Genomic and phenotypic adaptations of Rattus tanezumi to cold limit its further northward expansion and range overlap with R. norvegicus.

Global climate change has led to shifts in the distribution ranges of many terrestrial species, promoting their migration from lower altitudes or latitudes to higher ones. Meanwhile, successful invaders have developed genetic adaptations enabling the colonization of new environments. Over the past 40 years, Rattus tanezumi (RT) has expanded into northern China (Northwest and North China) from its southern origins. We studied the cold adaptation of RT and its potential for northward expansion by comparing it with sympatric R. norvegicus (RN), which is well adapted to cold regions. Through population genomic analysis, we revealed that the invading RT rats have split into three distinct populations: the North, Northwest and Tibetan populations. The first two populations exhibited high genetic diversity, while the latter population showed remarkably low genetic diversity. These rats have developed various genetic adaptations to cold, arid, hypoxic, and high-UV conditions. Cold acclimation tests revealed divergent thermoregulation between RT and RN. Specifically, RT exhibited lower brown adipose tissue (BAT) activity and higher metabolic rates than did RN. Transcriptome analysis highlighted changes in genes regulating triglyceride catabolic processes in RT, including Apoa1 and Apoa4, which were upregulated, under selection and associated with local adaptation. In contrast, RN showed changes in carbohydrate metabolism genes. Despite the cold adaptation of RT, we observed genotypic and phenotypic constraints that may limit its ability to cope with severe low temperatures farther north. Consequently, it is less likely that RT rats will invade and overlap with RN rats in farther northern regions.

Reinvestigating the performance of artificial intelligence classification algorithms on COVID-19 X-Ray and CT images.

There are concerns that artificial intelligence (AI) algorithms may create underdiagnosis bias by mislabeling patient individuals with certain attributes (e.g., female and young) as healthy. Addressing this bias is crucial given the urgent need for AI diagnostics facing rapidly spreading infectious diseases like COVID-19. We find the prevalent AI diagnostic models show an underdiagnosis rate among specific patient populations, and the underdiagnosis rate is higher in some intersectional specific patient populations (for example, females aged 20-40 years). Additionally, we find training AI models on heterogeneous datasets (positive and negative samples from different datasets) may lead to poor model generalization. The model's classification performance varies significantly across test sets, with the accuracy of the better performance being over 40% higher than that of the poor performance. In conclusion, we developed an AI bias analysis pipeline to help researchers recognize and address biases that impact medical equality and ethics.

Promoting Oxygen Evolution Electrocatalysis by Coordination Engineering in Cobalt Phosphate.

Understanding the structure-activity correlation is an important prerequisite for the rational design of high-efficiency electrocatalysts at the atomic level. However, the effect of coordination environment on electrocatalytic oxygen evolution reaction (OER) remains enigmatic. In this work, the regulation of proton transfer involved in water oxidation by coordination engineering based on Co3(PO4)2 and CoHPO4 is reported. The HPO4 2- anion has intermediate pKa value between Co(II)-H2O and Co(III)-H2O to be served as an appealing proton-coupled electron transfer (PCET) induction group. From theoretical calculations, the pH-dependent OER properties, deuterium kinetic isotope effects, operando electrochemical impedance spectroscopy (EIS) and Raman studies, the CoHPO4 catalyst beneficially reduces the energy barrier of proton hopping and modulates the formation energy of high-valent Co species, thereby enhancing OER activity. This work demonstrates a promising strategy that involves tuning the local coordination environment to optimize PCET steps and electrocatalytic activities for electrochemical applications. In addition, the designed system offers a motif to understand the structure-efficiency relationship from those amino-acid residue with proton buffer ability in natural photosynthesis.

A dual-responsive RhB-doped MOF probe for simultaneous recognition of Cu2+ and Fe3.

