Helicobacter pylori causes gastric dysbacteriosis in chronic gastritis patients.

Gastric mucosal samples were procured and underwent the sequencing of 16S ribosomal RNA (16S rRNA) via Illumina high-throughput sequencing technology to explore the impact of Helicobacter pylori (H. pylori) infection on the composition of gastric flora in chronic gastritis (CG) patients. In the results, the operational taxonomic unit (OTU) analysis revealed an overlap of 5706 OTUs shared between the two groups. The top 5 abundance ranking (TOP5) phyla comprised Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Epsilonbacteraeota, while the TOP5 genus was Lachnospiraceae_NK4A136_group, Helicobacter, Bacteroides, Klebsiella, and Pseudomonas. In the metabolic pathways at the Kyoto Encyclopedia of Genes and Genomes (KEGG)_L3 level, conspicuous variations across seven functions were observed between the H. pylori-positive (HP_Pos) and H. pylori-negative (HP_Neg) groups. Subsequently, functional gene enrichment in KEGG pathways was further validated through animal experimentation. In contrast to the mice in the HP_Neg group, those infected with H. pylori manifested an infiltration of inflammatory cells, an augmentation in gastric acid secretion, and conspicuously elevated scores regarding gastric activity, along with heightened levels of malondialdehyde. In conclusion, CG patients infected with H. pylori displayed a disorder in gastric flora, furnishing a theoretical basis for the prophylaxis of H. pylori infection and its associated pathogenic ramifications.

CagA-positive Helicobacter pylori may promote and aggravate scrub typhus.

Helicobacter pylori (H. pylori) infection may alter the host's resistance to tsutsugamushi disease pathogens through the Th1 immune response, leading to potential synergistic pathogenic effects. A total of 117 scrub typhus cases at Beihai People's Hospital and affiliated hospitals of Youjiang University for Nationalities and Medical Sciences were studied from January to December 2022, alongside 130 healthy individuals forming the control group. All participants underwent serum H. pylori antibody testing. The prevalence of H. pylori infection was significantly higher among scrub typhus patients (89.7%) compared to healthy individuals (54.6%) (p < 0.05). Moreover, type I H. pylori infection was notably more prevalent in scrub typhus cases (67.5%) compared to healthy individuals (30%) (p < 0.05). Multifactorial analysis demonstrated type I H. pylori infection as an independent risk factor for scrub typhus (adjusted odds ratio: 2.407, 95% confidence interval: 1.249-4.64, p = 0.009). Among scrub typhus patients with multiple organ damage, the prevalence of type I H. pylori infection was significantly higher (50.6%) than type II H. pylori infection (15.4%) (χ2 = 4.735, p = 0.030). These results highlight a higher incidence of H. pylori infection in scrub typhus patients compared to the healthy population. Additionally, type I H. pylori strain emerged as an independent risk factor for scrub typhus development. Moreover, individuals infected with type I H. pylori are more susceptible to multiple organ damage. These findings suggest a potential role of H. pylori carrying the CagA gene in promoting and exacerbating scrub typhus.

Boosting the oxygen reduction reaction activity of dual-atom catalysts on N-doped graphene by regulating the N coordination environment.

Development of low-cost and high-efficiency oxygen reduction reaction (ORR) catalysts is of significance for fuel cells and metal-air batteries. Here, by regulating the N environment, a series of dual-atom embedded N5-coordinated graphene catalysts, namely M1M2N5 (M1, M2 = Fe, Co, and Ni), were constructed and systematically investigated by DFT calculations. The results reveal that all M1M2N5 configurations are structurally and thermodynamically stable. The strong adsorption of *OH hinders the proceeding of ORR on the surface of M1M2N5, but M1M2N5(OH2) complexes are formed to improve their catalytic activity. In particular, FeNiN5(OH2) and CoNiN5(OH2) with the overpotentials of 0.33 and 0.41 V, respectively, possess superior ORR catalytic activity. This superiority should be attributed to the reduced occupation of d-orbitals of Fe and Co atoms in the Fermi level and the apparent shift of dyz and dz2 orbitals of Ni atoms towards the Fermi level after adsorbing *OH, thus regulating the active sites and exhibiting appropriate adsorption strength for reaction intermediates. This work provides significant insight into the ORR mechanism and theoretical guidance for the discovery and design of low-cost and high-efficiency graphene-based dual-atom ORR catalysts.

Experimental study on flow resistance characteristics of the uniform steam injection outflow control device.

