DNA methylation signatures in airway cells from adult children of asthmatic mothers reflect subtypes of severe asthma.

Maternal asthma (MA) is among the most consistent risk factors for asthma in children. Possible mechanisms for this observation are epigenetic modifications in utero that have lasting effects on developmental programs in children of mothers with asthma. To test this hypothesis, we performed differential DNA methylation analyses of 398,186 individual CpG sites in primary bronchial epithelial cells (BECs) from 42 nonasthma controls and 88 asthma cases, including 56 without MA (NMA) and 32 with MA. We used weighted gene coexpression network analysis (WGCNA) of 69 and 554 differentially methylated CpGs (DMCs) that were specific to NMA and MA cases, respectively, compared with controls. WGCNA grouped 66 NMA-DMCs and 203 MA-DMCs into two and five comethylation modules, respectively. The eigenvector of one MA-associated module (turquoise) was uniquely correlated with 85 genes expressed in BECs and enriched for 36 pathways, 16 of which discriminated between NMA and MA using machine learning. Genes in all 16 pathways were decreased in MA compared with NMA cases (P = 7.1 × 10−3), a finding that replicated in nasal epithelial cells from an independent cohort (P = 0.02). Functional interpretation of these pathways suggested impaired T cell signaling and responses to viral and bacterial pathogens. The MA-associated turquoise module eigenvector was additionally correlated with clinical features of severe asthma and reflective of type 2 (T2)-low asthma (i.e., low total serum immunoglobulin E, fractional exhaled nitric oxide, and eosinophilia). Overall, these data suggest that MA alters diverse epigenetically mediated pathways that lead to distinct subtypes of severe asthma in adults, including hard-to-treat T2-low asthma.

Ground-state phase diagram of the t-t'-J model.

We report results of large-scale ground-state density matrix renormalization group (DMRG) calculations on t-[Formula: see text]-J cylinders with circumferences 6 and 8. We determine a rough phase diagram that appears to approximate the two-dimensional (2D) system. While for many properties, positive and negative [Formula: see text] values ([Formula: see text]) appear to correspond to electron- and hole-doped cuprate systems, respectively, the behavior of superconductivity itself shows an inconsistency between the model and the materials. The [Formula: see text] (hole-doped) region shows antiferromagnetism limited to very low doping, stripes more generally, and the familiar Fermi surface of the hole-doped cuprates. However, we find [Formula: see text] strongly suppresses superconductivity. The [Formula: see text] (electron-doped) region shows the expected circular Fermi pocket of holes around the [Formula: see text] point and a broad low-doped region of coexisting antiferromagnetism and d-wave pairing with a triplet p component at wavevector [Formula: see text] induced by the antiferromagnetism and d-wave pairing. The pairing for the electron low-doped system with [Formula: see text] is strong and unambiguous in the DMRG simulations. At larger doping another broad region with stripes in addition to weaker d-wave pairing and striped p-wave pairing appears. In a small doping region near [Formula: see text] for [Formula: see text], we find an unconventional type of stripe involving unpaired holes located predominantly on chains spaced three lattice spacings apart. The undoped two-leg ladder regions in between mimic the short-ranged spin correlations seen in two-leg Heisenberg ladders.

Treating asthma in the time of COVID.

The Precision Interventions for Severe and/or Exacerbation-Prone Asthma clinical trials network is actively assessing novel treatments for severe asthma during the coronavirus disease (COVID-19) pandemic and has needed to adapt to various clinical dilemmas posed by the COVID-19 pandemic. Pharmacologic interactions between established asthma therapies and novel drug interventions for COVID-19 infection, including antivirals, biologics, and vaccines, have emerged as a critical and unanticipated issue in the clinical care of asthma. In particular, impaired metabolism of some long-acting beta-2 agonists by the cytochrome P4503A4 enzyme in the setting of antiviral treatment using ritonavir-boosted nirmatrelvir (NVM/r, brand name Paxlovid) may increase risk for adverse cardiovascular events. Although available data have documented the potential for such interactions, these issues are largely unappreciated by clinicians who treat asthma, or those dispensing COVID-19 interventions in patients who happen to have asthma. Because these drug-drug interactions have not previously been relevant to patient care, clinicians have had no guidance on management strategies to reduce potentially serious interactions between treatments for asthma and COVID-19. The Precision Interventions for Severe and/or Exacerbation-Prone Asthma network considered the available literature and product information, and herein share our considerations and plans for treating asthma within the context of these novel COVID-19-related therapies.

