Commonly used software tools produce conflicting and overly-optimistic AUPRC values.

The precision-recall curve (PRC) and the area under the precision-recall curve (AUPRC) are useful for quantifying classification performance. They are commonly used in situations with imbalanced classes, such as cancer diagnosis and cell type annotation. We evaluate 10 popular tools for plotting PRC and computing AUPRC, which were collectively used in more than 3000 published studies. We find the AUPRC values computed by the tools rank classifiers differently and some tools produce overly-optimistic results.

Dynamic structural evolution of MgO-supported palladium catalysts: from metal to metal oxide nanoparticles to surface then subsurface atomically dispersed cations.

Supported noble metal catalysts, ubiquitous in chemical technology, often undergo dynamic transformations between reduced and oxidized states-which influence the metal nuclearities, oxidation states, and catalytic properties. In this investigation, we report the results of in situ X-ray absorption spectroscopy, scanning transmission electron microscopy, and other physical characterization techniques, bolstered by density functional theory, to elucidate the structural transformations of a set of MgO-supported palladium catalysts under oxidative treatment conditions. As the calcination temperature increased, the as-synthesized supported metallic palladium nanoparticles underwent oxidation to form palladium oxides (at approximately 400 °C), which, at approximately 500 °C, were oxidatively fragmented to form mixtures of atomically dispersed palladium cations. The data indicate two distinct types of atomically dispersed species: palladium cations located at MgO steps and those embedded in the first subsurface layer of MgO. The former exhibit significantly higher (>500 times) catalytic activity for ethylene hydrogenation than the latter. The results pave the way for designing highly active and stable supported palladium hydrogenation catalysts with optimized metal utilization.

High-sensitivity refractive index sensor based on strong localized surface plasmon resonance.

This study proposes two types of composite structures based on gold nano circular and nano square rings on a gold thin film for plasmonic refractive index sensing. The finite-difference time-domain method was used for simulation and analysis. The nano square ring composite structure showed superior performance, with five surface plasmon resonance modes, and a peak sensitivity and figure of merit in a liquid environment of 1600 nm/RIU and 86R I U -1, respectively. The sensing performances of localized surface plasmon resonance modes of both structures are superior to those of the propagating surface plasmon resonance modes. The proposed composite structures can provide a reference for refractive index sensing and have broad application prospects in bio-chemistry.

Optimizing antigen selection for the development of tuberculosis vaccines.

Tuberculosis (TB) remains a prevalent global infectious disease caused by genetically closely related tubercle bacilli in Mycobacterium tuberculosis complex (MTBC). For a century, the Bacillus Calmette-Guérin (BCG) vaccine has been the primary preventive measure against TB. While it effectively protects against extrapulmonary forms of pediatric TB, it lacks consistent efficacy in providing protection against pulmonary TB in adults. Consequently, the exploration and development of novel TB vaccines, capable of providing broad protection to populations, have consistently constituted a prominent area of interest in medical research. This article presents a concise overview of the novel TB vaccines currently undergoing clinical trials, discussing their classification, protective efficacy, immunogenicity, advantages, and limitations. In vaccine development, the careful selection of antigens that can induce strong and diverse specific immune responses is essential. Therefore, we have summarized the molecular characteristics, biological function, immunogenicity, and relevant studies associated with the chosen antigens for TB vaccines. These insights gained from vaccines and immunogenic proteins will inform the development of novel mycobacterial vaccines, particularly mRNA vaccines, for effective TB control.

Dynamic chloride ion adsorption on single iridium atom boosts seawater oxidation catalysis.

Seawater electrolysis offers a renewable, scalable, and economic means for green hydrogen production. However, anode corrosion by Cl- pose great challenges for its commercialization. Herein, different from conventional catalysts designed to repel Cl- adsorption, we develop an atomic Ir catalyst on cobalt iron layered double hydroxide (Ir/CoFe-LDH) to tailor Cl- adsorption and modulate the electronic structure of the Ir active center, thereby establishing a unique Ir-OH/Cl coordination for alkaline seawater electrolysis. Operando characterizations and theoretical calculations unveil the pivotal role of this coordination state to lower OER activation energy by a factor of 1.93. The Ir/CoFe-LDH exhibits a remarkable oxygen evolution reaction activity (202 mV overpotential and TOF = 7.46 O2 s-1) in 6 M NaOH+2.8 M NaCl, superior over Cl--free 6 M NaOH electrolyte (236 mV overpotential and TOF = 1.05 O2 s-1), with 100% catalytic selectivity and stability at high current densities (400-800 mA cm-2) for more than 1,000 h.

An Isolable One-Coordinate Lead(I) Radical with Strong g-Factor Anisotropy.