Introduction: Multi-point steam injection technology is a new completion method for heavy oil horizontal wells to solve the uneven distribution of the intake profile in the horizontal section. It is equipped with the flow control device to achieve the effect of balanced steam injection. Methods: The steady-state experiment method was adopted; Considering the variable mass complex flow of the steam-liquid two-phase flow in the downhole flow device, the pressure loss of downhole tools through uniform steam injection with different steam-liquid compositions was tested, the influencing factors of the pressure drop were analyzed, and a more reliable pressure drop calculation method was established. Results: The overflow pressure drop can be adjusted by changing the aperture, steam dryness, and fluid flow of the downhole outflow control device (OCD). Discussion: By comparing the experimental and theoretical results, the calculation method of the overflow resistance of single-phase and steam-liquid two-phase fluids in OCD is given, and the error is within the usable range.

The s-p Nonhybrid Nature Causes Adaptive Superatomic States of Bismuth Clusters.

We report a joint experimental and theoretical study on the stability and reactivity of Bin + (n=5-33) clusters. The alternating odd-even effect on the reaction rates of Bin + clusters with NO is observed, and Bi7 + finds the most inertness. First-principles calculation results reveal that the lowest energy structures of Bi6-9 + exhibit quasi-spherical geometry pertaining to the jellium shell model; however, the Bin + (n≥10) clusters adopt assembly structures. The prominent stability of Bi7 + is associated with its highly symmetric structure and superatomic states with a magic number of 34e closed shell. For the first time, we demonstrate that the unique s-p nonhybrid feature in bismuth rationalizes the stability of Bi6-9 + clusters within the jellium model, by filling the 6s electrons into the superatomic orbitals (forming "s-band"). Interestingly, the stability of 18e "s-band" coincides with the compact structure for Bin + at n≤9 but assembly structures for n≥10, showing an accommodation of the s electrons to the geometric structure. The atomic p-orbitals also allow to form superatomic orbitals at higher energy levels, contributing to the preferable structures of tridentate binding units. We illustrate the s-p nonhybrid nature accommodates the structure and superatomic states of bismuth clusters.

Single atom alloy clusters Agn-1X- (X = Cu, Au; n = 7-20) reacting with O2: Symmetry-adapted orbital model.

Single atom alloy AgCu catalysts have attracted great attention, since doping the single Cu atom introduces narrow free-atom-like Cu 3d states in the electronic structure. These peculiar electronic states can reduce the activation energies in some reactions and offer valuable guidelines for improving catalytic performance. However, the geometric tuning effect of single Cu atoms in Ag catalysts and the structure-activity relationship of AgCu catalysts remain unclear. Here, we prepared well-resolved pristine Agn - as well as single atom alloy Agn-1Cu- and Agn-1Au- (n = 7-20) clusters and investigated their reactivity with O2. We found that replacing an Ag atom in Agn - (n = 15-18) with a Cu atom significantly increases the reactivity with O2, while replacement of an Ag with an Au atom has negligible effects. The adsorption of O2 on Agn - or Agn-1Cu- clusters follows the single electron transfer mechanism, in which the cluster activity is dependent on two descriptors, the energy level of α-HOMO (strong correlation) and the α-HOMO-LUMO gap (weak correlation). Our calculation demonstrated that the cluster arrangements caused by single Cu atom alloying would affect the above activity descriptors and, therefore, regulates clusters' chemical activity. In addition, the observed reactivity of clusters in the representative sizes with n = 17-19 can also be interpreted using the symmetry-adapted orbital model. Our work provides meaningful information to understand the chemical activities of related single-atom-alloy catalysts.

METTL3 potentiates progression of cervical cancer by suppressing ER stress via regulating m6A modification of TXNDC5 mRNA.

N6-methyladenosine (m6A) is the most abundant chemical modification on mRNA and plays significant roles in many bioprocesses. However, the functions of m6A on cervical cancer (CC) tumorigenesis remain unclear. Here we found methyltransferase-like 3 (METTL3), a core member of the m6A methyltransferase family, was greatly upregulated as an independent prognostic factor in CC. Mechanistically, the transcription factor ETS1 recruited P300 and WDR5 which separately mediated H3K27ac and H3K4me3 histone modification in the promoter of METTL3 and induced METTL3 transcription activation. Furthermore, we identified TXNDC5 as a target of METTL3-mediated m6A modification through MeRIP-seq, and revealed that METTL3-mediated TXNDC5 expression relied on the m6A reader-dependent manner. Functionally, we verified that METTL3 promoted proliferation and metastasis of CC cells by regulating of TXNDC5 expression through in vitro and in vivo experiments. In addition, our study verified the effect of METTL3/TXNDC5 axis on ER stress. Taken together, METTL3 facilitates the malignant progression of CC, suggesting that METTL3 might be a potential prognostic biomarker and therapeutic target for CC.

The biological function of IGF2BPs and their role in tumorigenesis.

