The NiFe NNG catalyst exhibits outstanding performance, characterized by a low overpotential of 292.3 mV and a Tafel slope of 48 mV dec-1, achieved at a current density of 10 mA cm- 2. Moreover, the catalyst exhibits remarkable stability over extended durations. The OER performance of NiFe NNG is on par with that of commercial IrO2 in alkaline media. Such superb OER catalytic performance can be attributed to the synergistic effect between the NiFe nanoparticle nests and graphene, which arises from their large surface area and outstanding intrinsic catalytic activity. The excellent electrochemical properties of NiFe NNG hold great promise for further applications in energy storage and conversion devices.

Active Sites of Cobalt Phthalocyanine in Electrocatalytic CO2 Reduction to Methanol.

Many metal coordination compounds catalyze CO2 electroreduction to CO, but cobalt phthalocyanine hybridized with conductive carbon such as carbon nanotubes is currently the only one that can generate methanol. The underlying structure-reactivity correlation and reaction mechanism desperately demand elucidation. Here we report the first in situ X-ray absorption spectroscopy characterization, combined with ex situ spectroscopic and electrocatalytic measurements, to study CoPc-catalyzed CO2 reduction to methanol. Molecular dispersion of CoPc on CNT surfaces, as evidenced by the observed electronic interaction between the two, is crucial to fast electron transfer to the active sites and multi-electron CO2 reduction. CO, the key intermediate in the CO2 -to-methanol pathway, is found to be labile on the active site, which necessitates a high local concentration in the microenvironment to compete with CO2 for active sites and promote methanol production. A comparison of the electrocatalytic performance of structurally related porphyrins indicates that the bridging aza-N atoms of the Pc macrocycle are critical components of the CoPc active site that produces methanol. In situ X-ray absorption spectroscopy identifies the active site as Co(I) and supports an increasingly non-centrosymmetric Co coordination environment at negative applied potential, likely due to the formation of a Co-CO adduct during the catalysis.

Regulating Catalytic Properties and Thermal Stability of Pt and PtCo Intermetallic Fuel-Cell Catalysts via Strong Coupling Effects between Single-Metal Site-Rich Carbon and Pt.

Developing low platinum-group-metal (PGM) catalysts for the oxygen reduction reaction (ORR) in proton-exchange membrane fuel cells (PEMFCs) for heavy-duty vehicles (HDVs) remains a great challenge due to the highly demanded power density and long-term durability. This work explores the possible synergistic effect between single Mn site-rich carbon (MnSA-NC) and Pt nanoparticles, aiming to improve intrinsic activity and stability of PGM catalysts. Density functional theory (DFT) calculations predicted a strong coupling effect between Pt and MnN4 sites in the carbon support, strengthening their interactions to immobilize Pt nanoparticles during the ORR. The adjacent MnN4 sites weaken oxygen adsorption at Pt to enhance intrinsic activity. Well-dispersed Pt (2.1 nm) and ordered L12-Pt3Co nanoparticles (3.3 nm) were retained on the MnSA-NC support after indispensable high-temperature annealing up to 800 °C, suggesting enhanced thermal stability. Both PGM catalysts were thoroughly studied in membrane electrode assemblies (MEAs), showing compelling performance and durability. The Pt@MnSA-NC catalyst achieved a mass activity (MA) of 0.63 A mgPt-1 at 0.9 ViR-free and maintained 78% of its initial performance after a 30,000-cycle accelerated stress test (AST). The L12-Pt3Co@MnSA-NC catalyst accomplished a much higher MA of 0.91 A mgPt-1 and a current density of 1.63 A cm-2 at 0.7 V under traditional light-duty vehicle (LDV) H2-air conditions (150 kPaabs and 0.10 mgPt cm-2). Furthermore, the same catalyst in an HDV MEA (250 kPaabs and 0.20 mgPt cm-2) delivered 1.75 A cm-2 at 0.7 V, only losing 18% performance after 90,000 cycles of the AST, demonstrating great potential to meet the DOE targets.

Spontaneous Lithiation of Binary Oxides during Epitaxial Growth on LiCoO2.