Lead-based radicals in the oxidation state of +1 are elusive species and are highly challenging to isolate in the condensed phase. In this study, we present the synthesis and characterization of the first isolable free plumbylyne radical 2 bearing a one-coordinate Pb(I) atom. It reacts with an N-heterocyclic carbene (NHC) to afford a two-coordinate NHC-ligated Pb(I) radical 3. 2 and 3 represent the first isolable Pb(I)-based radicals. Theoretical calculations and electron paramagnetic resonance analysis revealed that the unpaired electron mainly resides at the Pb 6p orbital in both radicals. Owing to the unique one-coordinate nature of the Pb atom in 2, it possesses two-fold orbital pseudo-degeneracy and substantial unquenched orbital angular momentum, and exhibits hitherto strongest g-factor anisotropy (gx,y,z=1.496, 1.166, 0.683) amongst main group radicals. Preliminary investigations into the reactivity of 2 unveiled its Pb-centered radical nature, and plumbylenes were isolated as products.

Commonly used software tools produce conflicting and overly-optimistic AUPRC values.

The precision-recall curve (PRC) and the area under it (AUPRC) are useful for quantifying classification performance. They are commonly used in situations with imbalanced classes, such as cancer diagnosis and cell type annotation. We evaluated 10 popular tools for plotting PRC and computing AUPRC, which were collectively used in >3,000 published studies. We found the AUPRC values computed by the tools rank classifiers differently and some tools produce overly-optimistic results.

An integrated meta-omics approach reveals the different response mechanisms of two anammox bacteria towards fluoroquinolone antibiotics.

The emerging fluoroquinolone antibiotics (FQs) are highly influential in nitrogen removal from livestock wastewater. However, beyond the capability of nitrogen removal, little is known about the molecular mechanisms (e.g., shift of core metabolism and energy allocation) of different anaerobic ammonium-oxidizing bacteria (AnAOB) under continuous FQ stress. This study investigated the effects of ciprofloxacin, ofloxacin and their mixture at concentrations detected in livestock wastewater on two key anammox species in membrane bioreactors. It was found 20 µg/L FQs promoted nitrogen removal efficiency and community stability, and42-51 % of FQs were removed simultaneously. Integrated meta-omics analysis revealed varied gene expression patterns between the two dominant AnAOB, Candidatus Brocadia sapporoensis (B AnAOB) and Candidatus Kuenenia stuttgartiensis (K AnAOB). The nitrogen metabolic processes were bolstered in B AnAOB, while those involved in anammox pathway of K AnAOB were inhibited. This difference was tentatively attributed to the up-regulation of reactive oxygen species scavenger genes (ccp and dxf) and FQ resistance gene (qnrB72) in B AnAOB. Importantly, most enhanced core biosynthesis/metabolism of AnAOB and close cross-feeding with accompanying bacteria were also likely to contribute to their higher levels of biomass yield and metabolism activity under FQ stress. This finding suggests that B AnAOB has the advantage of higher nitrogen metabolism capacity over K AnAOB in livestock wastewater containing FQs, which is helpful for efficient and stable nitrogen removal by the functional anammox species.

Interleukin-10 gene intervention ameliorates liver fibrosis by enhancing the immune function of natural killer cells in liver tissue.

BACKGROUND AND AIMS: Interleukin 10 (IL-10) and natural killer (NK) cells have the potential to combat liver fibrosis. However, whether NK cells play an important role in the anti-fibrotic effects of IL-10 is not sufficiently elucidated. In this study, we investigated the regulatory effects of IL-10 on NK cells during liver fibrosis. METHODS: Fibrotic mice induced with carbon tetrachloride were treated with or without IL-10 in the presence or absence of NK cells. Liver damage and fibrosis were assessed using hematoxylin and eosin and Sirius Red staining and serum transaminase and liver hydroxyproline assays, respectively. NK cell distribution, quantity, activation, cytotoxicity, development, and origin were analyzed using immunohistochemistry, immunofluorescence, and flow cytometry. Enzyme-linked immunosorbent assay was used to determine chemokine levels. RESULTS: In the presence of NK cells, IL-10 gene intervention improved liver fibrosis and enhanced NK cell accumulation and function in the liver, as evidenced by increased NKG2D, interferon-γ, and CD107a expression. Furthermore, IL-10 promoted the migration of circulating NK cells to the fibrotic liver and elevated C-C motif ligand 5 levels. However, depletion of NK cells exacerbated liver fibrosis and impaired the anti-fibrotic effect of IL-10. CONCLUSIONS: The anti-fibrotic effect of IL-10 relies on the enhancement of NK cell immune function, including activation, cytotoxicity, development, and migration. These results provide valuable insights into the mechanisms through which IL-10 regulates NK cells to limit the progression of liver fibrosis.