The insulin-like growth factor-2 mRNA-binding proteins (IGF2BPs) pertain to a highly conservative RNA-binding family that works as a post-transcriptional fine-tuner for target transcripts. Emerging evidence suggests that IGF2BPs regulate RNA processing and metabolism, including stability, translation, and localization, and are involved in various cellular functions and pathophysiologies. In this review, we summarize the roles and molecular mechanisms of IGF2BPs in cancer development and progression. We mainly discuss the functional relevance of IGF2BPs in embryo development, neurogenesis, metabolism, RNA processing, and tumorigenesis. Understanding IGF2BPs role in tumor progression will provide new insight into cancer pathophysiology.

METTL3-mediated m6A methylation of SPHK2 promotes gastric cancer progression by targeting KLF2.

N6-methyladenosine (m6A) RNA methylation is profoundly involved in epigenetic regulation, especially for carcinogenesis and tumor progression. Mounting evidence suggests that methyltransferase METTL3 regulates malignant behaviors of gastric cancer (GC). However, the clinical significance and biological implication of SPHK2 and its related m6A modification in GC remain unclear. In this study, quantitative real-time PCR (qRT-PCR), western blot and immunohistochemistry were utilized to detect the expression profiles and prognostic significance of SPHK2 in GC. Here, we showed that increased SPHK2 was signified a poor prognosis of GC patients. Phosphorylation and ubiquitination assays were used to investigate the possible mechanisms of SPHK2-mediated KLF2 expression. SPHK2 can promote the phosphorylation of KLF2, which triggers the ubiquitination and degradation of KLF2 protein in GC. Methylated RNA immunoprecipitation (MeRIP) was performed to uncover the m6A modification of SPHK2 mRNA. METTL3 promotes translation of SPHK2 mRNA via an m6A-YTHDF1-dependent manner. Functionally, SPHK2 facilitates GC cell proliferation, migration and invasion by inhibiting KLF2 expression. SPHK2/KLF2 regulates the cell proliferation, migration, and invasion induced by METTL3 in GC. Overall, our findings reveal that METTL3-mediated m6A modification of SPHK2 contributes to GC progression, which extends the understanding of the importance m6A methylation in GC and represents a potential target for GC therapy.

TM4B18 0/- (TM = Hf, Ta, W, Re, Os): new structure construction with TM doped B wheel units.

We report the global search for the lowest energy structures of the transition metal (TM) doped B clusters, TM4B18 0/- (TM = Hf, Ta, W, Re, Os) and their electronic properties. A combination of the comprehensive genetic algorithm (CGA) method with density functional theory (DFT) calculations shows that they are composed of four planar TM@B9 wheel units by sharing B atoms, except for Os4B18 0/-, which consists of two types of planar molecular wheels of Os@B7 and Os@B8. Among these nanoclusters, it is found that the Ta4B18 cluster has a closed-shell with a large HOMO-LUMO gap of 2.61 eV. Adaptive natural density partitioning analysis (AdNDP) reveals that the Ta4B18 cluster has σ antiaromaticity and π aromaticity, i.e., a conflicting aromaticity. The simulated photoelectron spectra (PES) of all anionic clusters are also provided for future experimental investigations.

Endohedrally Doped Cage Clusters.

The discovery of carbon fullerene cages and their solids opened a new avenue to build materials from stable cage clusters as "artificial atoms" or "superatoms" instead of atoms. However, cage clusters of other elements are generally not stable. In 2001, ab initio calculations showed that endohedral doping of Zr and Ti atoms leads to highly stable Zr@Si16 fullerene and Ti@Si16 Frank-Kasper polyhedral clusters with large HOMO-LUMO gaps. In 2002, Zr@Ge16 was shown to form a Frank-Kasper polyhedron, suggesting the possibility of designing novel clusters by tuning endohedral and cage atoms. These results were subsequently confirmed from experiments. In the past nearly two decades, many experimental and theoretical studies have been carried out on different clusters, and many very stable cage clusters with possibly high abundance have been found by endohedral doping. Indeed in 2017, Ta@Si16 and Ti@Si16 cage clusters have been synthesized in bulk quantity of about 100 mg using a dry-chemistry method, giving rise to a new hope of developing cluster-based materials in macroscopic quantity besides the well-known C60 fullerene solid. Also, wet-chemistry methods have been used to synthesize endohedrally doped clusters as well as ligated clusters and their solids, which auger well for the development of novel nanostructured materials using atomically precise clusters with unique properties. In this comprehensive review, we present results of many such developments in this fast-growing field including (i) endohedrally doped Al, Ga, and In clusters, (ii) small endohedral carbon fullerene cages with ≤ 28 carbon atoms, (iii) metal doped boron cages, (iv) endohedrally doped cages of group 14 elements (Si, Ge, Sn, and Pb), (v) coinage metal (Cu, Ag, Au) cages doped with a transition metal atom as well as their ligated clusters and crystals, (vi) endohedrally doped cages of compound semiconductors, and (vii) multilayer Matryoshka cages and core-shell structures. In a large number of cases, we have performed ab initio calculations to present updated results of the most stable atomic structures and fundamental electronic properties of the endohedrally doped cage clusters. We discuss electronic, magnetic, optical, and catalytic properties in order to shed light on their potential applications. The stability of the doped cage clusters has been correlated to the concept of filling the electronic shells for superatoms such as within a spherical potential model and also using various electron counting rules including Wade-Mingos rules, systems with 18 and 32 electrons, and the spherical aromaticity rule. We also discuss cluster-cluster interaction in cluster dimers and assemblies of some of the promising doped cage clusters in different dimensions. Finally, we give a perspective of this field with a bright future.