Epitaxial growth is a powerful tool for synthesizing heterostructures and integrating multiple functionalities. However, interfacial mixing can readily occur and significantly modify the properties of layered structures, particularly for those containing energy storage materials with smaller cations. Here, we show a two-step sequence involving the growth of an epitaxial LiCoO2 cathode layer followed by the deposition of a binary transition metal oxide. Orientation-controlled epitaxial synthesis of the model solid-state-electrolyte Li2WO4 and anode material Li4Ti5O12 occurs as WO3 and TiO2 nucleate and react with Li ions from the underlying cathode. We demonstrate that this lithiation-assisted epitaxy approach can be used for energy materials discovery and exploring different combinations of epitaxial interfaces that can serve as well-defined model systems for mechanistic studies of energy storage and conversion processes.

Atomically Local Electric Field Induced Interface Water Reorientation for Alkaline Hydrogen Evolution Reaction.

The slow water dissociation process in alkaline electrolyte severely limits the kinetics of HER. The orientation of H2 O is well known to affect the dissociation process, but H2 O orientation is hard to control because of its random distribution. Herein, an atomically asymmetric local electric field was designed by IrRu dizygotic single-atom sites (IrRu DSACs) to tune the H2 O adsorption configuration and orientation, thus optimizing its dissociation process. The electric field intensity of IrRu DSACs is over 4.00×1010  N/C. The ab initio molecular dynamics simulations combined with in situ Raman spectroscopy analysis on the adsorption behavior of H2 O show that the M-H bond length (M=active site) is shortened at the interface due to the strong local electric field gradient and the optimized water orientation promotes the dissociation process of interfacial water. This work provides a new way to explore the role of single atomic sites in alkaline hydrogen evolution reaction.

Predicting Ca2+ and Mg2+ ligand binding sites by deep neural network algorithm.

BACKGROUND: Alkaline earth metal ions are important protein binding ligands in human body, and it is of great significance to predict their binding residues. RESULTS: In this paper, Mg2+ and Ca2+ ligands are taken as the research objects. Based on the characteristic parameters of protein sequences, amino acids, physicochemical characteristics of amino acids and predicted structural information, deep neural network algorithm is used to predict the binding sites of proteins. By optimizing the hyper-parameters of the deep learning algorithm, the prediction results by the fivefold cross-validation are better than those of the Ionseq method. In addition, to further verify the performance of the proposed model, the undersampling data processing method is adopted, and the prediction results on independent test are better than those obtained by the support vector machine algorithm. CONCLUSIONS: An efficient method for predicting Mg2+ and Ca2+ ligand binding sites was presented.

Single-Atomic Iron Doped Carbon Dots with Both Photoluminescence and Oxidase-Like Activity.

Multifunctional nanozymes can benefit biochemical analysis via expanding sensing modes and enhancing analytical performance, but designing multifunctional nanozymes to realize the desired sensing of targets is challenging. In this work, single-atomic iron doped carbon dots (SA Fe-CDs) are designed and synthesized via a facile in situ pyrolysis process. The small-sized CDs not only maintain their tunable fluorescence, but also serve as a support for loading dispersed active sites. Monoatomic Fe offers SA Fe-CDs exceptional oxidase-mimetic activity to catalyze 3,3',5,5'-tetramethylbenzidine (TMB) oxidation with fast response (Vmax  = 10.4 nM s-1 ) and strong affinity (Km  = 168 µM). Meanwhile, their photoluminescence is quenched by the oxidation product of TMB due to inner filter effect. Phosphate ions (Pi) can suppress the oxidase-mimicking activity and restore the photoluminescence of SA Fe-CDs by interacting with Fe active sites. Based on this principle, a dual-mode colorimetric and fluorescence assay of Pi with high sensitivity, selectivity, and rapid response is established. This work paves a path to develop multifunctional enzyme-like catalysts, and offers a simple but efficient dual-mode method for phosphate monitoring, which will inspire the exploration of multi-mode sensing strategies based on nanozyme catalysis.

Prognostic and Immunological Role of FAT Family Genes in Non-Small Cell Lung Cancer.

