One panel with four single nucleotide polymorphisms for Chinese children with asthma: Integrating public data and whole exome sequencing.

BACKGROUND: Polymorphisms in susceptibility genes are a major risk factor for the development of asthma. Understanding these genetic variants helps elucidate asthma's pathogenesis, predict its onset, expedite antiasthma medication development, and achieve precise targeted individualized treatment. This study developed a test kit based on susceptibility genes for predicting asthma in Chinese children. METHODS: The present study constructed a VariantPro Targeted Library Preparation System with 72 single nucleotide polymorphism (SNP) loci associated with asthma from the ClinVar, OMIM, and SNPedia databases. These SNP loci were detected in the peripheral blood of 499 children with asthma and 500 healthy children. Significant differences were discovered for seven SNP loci. Simultaneously, whole exome sequencing of 46 children with asthma and 50 healthy children identified eight SNP loci with significant differences. The 15 SNP loci identified from Chinese children with asthma were validated in an independent population of 97 children with asthma and 93 healthy children by conducting multiplex polymerase chain reaction (PCR)-next-generation sequencing genotyping. RESULTS: Four loci (rs12422149, rs7216389, rs4065275, and rs41453444) were identified, and a single-tube multifluorescent qPCR (real-time quantitative PCR) test kit was developed using these four SNP loci. The kit was tested on 269 children with asthma and 724 children with bronchopneumonia. CONCLUSIONS: We identified four loci as susceptibility genes and developed a quantitative PCR test kit for predicting asthma development in Chinese children.

A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species.

Background: Genome data have been used to find novel allergen from house dust mites. Here, we aim to construct a chromosome-level genome assembly of Dermatophagoides farinae, a common allergenic mite species. Methods: We achieved a chromosome-level assembly of D. farinae's genome by integrating PacBio single-molecule real-time sequencing, Illumina paired-end sequencing, and Hi-C technology, followed by annotating allergens and mapping them to specific chromosomes. Results: A 62.43 Mb genome was assembled with a 0.52% heterozygosity rate and a 36.11 Merqury-estimated quality value. The assembled genome represents 92.1% completeness benchmarking universal single-copy orthologs with a scaffold N50 value of 7.11 Mb. Hi-C scaffolding of the genome resulted in construction of 10 pseudochromosomes. The genome comprises 13.01% (7.66 Mb) repetitive sequences and predicts 10,709 protein-coding genes, 96.57% of which are functionally annotated. Moreover, we identified and located 36 allergen groups on specific chromosomes, including allergens Der f 1, Der f 2, Der f 23, Der f 4, Der f 5, Der f 7, and Der f 21 located on chromosomes 2, 1, 7, 3, 4, 6, and 4, respectively. Conclusion: This comprehensive genomic data provides valuable insights into mite biology and evolutionary adaptations, potentially advancing D. farinae allergy research and treatment strategies.

Visualizing a single wavefront dislocation induced by orbital angular momentum in graphene.

Phase singularities are phase-indeterminate points where wave amplitudes are zero, which manifest as phase vertices or wavefront dislocations. In the realm of optical and electron beams, the phase singularity has been extensively explored, demonstrating a profound connection to orbital angular momentum. Direct local imaging of the impact of orbital angular momentum on phase singularities at the nanoscale, however, remains challenging. Here, we study the role of orbital angular momentum in phase singularities in graphene, particularly at the atomic level, through scanning tunneling microscopy and spectroscopy. Our experiments demonstrate that the scatterings between different orbital angular momentum states, which are induced by local rotational symmetry-breaking potentials, can generate additional phase singularities, and result in robust single-wavefront dislocations in real space. Our results pave the way for exploring the effects of orbital degree of freedom on quantum phases in quasiparticle interference processes.

Immunobiological properties and structure analysis of group 13 allergen from Blomia tropicalis and its IgE-mediated cross-reactivity.

