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Abstract Perovskite solar cells (PSCs) offer an efficient, inexpensive alternative to current photovoltaic technologies, with the potential for manufacture via high-throughput coating methods. However, challenges for commercial-scale solution-processing of metal-halide perovskites include the use of harmful solvents, the expense of maintaining controlled atmospheric conditions, and the inherent instabilities of PSCs under operation. Here, we address these challenges by introducing a high volatility, low toxicity, biorenewable solvent system to fabricate a range of 2D perovskites, which we use as highly effective precursor phases for subsequent transformation to α-formamidinium lead triiodide (α-FAPbI3), fully processed under ambient conditions. PSCs utilising our α-FAPbI3 reproducibly show remarkable stability under illumination and elevated temperature (ISOS-L-2) and “damp heat” (ISOS-D-3) stressing, surpassing other state-of-the-art perovskite compositions. We determine that this enhancement is a consequence of the 2D precursor phase crystallisation route, which simultaneously avoids retention of residual low-volatility solvents (such as DMF and DMSO) and reduces the rate of degradation of FA+ in the material. Our findings highlight both the critical role of the initial crystallisation process in determining the operational stability of perovskite materials, and that neat FA+-based perovskites can be competitively stable despite the inherent metastability of the α-phase.

Abstract Mixed lineage kinase domain-like (MLKL) is a pseudokinase, best known for its role as the terminal effector of the necroptotic cell death pathway. MLKL-mediated necroptosis has long been linked to various age-related pathologies including neurodegeneration, atherosclerosis and male reproductive decline, however many of these attributions remain controversial. Here, we investigated the role of MLKL and necroptosis in the adult mouse testis: an organ divided into sperm-producing seminiferous tubules and the surrounding testosterone-producing interstitium. We find that sperm-producing cells within seminiferous tubules lack expression of key necroptotic mediators and thus are resistant to a pro-necroptotic challenge. By comparison, coordinated expression of the necroptotic pathway occurs in the testicular interstitium, rendering cells within this compartment, especially the lysozyme-positive macrophages, vulnerable to necroptotic cell death. We also uncover a non-necroptotic role for MLKL in regulating testosterone levels. Thus, MLKL serves two roles in the mouse testes – one involving the canonical response of macrophages to necroptotic insult, and the other a non-canonical function in male reproductive hormone control.

Abstract Objectives Serum protein abundance was assessed in adult and juvenile dermatomyositis (DM and JDM) patients to determine differentially regulated proteins, altered pathways, and candidate disease activity biomarkers. Methods Serum protein expression from 17 active adult DM and JDM patients each was compared to matched, healthy control subjects by a multiplex immunoassay. Pathway analysis and protein clustering of the differentially regulated proteins were examined to assess underlying mechanisms. Candidate disease activity biomarkers were identified by correlating protein expression with disease activity measures. Results Seventy-eight of 172 proteins were differentially expressed in the sera of DM and JDM patients compared to healthy controls. Forty-eight proteins were differentially expressed in DM, 32 proteins in JDM, and 14 proteins in both DM and JDM. Twelve additional differentially expressed proteins were identified after combining the DM and JDM cohorts. C-X-C motif chemokine ligand 10 (CXCL10) was the most strongly upregulated protein in both DM and JDM sera. Other highly upregulated proteins in DM included S100 calcium binding protein A12 (S100A12), CXCL9, and nicotinamide phosphoribosyltransferase (NAMPT), while highly upregulated proteins in JDM included matrix metallopeptidase 3 (MMP3), growth differentiation factor 15 (GDF15), and von Willebrand factor (vWF). Pathway analysis indicated that phosphoinositide 3-kinase (PI3K), p38 mitogen-activated protein kinase (MAPK), and toll-like receptor 7 (TLR7) signaling were activated in DM and JDM. Additional pathways specific to DM or JDM were identified. A protein cluster associated with neutrophils and mononuclear leukocytes and a cluster of interferon-associated proteins were observed in both DM and JDM. Twenty-two proteins in DM and 24 proteins in JDM sera correlated with global, muscle, and/or skin disease activity. Seven proteins correlated with disease activity measures in both DM and JDM sera. IL-1 receptor like 1 (IL1RL1) emerged as a candidate global disease activity biomarker in DM and JDM. Conclusion Coordinate analysis of protein expression in DM and JDM patient sera by a multiplex immunoassay validated previous gene expression studies and identified novel dysregulated proteins, altered signaling pathways, and candidate disease activity biomarkers. These findings may further inform the assessment of DM and JDM patients and aid in the identification of potential therapeutic targets.