BACKGROUND: The FAT atypical cadherin 1/2/3/4 (FAT1/2/3/4) has been linked to the occurrence and development of various cancers. However, the prognostic and immunological role of FAT1/2/3/4 in non-small cell lung cancer (NSCLC) has not been clarified. METHODS: The association of FAT1/2/3/4 mutations with tumor mutation burden (TMB), tumor immunity in the microenvironment, and response to ICIs in NSCLC was investigated. Whole-exome sequencing data of lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC) samples from the Cancer Genome Atlas (TCGA), and an immunotherapy data set comprising mutation and survival data of 75 NSCLC patients were analyzed. Two independent pan-cancer cohorts with large samples were used to validate the prognostic value of FAT1/2/3/4 mutations in immunotherapy. RESULTS: A high mutation rate of FAT1/2/3/4 (57.3%, 603/1052) was observed in NSCLC patients. TMB was significantly higher in samples with mutated FAT1/2/3/4 compared to samples with wildtype FAT1/2/3/4 (P < .05). FAT2 mutation was found to be an independent prognostic biomarker in LUAD. FAT1/2/3/4 were aberrantly expressed in LUAD and LUSC, and high FAT2 expression strongly correlated with high PD-L1 levels in LUAD. Moreover, LUAD patients with FAT1 mutations showed significantly high activated dendritic cells infiltration, whereas those with FAT2/3/4 mutations had high infiltration of CD8+ T-cells, M1 macrophages, activated memory CD4+ T-cells, and helper follicular T-cells. It was also observed that FAT1/2/4 mutations were significantly associated with better enhanced objective response and durable clinical benefit, whereas FAT1/2/3 mutations correlated with longer progression-free survival in ICI-treated NSCLC cohort. FAT1/4 mutations were related to better overall survival in pan-cancer patients treated with ICIs. CONCLUSIONS: FAT family genes are potential prognostic and immunological biomarkers and correlate with response to ICIs in NSCLC.

Understanding the Electronic Structure Evolution of Epitaxial LaNi1-xFexO3 Thin Films for Water Oxidation.

Rare earth nickelates including LaNiO3 are promising catalysts for water electrolysis to produce oxygen gas. Recent studies report that Fe substitution for Ni can significantly enhance the oxygen evolution reaction (OER) activity of LaNiO3. However, the role of Fe in increasing the activity remains ambiguous, with potential origins that are both structural and electronic in nature. On the basis of a series of epitaxial LaNi1-xFexO3 thin films synthesized by molecular beam epitaxy, we report that Fe substitution tunes the Ni oxidation state in LaNi1-xFexO3 and a volcano-like OER trend is observed, with x = 0.375 being the most active. Spectroscopy and ab initio modeling reveal that high-valent Fe3+δ cationic species strongly increase the transition-metal (TM) 3d bandwidth via Ni-O-Fe bridges and enhance TM 3d-O 2p hybridization, boosting the OER activity. These studies deepen our understanding of structural and electronic contributions that give rise to enhanced OER activity in perovskite oxides.

From Copper to Basic Copper Carbonate: A Reversible Conversion Cathode in Aqueous Anion Batteries.

Dual-ion batteries that use anions and cations as charge carriers represent a promising energy-storage technology. However, an uncharted area is to explore transition metals as electrodes to host carbonate in conversion reactions. Here we report the reversible conversion reaction from copper to Cu2 CO3 (OH)2 , where the copper electrode comprising K2 CO3 and KOH solid is self-sufficient with anion-charge carriers. This electrode dissociates and associates K+ ions during battery charge and discharge. The copper active mass and the anion-bearing cathode exhibit a reversible capacity of 664 mAh g-1 and 299 mAh g-1 , respectively, and relatively stable cycling in a saturated mixture electrolyte of K2 CO3 and KOH. The results open an avenue to use carbonate as a charge carrier for batteries to serve for the consumption and storage of CO2 .

Atomically Dispersed Dual-Metal Site Catalysts for Enhanced CO2 Reduction: Mechanistic Insight into Active Site Structures.