Based on the dual response of RhB@UiO-67 (1:6) to Cu2+ and Fe3+, a proportional fluorescent probe with (I392/I581) as the output signal was developed to recognize Cu2+ and Fe3+. Developing highly sensitive and selective trace metal ions probes is crucial to human health and ecological sustainability. In this work, a series of ratio fluorescent probes (RhB@UiO-67) were successfully synthesized using a one-pot method to enable fluorescence sensing of Cu2+ and Fe3+ at low concentrations. The proportional fluorescent probe RhB@UiO-67 (1:6) exhibited simultaneous quenching of Cu2+ and Fe3+, which was found to be of interest. Furthermore, the limits of detection (LODs) for Cu2+ and Fe3+ were determined to be 2.76 µM and 0.76 µM, respectively, for RhB@UiO-67 (1:6). These values were significantly superior to those reported for previous sensors, indicating the probe's effectiveness in detecting Cu2+ and Fe3+ in an ethanol medium. Additionally, RhB@UiO-67 (1:6) demonstrated exceptional immunity and reproducibility towards Cu2+ and Fe3+. The observed fluorescence quenching of Cu2+ and Fe3+ was primarily attributed to the mechanisms of fluorescence resonance energy transfer (FRET), photoinduced electron transfer (PET), and competitive absorption (CA). This work establishes a valuable foundation for the future study and utilization of Cu2+ and Fe3+ sensing technologies.

Trajectory Tracking Control of Variable Sweep Aircraft Based on Reinforcement Learning.

An incremental deep deterministic policy gradient (IDDPG) algorithm is devised for the trajectory tracking control of a four-wing variable sweep (FWVS) aircraft with uncertainty. The IDDPG algorithm employs the line-of-sight (LOS) method for path tracking, formulates a reward function based on position and attitude errors, and integrates long short-term memory (LSTM) units into IDDPG algorithm to enhance its adaptability to environmental changes during flight. Finally, environmental disturbance factors are introduced in simulation to validate the designed controller's ability to track climbing trajectories of morphing aircraft in the presence of uncertainty.

A combination influenza mRNA vaccine candidate provided broad protection against diverse influenza virus challenge.

Influenza viruses present a significant threat to global health. The production of a universal vaccine is considered essential due to the ineffectiveness of current seasonal influenza vaccines against mutant strains. mRNA technology offers new prospects in vaccinology, with various candidates for different infectious diseases currently in development and testing phases. In this study, we encapsulated a universal influenza mRNA vaccine. The vaccine encoded influenza hemagglutinin (HA), nucleoprotein (NP), and three tandem repeats of matrix protein 2 (3M2e). Twice-vaccinated mice exhibited strong humoral and cell-mediated immune responses in vivo. Notably, these immune responses led to a significant reduction in viral load of the lungs in challenged mice, and also conferred protection against future wild-type H1N1, H3N2, or H5N1 influenza virus challenges. Our findings suggest that this mRNA-universal vaccine strategy for influenza virus may be instrumental in mitigating the impact of future influenza pandemics.

Polygenic risk score for acute rejection based on donor-recipient non-HLA genotype mismatch.

BACKGROUND: Acute rejection (AR) after kidney transplantation is an important allograft complication. To reduce the risk of post-transplant AR, determination of kidney transplant donor-recipient mismatching focuses on blood type and human leukocyte antigens (HLA), while it remains unclear whether non-HLA genetic mismatching is related to post-transplant complications. METHODS: We carried out a genome-wide scan (HLA and non-HLA regions) on AR with a large kidney transplant cohort of 784 living donor-recipient pairs of European ancestry. An AR polygenic risk score (PRS) was constructed with the non-HLA single nucleotide polymorphisms (SNPs) filtered by independence (r2 < 0.2) and P-value (< 1×10-3) criteria. The PRS was validated in an independent cohort of 352 living donor-recipient pairs. RESULTS: By the genome-wide scan, we identified one significant SNP rs6749137 with HR = 2.49 and P-value = 2.15×10-8. 1,307 non-HLA PRS SNPs passed the clumping plus thresholding and the PRS exhibited significant association with the AR in the validation cohort (HR = 1.54, 95% CI = (1.07, 2.22), p = 0.019). Further pathway analysis attributed the PRS genes into 13 categories, and the over-representation test identified 42 significant biological processes, the most significant of which is the cell morphogenesis (GO:0000902), with 4.08 fold of the percentage from homo species reference and FDR-adjusted P-value = 8.6×10-4. CONCLUSIONS: Our results show the importance of donor-recipient mismatching in non-HLA regions. Additional work will be needed to understand the role of SNPs included in the PRS and to further improve donor-recipient genetic matching algorithms. Trial registry: Deterioration of Kidney Allograft Function Genomics (NCT00270712) and Genomics of Kidney Transplantation (NCT01714440) are registered on ClinicalTrials.gov.

