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Secondary bacterial pneumonia (2°BP) is associated with significant morbidity following respiratory viral infection, yet remains incompletely understood. In a prospective cohort of 112 critically ill adults intubated for COVID-19, we comparatively assess longitudinal airway microbiome dynamics and the pulmonary transcriptome of patients who developed 2°BP versus controls who did not. We find that 2°BP is significantly associated with both mortality and corticosteroid treatment. The pulmonary microbiome in 2°BP is characterized by increased bacterial RNA mass and dominance of culture-confirmed pathogens, detectable days prior to 2°BP clinical diagnosis, and frequently also present in nasal swabs. Assessment of the pulmonary transcriptome reveals suppressed TNFα signaling in patients with 2°BP, and sensitivity analyses suggest this finding is mediated by corticosteroid treatment. Further, we find that increased bacterial RNA mass correlates with reduced expression of innate and adaptive immunity genes in both 2°BP patients and controls. Taken together, our findings provide fresh insights into the microbial dynamics and host immune features of COVID-19-associated 2°BP, and suggest that suppressed immune signaling, potentially mediated by corticosteroid treatment, permits expansion of opportunistic bacterial pathogens.

Mucus plugs occlude airways to obstruct airflow in asthma. Studies in patients and in mouse models show that mucus plugs occur in the context of type 2 inflammation, and studies in human airway epithelial cells (HAECs) show that IL-13-activated cells generate pathologic mucus independently of immune cells. To determine how HAECs autonomously generate pathologic mucus, we used a magnetic microwire rheometer to characterize the viscoelastic properties of mucus secreted under varying conditions. We found that normal HAEC mucus exhibited viscoelastic liquid behavior and that mucus secreted by IL-13-activated HAECs exhibited solid-like behavior caused by mucin cross-linking. In addition, IL-13-activated HAECs shows increased peroxidase activity in apical secretions, and an overlaid thiolated polymer (thiomer) solution shows an increase in solid behavior that was prevented by peroxidase inhibition. Furthermore, gene expression for thyroid peroxidase (TPO), but not lactoperoxidase (LPO), was increased in IL-13-activated HAECs and both TPO and LPO catalyze the formation of oxidant acids that cross-link thiomer solutions. Finally, gene expression for TPO in airway epithelial brushings was increased in patients with asthma with high airway mucus plug scores. Together, our results show that IL-13-activated HAECs autonomously generated pathologic mucus via peroxidase-mediated cross-linking of mucin polymers.

BACKGROUND: Qualitative methods are incredibly beneficial to the dissemination and implementation of new digital health interventions; however, these methods can be time intensive and slow down dissemination when timely knowledge from the data sources is needed in ever-changing health systems. Recent advancements in generative artificial intelligence (GenAI) and their underlying large language models (LLMs) may provide a promising opportunity to expedite the qualitative analysis of textual data, but their efficacy and reliability remain unknown. OBJECTIVE: The primary objectives of our study were to evaluate the consistency in themes, reliability of coding, and time needed for inductive and deductive thematic analyses between GenAI (ie, ChatGPT and Bard) and human coders. METHODS: The qualitative data for this study consisted of 40 brief SMS text message reminder prompts used in a digital health intervention for promoting antiretroviral medication adherence among people with HIV who use methamphetamine. Inductive and deductive thematic analyses of these SMS text messages were conducted by 2 independent teams of human coders. An independent human analyst conducted analyses following both approaches using ChatGPT and Bard. The consistency in themes (or the extent to which the themes were the same) and reliability (or agreement in coding of themes) between methods were compared. RESULTS: The themes generated by GenAI (both ChatGPT and Bard) were consistent with 71% (5/7) of the themes identified by human analysts following inductive thematic analysis. The consistency in themes was lower between humans and GenAI following a deductive thematic analysis procedure (ChatGPT: 6/12, 50%; Bard: 7/12, 58%). The percentage agreement (or intercoder reliability) for these congruent themes between human coders and GenAI ranged from fair to moderate (ChatGPT, inductive: 31/66, 47%; ChatGPT, deductive: 22/59, 37%; Bard, inductive: 20/54, 37%; Bard, deductive: 21/58, 36%). In general, ChatGPT and Bard performed similarly to each other across both types of qualitative analyses in terms of consistency of themes (inductive: 6/6, 100%; deductive: 5/6, 83%) and reliability of coding (inductive: 23/62, 37%; deductive: 22/47, 47%). On average, GenAI required significantly less overall time than human coders when conducting qualitative analysis (20, SD 3.5 min vs 567, SD 106.5 min). CONCLUSIONS: The promising consistency in the themes generated by human coders and GenAI suggests that these technologies hold promise in reducing the resource intensiveness of qualitative thematic analysis; however, the relatively lower reliability in coding between them suggests that hybrid approaches are necessary. Human coders appeared to be better than GenAI at identifying nuanced and interpretative themes. Future studies should consider how these powerful technologies can be best used in collaboration with human coders to improve the efficiency of qualitative research in hybrid approaches while also mitigating potential ethical risks that they may pose.