Carbon-supported nitrogen-coordinated single-metal site catalysts (i.e., M-N-C, M: Fe, Co, or Ni) are active for the electrochemical CO2 reduction reaction (CO2 RR) to CO. Further improving their intrinsic activity and selectivity by tuning their N-M bond structures and coordination is limited. Herein, we expand the coordination environments of M-N-C catalysts by designing dual-metal active sites. The Ni-Fe catalyst exhibited the most efficient CO2RR activity and promising stability compared to other combinations. Advanced structural characterization and theoretical prediction suggest that the most active N-coordinated dual-metal site configurations are 2N-bridged (Fe-Ni)N6 , in which FeN4 and NiN4 moieties are shared with two N atoms. Two metals (i.e., Fe and Ni) in the dual-metal site likely generate a synergy to enable more optimal *COOH adsorption and *CO desorption than single-metal sites (FeN4 or NiN4 ) with improved intrinsic catalytic activity and selectivity.

Single Iridium Atom Doped Ni2P Catalyst for Optimal Oxygen Evolution.

Single-atom catalysts (SACs) with 100% active sites have excellent prospects for application in the oxygen evolution reaction (OER). However, further enhancement of the catalytic activity for OER is quite challenging, particularly for the development of stable SACs with overpotentials <180 mV. Here, we report an iridium single atom on Ni2P catalyst (IrSA-Ni2P) with a record low overpotential of 149 mV at a current density of 10 mA·cm-2 in 1.0 M KOH. The IrSA-Ni2P catalyst delivers a current density up to ∼28-fold higher than that of the widely used IrO2 at 1.53 V vs RHE. Both the experimental results and computational simulations indicate that Ir single atoms preferentially occupy Ni sites on the top surface. The reconstructed Ir-O-P/Ni-O-P bonding environment plays a vital role for optimal adsorption and desorption of the OER intermediate species, which leads to marked enhancement of the OER activity. Additionally, the dynamic "top-down" evolution of the specific structure of the Ni@Ir particles is responsible for the robust single-atom structure and, thus, the stability property. This IrSA-Ni2P catalyst offers novel prospects for simplifying decoration strategies and further enhancing OER performance.

Engineering Atomically Dispersed FeN4 Active Sites for CO2 Electroreduction.

Atomically dispersed FeN4 active sites have exhibited exceptional catalytic activity and selectivity for the electrochemical CO2 reduction reaction (CO2RR) to CO. However, the understanding behind the intrinsic and morphological factors contributing to the catalytic properties of FeN4 sites is still lacking. By using a Fe-N-C model catalyst derived from the ZIF-8, we deconvoluted three key morphological and structural elements of FeN4 sites, including particle sizes of catalysts, Fe content, and Fe-N bond structures. Their respective impacts on the CO2RR were comprehensively elucidated. Engineering the particle size and Fe doping is critical to control extrinsic morphological factors of FeN4 sites for optimal porosity, electrochemically active surface areas, and the graphitization of the carbon support. In contrast, the intrinsic activity of FeN4 sites was only tunable by varying thermal activation temperatures during the formation of FeN4 sites, which impacted the length of the Fe-N bonds and the local strains. The structural evolution of Fe-N bonds was examined at the atomic level. First-principles calculations further elucidated the origin of intrinsic activity improvement associated with the optimal local strain of the Fe-N bond.

Ultrahigh-Loading of Ir Single Atoms on NiO Matrix to Dramatically Enhance Oxygen Evolution Reaction.

Engineering single-atom electrocatalysts with high-loading amount holds great promise in energy conversion and storage application. Herein, we report a facile and economical approach to achieve an unprecedented high loading of single Ir atoms, up to ∼18wt%, on the nickel oxide (NiO) matrix as the electrocatalyst for oxygen evolution reaction (OER). It exhibits an overpotential of 215 mV at 10 mA cm-2 and a remarkable OER current density in alkaline electrolyte, surpassing NiO and IrO2 by 57 times and 46 times at 1.49 V vs RHE, respectively. Systematic characterizations, including X-ray absorption spectroscopy and aberration-corrected Z-contrast imaging, demonstrate that the Ir atoms are atomically dispersed at the outermost surface of NiO and are stabilized by covalent Ir-O bonding, which induces the isolated Ir atoms to form a favorable ∼4+ oxidation state. Density functional theory calculations reveal that the substituted single Ir atom not only serves as the active site for OER but also activates the surface reactivity of NiO, which thus leads to the dramatically improved OER performance. This synthesis method of developing high-loading single-atom catalysts can be extended to other single-atom catalysts and paves the way for industrial applications of single-atom catalysts.