Synthesis and Reactivity of N-Heterocyclic Carbene Coordinated Formal Germanimidoyl-Phosphinidenes.

Treatment of N-heterocyclic carbene (NHC) ligated germylidenylphosphinidene MsFluidtBu-GeP(NHCiPr) (where MsFluidtBu is a bulky hydrindacene substituent, and NHCiPr is 1,3-diisopropyl-4,5-dimethyl-imidazolin-2-ylidene) with mesityl azide and 4-tertbutylphenyl azide afforded NHC coordinated formal germanimidoyl-phosphinidenes, which represent the first compounds bearing both Ge═N double bond and phosphinidene functionalities. Studies of the chemical properties revealed that the reactions preferred to occur at the Ge═N double bond, which underwent [2 + 2] cycloadditions with CO2 and ethyl isocyanate, and coordinated with coinage metals through the nitrogen atom.

Gut microbiota and immune mediation: a Mendelian randomization study on granulomatosis with polyangiitis.

Background: The gut microbiota plays a pivotal role in influencing various health outcomes, including immune-mediated conditions. Granulomatosis with Polyangiitis (GPA) is one such condition, and its potential associations with gut microbiota remain underexplored. Method: Using a two-sample Mendelian randomization approach, we investigated the causal links between gut microbiota and GPA. We sourced our data from multiple cohorts and consortiums, including the MiBioGen consortium. Our study design incorporated both direct associations and mediation effects of immune traits on the relationship between gut microbiota and GPA. Results: Our analysis revealed significant associations between 1 phylum, 1 family 9 genus microbiota taxa and GPA. Furthermore, we identified several immune cell traits that mediated the effects of gut microbiota on GPA. For instance, the family Defluviitaleaceae and genus Defluviitaleaceae UCG011 influenced GPA through CD11c in granulocytes. The mediation effect proportions further elucidated the complex dynamics between gut microbiota exposures, immune markers, and their combined influence on GPA. Conclusion: Our findings underscore the intricate relationship between gut microbiota, immune markers, and GPA. The identified associations and mediation effects provide valuable insights into the potential therapeutic avenues targeting gut microbiota to manage GPA.

[Meteorological Impact Assessment of PM2.5 and O3 Complex Pollution in Key Regions of China Based on Meteorological Conditions Index].

Meteorological conditions play a key role in the occurrence and evolution of atmospheric complex pollution. Considering the different pollution formation mechanisms of PM2.5 and O3, statistical calculation and in-depth learning methods were used to construct the PM2.5 and O3 meteorological condition indexes based on long-term pollution meteorological observation data. A research method was developed to study the meteorological characteristics and impact contribution of atmospheric complex pollution by using the meteorological condition index, and quantitative analysis of the distribution and variation of pollution excluding the influence of regional meteorological differences was also conducted. The results showed that in the summer of 2021, the pollution meteorological conditions in the key regions in central and eastern China were generally worse in the north and better in the south(index:"2+26" cities>the border area of Jiangsu, Anhui, Shandong, and Henan>the Yangtze River Delta) and the worst in June and the best in July. The "double high" pollution began to appear when the PM2.5 meteorological condition index>30 and O3 meteorological condition index>100; meanwhile, the unfavorable meteorological conditions for O3 also promoted the increase in PM2.5 concentration, resulting in the frequency of "double high" increases with the increase in O3 meteorological condition index. Compared with that during the same period last year, ρ(PM2.5) of each region decreased by 3.9 µg·m-3, 3.3 µg·m-3, and 1.4 µg·m-3 due to the contribution of the improvement in the pollution meteorological conditions, which is nearly 58.5% on average of the total decrease in PM2.5 concentration. However, the change in O3 pollution meteorological conditions was better in the north and worse in the south, and the overall deterioration in the Yangtze River Delta Region led to approximately 2.8 µg·m-3 growth for the O3 concentration. The PM2.5 and O3 concentrations after excluding the impact of meteorological differences showed different distribution characteristics from the air quality monitoring, in which the high concentrations of PM2.5 were distributed along the Bohai Sea, the inter-provincial border, and the south of the region, whereas the high concentrations of O3 were concentrated along the Taihang Mountains, around Mount Tai, and in parts of the Yangtze River Delta. The daily concentration variations in a single city during a specific pollution control period could be used as a basis for evaluating the effectiveness of local supervision and control, which will provide a reference for the dynamic supervision and daily scheduling of local control management.