In the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, epithelial populations in the distal lung expressing Angiotensin-converting enzyme 2 (ACE2) are infrequent, and therefore, the model of viral expansion and immune cell engagement remains incompletely understood. Using human lungs to investigate early host-viral pathogenesis, we found that SARS-CoV-2 had a rapid and specific tropism for myeloid populations. Human alveolar macrophages (AMs) reliably expressed ACE2 allowing both spike-ACE2-dependent viral entry and infection. In contrast to Influenza A virus, SARS-CoV-2 infection of AMs was productive, amplifying viral titers. While AMs generated new viruses, the interferon responses to SARS-CoV-2 were muted, hiding the viral dissemination from specific antiviral immune responses. The reliable and veiled viral depot in myeloid cells in the very early phases of SARS-CoV-2 infection of human lungs enables viral expansion in the distal lung and potentially licenses subsequent immune pathologies.

As part of biodiversity monitoring in the Kisangani Forest Region, a survey of bats was conducted in three protected areas, specifically Lomami, Yangambi and Epulu. In this pilot study, a total of 201 specimens were collected using Japanese nets of different lengths (6, 9 and 12 m long) and a height of 2 m with a mesh size of 2 × 2 cm to capture bats. Captured specimens were identified using determination keys appropriate for the study area. The results of inventories in the three sites revealed that 201 specimens of captured bats belong to 2 sub-orders, 4 families, 9 genera and 12 species. The most abundant species were Epomops franqueti, Megaloglossus woermannii and Myotis bocagii. The following species, Epomops franqueti, Megaloglossus woermanii, Casinycteris argynnis, and Hipposideros caffer were found at all three sites. Based on the Shannon Index, it was observed that the Lomami site has a higher specific diversity than the two other areas (Yangambi and Epulu) 1.74 against 1.51 and 1.42 respectively.

Cisheteronormative ideologies are infused into every aspect of society, including undergraduate science. We set out to identify the extent to which students can identify cisheteronormative language in biology textbooks by posing several hypothetical textbook questions and asking students to modify them to make the language more accurate (defined as "correct; precise; using language that applies to all people"). First, we confirmed that textbooks commonly use language that conflates or confuses sex and gender. We used this information to design two sample questions that used similar language. We examined what parts of the questions students modified, and the changes they recommended. When asked to modify sample textbook questions, we found the most common terms or words that students identified as inaccurate were related to infant gender identity. The most common modifications that students made were changing gender terms to sex terms. Students' decisions in this exercise differed little across three large biology courses or by exam performance. As the science community strives to promote inclusive classrooms and embrace the complexity of human gender identities, we provide foundational information about students' ability to notice and correct inaccurate language related to sex and gender in biology.

This paper presents the development of heritage-focused outreach materials with the objectives of positively impacting traffic safety culture for Indigenous youth to reduce the number and severity of traffic crashes impacting these communities. The approach presented in this paper includes involving local community leaders in traffic safety education and incorporating culturally based material in outreach education. This could empower Tribal communities to preserve their cultural identities while acquiring the expertise needed to promote traffic safety.

By incompletely understood mechanisms, type 2 (T2) inflammation present in the airways of severe asthmatics drives the formation of pathologic mucus which leads to airway mucus plugging. Here we investigate the molecular role and clinical significance of intelectin-1 (ITLN-1) in the development of pathologic airway mucus in asthma. Through analyses of human airway epithelial cells we find that ITLN1 gene expression is highly induced by interleukin-13 (IL-13) in a subset of metaplastic MUC5AC+ mucus secretory cells, and that ITLN-1 protein is a secreted component of IL-13-induced mucus. Additionally, we find ITLN-1 protein binds the C-terminus of the MUC5AC mucin and that its deletion in airway epithelial cells partially reverses IL-13-induced mucostasis. Through analysis of nasal airway epithelial brushings, we find that ITLN1 is highly expressed in T2-high asthmatics, when compared to T2-low children. Furthermore, we demonstrate that both ITLN-1 gene expression and protein levels are significantly reduced by a common genetic variant that is associated with protection from the formation of mucus plugs in T2-high asthma. This work identifies an important biomarker and targetable pathways for the treatment of mucus obstruction in asthma.