Recognizing five molecular ligand-binding sites with similar chemical structure.

Accurate identification of ligand-binding sites and discovering the protein-ligand interaction mechanism are important for understanding proteins' functions and designing new drugs. Meanwhile, accurate computational prediction and mechanism research are two grand challenges in proteomics. In this article, ligand-binding residues of five ligands (ATP, ADP, GTP, GDP, and NAD) are predicted as a group, due to their similar chemical structures and close biological function relations. The data set of binding sites by five ligands (ATP, ADP, GTP, GDP, and NAD) are collated from Biolip database. Then, five features, containing increment of diversity value, matrix scoring value, auto-covariance, secondary structure information, and surface accessibility information are used in binding site predictions. The support vector machine (SVM) model is used with the five features to predict ligand-binding sites. Finally, prediction results are tested by fivefold cross validation. Accuracy (Acc) of five ligands (ATP, ADP, GTP, GDP, and NAD) achieves 77.4%, 71.2%, 82.1%, 82.9%, and 85.3%, respectively; and Matthew correlation coefficient (MCC) of the above five ligands achieves 0.549, 0.424, 0.643, 0.659, and 0.702, respectively. The research result shows that for ligands with similar chemical structures, microenvironment of their binding sites and their sensitivities to features are similar, while, differences of their ligand-binding properties exist at the same time. © 2019 Wiley Periodicals, Inc.

Chemical Vapor Deposition for Atomically Dispersed and Nitrogen Coordinated Single Metal Site Catalysts.

Atomically dispersed and nitrogen coordinated single metal sites (M-N-C, M=Fe, Co, Ni, Mn) are the popular platinum group-metal (PGM)-free catalysts for many electrochemical reactions. Traditional wet-chemistry catalyst synthesis often requires complex procedures with unsatisfied reproducibility and scalability. Here, we report a facile chemical vapor deposition (CVD) strategy to synthesize the promising M-N-C catalysts. The deposition of gaseous 2-methylimidazole onto M-doped ZnO substrates, followed by an in situ thermal activation, effectively generated single metal sites well dispersed into porous carbon. In particular, an optimal CVD-derived Fe-N-C catalyst exclusively contains atomically dispersed FeN4 sites with increased Fe loading relative to other catalysts from wet-chemistry synthesis. The catalyst exhibited outstanding oxygen-reduction activity in acidic electrolytes, which was further studied in proton-exchange membrane fuel cells with encouraging performance.

Sr3CrN3: A New Electride with a Partially Filled d-Shell Transition Metal.

Electrides are ionic crystals in which the electrons prefer to occupy free space, serving as anions. Because the electrons prefer to be in the pockets, channels, or layers to the atomic orbitals around the nuclei, it has been challenging to find electrides with partially filled d-shell transition metals, since an unoccupied d-shell provides an energetically favorable location for the electrons to occupy. We recently predicted the existence of electrides with partially filled d-shells using high-throughput computational screening. Here, we provide experimental support using X-ray absorption spectroscopy and X-ray and neutron diffraction to show that Sr3CrN3 is indeed an electride despite its partial d-shell configuration. Our findings indicate that Sr3CrN3 is the first known electride with a partially filled d-shell transition metal, in agreement with theory, which significantly broadens the criteria for the search for new electride materials.

Thermally Driven Structure and Performance Evolution of Atomically Dispersed FeN4 Sites for Oxygen Reduction.

FeN4 moieties embedded in partially graphitized carbon are the most efficient platinum group metal free active sites for the oxygen reduction reaction in acidic proton-exchange membrane fuel cells. However, their formation mechanisms have remained elusive for decades because the Fe-N bond formation process always convolutes with uncontrolled carbonization and nitrogen doping during high-temperature treatment. Here, we elucidate the FeN4 site formation mechanisms through hosting Fe ions into a nitrogen-doped carbon followed by a controlled thermal activation. Among the studied hosts, the ZIF-8-derived nitrogen-doped carbon is an ideal model with well-defined nitrogen doping and porosity. This approach is able to deconvolute Fe-N bond formation from complex carbonization and nitrogen doping, which correlates Fe-N bond properties with the activity and stability of FeN4 sites as a function of the thermal activation temperature.