Where is the Quantum Spin Nematic?

We provide strong evidence of the spin-nematic state in a paradigmatic ferro-antiferromagnetic J_{1}-J_{2} model using analytical and density-matrix renormalization group methods. In zero field, the attraction of spin-flip pairs leads to a first-order transition and no nematic state, while pair repulsion at larger J_{2} stabilizes the nematic phase in a narrow region near the pair-condensation field. A devil's staircase of multipair condensates is conjectured for weak pair attraction. A suppression of the spin-flip gap by many-body effects leads to an order-of-magnitude contraction of the nematic phase compared to naïve expectations. The proposed phase diagram should be broadly valid.

Validating Phase-Space Methods with Tensor Networks in Two-Dimensional Spin Models with Power-Law Interactions.

Using a recently developed extension of the time-dependent variational principle for matrix product states, we evaluate the dynamics of 2D power-law interacting XXZ models, implementable in a variety of state-of-the-art experimental platforms. We compute the spin squeezing as a measure of correlations in the system, and compare to semiclassical phase-space calculations utilizing the discrete truncated Wigner approximation (DTWA). We find the latter efficiently and accurately captures the scaling of entanglement with system size in these systems, despite the comparatively resource-intensive tensor network representation of the dynamics. We also compare the steady-state behavior of DTWA to thermal ensemble calculations with tensor networks. Our results open a way to benchmark dynamical calculations for two-dimensional quantum systems, and allow us to rigorously validate recent predictions for the generation of scalable entangled resources for metrology in these systems.

Effectiveness of a Bundled Payments for Care Improvement Program for Chronic Obstructive Pulmonary Disease.

BACKGROUND: The Medicare Bundled Payments for Care Improvement (BPCI) program reimburses 90-day care episodes post-hospitalization. COPD is a leading cause of early readmissions making it a target for value-based payment reform. OBJECTIVE: Evaluate the financial impact of a COPD BPCI program. DESIGN, PARTICIPANTS, INTERVENTIONS: A single-site retrospective observational study evaluated the impact of an evidence-based transitions of care program on episode costs and readmission rates, comparing patients hospitalized for COPD exacerbations who received versus those who did not receive the intervention. MAIN MEASURES: Mean episode costs and readmissions. KEY RESULTS: Between October 2015 and September 2018, 132 received and 161 did not receive the program, respectively. Mean episode costs were below target for six out of eleven quarters for the intervention group, as opposed to only one out of twelve quarters for the control group. Overall, there were non-significant mean savings of $2551 (95% CI: - $811 to $5795) in episode costs relative to target costs for the intervention group, though results varied by index admission diagnosis-related group (DRG); there were additional costs of $4184 per episode for the least-complicated cohort (DRG 192), but savings of $1897 and $1753 for the most complicated index admissions (DRGs 191 and 190, respectively). A significant mean decrease of 0.24 readmissions per episode was observed in 90-day readmission rates for intervention relative to control. Readmissions and hospital discharges to skilled nursing facilities were factors of higher costs (mean increases of $9098 and $17,095 per episode respectively). CONCLUSIONS: Our COPD BPCI program had a non-significant cost-saving effect, although sample size limited study power. The differential impact of the intervention by DRG suggests that targeting interventions to more clinically complex patients could increase the financial impact of the program. Further evaluations are needed to determine if our BPCI program decreased care variation and improved quality of care. PRIMARY SOURCE OF FUNDING: This research was supported by NIH NIA grant #5T35AG029795-12.

Nested gausslet basis sets.

We introduce nested gausslet bases, an improvement on previous gausslet bases that can treat systems containing atoms with much larger atomic numbers. We also introduce pure Gaussian distorted gausslet bases, which allow the Hamiltonian integrals to be performed analytically, as well as hybrid bases in which the gausslets are combined with standard Gaussian-type bases. All these bases feature the diagonal approximation for the electron-electron interactions so that the Hamiltonian is completely defined by two Nb × Nb matrices, where Nb ≈ 104 is small enough to permit fast calculations at the Hartree-Fock level. In constructing these bases, we have gained new mathematical insight into the construction of one-dimensional diagonal bases. In particular, we have proved an important theorem relating four key basis set properties: completeness, orthogonality, zero-moment conditions, and diagonalization of the coordinate operator matrix. We test our basis sets on small systems with a focus on high accuracy, obtaining, for example, an accuracy of 2 × 10-5 Ha for the total Hartree-Fock energy of the neon atom in the complete basis set limit.