The meso-substituent electronic effect of Fe porphyrins on the electrocatalytic CO2 reduction reaction.

We report Fe porphyrins bearing different meso-substituents for the electrocatalytic CO2 reduction reaction (CO2RR). By replacing two and four meso-phenyl groups of Fe tetraphenylporphyrin (FeTPP) with strong electron-withdrawing pentafluorophenyl groups, we synthesized FeF10TPP and FeF20TPP, respectively. We showed that FeTPP and FeF10TPP are active and selective for CO2-to-CO conversion in dimethylformamide with the former being more active, but FeF20TPP catalyzes hydrogen evolution rather than the CO2RR under the same conditions. Experimental and theoretical studies revealed that with more electron-withdrawing meso-substituents, the Fe center becomes electron-deficient and it becomes difficult for it to bind a CO2 molecule in its formal Fe0 state. This work is significant to illustrate the electronic effects of catalysts on binding and activating CO2 molecules and provide fundamental knowledge for the design of new CO2RR catalysts.

Flowering genes identification, network analysis, and database construction for 837 plants.

Flowering is one of the most important biological phenomena in the plant kingdom, which not only has important ecological significance, but also has substantial horticultural ornamental value. In this study, we undertook an exhaustive review of the advancements in our understanding of plant flowering genes. We delved into the identification and conducted comparative analyses of flowering genes across virtually all sequenced angiosperm plant genomes. Furthermore, we established an extensive angiosperm flowering atlas, encompassing a staggering 183 720 genes across eight pathways, along with 10 155 ABCDE mode genes, which play a pivotal role in plant flowering regulation. Through the examination of expression patterns, we unveiled the specificities of these flowering genes. An interaction network between flowering genes of the ABCDE model and their corresponding upstream genes offered a blueprint for comprehending their regulatory mechanisms. Moreover, we predicted the miRNA and target genes linked to the flowering processes of each species. To culminate our efforts, we have built a user-friendly web interface, named the Plant Flowering-time Gene Database (PFGD), accessible at http://pfgd.bio2db.com/. We firmly believe that this database will serve as a cornerstone in the global research community, facilitating the in-depth exploration of flowering genes in the plant kingdom. In summation, this pioneering endeavor represents the first comprehensive collection and comparative analysis of flowering genes in plants, offering valuable resources for the study of plant flowering genetics.

Integrative Single Cell Atlas Revealed Intratumoral Heterogeneity Generation from an Adaptive Epigenetic Cell State in Human Bladder Urothelial Carcinoma.

Intratumor heterogeneity (ITH) of bladder cancer (BLCA) contributes to therapy resistance and immune evasion affecting clinical prognosis. The molecular and cellular mechanisms contributing to BLCA ITH generation remain elusive. It is found that a TM4SF1-positive cancer subpopulation (TPCS) can generate ITH in BLCA, evidenced by integrative single cell atlas analysis. Extensive profiling of the epigenome and transcriptome of all stages of BLCA revealed their evolutionary trajectories. Distinct ancestor cells gave rise to low-grade noninvasive and high-grade invasive BLCA. Epigenome reprograming led to transcriptional heterogeneity in BLCA. During early oncogenesis, epithelial-to-mesenchymal transition generated TPCS. TPCS has stem-cell-like properties and exhibited transcriptional plasticity, priming the development of transcriptionally heterogeneous descendent cell lineages. Moreover, TPCS prevalence in tumor is associated with advanced stage cancer and poor prognosis. The results of this study suggested that bladder cancer interacts with its environment by acquiring a stem cell-like epigenomic landscape, which might generate ITH without additional genetic diversification.

Dual-ligand quasi-2D perovskites with chiral-induced spin selectivity for room temperature spin-LEDs.

