First-line Osimertinib for Lung Cancer With Uncommon EGFR Exon 19 Mutations and EGFR Compound Mutations.

Introduction: Up to 20% of EGFR-mutated NSCLC cases harbor uncommon EGFR mutations, including atypical exon 19 and compound mutations. Relatively little is known about the efficacy of osimertinib in these cases. Methods: Patients treated with first-line osimertinib for NSCLC with rare EGFR exon 19 (non E746_A750del) or compound mutations were included. Response assessment and time to progression were determined using Response Evaluation Criteria in Solid Tumors version 1.1 criteria. Kaplan-Meier analyses were used to estimate progression-free survival (PFS), time to treatment discontinuation (TTD), and overall survival (OS). Results: Thirty-seven patients with NSCLC harboring an atypical EGFR exon 19 mutation or compound mutation were treated with first-line osimertinib at Johns Hopkins from 2016 to 2021. Overall response rate (ORR) was 76% and median PFS, TTD, and OS were 13 months (95% confidence interval [CI]: 10-15), 22 months (95% CI: 17-32) and 36 months (95% CI, 29-48), respectively. Among atypical exon 19 mutations (n = 25), ORR was 80%, median PFS was 12 months (95% CI: 10-15), median TTD was 19 months (95% CI: 17-38), and median OS was 48 months (95% CI: 25-not reached). Compound mutations (n = 12) had an ORR of 67%, median PFS of 14 months (95% CI: 5-22), median TTD of 26 months (95% CI: 5-36), and median OS of 36 months (95% CI: 20-46). Twelve patients (32%) continued first-line osimertinib after local therapy for oligoprogression. Conclusions: Osimertinib exhibited favorable outcomes for rare EGFR exon 19 and compound mutations. The heterogeneity in outcomes among these groups of tumors with similar mutations underscores the need for continued reporting and further study of outcomes among rare variants to optimize management for each patient.

Machine learning classification of new firearm injury encounters in the St Louis region: 2010-2020.

OBJECTIVES: To improve firearm injury encounter classification (new vs follow-up) using machine learning (ML) and compare our ML model to other common approaches. MATERIALS AND METHODS: This retrospective study used data from the St Louis region-wide hospital-based violence intervention program data repository (2010-2020). We randomly selected 500 patients with a firearm injury diagnosis for inclusion, with 808 total firearm injury encounters split (70/30) for training and testing. We trained a least absolute shrinkage and selection operator (LASSO) regression model with the following predictors: admission type, time between firearm injury visits, number of prior firearm injury emergency department (ED) visits, encounter type (ED or other), and diagnostic codes. Our gold standard for new firearm injury encounter classification was manual chart review. We then used our test data to compare the performance of our ML model to other commonly used approaches (proxy measures of ED visits and time between firearm injury encounters, and diagnostic code encounter type designation [initial vs subsequent or sequela]). Performance metrics included area under the curve (AUC), sensitivity, and specificity with 95% confidence intervals (CIs). RESULTS: The ML model had excellent discrimination (0.92, 0.88-0.96) with high sensitivity (0.95, 0.90-0.98) and specificity (0.89, 0.81-0.95). AUC was significantly higher than time-based outcomes, sensitivity was slightly (but not significantly) lower than other approaches, and specificity was higher than all other methods. DISCUSSION: ML successfully delineated new firearm injury encounters, outperforming other approaches in ruling out encounters for follow-up. CONCLUSION: ML can be used to identify new firearm injury encounters and may be particularly useful in studies assessing re-injuries.

How Feminist Heterosexual Men Navigate Their Sexual Desire While Following Feminist Principles.

Feminist considerations have influenced how women and men view sex, affecting not only women's perspectives but also men's feelings about sexual desire with regard to gender equity. This might be especially the case among men who self-identify as feminist. However, how men should manage their sexual desire or communicate about it within relationships with women is not always clear in this evolving social climate. Thus, the current study aimed to explore the successes and/or struggles feminist heterosexual men experience while navigating their desires alongside feminist considerations. To explore this, we recruited feminist-identified heterosexual men in long-term relationships. We asked participants (N = 30) a series of questions regarding their sexual desire, considering the context of their long-term relationships and evolving gender norms, during a one-on-one interview via Zoom. Using thematic analysis, we identified 11 themes from the interview data. We found that, though the feminist men in this study were all aware of negative societal perceptions of heterosexual men's sexual desire, most men in this study did not feel conflicts between their feminist principles and their own sexual desires. This is because they reported already following feminist principles; those who felt ambivalent navigated this by communicating with their partners. Findings demonstrate the usefulness and positive impact men report feminism having on them, their sexuality, and their long-term relationships, by allowing them to better engage with their sexuality and partners.