Blomia tropicalis is an important species of allergenic mite. Structurally related cross-reactive allergens are involved in pathogenesis of clinical symptoms. The present study focused on recombinant allergen rBlo t 13 from B. tropicalis, including investigation of its structure, immunological properties, IgE-mediated cross-reactivity. In this work, the prokaryotic expression plasmids pET-28(a)-Blo t 13, pET-28(a)-Der f 13, and pET-28(a)-Tyr p 13 were constructed, transformed into E. coli Rosetta (DE3) pLysS, and purified by nickel affinity chromatography, respectively. By using ELISA, the IgE-binding rates were detected for rBlo t 13 and its epitope peptides, as well as the cross-reactivity among rBlo t 13, rDer f 13, and rTyr p 13. The tertiary structure of rBlo t 13 was resolved using X-ray diffraction at 2.0 Å resolution. Using IgE-ELISA, the IgE binding rate of rBlo t 13 was 60 % with Blomia tropicalis-positive sera. In the experiments of ELISA for cross-reactivity with rBlo t 13 on solid phase, the inhibition rates were 65 %, 57 % and 63 % for rBlo t 13, rDer f 13, and rTyr p 13, respectively. The structure of Blo t 13 protein contains a ß-barrel structure which is composed of 10 ß strands and has 2 α helices at the end of the barrel. Comparison of the tertiary structures of rBlo t 13, rDer f 13, and rTyr p 13 revealed that the ß-barrel structure is highly conserved, consistent with the alignment of amino acid sequences. We obtained the recombinant protein rBlo t 13, demonstrated its cross-reactivity with Der f 13 and Tyr p 13 due to their structural similarity.

Expression, purification, and activity of novel allergen Tyr p 31 from Tyrophagus putrescentiae.

Allergen component products, such as recombinant proteins and epitope peptides of allergic components, are used as an adjunct to allergen-specific immunotherapy. We characterized a novel allergen, Tyr p 31, from Tyrophagus putrescentiae, a common allergenic mite. T. putrescentiae total RNA was amplified to Tyr p 31-encoding cDNA, which was inserted into pET28a(+). pET28a(+)-Tyr p 31 was then transformed into Rosetta 2 (DE3) pLysS cells and expressed under isopropyl ß-D-thiogalactoside induction. Next, we visualized Tyr p 31 through sodium dodecyl sulfate polyacrylamide gel electrophoresis and Western blotting based on its theoretical molecular weight. Recombinant Tyr p 31 (rTyr p 31) was purified, and its secondary structure was noted to comprise α-helices, antiparallel coils, ß-turns, parallel coils, and random coils. Our enzyme-linked immunosorbent assay and Western blotting results for T. putrescentiae-positive sera from children with allergic disorders demonstrated rTyr p 31-specific IgE-positivity rates of 72.41 % and 85.7 %, respectively. In BEAS-2B cells, rTyr p 31 increased IL-6 and IL-8 expression; furthermore, BEAS-2B cells treated with 30 µg/mL rTyr p 31 demonstrated 100 upregulated and 12 downregulated genes. In summary, we identified Tyr p 31, a novel T. putrescentiae allergen component, and noted rTyr p 31 to have a high IgE-binding rate and strong immunogenicity.

Multi feature fusion network for schizophrenia classification and abnormal brain network recognition.

Schizophrenia classification and abnormal brain network recognition have an important research significance. Researchers have proposed many classification methods based on machine learning and deep learning. However, fewer studies utilized the advantages of complementary information from multi feature to learn the best representation of schizophrenia. In this study, we proposed a multi-feature fusion network (MFFN) using functional network connectivity (FNC) and time courses (TC) to distinguish schizophrenia patients from healthy controls. DNN backbone was adopted to learn the feature map of functional network connectivity, C-RNNAM backbone was designed to learn the feature map of time courses, and Deep SHAP was applied to obtain the most discriminative brain networks. We proved the effectiveness of this proposed model using the combining two public datasets and evaluated this model quantitatively using the evaluation indexes. The results showed that the functional network connectivity generated by independent component analysis has advantage in schizophrenia classification by comparing static and dynamic functional connections. This method obtained the best classification accuracy (ACC=87.30%, SPE=89.28%, SEN=85.71%, F1 =88.23%, and AUC=0.9081), and it demonstrated the superiority of this proposed model by comparing state-of-the-art methods. Ablation experiment also demonstrated that multi feature fusion and attention module can improve classification accuracy. The most discriminative brain networks showed that default mode network and visual network of schizophrenia patients have aberrant connections in brain networks. In conclusion, this method can identify schizophrenia effectively and visualize the abnormal brain network, and it has important clinical application value.

Natural killer cells contribute to 'hot' tumor regression in the allergic inflammatory environment.