Spin-LEDs have been a central topic in semiconductor spintronics research and represent a promising avenue for advanced optoelectronic devices and applications. The future advancements of spin-LEDs will undoubtedly hinge on the generation and manipulation of spin-polarized population at room temperature. In this research, we elucidate the development of room-temperature spin-LEDs using quasi-2D perovskites, based on the chiral-induced spin selectivity (CISS) effect. During the carrier transfer from the chiral n2 phase to the randomly oriented high-n phase caused by the bandgap gradient distribution, CISS works to generate non-equilibrium spin population, leading to room-temperature spin-polarized fluorescence. A spin-polarization of ∼93% is observed for the films. Finally, we realize spin-LEDs at room temperature, exhibiting a |gCP-EL| value of 0.05 and an EQE of 3.8%. This work highlights the potential of integrating dual ligands to optimize the phase distribution and crystalline orientation in quasi-2D films to achieve efficient CISS for spin-LED applications.

DeepFGRN: inference of gene regulatory network with regulation type based on directed graph embedding.

The inference of gene regulatory networks (GRNs) from gene expression profiles has been a key issue in systems biology, prompting many researchers to develop diverse computational methods. However, most of these methods do not reconstruct directed GRNs with regulatory types because of the lack of benchmark datasets or defects in the computational methods. Here, we collect benchmark datasets and propose a deep learning-based model, DeepFGRN, for reconstructing fine gene regulatory networks (FGRNs) with both regulation types and directions. In addition, the GRNs of real species are always large graphs with direction and high sparsity, which impede the advancement of GRN inference. Therefore, DeepFGRN builds a node bidirectional representation module to capture the directed graph embedding representation of the GRN. Specifically, the source and target generators are designed to learn the low-dimensional dense embedding of the source and target neighbors of a gene, respectively. An adversarial learning strategy is applied to iteratively learn the real neighbors of each gene. In addition, because the expression profiles of genes with regulatory associations are correlative, a correlation analysis module is designed. Specifically, this module not only fully extracts gene expression features, but also captures the correlation between regulators and target genes. Experimental results show that DeepFGRN has a competitive capability for both GRN and FGRN inference. Potential biomarkers and therapeutic drugs for breast cancer, liver cancer, lung cancer and coronavirus disease 2019 are identified based on the candidate FGRNs, providing a possible opportunity to advance our knowledge of disease treatments.

Exploring research hotspots and future directions in neural tube defects field by bibliometric and bioinformatics analysis.

Background: Neural tube defects (NTDs) is the most common birth defect of the central nervous system (CNS) which causes the death of almost 88,000 people every year around the world. Much efforts have been made to investigate the reasons that contribute to NTD and explore new ways to for prevention. We trawl the past decade (2013-2022) published records in order to get a worldwide view about NTDs research field. Methods: 7,437 records about NTDs were retrieved from the Web of Science (WOS) database. Tools such as shell scripts, VOSviewer, SCImago Graphica, CiteSpace and PubTator were used for data analysis and visualization. Results: Over the past decade, the number of publications has maintained an upward trend, except for 2022. The United States is the country with the highest number of publications and also with the closest collaboration with other countries. Baylor College of Medicine has the closest collaboration with other institutions worldwide and also was the most prolific institution. In the field of NTDs, research focuses on molecular mechanisms such as genes and signaling pathways related to folate metabolism, neurogenic diseases caused by neural tube closure disorders such as myelomeningocele and spina bifida, and prevention and treatment such as folate supplementation and surgical procedures. Most NTDs related genes are related to development, cell projection parts, and molecular binding. These genes are mainly concentrated in cancer, Wnt, MAPK, PI3K-Akt and other signaling pathways. The distribution of NTDs related SNPs on chromosomes 1, 3, 5, 11, 14, and 17 are relatively concentrated, which may be associated with high-risk of NTDs. Conclusion: Bibliometric analysis of the literature on NTDs field provided the current status, hotspots and future directions to some extant. Further bioinformatics analysis expanded our understanding of NTDs-related genes function and revealed some important SNP clusters and loci. This study provided some guidance for further studies. More extensive cooperation and further research are needed to overcome the ongoing challenge in pathogenesis, prevention and treatment of NTDs.

De-aberration for transcranial photoacoustic computed tomography through an adult human skull.