Seat Belt Injury and Efferent Loop Laceration Following a Single Anastomosis Duodenal Switch: A Case Report.

Blunt abdominal trauma patients who have had prior bariatric procedures may present a diagnostic and therapeutic challenge. The single anastomosis duodenal-ileal bypass with sleeve (SADI-S) is a modified duodenal switch procedure that is relatively uncommon. This case report describes a patient who previously underwent a SADI-S for the management of obesity and subsequently sustained a seat belt injury in a motor vehicle collision resulting in a laceration of the efferent loop. The patient presented with symptoms of acute abdominal pain and was diagnosed through imaging studies. Prompt surgical intervention was performed with resection and primary anastomosis of the damaged section of the jejunum, and repair of a large mesenteric laceration. We discuss the importance of early recognition and intraoperative decision-making in the case of this patient concerning her SADI-S.

Protocol to electroporate DNA plasmids into Ciona robusta embryos at the 1-cell stage.

Electroporation is a technique to introduce DNA constructs into cells using electric current. Here, we present a protocol to electroporate DNA plasmids into Ciona robusta embryos at the 1-cell stage. We describe steps for setting up and conducting electroporation. We then detail procedures for collecting, fixing, and mounting embryos and counting expression. This protocol can be used to study the expression of enhancers via reporter assays, manipulating cells using genes or modified genes such as dominant negatives, and genome editing. For complete details on the use and execution of this protocol, please refer to Song, et al.1.

CB2 stimulation of adipose resident ILC2s orchestrates immune balance and ameliorates type 2 diabetes mellitus.

Development of type 2 diabetes mellitus (T2DM) is associated with low-grade chronic type 2 inflammation and disturbance of glucose homeostasis. Group 2 innate lymphoid cells (ILC2s) play a critical role in maintaining adipose homeostasis via the production of type 2 cytokines. Here, we demonstrate that CB2, a G-protein-coupled receptor (GPCR) and member of the endocannabinoid system, is expressed on both visceral adipose tissue (VAT)-derived murine and human ILC2s. Moreover, we utilize a combination of ex vivo and in vivo approaches to explore the functional and therapeutic impacts of CB2 engagement on VAT ILC2s in a T2DM model. Our results show that CB2 stimulation of ILC2s protects against insulin-resistance onset, ameliorates glucose tolerance, and reverses established insulin resistance. Our mechanistic studies reveal that the therapeutic effects of CB2 are mediated through activation of the AKT, ERK1/2, and CREB pathways on ILC2s. The results reveal that the CB2 agonist can serve as a candidate for the prevention and treatment of T2DM.

Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis.

Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with poor prognosis and limited treatment options. Efforts to identify effective treatments are thwarted by limited understanding of IPF pathogenesis and poor translatability of available preclinical models. Here we generated spatially resolved transcriptome maps of human IPF (n = 4) and bleomycin-induced mouse pulmonary fibrosis (n = 6) to address these limitations. We uncovered distinct fibrotic niches in the IPF lung, characterized by aberrant alveolar epithelial cells in a microenvironment dominated by transforming growth factor beta signaling alongside predicted regulators, such as TP53 and APOE. We also identified a clear divergence between the arrested alveolar regeneration in the IPF fibrotic niches and the active tissue repair in the acutely fibrotic mouse lung. Our study offers in-depth insights into the IPF transcriptional landscape and proposes alveolar regeneration as a promising therapeutic strategy for IPF.

CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes.