Systemic immune status influences the elimination of tumor cells. However, it remains unclear how chronic inflammation in allergic diseases affects the tumor microenvironment and tumorigenesis. To investigate tumor progression in a state of heightened allergic inflammation, we established a mouse model of allergic inflammation. We used house dust mite extract to induce a hyper-reactive systemic immune response. Additionally, we subcutaneously inoculated two types of cancer cells (CT26 and 4T1 tumors). We conducted immune profiling of the ex-vivo tumor mass using multicolor flow cytometry staining and performed dynamic analysis of peripheral cytokines to explore the significant relationship between the development of allergic inflammation and tumorigenesis. We found that mice in a state of allergic inflammation were more susceptible to developing tumors. Interestingly, the growth of T cell-inflamed was inhibited in the allergic state, while growth of non-T cell-inflamed was promoted. Further research revealed that natural killer (NK) cells with enhanced tumor-killing or immune-regulating abilities were more active in " hot " tumors. Inhibiting NK cell activity can partially alleviate the impact of allergic inflammation on tumor growth. In summary, our results suggest that NK cells play significant role in suppressing tumor growth in an allergic inflammation mouse model. This phenomenon seems to be closely linked to both the inherent characteristics of the tumor and its interaction with the immune system. The innate immune system can be mobilized to synergize with the adaptive immune system to inhibit tumor growth, which opens a new way for a tumor immunotherapy.

Observation of Robust and Long-Ranged Superperiodicity of Electronic Density Induced by Intervalley Scattering in Graphene/Transition Metal Dichalcogenide Heterostructures.

Two-dimensional (2D) h-BN and transition metal dichalcogenides (TMDs) are widely used as substrates of graphene because they are insulating, atomically flat, and without dangling bonds. Usually, it is believed that such insulating substrates will not affect the electronic properties of graphene, especially when the moiré pattern generated between them is quite small. Here, we present a systematic study of the electronic properties of graphene/TMD heterostructures with the period of the moiré pattern <1 nm, and our results reveal an unexpected sensitivity of electronic properties in graphene to the 2D insulating substrates. We demonstrate that there is a robust and long-ranged superperiodicity of electronic density in graphene, which arises from the scattering of electrons between the two valleys of graphene in the graphene/TMD heterostructures. By using scanning tunneling microscope and spectroscopy, three distinct atomic-scale patterns of the electronic density are directly imaged in every graphene/TMD heterostructure.

Molecular Collapse States in Graphene/WSe_{2} Heterostructure Quantum Dots.

In relativistic physics, both atomic collapse in a heavy nucleus and Hawking radiation in a black hole are predicted to occur through the Klein tunneling process that couples particles and antiparticles. Recently, atomic collapse states (ACSs) were explicitly realized in graphene because of its relativistic Dirac excitation with a large "fine structure constant." However, the essential role of the Klein tunneling in the ACSs remains elusive in experiment. Here we systematically study the quasibound states in elliptical graphene quantum dots (GQDs) and two coupled circular GQDs. Bonding and antibonding molecular collapse states formed by two coupled ACSs are observed in both systems. Our experiments supported by theoretical calculations indicate that the antibonding state of the ACSs will change into a Klein-tunneling-induced quasibound state revealing deep connection between the ACSs and the Klein tunneling.

Endogenous Plasmids and Chromosomal Genome Reduction in the Cardinium Endosymbiont of Dermatophagoides farinae.

Cardinium bacteria are well known as endosymbionts that infect a wide range of arthropods and can manipulate host reproduction to promote their vertical transmission. As intracellular bacteria, Cardinium species undergo dramatic genome evolution, especially their chromosomal genome reduction. Although Cardinium plasmids have been reported to harbor important genes, the role of these plasmids in the genome evolution is yet to be fully understood. In this study, 2 genomes of Cardinium endosymbiont bacteria in astigmatic mites were de novo assembled, including the complete circular chromosomal genome of Cardinium sp. DF that was constructed in high quality using high-coverage long-read sequencing data. Intriguingly, 2 circular plasmids were assembled in Cardinium sp. DF and were identified to be endogenous for over 10 homologous genes shared with the chromosomal genome. Comparative genomics analysis illustrated an outline of the genome evolution of Cardinium bacteria, and the in-depth analysis of Cardinium sp. DF shed light on the multiple roles of endogenous plasmids in the molecular process of the chromosomal genome reduction. The endogenous plasmids of Cardinium sp. DF not only harbor massive homologous sequences that enable homologous recombination with the chromosome, but also can provide necessary functional proteins when the coding genes decayed in the chromosomal genome. IMPORTANCE As bacterial endosymbionts, Cardinium typically undergoes genome reduction, but the molecular process is still unclear, such as how plasmids get involved in chromosome reduction. Here, we de novo assembled 2 genomes of Cardinium in astigmatic mites, especially the chromosome of Cardinium sp. DF was assembled in a complete circular DNA using high-coverage long-read sequencing data. In the genome assembly of Cardinium sp. DF, 2 circular endogenous plasmids were identified to share at least 10 homologous genes with the chromosomal genome. In the comparative analysis, we identified a range of genes decayed in the chromosomal genome of Cardinium sp. DF but preserved in the 2 plasmids. Taken together with in-depth analyses, our results unveil that the endogenous plasmids harbor homologous sequences of chromosomal genome and can provide a structural basis of homologous recombination. Overall, this study reveals that endogenous plasmids participate in the ongoing chromosomal genome reduction of Cardinium sp. DF.