Noninvasive transcranial photoacoustic computed tomography (PACT) of the human brain, despite its clinical potential, remains impeded by the acoustic distortion induced by the human skull. The distortion, which is attributed to the markedly different material properties of the skull relative to soft tissue, results in heavily aberrated PACT images -- a problem that has remained unsolved in the past two decades. Herein, we report the first successful experimental demonstration of the de-aberration of PACT images through an ex-vivo adult human skull using a homogeneous elastic model for the skull. Using only the geometry, position, and orientation of the skull, we accurately de-aberrate the PACT images of light-absorbing phantoms acquired through an ex-vivo human skull, in terms of the recovered phantom features, for different levels of phantom complexity and positions. Our work addresses the longstanding challenge of skull-induced aberrations in transcranial PACT and advances the field towards unlocking the full potential of transcranial human brain PACT.

G6PD maintains the VSMC synthetic phenotype and accelerates vascular neointimal hyperplasia by inhibiting the VDAC1-Bax-mediated mitochondrial apoptosis pathway.

BACKGROUND: Glucose-6-phosphate dehydrogenase (G6PD) plays an important role in vascular smooth muscle cell (VSMC) phenotypic switching, which is an early pathogenic event in various vascular remodeling diseases (VRDs). However, the underlying mechanism is not fully understood. METHODS: An IP‒LC‒MS/MS assay was conducted to identify new binding partners of G6PD involved in the regulation of VSMC phenotypic switching under platelet-derived growth factor-BB (PDGF-BB) stimulation. Co-IP, GST pull-down, and immunofluorescence colocalization were employed to clarify the interaction between G6PD and voltage-dependent anion-selective channel protein 1 (VDAC1). The molecular mechanisms involved were elucidated by examining the interaction between VDAC1 and apoptosis-related biomarkers, as well as the oligomerization state of VDAC1. RESULTS: The G6PD level was significantly elevated and positively correlated with the synthetic characteristics of VSMCs induced by PDGF-BB. We identified VDAC1 as a novel G6PD-interacting molecule essential for apoptosis. Specifically, the G6PD-NTD region was found to predominantly contribute to this interaction. G6PD promotes VSMC survival and accelerates vascular neointimal hyperplasia by inhibiting VSMC apoptosis. Mechanistically, G6PD interacts with VDAC1 upon stimulation with PDGF-BB. By competing with Bax for VDAC1 binding, G6PD reduces VDAC1 oligomerization and counteracts VDAC1-Bax-mediated apoptosis, thereby accelerating neointimal hyperplasia. CONCLUSION: Our study showed that the G6PD-VDAC1-Bax axis is a vital switch in VSMC apoptosis and is essential for VSMC phenotypic switching and neointimal hyperplasia, providing mechanistic insight into early VRDs.

Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants.

The auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA) family of genes are central components of the auxin signaling pathway and play essential roles in plant growth and development. Their large-scale analysis and evolutionary trajectory of origin are currently not known. Here, we identified the corresponding ARF and Aux/IAA family members and performed a large-scale analysis by scanning 406 plant genomes. The results showed that the ARF and Aux/IAA gene families originated from charophytes. The ARF family sequences were more conserved than the Aux/IAA family sequences. Dispersed duplications were the common expansion mode of ARF and Aux/IAA families in bryophytes, ferns, and gymnosperms; however, whole-genome duplication was the common expansion mode of the ARF and Aux/IAA families in basal angiosperms, magnoliids, monocots, and dicots. Expression and regulatory network analyses revealed that the Arabidopsis thaliana ARF and Aux/IAA families responded to multiple hormone, biotic, and abiotic stresses. The APETALA2 and serum response factor-transcription factor gene families were commonly enriched in the upstream and downstream genes of the ARF and Aux/IAA gene families. Our study provides a comprehensive overview of the evolutionary trajectories, structural functions, expansion mechanisms, expression patterns, and regulatory networks of these two gene families.

Microstructural Characteristics and Properties of Laser-Welded Diamond Saw Blade with 30CrMo Steel.