Genome-wide association study identifies kallikrein 5 in type 2 inflammation-low asthma.

BACKGROUND: Clinical studies of type 2 (T2) cytokine-related neutralizing antibodies in asthma have identified a substantial subset of patients with low levels of T2 inflammation who do not benefit from T2 cytokine neutralizing antibody treatment. Non-T2 mechanisms are poorly understood in asthma but represent a redefined unmet medical need. OBJECTIVE: We sought to gain a better understanding of genetic contributions to T2-low asthma. METHODS: We utilized an unbiased genome-wide association study of patients with moderate to severe asthma stratified by T2 serum biomarker periostin. We also performed additional expression and biological analysis for the top genetic hits. RESULTS: We identified a novel protective single nucleotide polymorphism at chr19q13.41, which is selectively associated with T2-low asthma and establishes Kallikrein-related peptidase 5 (KLK5) as the causal gene mediating this association. Heterozygous carriers of the single nucleotide polymorphisms have reduced KLK5 expression. KLK5 is secreted by human bronchial epithelial cells and elevated in asthma bronchial alveolar lavage. T2 cytokines IL-4 and IL-13 downregulate KLK5 in human bronchial epithelial cells. KLK5, dependent on its catalytic function, induces epithelial chemokine/cytokine expression. Finally, overexpression of KLK5 in airway or lack of an endogenous KLK5 inhibitor, SPINK5, leads to spontaneous airway neutrophilic inflammation. CONCLUSION: Our data identify KLK5 to be the causal gene at a novel locus at chr19q13.41 associated with T2-low asthma.

A-to-I editing of miR-200b-3p in airway cells is associated with moderate-to-severe asthma.

BACKGROUND: Asthma is a chronic lung disease characterised by persistent airway inflammation. Altered microRNA (miRNA)-mediated gene silencing in bronchial epithelial cells (BECs) has been reported in asthma, yet adenosine deaminase acting on RNA (ADAR)-mediated miRNA editing in asthma remains unexplored. METHODS: We first identified adenosine to inosine (A-to-I) edited sites in miRNAs in BECs from 142 adult asthma cases and controls. A-to-I edited sites were tested for associations with asthma severity and clinical measures of asthma. Paired RNA sequencing data were used to perform pathway enrichments and test for associations with bioinformatically predicted target genes of the unedited and edited miRNAs. RESULTS: Of 19 A-to-I edited sites detected in these miRNAs, one site at position 5 of miR-200b-3p was edited less frequently in cases compared with controls (pcorrected=0.013), and especially compared with cases with moderate (pcorrected=0.029) and severe (pcorrected=3.9×10-4), but not mild (pcorrected=0.38), asthma. Bioinformatic prediction revealed 232 target genes of the edited miR-200b-3p, which were enriched for both interleukin-4 and interferon-γ signalling pathways, and included the SOCS1 (suppressor of cytokine signalling 1) gene. SOCS1 was more highly expressed in moderate (pcorrected=0.017) and severe (pcorrected=5.4×10-3) asthma cases compared with controls. Moreover, both miR-200b-3p editing and SOCS1 were associated with bronchoalveolar lavage eosinophil levels. CONCLUSIONS: Reduced A-to-I editing of position 5 of miR-200b-3p in lower airway cells from moderate-to-severe asthmatic subjects may lead to overexpression of SOCS1 and impaired cytokine signalling. We propose ADAR-mediated editing as an epigenetic mechanism contributing to features of moderate-to-severe asthma in adulthood.

Publisher's Note: Sliced Basis Density Matrix Renormalization Group for Electronic Structure [Phys. Rev. Lett. 119, 046401 (2017)].

This corrects the article DOI: 10.1103/PhysRevLett.119.046401.

Hybrid gausslet/Gaussian basis sets.