BACKGROUNDInformation about the size, airway location, and longitudinal behavior of mucus plugs in asthma is needed to understand their role in mechanisms of airflow obstruction and to rationally design muco-active treatments.METHODSCT lung scans from 57 patients with asthma were analyzed to quantify mucus plug size and airway location, and paired CT scans obtained 3 years apart were analyzed to determine plug behavior over time. Radiologist annotations of mucus plugs were incorporated in an image-processing pipeline to generate size and location information that was related to measures of airflow.RESULTSThe length distribution of 778 annotated mucus plugs was multimodal, and a 12 mm length defined short ("stubby", ≤12 mm) and long ("stringy", >12 mm) plug phenotypes. High mucus plug burden was disproportionately attributable to stringy mucus plugs. Mucus plugs localized predominantly to airway generations 6-9, and 47% of plugs in baseline scans persisted in the same airway for 3 years and fluctuated in length and volume. Mucus plugs in larger proximal generations had greater effects on spirometry measures than plugs in smaller distal generations, and a model of airflow that estimates the increased airway resistance attributable to plugs predicted a greater effect for proximal generations and more numerous mucus plugs.CONCLUSIONPersistent mucus plugs in proximal airway generations occur in asthma and demonstrate a stochastic process of formation and resolution over time. Proximal airway mucus plugs are consequential for airflow and are in locations amenable to treatment by inhaled muco-active drugs or bronchoscopy.TRIAL REGISTRATIONClinicaltrials.gov; NCT01718197, NCT01606826, NCT01750411, NCT01761058, NCT01761630, NCT01716494, and NCT01760915.FUNDINGAstraZeneca, Boehringer-Ingelheim, Genentech, GlaxoSmithKline, Sanofi-Genzyme-Regeneron, and TEVA provided financial support for study activities at the Coordinating and Clinical Centers beyond the third year of patient follow-up. These companies had no role in study design or data analysis, and the only restriction on the funds was that they be used to support the SARP initiative.

Post-acute sequelae of SARS-CoV-2 (PASC) is a significant public health concern. We describe Patient Reported Outcomes (PROs) on 590 participants prospectively assessed from hospital admission for COVID-19 through one year after discharge. Modeling identified 4 PRO clusters based on reported deficits (minimal, physical, mental/cognitive, and multidomain), supporting heterogenous clinical presentations in PASC, with sub-phenotypes associated with female sex and distinctive comorbidities. During the acute phase of disease, a higher respiratory SARS-CoV-2 viral burden and lower Receptor Binding Domain and Spike antibody titers were associated with both the physical predominant and the multidomain deficit clusters. A lower frequency of circulating B lymphocytes by mass cytometry (CyTOF) was observed in the multidomain deficit cluster. Circulating fibroblast growth factor 21 (FGF21) was significantly elevated in the mental/cognitive predominant and the multidomain clusters. Future efforts to link PASC to acute anti-viral host responses may help to better target treatment and prevention of PASC.

VMXm joins the suite of operational macromolecular crystallography beamlines at Diamond Light Source. It has been designed to optimize rotation data collections from protein crystals less than 10 µm and down to below 1 µm in size. The beamline has a fully focused beam of 0.3 × 2.3 µm (vertical × horizontal) with a tuneable energy range (6–28 keV) and high flux (1.6 × 1012 photons s−1 at 12.5 keV). The crystals are housed within a vacuum chamber to minimize background scatter from air. Crystals are plunge-cooled on cryo-electron microscopy grids, allowing much of the liquid surrounding the crystals to be removed. These factors improve the signal-to-noise during data collection and the lifetime of the microcrystals can be prolonged by exploiting photoelectron escape. A novel in vacuo sample environment has been designed which also houses a scanning electron microscope to aid with sample visualization. This combination of features at VMXm allows measurements at the physical limits of X-ray crystallography on biomacromolecules to be explored and exploited.