Real-Space Mapping of Local Subdegree Lattice Rotations in Low-Angle Twisted Bilayer Graphene.

In two-dimensional small-angle twisted bilayers, van der Waals (vdW) interlayer interaction introduces an atomic-scale reconstruction, which consists of a moiré-periodic network of local subdegree lattice rotations. However, real-space measurement of the subdegree lattice rotation requires extremely high spatial resolution, which is an outstanding challenge in an experiment. Here, a topmost small-period graphene moiré pattern is introduced as a magnifying lens to magnify sub-Angstrom lattice distortions in small-angle twisted bilayer graphene (TBG) by about 2 orders of magnitude. Local moiré periods of the topmost graphene moiré patterns and low-energy van Hove singularities of the system are spatially modified by the atomic-scale reconstruction of the underlying TBG, thus enabling real-space mapping of the networks of the subdegree lattice rotations both in structure and in electronic properties. Our results indicate that it is quite facile to study subdegree lattice rotation in vdW systems by measuring the periods of the topmost moiré superlattice.

Neutrophil-lymphocyte ratios in blood to distinguish children with asthma exacerbation from healthy subjects.

OBJECTIVE: Airway inflammation is a prominent feature of asthma and may play an important role in disease pathophysiology. Despite the increasing incidence of asthma worldwide, reliable diagnostic biomarkers are lacking and widely lead to asthma misdiagnosis. Neutrophil-lymphocyte ratio (NLR) is a biomarker of systemic inflammation, in addition to NLR-alanine aminotransferase ratio (NAR) and NLR-albumin ratio (NBR). The aim of this study was to evaluate associations of NLR, NAR, and NBR with diagnosis of childhood asthma to determine if they can aid clinical childhood asthma diagnosis. METHODS: This retrospective case-control study included 89 children with asthma and 53 healthy children from the Wuxi Children's Hospital affiliated with Nanjing Medical University. We applied various statistical tests to the dataset: Mann-Whitney U test to compare characteristics of the case and control groups; chi-squared test to compare categorical variables; Kruskal-Wallis test to compare statistical differences of asthma indicators among groups; receiver operating characteristic (ROC) curves to assess the diagnostic value of indices; and Spearman correlation analysis to evaluate relationships between NLR and lactate dehydrogenase, albumin, aspartate transaminase, and alanine transaminase levels. RESULTS: Compared with controls, the asthma case group had significantly higher white blood cell (p < 0.01), neutrophil, lactate dehydrogenase, C-reactive protein, and NLR levels (p < 0.01) and significantly lower lymphocyte (p = 0.001), platelet (p = 0.039), and albumin levels (p = 0.04). We determined optimal cutoff levels for several metrics: 1.723 for NLR, with sensitivity of 0.73 and specificity of 0.906; 0.135 for NAR, with sensitivity of 0.685 and specificity of 0.887; and 0.045 for NBR, with sensitivity of 0.674 and specificity of 0.906. The areas under the curve (AUCs) were 0.824 for NLR, 0.788 for NAR, 0.818 for NBR, and 0.83 for the combination of NLR + NAR + NBR. CONCLUSION: The combination of NLR, NAR, and NBR biomarkers distinguished asthmatic ones suffering from exacerbation of the condition from healthy children. Thus, our results indicate NLR + NAR + NBR could be used as a clinical biomarker for asthma in children.

Magnetic-Field-Tunable Valley-Contrasting Pseudomagnetic Confinement in Graphene.

Introducing quantum confinement has uncovered a rich set of interesting quantum phenomena and allows one to directly probe the physics of confined (quasi-)particles. In most experiments, however, an electrostatic potential is the only available method to generate quantum dots in a continuous system to confine (quasi-)particles. Here we demonstrate experimentally that inhomogeneous pseudomagnetic fields in strained graphene can introduce exotic quantum confinement of massless Dirac fermions. The pseudomagnetic fields have opposite directions in the two distinct valleys of graphene. By adding and tuning real magnetic fields, the total effective magnetic fields in the two valleys are imbalanced. By that we realized valley-contrasting spatial confinement, which lifts the valley degeneracy and results in field-tunable valley-polarized confined states in graphene. Our results provide a new avenue to manipulate the valley degree of freedom.