We introduce hybrid gausslet/Gaussian basis sets, where a standard Gaussian basis is added to a gausslet basis in order to increase accuracy near the nuclei while keeping the spacing of the grid of gausslets relatively large. The Gaussians are orthogonalized to the gausslets, which are already orthonormal, and approximations are introduced to maintain the diagonal property of the two electron part of the Hamiltonian so that it continues to scale as the second power of the number of basis functions rather than the fourth. We introduce several corrections to the Hamiltonian designed to enforce certain exact properties, such as the values of certain two-electron integrals. We also introduce a simple universal energy correction that compensates for the incompleteness of the basis stemming from the electron-electron cusps based on the measured double occupancy of each basis function. We perform a number of Hartree Fock and full configuration interaction (full-CI) test calculations on two electron systems and Hartree Fock on a ten-atom hydrogen chain to benchmark these techniques. The inclusion of the cusp correction allows us to obtain complete basis set full-CI results for the two electron cases at the level of several micro-Hartrees, and we see similar apparent accuracy for Hartree Fock on the ten-atom hydrogen chain.

Distinct associations of sputum and oral microbiota with atopic, immunologic, and clinical features in mild asthma.

BACKGROUND: Whether microbiome characteristics of induced sputum or oral samples demonstrate unique relationships to features of atopy or mild asthma in adults is unknown. OBJECTIVE: We sought to determine sputum and oral microbiota relationships to clinical or immunologic features in mild atopic asthma and the impact on the microbiota of inhaled corticosteroid (ICS) treatment administered to ICS-naive subjects with asthma. METHODS: Bacterial microbiota profiles were analyzed in induced sputum and oral wash samples from 32 subjects with mild atopic asthma before and after inhaled fluticasone treatment, 18 atopic subjects without asthma, and 16 nonatopic healthy subjects in a multicenter study (NCT01537133). Associations with clinical and immunologic features were examined, including markers of atopy, type 2 inflammation, immune cell populations, and cytokines. RESULTS: Sputum bacterial burden inversely associated with bronchial expression of type 2 (T2)-related genes. Differences in specific sputum microbiota also associated with T2-low asthma phenotype, a subgroup of whom displayed elevations in lung inflammatory mediators and reduced sputum bacterial diversity. Differences in specific oral microbiota were more reflective of atopic status. After ICS treatment of patients with asthma, the compositional structure of sputum microbiota showed greater deviation from baseline in ICS nonresponders than in ICS responders. CONCLUSIONS: Novel associations of sputum and oral microbiota to immunologic features were observed in this cohort of subjects with or without ICS-naive mild asthma. These findings confirm and extend our previous report of reduced bronchial bacterial burden and compositional complexity in subjects with T2-high asthma, with additional identification of a T2-low subgroup with a distinct microbiota-immunologic relationship.

Bypassing the Energy Functional in Density Functional Theory: Direct Calculation of Electronic Energies from Conditional Probability Densities.

Density functional calculations can fail for want of an accurate exchange-correlation approximation. The energy can instead be extracted from a sequence of density functional calculations of conditional probabilities (CP DFT). Simple CP approximations yield usefully accurate results for two-electron ions, the hydrogen dimer, and the uniform gas at all temperatures. CP DFT has no self-interaction error for one electron, and correctly dissociates H_{2}, both major challenges. For warm dense matter, classical CP DFT calculations can overcome the convergence problems of Kohn-Sham DFT.

The precision interventions for severe and/or exacerbation-prone asthma (PrecISE) adaptive platform trial: statistical considerations.

The Precision Interventions for Severe and/or Exacerbation-prone Asthma (PrecISE) study is an adaptive platform trial designed to investigate novel interventions to severe asthma. The study is conducted under a master protocol and utilizes a crossover design with each participant receiving up to five interventions and at least one placebo. Treatment assignments are based on the patients' biomarker profiles and precision health methods are incorporated into the interim and final analyses. We describe key elements of the PrecISE study including the multistage adaptive enrichment strategy, early stopping of an intervention for futility, power calculations, and the primary analysis strategy.

Associations between fungal and bacterial microbiota of airways and asthma endotypes.

