TMErisk score: A tumor microenvironment-based model for predicting prognosis and immunotherapy in patients with head and neck squamous cell carcinoma.

Tumor microenvironment (TME) is closely associated with the progression and prognosis of head and neck squamous cell carcinoma (HNSCC). To investigate potential biomarkers for predicting therapeutic outcomes in HNSCC, we analyzed the immune and stromal status of HNSCC based on the genes associated with TME using the ESTIMATE algorithm. Immune and stromal genes were identified with differential gene expression and weighted gene co-expression network analysis (WGCNA). From these genes, 118 were initially selected through Cox univariate regression and then further input into least absolute shrinkage and selection operator (LASSO) regression analysis. As a result, 11 genes were screened out for the TME-related risk (TMErisk) score model which presented promising overall survival predictive potential. The TMErisk score was negatively associated with immune and stromal scores but positively associated with tumor purity. Individuals with high TMErisk scores exhibited decreased expression of most immune checkpoints and all human leukocyte antigen family genes, and reduced abundance of infiltrating immune cells. Divergent genes were mutated in HNSCC. In both high and low TMErisk score groups, the tumor protein P53 exhibited the highest mutation frequency. A higher TMErisk score was found to be associated with reduced overall survival probability and worse outcomes of immunotherapy. Therefore, the TMErisk score could serve as a valuable model for the outcome prediction of HNSCC in clinic.

Recent Advances in Bacterial Persistence Mechanisms.

The recurrence of bacterial infectious diseases is closely associated with bacterial persisters. This subpopulation of bacteria can escape antibiotic treatment by entering a metabolic status of low activity through various mechanisms, for example, biofilm, toxin-antitoxin modules, the stringent response, and the SOS response. Correspondingly, multiple new treatments are being developed. However, due to their spontaneous low abundance in populations and the lack of research on in vivo interactions between persisters and the host's immune system, microfluidics, high-throughput sequencing, and microscopy techniques are combined innovatively to explore the mechanisms of persister formation and maintenance at the single-cell level. Here, we outline the main mechanisms of persister formation, and describe the cutting-edge technology for further research. Despite the significant progress regarding study techniques, some challenges remain to be tackled.

Association between Intestinal Colonization and Extraintestinal Infection with Carbapenem-Resistant Klebsiella pneumoniae in Children.

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a critical public health threat. However, the association between intestinal colonization and parenteral infection among pediatric patients has not been elucidated. We collected 8 fecal CRKP strains and 10 corresponding CRKP strains responsible for extraintestinal infection from eight patients who did not manifest infection upon admission to the hospital. Paired isolates showed identical resistance to antimicrobials and identical virulence in vitro and in vivo. wzi capsule typing, multilocus sequence typing, and whole-genome sequencing (WGS) indicated high similarity between paired colonizing and infecting isolates. Mutations between colonizing and infecting isolate pairs found by WGS had a distinctive molecular signature of a high proportion of complex structural variants. The mutated genes were involved in pathways associated with infection-related physiological and pathogenic functions, including antibiotic resistance, virulence, and response to the extracellular environment. The latter is important for bacterial infection of environmental niches. Various mutations related to antibiotic resistance, virulence, and colonization that were not associated with any particular mutational hot spot correlated with an increased risk of extraintestinal infection. Notably, novel subclone carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) KL19-ST15 exhibited hypervirulence in experimental assays that reflected the severe clinical symptoms of two patients infected with the clonal strains. Taken together, our findings indicate the association between CRKP intestinal colonization and extraintestinal infection, suggesting that active screening for colonization on admission could decrease infection risk in children. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKP) causes an increasing number of nosocomial infections, which can be life-threatening, as carbapenems are last-resort antibiotics. K. pneumoniae is part of the healthy human microbiome, and this provides a potential advantage for infection. This study demonstrated that CRKP intestinal colonization is strongly linked to extraintestinal infection, based on the evidence given by whole-genome sequencing data and phenotypic assays of antimicrobial resistance and virulence. Apart from these findings, our in-depth analysis of point mutations and chromosome structural variants in patient-specific infecting isolates compared with colonizing isolates may contribute insights into bacterial adaptation underlying CRKP infection. In addition, a novel subclone of carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) was observed in the study. This finding highlights the importance of CRKP active surveillance among children, targeting in particular the novel high-risk CR-hvKP clone.

Reconfigurable Hexapartite Entanglement by Spatially Multiplexed Four-Wave Mixing Processes.

Multipartite entanglement serves as a vital resource for quantum information processing. Generally, its generation requires complex beam splitting processes which limit scalability. A promising trend is to integrate multiple nonlinear processes into a single device via frequency or time multiplexing. The generated states in these schemes are useful for quantum computation. However, they are confined in one or two beams and hard to be spatially separated for applications in quantum communication. Here, we experimentally demonstrate a scheme to generate spatially separated hexapartite entangled states by means of spatially multiplexing seven concurrent four-wave mixing processes. In addition, we show that the entanglement structure characterized by subsystem entanglement distribution can be modified by appropriately shaping the pump characteristics. Such reconfigurability of the entanglement structure gives the possibility to target a desired multipartite entangled state for a specific quantum communication protocol. Our results here provide a new platform for generating large scale spatially separated reconfigurable multipartite entangled beams.