Abstract Secondary bacterial pneumonia (2°BP) is associated with significant morbidity following respiratory viral infection, yet remains incompletely understood. In a prospective cohort of 112 critically ill adults intubated for COVID-19, we comparatively assess longitudinal airway microbiome dynamics and the pulmonary transcriptome of patients who developed 2°BP versus controls who did not. We find that 2°BP is significantly associated with both mortality and corticosteroid treatment. The pulmonary microbiome in 2°BP is characterized by increased bacterial RNA mass and dominance of culture-confirmed pathogens, detectable days prior to 2°BP clinical diagnosis, and frequently also present in nasal swabs. Assessment of the pulmonary transcriptome reveals suppressed TNFα signaling in patients with 2°BP, and sensitivity analyses suggest this finding is mediated by corticosteroid treatment. Further, we find that increased bacterial RNA mass correlates with reduced expression of innate and adaptive immunity genes in both 2°BP patients and controls. Taken together, our findings provide fresh insights into the microbial dynamics and host immune features of COVID-19-associated 2°BP, and suggest that suppressed immune signaling, potentially mediated by corticosteroid treatment, permits expansion of opportunistic bacterial pathogens.

In today's higher education landscape, there are numerous conflicting pressures that influence how the mix of academic programs institutions choose to offer will evolve. This article describes: (1) The need to understand better how institutions' program arrays are evolving over time in the face of a variety of student, workforce, competitive, financial, and regulatory pressures; (2) How the use of the Integrated Postsecondary Education Data System data to examine changes in institutions' program offerings over time reveal which kinds of programs are increasing and which are decreasing; (3) The overall number of programs offered by U.S. institutions of higher education increased from 2014 to 2019, even as enrollments declined. Trends varied by state, sector, program level, and discipline; and (4) The available data may help policy makers and institutional leaders understand how individual program-level decisions translate into bigger picture trends, so they can put those decisions in context and consider strategic investments.

While many previous studies have indicated that encouraging a growth mindset can improve student learning outcomes, this conclusion's applicability to college-level astronomy classrooms remains poorly understood owing to the variation in students' overall and domain-specific learning attitudes. To address this, we surveyed undergraduate students in an introductory astronomy class about their attitudes towards learning astronomy over the course of five semesters. Overall, students felt an affinity for astronomy, felt moderately competent, perceived astronomy to be intermediate in terms of difficulty, and agreed strongly with standard statements reflecting a "growth mindset," i.e., the belief that intelligence is malleable rather than fixed from birth. Their responses were stable over the course of the semester and did not appear to depend strongly on student demographics. The unexpected start of the COVID-19 pandemic and the associated shift to all-virtual learning correlated with a drop in their affinity for astronomy, a small decrease in their perceived competence, and an increase in the perceived difficulty of the topic. Their overall learning mindset showed negligible change during this time, emphasizing the stability of their belief in a growth mindset as compared to other measured learning attitudes. However, more nuanced questions about their behaviors and interpretations in the classroom, about how they felt "in the moment," and about what factors were most important for their success in the class revealed significantly lower alignment with a growth mindset. This suggests that while introductory astronomy students may believe that they have a growth mindset, this mindset is not necessarily reflected in their self-reported classroom behaviors or measured responses to actual learning challenges.

"Purpose:" ASD is associated with relative strengths in the visuospatial domain but varying abilities in the linguistic domain. Previous studies suggest parallels between spatial language and spatial cognition in older autistic individuals, but no research to date has examined this relationship in young autistic children. Therefore, the purpose of the present study was to investigate the connection between children's spatial language production and nonverbal spatial cognition over time. We also examined two potential predictors of spatial language observed in previous literature, ASD symptom severity and parent spatial language input. "Methods:" In past work investigating spatial language in NT children of the same age, parent-child interactions have been a primary context for study. Therefore, in the present study, we analyzed transcripts of dyadic naturalistic play interactions between autistic children and their parents over three visits from age 30 to 66 months and administered standardized cognitive and ASD diagnostic assessments at each visit. "Results:" Spatial language production was related to nonverbal spatial cognition even when accounting for overall language production, though the strength of that relationship decreased over time. Parent spatial input (but not ASD severity) significantly predicted children's spatial language production over and above the effect of overall language production. "Conclusion:" Spatial language is associated with spatial cognition in young autistic children and appears to reflect the interaction of overall linguistic skills and nonverbal spatial cognitive ability regardless of autism severity. Parent-mediated interventions may be a promising context for increasing spatial language in autistic preschoolers.