Anionic Copper Clusters Reacting with NO: An Open-Shell Superatom Cu18.

Gas-phase metal clusters have been a subject of research interest for allowing reliable strategies to explore the stability and reactivity of materials at reduced sizes with atomic precision. Here we have prepared well-resolved copper cluster anions Cun- (n = 7-37) and systematically studied their reactivity with O2, NO, and CO. We found remarkable stability of an open-shell cluster Cu18-, which is comparable with the closed-shell clusters Cu17- and Cu19- within the picture of an electronic shell model. Even without having a magic number of valence electrons, intriguingly, the unpaired electron on the singly occupied molecular orbital of Cu18- is mainly contributed by the central copper atom, while the other 18 delocalized valence electrons occupy the lower-energy superatomic orbitals of the cluster. The finding of such an open-shell superatom Cu18-, with an electron configuration of 1S21P61D102S1||1F0, is interesting in the sense that an elementary cluster of coinage metal atoms could still behave as a superatom mimicking coinage metals like silver or gold atoms with an empty f orbital. The superatomic stability of this Cu18- cluster is reinforced by the unique electrostatic interaction between the Cu- core and Cu17 shell, which provides new insights into the chemistry of metal clusters.

Evolution of atomic structures of SnN, SnN -, and SnNCl- clusters (N = 4-20): Insight from ab initio calculations.

An unbiased global search was employed to explore the low-energy structures of SnN, SnN -, and SnNCl- clusters with N = 4-20 atoms based on the genetic algorithm combined with density functional theory calculations. Some unprecedented low-energy isomers are reported for SnN and SnNCl- clusters. The theoretical electronic properties such as binding energy per atom, ionization potential, adiabatic detachment energy, and vertical detachment energy compare well with the experimental data. Based on the equilibrium structures, the simulated photoelectron spectra are in good agreement with the experimental data in the range of N = 4-20. With addition of a Cl atom on the SnN - cluster, which causes almost no rearrangement on the structural framework, the first peaks in all original photoelectron spectra of SnN - clusters disappear and other peaks nearly retain the original feature at most sizes.

Foreign atom encapsulated Au12 golden cages for catalysis of CO oxidation.

Gold clusters are known for their unique catalytic properties, among which, endohedral gold clusters doped with heteroatoms have remarkable stabilities, with electronic structures tunable by both cluster size and doping element. Thus, it is intriguing and imperative to understand the principles for modulating the catalytic behaviors of these novel clusters. Here, we exploit experimentally produced M@Au12 (M = transition metal) cage clusters for catalysis of CO oxidation. The doping effects of 3d, 4d and 5d transition metals (V, Cr, Mn, Nb, Mo, Ta, W and Re) on the catalytic properties were systematically explored by first-principles calculations. Among the considered M@Au12 clusters, Cr@Au12 and Mn@Au12 provide a suitable binding strength with reaction intermediates and are highly active for CO oxidation with reaction barriers of 0.41 eV under the Langmuir-Hinshelwood mechanism. More importantly, we establish a distinct relationship between catalytic activity and the M-Au bond order and the d orbital center of the M@Au12 clusters, which would help tailor their catalytic performance with atomistic precision and enable utilization of these stable gold cages for catalysis of various chemical processes.

Medium-sized [Formula: see text] (n = 14-20) clusters: a combined study of photoelectron spectroscopy and DFT calculations.

Size-selected anionic silicon clusters, [Formula: see text] (n = 14-20), have been investigated by photoelectron spectroscopy and density functional theory (DFT) calculations. Low-energy structures of the clusters are globally searched for by using a genetic algorithm based on DFT calculations. The electronic density of states and vertical detachment energies have been simulated by using ten DFT functionals and compared to the experimental results. We systematically evaluated the DFT functionals for the calculation of the energetics of silicon clusters. CCSD(T) single-point energies based on MP2 optimized geometries for selected isomers of [Formula: see text] are also used as benchmark for the energy sequence. The HSE06 functional with aug-cc-pVDZ basis set is found to show the best performance. Our global minimum search corroborates that most of the lowest-energy structures of [Formula: see text] (n = 14-20) clusters can be derived from assembling tricapped trigonal prisms in various ways. For most sizes previous structures are confirmed, whereas for [Formula: see text] a new structure has been found.