Triplet bismuthinidenes featuring unprecedented giant and positive zero field splittings.

Isolation of triplet pnictinidenes, which bear two unpaired electrons at the pnictogen centers, has long been a great challenge due to their intrinsic high reactivity. Herein, we report the syntheses and characterizations of two bismuthinidenes MsFluindtBu-Bi (3) and MsFluind*-Bi (4) stabilized by sterically encumbered hydrindacene ligands. They were facilely prepared through reductions of the corresponding dichloride precursors with 2 molar equivalents of potassium graphite. The structural analyses revealed that 3 and 4 contain a one-coordinate bismuth atom supported by a Bi-C single σ bond. As a consequence, the remaining two Bi 6p orbitals are nearly degenerate, and 3 and 4 possess triplet ground states. Experimental characterizations with multinuclear magnetic resonance, magnetometry and near infrared spectroscopy coupled to wavefunction based ab initio calculations concurred to evidence that there exist giant and positive zero field splittings (>4300 cm-1) in their S = 1 ground states. Hence even at room temperature the systems almost exclusively populate the lowest-energy nonmagnetic Ms = 0 level, which renders them seemingly diamagnetic.

Resolvin D1 promotes the resolution of inflammation in the ACLF rat model by increasing the proportion of Treg cells.

OBJECTIVE: Acute-on-chronic liver failure (ACLF) causes organ system failures in patients and increases the risk of mortality. One of the main predictors of ACLF development in patients is the severity of systemic inflammation. The purpose of this study was to explore the effects of resolvin D1 (RvD1) on the rat model of ACLF. METHODS: The ACLF rats were induced by first intraperitoneally (ip) injecting CCl4 and porcine serum for 6 weeks to establish the chronic liver injury, followed by once administration (ip) of lipopolysaccharide and d-galactose d-GalN to cause acute liver injury (ALI). An hour before the ALI-induced treatment, rats were administrated (ip) with 0.9% saline or different doses of RvD1 (0.3 or 1 µg/kg). Afterward, the control and treated rats were killed and samples were collected. Biochemical analysis, hematoxylin-eosin and Sirius red staining, flow cytometry assay, and real-time polymerase chain reaction were used to assess the rat liver histopathological injury, the percentage of Treg cells in the spleen, and the messenger RNA (mRNA) levels of transcription factors and immunologic cytokines in liver. RESULTS: The necroinflammatory scores and the serum levels of transaminase significantly increased in ACLF rats compared with those in control rats. These impaired changes observed in ACLF rats could be attenuated by the administration of a low dose of RvD1 before the induction of ALI, which was associated with the increased proportion of regulatory T cells (Treg) in the spleen together with the increased gene expression ratio of Foxp3/RORγt and decreased mRNA level of Il-17a and Il-6 in the liver. CONCLUSION: A low dose of RvD1 can promote the resolution of inflammation in ACLF rats by increasing the proportion of Treg cells. RvD1, therefore, may be used as a potential drug for the treatment of patients with ACLF.

High-efficiency plasmonic vortex generation with near-infrared bifunctional metasurfaces.

Plasmonic vortices have shown a wide range of applications in on-chip photonics due to their fascinating properties of the orbital angular momenta (OAM) and phase singularity. However, conventional devices to generate them suffer from issues of low efficiencies and limited functionalities. Here, we establish a systematic scheme to construct high-efficiency bifunctional metasurfaces that can generate two plasmonic vortices exhibiting distinct topological charges, based on a series of reflective meta-atoms exhibiting tailored reflection-phases dictated by both resonant and geometric origins. As a benchmark test, we first construct a meta-coupler with meta-atoms exhibiting geometric phases only, and experimentally demonstrate that it can generate a pre-designed plasmonic vortex at the wavelength of 1064 nm with an efficiency of 27% (56% in simulation). Next, we design/fabricate two bifunctional metasurfaces with meta-atoms integrated with both resonant and geometric phases, and experimentally demonstrate that they can generate divergent (or focused) or convergent (or defocused) plasmonic vortices with district OAM as shined by circularly polarized light with opposite helicity at 1064 nm wavelength. Our work provides an efficient platform to generate plasmonic vortices as desired, which can find many applications in on-chip photonics.

Efficacy and safety of totally laparoscopic gastrectomy with uncut Roux-en-Y for gastric cancer: a dual-center retrospective study.