Deterministic Generation of Orbital-Angular-Momentum Multiplexed Tripartite Entanglement.

We demonstrate the experimental generation of orbital angular momentum (OAM) multiplexed multipartite entanglement with cascaded four-wave mixing processes in a continuous variable (CV) system. In particular, we implement the simultaneous generation of 9 sets of OAM multiplexed tripartite entanglement over 27 Laguerre-Gauss (LG) modes, as well as 20 sets of OAM multiplexed bipartite entanglement over 40 LG modes, which show the rich entanglement structure of the system. In addition, we also generate tripartite entanglement of three types of coherent OAM superposition modes. Such OAM multiplexed multipartite entanglement opens the avenue to construct CV parallel quantum network for realizing parallel quantum information protocols.

Orbital-Angular-Momentum Multiplexed Continuous-Variable Entanglement from Four-Wave Mixing in Hot Atomic Vapor.

Multiplexing is crucial for the data-carrying capacity of information communication systems. Orbital angular momentum (OAM) with a topological charge ℓ (ℓ integer) provides a degree of freedom to realize multiplexing. In this Letter, we report an experimental implementation of OAM multiplexed continuous variables (CV) entanglement based on a four-wave mixing (FWM) process, in which 13 pairs of entangled Laguerre-Gauss (LG) modes, LG_{ℓ,pr} and LG_{-ℓ,conj}, are simultaneously and deterministically generated, where ℓ (ℓ integer) is the topological charge corresponding to the OAM mode and pr (conj) indicates a probe (conjugate) beam. In the meanwhile, we experimentally show that there is no entanglement between the modes of LG_{ℓ,pr} and LG_{ℓ,conj} (ℓ≠0). These results clearly confirm the conservation of OAM in the FWM process from the viewpoint of a CV system. In addition, we investigate the entanglement properties of three types of coherent superposition of OAM modes. In the end, we also study the effect of the pump beam radius on the number of OAM multiplexing. Such OAM multiplexed CV entanglement provides a new perspective and platform to study CV quantum information protocols.

An investigation into the role of ATP in the mammalian pre-mRNA 3' cleavage reaction.

RNA Polymerase II transcribes beyond what later becomes the 3' end of a mature messenger RNA (mRNA). The formation of most mRNA 3' ends results from pre-mRNA cleavage followed by polyadenylation. In vitro studies have shown that low concentrations of ATP stimulate the 3' cleavage reaction while high concentrations inhibit it, but the origin of these ATP effects is unknown. ATP might enable a cleavage factor kinase or activate a cleavage factor directly. To distinguish between these possibilities, we tested several ATP structural analogs in a pre-mRNA 3' cleavage reaction reconstituted from DEAE-fractionated cleavage factors. We found that adenosine 5'-(ß,γ-methylene)triphosphate (AMP-PCP) is an effective in vitro 3' cleavage inhibitor with an IC50 of ∼300 µM, but that most other ATP analogs, including adenosine 5'-(ß,γ-imido)triphosphate, which cannot serve as a protein kinase substrate, promoted 3' cleavage but less efficiently than ATP. In combination with previous literature data, our results do not support ATP stimulation of 3' cleavage through cleavage factor phosphorylation in vitro. Instead, the more likely mechanism is that ATP stimulates cleavage factor activity through direct cleavage factor binding. The mammalian 3' cleavage factors known to bind ATP include the cleavage factor II (CF IIm) Clp1 subunit, the CF Im25 subunit and poly(A) polymerase alpha (PAP). The yeast homolog of the CF IIm complex also binds ATP through yClp1. To investigate the mammalian complex, we used a cell-line expressing FLAG-tagged Clp1 to co-immunoprecipitate Pcf11 as a function of ATP concentration. FLAG-Clp1 co-precipitated Pcf11 with or without ATP and the complex was not affected by AMP-PCP. Diadenosine tetraphosphate (Ap4A), an ATP analog that binds the Nudix domain of the CF Im25 subunit with higher affinity than ATP, neither stimulated 3' cleavage in place of ATP nor antagonized ATP-stimulated 3' cleavage. The ATP-binding site of PAP was disrupted by site directed mutagenesis but a reconstituted 3' cleavage reaction containing a mutant PAP unable to bind ATP nevertheless underwent ATP-stimulated 3' cleavage. Fluctuating ATP levels might contribute to the regulation of pre-mRNA 3' cleavage, but the three subunits investigated here do not appear to be responsible for the ATP-stimulation of pre-mRNA cleavage.