Rationale: Indoor pollutants have been associated with chronic obstructive pulmonary disease morbidity, but it is unclear whether they contribute to disease progression. Objectives: We aimed to determine whether indoor particulate matter (PM) and nitrogen dioxide (NO2) are associated with lung function decline among current and former smokers. Methods: Of the 2,382 subjects with a history of smoking in SPIROMICS AIR, 1,208 participants had complete information to estimate indoor PM and NO2, using individual-based prediction models, in relation to measured spirometry at two or more clinic visits. We used a three-way interaction model between time, pollutant, and smoking status and assessed the indoor pollutant-associated difference in FEV1 decline separately using a generalized linear mixed model. Measurements and Main Results: Participants had an average rate of FEV1 decline of 60.3 ml/yr for those currently smoking compared with 35.2 ml/yr for those who quit. The association of indoor PM with FEV1 decline differed by smoking status. Among former smokers, every 10 μg/m3 increase in estimated indoor PM was associated with an additional 10 ml/yr decline in FEV1 (P = 0.044). Among current smokers, FEV1 decline did not differ by indoor PM. The results of indoor NO2 suggest trends similar to those for PM ⩽2.5 μm in aerodynamic diameter. Conclusions: Former smokers with chronic obstructive pulmonary disease who live in homes with high estimated PM have accelerated lung function loss, and those in homes with low PM have lung function loss similar to normal aging. In-home PM exposure may contribute to variability in lung function decline in people who quit smoking and may be a modifiable exposure.

OBJECTIVE: Genome-wide association studies (GWASs) have identified single nucleotide polymorphisms (SNPs) in chr11p15.5 region associated with asthma and idiopathic interstitial pneumonias (IIPs). We sought to identify functional genes for asthma by combining SNPs and mRNA expression in bronchial epithelial cells (BEC) in the Severe Asthma Research Program (SARP). METHODS: Correlation analyses of mRNA expression of six candidate genes (AP2A2, MUC6, MUC2, MUC5AC, MUC5B, and TOLLIP) and asthma phenotypes were performed in the longitudinal cohort (n = 156) with RNAseq in BEC, and replicated in the cross-sectional cohort (n = 155). eQTL (n = 114) and genetic association analysis of asthma severity (426 severe vs. 531 non-severe asthma) were performed, and compared with previously published GWASs of IIPs and asthma. RESULTS: Higher expression of AP2A2 and MUC5AC and lower expression of MUC5B in BEC were correlated with asthma, asthma exacerbations, and T2 biomarkers (P  0.8). CONCLUSIONS: SNPs associated with asthma in chr11p15.5 region are not associated with asthma severity neither with IIPs. Higher expression of MUC5AC and lower expression of MUC5B are risk for asthma but protective for IIPs.

The miR-15/16 family targets a large network of genes in T cells to restrict their cell cycle, memory formation, and survival. Upon T cell activation, miR-15/16 are downregulated, allowing rapid expansion of differentiated effector T cells to mediate a sustained response. Here, we used conditional deletion of miR-15/16 in regulatory T cells (Tregs) to identify immune functions of the miR-15/16 family in T cells. miR-15/16 are indispensable to maintain peripheral tolerance by securing efficient suppression by a limited number of Tregs. miR-15/16 deficiency alters expression of critical Treg proteins and results in accumulation of functionally impaired FOXP3loCD25loCD127hi Tregs. Excessive proliferation in the absence of miR-15/16 shifts Treg fate and produces an effector Treg phenotype. These Tregs fail to control immune activation, leading to spontaneous multi-organ inflammation and increased allergic inflammation in a mouse model of asthma. Together, our results demonstrate that miR-15/16 expression in Tregs is essential to maintain immune tolerance.

Altered myeloid inflammation and lymphopenia are hallmarks of severe infections. We identified the upregulated EN-RAGE gene program in airway and blood myeloid cells from patients with acute lung injury from SARS-CoV-2 or other causes across 7 cohorts. This program was associated with greater clinical severity and predicted future mechanical ventilation and death. EN-RAGEhi myeloid cells express features consistent with suppressor cell functionality, including low HLA-DR and high PD-L1. Sustained EN-RAGE program expression in airway and blood myeloid cells correlated with clinical severity and increasing expression of T cell dysfunction markers. IL-6 upregulated many EN-RAGE program genes in monocytes in vitro. IL-6 signaling blockade by tocilizumab in a placebo-controlled clinical trial led to rapid normalization of EN-RAGE and T cell gene expression. This identifies IL-6 as a key driver of myeloid dysregulation associated with worse clinical outcomes in COVID-19 patients and provides insights into shared pathophysiological mechanisms in non-COVID-19 ARDS.