BACKGROUND: Uncut Roux-en-Y (URY) effectively alleviates the prevalent complexities connected with RY, such as Roux-en-Y stasis syndrome (RSS). Nevertheless, for gastric cancer (GC) patients, it is still controversial whether URY has an impact on long-term prognosis and whether it has fewer afferent loop recanalization. Therefore, compare whether URY and RY have differences in prognosis and long-term complications of GC patients undergoing totally laparoscopic gastrectomy (TLG). METHODS: We analyzed the data of patients who underwent TLG combined with digestive tract reconstruction from dual-center between 2016 and 2022. Only patients undergoing URY and RY were selected for analysis. Relapse-free survival (RFS) and overall survival (OS) were estimated. Bias between the groups was reduced by propensity score matching (PSM). The Cox proportional hazard regression model was used to further analyze the influence of URY on prognosis. RESULTS: Two hundred forty two GC patients were enrolled. The URY had significantly shorter operation time, liquid food intake time, and in-hospital stays than the RY (P < 0.001). The URY had fewer long-term and short-term postoperative complications than the RY, especially with regard to RSS, reflux esophagitis, and reflux gastritis. The 3-year and 5-year OS of the URY group and the RY group before PSM: 87.5% vs. 65.6% (P < 0.001) and 81.4% vs. 61.7% (P = 0.001). PSM and Cox multivariate analysis confirmed that compared to RY, URY can improve the short-term and long-term prognosis of GC patients. CONCLUSION: TLG combined with URY for GC, especially for advanced, older, and poorly differentiated patients, may promote postoperative recovery and improve long-term prognosis.

Synergy of Cu/C3 N4 Interface and Cu Nanoparticles Dual Catalytic Regions in Electrolysis of CO to Acetic Acid.

Electrochemical reduction reaction of carbon monoxide (CORR) offers a promising way to manufacture acetic acid directly from gaseous CO and water at mild condition. Herein, we discovered that the graphitic carbon nitride (g-C3 N4 ) supported Cu nanoparticles (Cu-CN) with the appropriate size showed a high acetate faradaic efficiency of 62.8 % with a partial current density of 188 mA cm-2 in CORR. In situ experimental and density functional theory calculation studies revealed that the Cu/C3 N4 interface and metallic Cu surface synergistically promoted CORR into acetic acid. The generation of pivotal intermediate -*CHO is advantage around the Cu/C3 N4 interface and migrated *CHO facilitates acetic acid generation on metallic Cu surface with promoted *CHO coverage. Moreover, continuous production of acetic acid aqueous solution was achieved in a porous solid electrolyte reactor, indicating the great potential of Cu-CN catalyst in the industrial application.

Efficient Meta-couplers Squeezing Propagating Light into On-Chip Subwavelength Devices in a Controllable Way.

On-chip photonic systems play crucial roles in nanoscience and nanoapplications, but coupling external light to these subwavelength devices is challenging due to a large mode mismatch. Here, we establish a new scheme for realizing highly miniaturized couplers for efficiently exciting on-chip photonic devices in a controllable way. Relying on both resonant and Pancharatnam-Berry mechanisms, our meta-device can couple circularly polarized light to a surface plasmon, which is then focused into a spot placed with a target on-chip device. We experimentally demonstrate two meta-couplers. The first can excite an on-chip waveguide (with a 0.1λ × 0.2λ cross section) with an absolute efficiency of 51%, while the second can achieve incident spin-selective excitation of a dual-waveguide system. Background-free excitation of a gap-plasmon nanocavity with the local field enhanced by >1000 times is numerically demonstrated. Such a scheme connects efficiently propagating light in free space and localized fields in on-chip devices, being highly favored in many integration-optics applications.

Molecular Characterization of the Acyl-CoA-Binding Protein Genes Reveals Their Significant Roles in Oil Accumulation and Abiotic Stress Response in Cotton.

Members of the acyl-CoA-binding protein (ACBP) gene family play vital roles in diverse processes related to lipid metabolism, growth and development, and environmental response. Plant ACBP genes have been well-studied in a variety of species including Arabidopsis, soybean, rice and maize. However, the identification and functions of ACBP genes in cotton remain to be elucidated. In this study, a total of 11 GaACBP, 12 GrACBP, 20 GbACBP, and 19 GhACBP genes were identified in the genomes of Gossypium arboreum, Gossypium raimondii, Gossypium babardense, and Gossypium hirsutum, respectively, and grouped into four clades. Forty-nine duplicated gene pairs were identified in Gossypium ACBP genes, and almost all of which have undergone purifying selection during the long evolutionary process. In addition, expression analyses showed that most of the GhACBP genes were highly expressed in the developing embryos. Furthermore, GhACBP1 and GhACBP2 were induced by salt and drought stress based on a real-time quantitative PCR (RT-qPCR) assay, indicating that these genes may play an important role in salt- and drought-stress tolerance. This study will provide a basic resource for further functional analysis of the ACBP gene family in cotton.