In order to enhance the quality of diamond composite materials, this work employs a Cu-Co-Fe and Ni-Cr-Cu pre-alloyed powder mixture as a transition layer, and utilizes laser-welding technology for saw blade fabrication. By adjusting the laser-welding process parameters, including welding speed and welding power, well-formed welded joints were achieved, and the microstructure and mechanical properties of the welded joints were investigated. The results demonstrate that the best welding performance was achieved at a laser power of 1600 W and a welding speed of 1400 mm/min, with a remarkable tooth engagement strength of up to 819 MPa. The fusion zone can be divided into rich Cu phase and rich Fe phase regions, characterized by coarse grains without apparent preferred orientation. The microstructure of the heat-affected zone primarily consists of high-hardness brittle quenched needle-like martensite, exhibiting a sharp increase in microhardness up to 550 HV. Fracture occurred at the boundary between the fusion zone and the heat-affected zone of the base material, where stress concentration was observed. By adjusting the welding parameters and transition layer materials, the mechanical properties of the joints were improved, thereby achieving a reliable connection between diamond composite materials and the metal substrate.

CO Intermediate-Assisted Dynamic Cu Sintering During Electrocatalytic CO2 Reduction on Cu-N-C Catalysts.

The electrochemical CO2 reduction reaction (eCO2RR) to multicarbon products has been widely recognized for Cu-based catalysts. However, the structural changes in Cu-based catalysts during the eCO2RR pose challenges to achieving an in-depth understanding of the structure-activity relationship, thereby limiting catalyst development. Herein, we employ constant-potential density functional theory calculations to investigate the sintering process of Cu single atoms of Cu-N-C single-atom catalysts into clusters under eCO2RR conditions. Systematic constant-potential ab initio molecular dynamics simulations revealed that the leaching of Cu-(CO)x moieties and subsequent agglomeration into clusters can be facilitated by synergistic adsorption of H and eCO2RR intermediates (e.g., CO). Increasing the Cu2+ concentration or the applied potential can efficiently suppress Cu sintering. Both microkinetic simulations and experimental results further confirm that sintered Cu clusters play a crucial role in generating C2 products. These findings provide significant insights into the dynamic evolution of Cu-based catalysts and the origin of their activity toward C2 products during the eCO2RR.

The mechanism of water oxidation using transition metal-based heterogeneous electrocatalysts.

The water oxidation reaction, a crucial process for solar energy conversion, has garnered significant research attention. Achieving efficient energy conversion requires the development of cost-effective and durable water oxidation catalysts. To design effective catalysts, it is essential to have a fundamental understanding of the reaction mechanisms. This review presents a comprehensive overview of recent advancements in the understanding of the mechanisms of water oxidation using transition metal-based heterogeneous electrocatalysts, including Mn, Fe, Co, Ni, and Cu-based catalysts. It highlights the catalytic mechanisms of different transition metals and emphasizes the importance of monitoring of key intermediates to explore the reaction pathway. In addition, advanced techniques for physical characterization of water oxidation intermediates are also introduced, for the purpose of providing information for establishing reliable methodologies in water oxidation research. The study of transition metal-based water oxidation electrocatalysts is instrumental in providing novel insights into understanding both natural and artificial energy conversion processes.

Regulation of nitrogen transformation and microbial community by inoculation during livestock manure composting.

This study examined the effects of three Bacillus strains and one Saccharomyces cerevisiae strain on nitrogen transformation and microbial communities in pig and chicken manure compost. The findings revealed that the use of compound microbial inoculants increased the compost temperature, accelerated moisture reduction, enhanced cellulase activity, and stimulated the accumulation of NH4 +-N, NO3 --N, and total nitrogen (TN), resulting in a 9% increase in TN content. The abundance of Firmicutes decreased by 3.95% at the maturation phase, while Actinobacteria and Bacteroidetes increased by 1.64% and 1.85%, respectively. Inoculation led to an increase in amoA, nxrA and nifH gene copy numbers, while simultaneously reducing the abundance of nirK, nosZ and nirS genes. It also resulted in an increase in functional enzyme levels, specifically nif and amo, with a corresponding decrease in nor. Clostridium, Phascolarctobacterium, Eubacterium and Faecalibacterium from the class Clostridium, which have a significant correlation with nifH and nxrA genes, suggest their likely crucial role in nitrogen retention and fixation. Inoculation aided in the removal of pathogenic bacteria and antibiotic resistance genes (ARGs) like fluoroquinolones, nucleosides and nitroimidazole. This study provides effective theoretical support for the mechanism of nitrogen retention and fixation, and for improving the quality of compost.