BACKGROUND: The relationship between asthma, atopy, and underlying type 2 (T2) airway inflammation is complex. Although the bacterial airway microbiota is known to differ in asthmatic patients, the fungal and bacterial markers that discriminate T2-high (eosinophilic) and T2-low (neutrophilic/mixed-inflammation) asthma and atopy are still incompletely identified. OBJECTIVES: The aim of this study was to demonstrate the fungal microbiota structure of airways in asthmatic patients associated with T2 inflammation, atopy, and key clinical parameters. METHODS: We collected endobronchial brush (EB) and bronchoalveolar lavage (BAL) samples from 39 asthmatic patients and 19 healthy subjects followed by 16S gene and internal transcribed spacer-based microbiota sequencing. The microbial sequences were classified into exact sequence variants. The T2 phenotype was defined by using a blood eosinophil count with a threshold of 300 cells/µL. RESULTS: Fungal diversity was significantly lower in EB samples from patients with T2-high compared with T2-low inflammation; key fungal genera enriched in patients with T2-high inflammation included Trichoderma species, whereas Penicillium species was enriched in patients with atopy. In BAL fluid samples the dominant genera were Cladosporium, Fusarium, Aspergillus, and Alternaria. Using generalized linear models, we identified significant associations between specific fungal exact sequence variants and FEV1, fraction of exhaled nitric oxide values, BAL fluid cell counts, and corticosteroid use. Investigation of interkingdom (bacterial-fungal) co-occurrence patterns revealed different topologies between asthmatic patients and healthy control subjects. Random forest models with fungal classifiers predicted asthma status with 75% accuracy for BAL fluid samples and 80% accuracy for EB samples. CONCLUSIONS: We demonstrate clear differences in bacterial and fungal microbiota in asthma-associated phenotypes. Our study provides additional support for considering microbial signatures in delineating asthma phenotypes.

Genetic-Epigenetic Interactions in Asthma Revealed by a Genome-Wide Gene-Centric Search.

OBJECTIVES: There is evidence to suggest that asthma pathogenesis is affected by both genetic and epigenetic variation independently, and there is some evidence to suggest that genetic-epigenetic interactions affect risk of asthma. However, little research has been done to identify such interactions on a genome-wide scale. The aim of this studies was to identify genes with genetic-epigenetic interactions associated with asthma. METHODS: Using asthma case-control data, we applied a novel nonparametric gene-centric approach to test for interactions between multiple SNPs and CpG sites simultaneously in the vicinities of 18,178 genes across the genome. RESULTS: Twelve genes, PF4, ATF3, TPRA1, HOPX, SCARNA18, STC1, OR10K1, UPK1B, LOC101928523, LHX6, CHMP4B, and LANCL1, exhibited statistically significant SNP-CpG interactions (false discovery rate = 0.05). Of these, three have previously been implicated in asthma risk (PF4, ATF3, and TPRA1). Follow-up analysis revealed statistically significant pairwise SNP-CpG interactions for several of these genes, including SCARNA18, LHX6, and LOC101928523 (p = 1.33E-04, 8.21E-04, 1.11E-03, respectively). CONCLUSIONS: Joint effects of genetic and epigenetic variation may play an important role in asthma pathogenesis. Statistical methods that simultaneously account for multiple variations across chromosomal regions may be needed to detect these types of effects on a genome-wide scale.

Topography of Spin Liquids on a Triangular Lattice.

Spin systems with frustrated anisotropic interactions are of significant interest due to possible exotic ground states. We have explored their phase diagram on a nearest-neighbor triangular lattice using the density-matrix renormalization group and mapped out the topography of the region that can harbor a spin liquid. We find that this spin-liquid phase is continuously connected to a previously discovered spin-liquid phase of the isotropic J_{1}-J_{2} model. The two limits show nearly identical spin correlations, making the case that their respective spin liquids are isomorphic to each other.

Insights about the economic impact of chronic obstructive pulmonary disease readmissions post implementation of the hospital readmission reduction program.