Realizing Valley-Polarized Energy Spectra in Bilayer Graphene Quantum Dots via Continuously Tunable Berry Phases.

The Berry phase plays an important role in determining many physical properties of quantum systems. However, tuning the energy spectrum of a quantum system via Berry phase is comparatively rare because the Berry phase is usually a fixed constant. Here, we report the realization of an unusual valley-polarized energy spectra via continuously tunable Berry phases in Bernal-stacked bilayer graphene quantum dots. In our experiment, the Berry phase of electron orbital states is continuously tuned from about π to 2π by perpendicular magnetic fields. When the Berry phase equals π or 2π, the electron states in the two inequivalent valleys are energetically degenerate. By altering the Berry phase to noninteger multiples of π, large and continuously tunable valley-polarized energy spectra are realized. Our result reveals the Berry phase's essential role in valleytronics and the observed valley splitting, on the order of 10 meV at a magnetic field of 1 T, is about 100 times larger than Zeeman splitting for spin, shedding light on graphene-based valleytronics.

Tunable Lattice Reconstruction, Triangular Network of Chiral One-Dimensional States, and Bandwidth of Flat Bands in Magic Angle Twisted Bilayer Graphene.

The interplay between interlayer van der Waals interaction and intralayer lattice distortion can lead to structural reconstruction in slightly twisted bilayer graphene (TBG) with the twist angle being smaller than a characteristic angle θ_{c}. Experimentally, the θ_{c} is demonstrated to be very close to the magic angle (θ≈1.08°). Here we address the transition between reconstructed and unreconstructed structures of the TBG across the magic angle by using scanning tunneling microscopy (STM). Our experiment demonstrates that both structures are stable in the TBG around the magic angle. By using a STM tip, we show that the two structures can be changed to each other and a triangular network of chiral one-dimensional states hosted by domain boundaries can be switched on and off. Consequently, the bandwidth of the flat band, which plays a vital role in the emergent strongly correlated states in the magic angle TBG, is tuned. This provides an extra control knob to manipulate the exotic electronic states of the TBG near the magic angle.

Spectroscopic Evidence for a Spin- and Valley-Polarized Metallic State in a Nonmagic-Angle Twisted Bilayer Graphene.

In the magic-angle twisted bilayer graphene (MA-TBG), strong electron-electron (e-e) correlations caused by the band-flattening lead to many exotic quantum phases such as superconductivity, correlated insulator, ferromagnetism, and quantum anomalous Hall effects, when its low-energy van Hove singularities (VHSs) are partially filled. Here our high-resolution scanning tunneling microscope and spectroscopy measurements demonstrate that the e-e correlation in a nonmagic-angle TBG with a twist angle θ = 1.49° still plays an important role in determining its electronic properties. Our most interesting observation on that sample is when one of its VHSs is partially filled, the one associated peak in the spectrum splits into four peaks. Simultaneously, the spatial symmetry of electronic states around the split VHSs is broken by the e-e correlation. Our analysis based on the continuum model suggests that such a one-to-four split of the VHS originates from the formation of an interaction-driven spin-valley-polarized metallic state near the VHS, which is a symmetry-breaking phase that has not been identified in the MA-TBG or in other systems.

Valley Polarization and Inversion in Strained Graphene via Pseudo-Landau Levels, Valley Splitting of Real Landau Levels, and Confined States.

It is quite easy to control spin polarization and the spin direction of a system via magnetic fields. However, there is no such direct and efficient way to manipulate the valley pseudospin degree of freedom. Here, we demonstrate experimentally that it is possible to realize valley polarization and valley inversion in graphene by using both strain-induced pseudomagnetic fields and real magnetic fields. Pseudomagnetic fields, which are quite different from real magnetic fields, point in opposite directions at the two distinct valleys of graphene. Therefore, the coexistence of pseudomagnetic fields and real magnetic fields leads to imbalanced effective magnetic fields at two distinct valleys of graphene. This allows us to control the valley in graphene as conveniently as the electron spin. In this work, we report a consistent observation of valley polarization and inversion in strained graphene via pseudo-Landau levels, splitting of real Landau levels, and valley splitting of confined states using scanning tunneling spectroscopy. Our results highlight a pathway to valleytronics in strained graphene-based platforms.