Deconvolution methods infer quantitative cell type estimates from bulk measurement of mixed samples including blood and tissue. DNA methylation sequencing measures multiple CpGs per read, but few existing deconvolution methods leverage this within-read information. We develop CelFiE-ISH, which extends an existing method (CelFiE) to use within-read haplotype information. CelFiE-ISH outperforms CelFiE and other existing methods, achieving 30% better accuracy and more sensitive detection of rare cell types. We also demonstrate the importance of marker selection and of tailoring markers for haplotype-aware methods. While here we use gold-standard short-read sequencing data, haplotype-aware methods will be well-suited for long-read sequencing.

Late Holocene relative sea-level records from coral microatolls in Singapore.

Late Holocene relative sea-level (RSL) data are important to understand the drivers of RSL change, but there is a lack of precise RSL records from the Sunda Shelf. Here, we produced a Late Holocene RSL reconstruction from coral microatolls in Singapore, demonstrating for the first time the utility of Diploastrea heliopora microatolls as sea-level indicators. We produced 12 sea-level index points and three marine limiting data with a precision of < ± 0.2 m (2σ) and < ± 26 years uncertainties (95% highest density region). The data show a RSL fall of 0.31 ± 0.18 m between 2.8 and 0.6 thousand years before present (kyr BP), at rates between - 0.1 ± 0.3 and - 0.2 ± 0.7 mm/year. Surface profiles of the fossil coral microatolls suggest fluctuations in the rate of RSL fall: (1) stable between 2.8 and 2.5 kyr BP; (2) rising at ~ 1.8 kyr BP; and (3) stable from 0.8 to 0.6 kyr BP. The microatoll record shows general agreement with published, high-quality RSL data within the Sunda Shelf. Comparison to a suite of glacial isostatic adjustment (GIA) models indicate preference for lower viscosities in the mantle. However, more high quality and precise Late Holocene RSL data are needed to further evaluate the drivers of RSL change in the region and better constrain GIA model parameters.

Oldest southern sauropterygian reveals early marine reptile globalization.

Sauropterygians were the stratigraphically longest-ranging clade of Mesozoic marine reptiles with a global fossil record spanning ∼180 million years1. However, their early evolution has only been known from what is now the Northern Hemisphere, extending across the northern and trans-equatorial western margins of the Tethys paleo-ocean1 after the late-Early Triassic (late Olenekian, ∼248.8 million years [Ma] ago2), and via possible trans-Arctic migration1 to the Eastern Panthalassa super-ocean prior to the earliest Middle Triassic (Olenekian-earliest Anisian3,4, ∼247 Ma). Here, we describe the geologically oldest sea-going reptile from the Southern Hemisphere - a nothosaur (basal sauropterygian5) from the Middle Triassic (Anisian, after ∼246 Ma6) of New Zealand. Time-scaled ancestral range estimations thus reveal an unexpected circum-Gondwanan high-paleolatitude (>60° S7) dispersal from a northern Tethyan origination center. This coincides with the adaptive diversification of sauropterygians after the end-Permian mass extinction8 and suggests that rapid globalization accompanied their initial radiation in the earliest Mesozoic.

Prevalence of cefixime-resistant Neisseria gonorrhoeae in Melbourne, Australia, 2021-2022.

While ceftriaxone remains the first-line treatment for gonorrhoea, the US CDC recommended cefixime as a second-line treatment in 2021. We tested 1176 Neisseria gonorrhoeae isolates among clients attending the Melbourne Sexual Health Centre in 2021-2022. The prevalence of cefixime resistance was 6.3% (74/1176), azithromycin resistance was 4.9% (58/1176) and ceftriaxone resistance was 0% (0/1176). Cefixime resistance was the highest among women (16.4%, 10/61), followed by men-who-have-sex-with-women (6.4%, 7/109), and men-who-have-sex-with-men (5.8%, 57/982). The prevalence of cefixime-resistant N. gonorrhoeae exceeds the threshold of the 5% resistance level recommended by the World Health Organization; and thus, cefixime treatment would have limited benefits in Australia.

Single-stranded DNA Gap Accumulation is a Functional Biomarker for USP1 Inhibitor Sensitivity.