PURPOSE OF REVIEW: Chronic obstructive pulmonary disease (COPD) affects over 12 million adults in the United States and is the third leading cause of 30-day readmissions. COPD is costly with almost $50 billion in direct costs annually. Total COPD costs can be up to double the identified direct costs because of comorbid disease and numerous indirect costs such as absenteeism. Acute exacerbations of COPD (AECOPD) are responsible for up to 70% of COPD-related healthcare costs; hospital readmissions alone account for over $15 billion annually. In this review, we aim to describe insights about the economic impact of COPD readmissions based on articles published over the last 18 months. RECENT FINDINGS: Interventions aimed at reducing readmission, particularly those using interdisciplinary teams with bundled care interventions, were uniformly successful at improving the quality of care provided and demonstrating improved process measures. However, success at reducing readmissions and cost savings based on these interventions varied across the studies. SUMMARY: The literature to date points to factors and conditions that may place patients at higher risk of readmissions and may lead to higher costs. Interventions aimed at reducing readmissions after index admissions for AECOPD have demonstrated variable results. Most interventions did not reflect cost-based analyses.

Gene Expression Profiling in Blood Provides Reproducible Molecular Insights into Asthma Control.

RATIONALE: Maintaining optimal symptom control remains the primary objective of asthma treatment. Better understanding of the biologic underpinnings of asthma control may lead to the development of improved clinical and pharmaceutical approaches. OBJECTIVES: To identify molecular pathways and interrelated genes whose differential expression was associated with asthma control. METHODS: We performed gene set enrichment analyses of asthma control in 1,170 adults with asthma, each with gene expression data derived from either whole blood (WB) or unstimulated CD4+ T lymphocytes (CD4), and a self-reported asthma control score representing either the preceding 6 months (chronic) or 7 days (acute). Our study comprised a discovery WB cohort (n = 245, chronic) and three independent, nonoverlapping replication cohorts: a second WB set (n = 448, acute) and two CD4 sets (n = 300, chronic; n = 77, acute). MEASUREMENTS AND MAIN RESULTS: In the WB discovery cohort, we found significant overrepresentation of genes associated with asthma control in 1,106 gene sets from the Molecular Signatures Database (false discovery rate, <5%). Of these, 583 (53%) replicated in at least one replication cohort (false discovery rate, <25%). Suboptimal control was associated with signatures of eosinophilic and granulocytic inflammatory signals, whereas optimal control signatures were enriched for immature lymphocytic patterns. These signatures included two related biologic processes related to activation by TREM-1 (triggering receptor expressed on myeloid cells 1) and lipopolysaccharide. CONCLUSIONS: Together, these results demonstrate the existence of specific, reproducible transcriptomic components in blood that vary with degree of asthma control and implicate a novel biologic target (TREM-1).

Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment.

BACKGROUND: Compositional differences in the bronchial bacterial microbiota have been associated with asthma, but it remains unclear whether the findings are attributable to asthma, to aeroallergen sensitization, or to inhaled corticosteroid treatment. OBJECTIVES: We sought to compare the bronchial bacterial microbiota in adults with steroid-naive atopic asthma, subjects with atopy but no asthma, and nonatopic healthy control subjects and to determine relationships of the bronchial microbiota to phenotypic features of asthma. METHODS: Bacterial communities in protected bronchial brushings from 42 atopic asthmatic subjects, 21 subjects with atopy but no asthma, and 21 healthy control subjects were profiled by using 16S rRNA gene sequencing. Bacterial composition and community-level functions inferred from sequence profiles were analyzed for between-group differences. Associations with clinical and inflammatory variables were examined, including markers of type 2-related inflammation and change in airway hyperresponsiveness after 6 weeks of fluticasone treatment. RESULTS: The bronchial microbiome differed significantly among the 3 groups. Asthmatic subjects were uniquely enriched in members of the Haemophilus, Neisseria, Fusobacterium, and Porphyromonas species and the Sphingomonodaceae family and depleted in members of the Mogibacteriaceae family and Lactobacillales order. Asthma-associated differences in predicted bacterial functions included involvement of amino acid and short-chain fatty acid metabolism pathways. Subjects with type 2-high asthma harbored significantly lower bronchial bacterial burden. Distinct changes in specific microbiota members were seen after fluticasone treatment. Steroid responsiveness was linked to differences in baseline compositional and functional features of the bacterial microbiome. CONCLUSION: Even in subjects with mild steroid-naive asthma, differences in the bronchial microbiome are associated with immunologic and clinical features of the disease. The specific differences identified suggest possible microbiome targets for future approaches to asthma treatment or prevention.