Recent studies suggest that PARP inhibitors and POLQ inhibitors confer synthetic lethality in BRCA1-deficient tumors by accumulation of single-stranded DNA (ssDNA) gaps at replication forks. Loss of USP1, a deubiquitinating enzyme, is also synthetic lethal with BRCA1 deficiency, and USP1 inhibitors are now undergoing clinical development for these cancers. Here, we show that USP1 inhibitors also promote the accumulation of ssDNA gaps during replication in BRCA1-deficient cells, and this phenotype correlates with the drug sensitivity. USP1 inhibition increased monoubiquitinated PCNA at replication forks, mediated by the ubiquitin ligase RAD18, and knockdown of RAD18 caused USP1 inhibitor resistance and suppression of ssDNA gaps. USP1 inhibition overcame PARP inhibitor resistance in a BRCA1-mutated xenograft model and induced ssDNA gaps. Furthermore, USP1 inhibition was synergistic with PARP and POLQ inhibition in BRCA1-mutant cells, with enhanced ssDNA gap accumulation. Finally, in patient-derived ovarian tumor organoids, sensitivity to USP1 inhibition alone or in combination correlated with the accumulation of ssDNA gaps. Assessment of ssDNA gaps in ovarian tumor organoids therefore represents a rapid approach for predicting response to USP1 inhibition in ongoing clinical trials.

Computer-Aided Design and Biological Evaluation of Diazaspirocyclic D4R Antagonists.

Parkinson's disease (PD) is a neurodegenerative disorder characterized by the progressive loss of dopaminergic neurons in the substantia nigra, resulting in motor dysfunction. Current treatments are primarily centered around enhancing dopamine signaling or providing dopamine replacement therapy and face limitations such as reduced efficacy over time and adverse side effects. To address these challenges, we identified selective dopamine receptor subtype 4 (D4R) antagonists not previously reported as potential adjuvants for PD management. In this study, a library screening and artificial neural network quantitative structure-activity relationship (QSAR) modeling with experimentally driven library design resulted in a class of spirocyclic compounds to identify candidate D4R antagonists. However, developing selective D4R antagonists suitable for clinical translation remains a challenge.

Mast Cell-related Prognosis Signature Characterizes Immune Landscape and Predicts Prognosis of Ovarian Cancer.

BACKGROUND/AIM: Ovarian cancer (OVC) is a common, aggressive, and heterogeneous malignancy, with a widely variable prognosis. With the advances of modern immunology, mast cells (MCs) have been shown to play a significant role in the prognosis of some malignant tumors. However, the role of mast cells in the prognosis of OVC is unknown. MATERIALS AND METHODS: In this study, MC-associated prognostic genes (MRGs) were used to classify OVC from The Cancer Genome Atlas (TCGA)-OVC cohort. Genes were evaluated using univariate cox regression analysis. Twenty-nine prognostic gene signatures were identified using LASSO-COX analysis. COX regression models and principal component analysis (PCA) algorithms were used to construct MRG scores and individual MRGs patterns. External validation was performed in the TCGA-breast cancer (BRCA) and IMvigor210 cohorts. Immunity analysis based on MRGs was performed using CIBERSORT, and GSVA methods, and immunotherapy response was evaluated using the TIDE website. RESULTS: Using TCGA-OVC data, we established a model for constructing MRG scores based on the twenty-nine identified prognostic gene signatures using the PCA algorithm. MRG scores were found to be strongly correlated with immune cell infiltration and were excellent predictors of prognosis in patients with OVC. Low MRG scores were associated with better prognosis and better response to immunotherapy and chemotherapy. CONCLUSION: MC-related prognosis signature characterizes the immune landscape and predicts the prognosis of OVC. Understanding the correlation between MC-related gene signatures and immunotherapy and chemotherapy may improve the development of personalized clinical treatment strategies.

Genomic Surveillance of Invasive Meningococcal Disease During a National MenW Outbreak in Australia, 2017-2018.

Background: In Australia, invasive meningococcal disease (IMD) incidence rapidly increased between 2014 and 2017 due to rising serogroup W (MenW) and MenY infections. We aimed to better understand the genetic diversity of IMD during 2017 and 2018 using whole genome sequencing data. Methods: Whole genome sequencing data from 440 Australian IMD isolates collected during 2017 and 2018 and 1737 international MenW:CC11 isolates collected in Europe, Africa, Asia, North America, and South America between 1974 and 2020 were used in phylogenetic analyses; genetic relatedness was determined from single-nucleotide polymorphisms. Results: Australian isolates were as follows: 181 MenW (41%), 144 MenB (33%), 88 MenY (20%), 16 MenC (4%), 1 MenW/Y (0.2%), and 10 nongenogroupable (2%). Eighteen clonal complexes (CCs) were identified, and 3 (CC11, CC23, CC41/44) accounted for 78% of isolates (343/440). These CCs were associated with specific serogroups: CC11 (n = 199) predominated among MenW (n = 181) and MenC (n = 15), CC23 (n = 80) among MenY (n = 78), and CC41/44 (n = 64) among MenB (n = 64). MenB isolates were highly diverse, MenY were intermediately diverse, and MenW and MenC isolates demonstrated the least genetic diversity. Thirty serogroup and CC-specific genomic clusters were identified. International CC11 comparison revealed diversification of MenW in Australia. Conclusions: Whole genome sequencing comprehensively characterized Australian IMD isolates, indexed their genetic variability, provided increased within-CC resolution, and elucidated the evolution of CC11 in Australia.

Sulfuric Acid Baking and Fe(III)-Cl--H2SO4 Leaching Behavior of Ni- and Cu-Containing Sulfide and Silicate Rich Suhanko Concentrate.

Ni- and Cu-rich concentrate from a new site in Suhanko, Finland, was investigated. Mineral phases identified included talc, chalcopyrite, kaolinite, and pyrrhotite with 3.2% Cu and 1.5% Ni, and the latter is associated with pyrrhotite. In addition, the concentrate contained the precious elements Pd (14.9 g/t), Ag (17.1 g/t), Pt (2.1 g/t), and Au (1.1 g/t). This concentrate was baked and leached using a Fe(III)-Cl--H2SO4 system. The results showed that the leaching efficiencies of Ni, Cu, and Si from raw concentrate were 60%, 40%, and 5%; however, those from baked concentrate were 96%, 60%, and below 0.1%, indicating that the baking process enhanced Ni and Cu extraction while simultaneously inhibiting the dissolution of Si, which was due to the baking process liberating the associated Ni and Cu by the oxidation of chalcopyrite and pyrrhotite and converting the acid-soluble silicate into an insoluble form. Sulfuric acid leaching solution with Fe(III) as oxidant and Cl- as lixiviant was shown to be effective at leaching Ni (97%), Cu (62%), and Ag (89%), while simultaneously enriching the PMs Pd, Pt, and Au in the residue.

Histone acylation at a glance.

An important mechanism of gene expression regulation is the epigenetic modification of histones. The cofactors and substrates for these modifications are often intermediary metabolites, and it is becoming increasingly clear that the metabolic and nutritional state of cells can influence these marks. These connections between the balance of metabolites, histone modifications and downstream transcriptional changes comprise a metabolic signaling program that can enable cells to adapt to changes in nutrient availability. Beyond acetylation, there is evidence now that histones can be modified by other acyl groups. In this Cell Science at a Glance article and the accompanying poster, we focus on these histone acylation modifications and provide an overview of the players that govern these acylations and their connections with metabolism.

Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight.

Maintenance of astronaut health during spaceflight will require monitoring and potentially modulating their microbiomes. However, documenting microbial shifts during spaceflight has been difficult due to mission constraints that lead to limited sampling and profiling. Here we executed a six-month longitudinal study to quantify the high-resolution human microbiome response to three days in orbit for four individuals. Using paired metagenomics and metatranscriptomics alongside single-nuclei immune cell profiling, we characterized time-dependent, multikingdom microbiome changes across 750 samples and 10 body sites before, during and after spaceflight at eight timepoints. We found that most alterations were transient across body sites; for example, viruses increased in skin sites mostly during flight. However, longer-term shifts were observed in the oral microbiome, including increased plaque-associated bacteria (for example, Fusobacteriota), which correlated with immune cell gene expression. Further, microbial genes associated with phage activity, toxin-antitoxin systems and stress response were enriched across multiple body sites. In total, this study reveals in-depth characterization of microbiome and immune response shifts experienced by astronauts during short-term spaceflight and the associated changes to the living environment, which can help guide future missions, spacecraft design and space habitat planning.