Abstract The rapid and repeatable characterization of individual morphology has advanced automated taxonomic classification. The most direct study of evolutionary processes is, however, not from taxonomic description, but rather of the evolution of the traits that comprise individuals and define species. Repeatable signatures of individual morphology are crucial for analysing the response to selection at scale, and thus tracking evolutionary trajectories through time and across species boundaries. Here, we introduce our 3DKMI—an open‐source MATLAB package designed for the study of morphology using three‐dimensional (3D) Krawtchouk moment invariants. The volumetric features derived from the 3D images remain stable under translation, scaling and rotation and, for an image of size 128 × 128 × 128 can be computed in less than 0.1 s. We applied our package as a case study on a collection of 300 X‐ray computed tomography scans of planktonic foraminifera specimens across five species to (1) assess the invariance of the features under different transformations and (2) analyse morphological differences among species based on the extracted characteristics. We show that 3DKMI has the capacity to efficiently and repeatedly characterize the signatures of individual morphology. In the future, we hope that the 3D feature extraction technique 3DKMI will be widely applied to digital collections to advance research in ecology and evolution.

Abstract Background Dynamic transmission models are often used to provide epidemiological guidance for pandemic policy decisions. However, how economic evaluation is typically incorporated into this technique to generate cost-effectiveness estimates of pandemic policy responses has not previously been reviewed. Methods We systematically searched the Embase, PubMed and Scopus databases for dynamic epidemiological modelling studies that incorporated economic evaluation of public health and social measures (PHSMs), with no date restrictions, on 7 July 2024. Results Of the 2,719 screened studies, 51 met the inclusion criteria. Most studies (n = 42, 82%) modelled SARS-CoV-2. A range of PHSMs were examined, including school closures, testing/screening, social distancing and mask use. Half of the studies utilised an extension of a Susceptible-Exposed-Infectious-Recovered (SEIR) compartmental model. The most common type of economic evaluation was cost-effectiveness analysis (n = 24, 47%), followed by cost-utility analysis (n = 17, 33%) and cost–benefit analysis (n = 17, 33%). Conclusions Economic evaluation is infrequently incorporated into dynamic epidemiological modelling studies of PHSMs. The scope of this research should be expanded, given the substantial cost implications of pandemic PHSM policy responses.

Graphene oxide (GO) undergoes multiple transformations when introduced to biological and environmental media. GO surface favors the adsorption of biomolecules through different types of interaction mechanisms, modulating the biological effects of the material. In this study, we investigated the interaction of GO with tannic acid (TA) and its consequences for GO toxicity. We focused on understanding how TA interacts with GO, its impact on the material surface chemistry, colloidal stability, as well as, toxicity and biodistribution using the Caenorhabditis elegans model. Employing computational modeling, including reactive classical molecular dynamics and ab initio calculations, we reveal that TA preferentially binds to the most reactive sites on GO surfaces via the oxygen-containing groups or the carbon matrix; van der Waals interaction forces dominate the binding energy. TA exhibits a dose-dependent mitigating effect on the toxicity of GO, which can be attributed not only to the surface interactions between the molecule and the material but also to the inherent biological properties of TA in C. elegans. Our findings contribute to a deeper understanding of GO’s environmental behavior and toxicity and highlight the potential of tannic acid for the synthesis and surface functionalization of graphene-based nanomaterials, offering insights into safer nanotechnology development.

Abstract Background Babies born via caesarean section in low-income settings face a higher risk of early-onset neonatal sepsis (EONS), which has greater mortality than late-onset sepsis. However, maternal factors contributing to EONS among caesarean-delivered babies in these settings, including Uganda, are not well documented. We determined maternal factors associated with EONS among term babies delivered by caesarian section at Mbarara Regional Referral Hospital (MRRH), southwestern Uganda. Methods We conducted an unmatched case-control study at MRRH from December 2019 to March 2020. Cases were caesarean section-delivered term babies with EONS (within 72 h). Controls were caesarean section-delivered term babies without EONS. We enrolled mother-baby pairs for both groups, obtaining maternal data via structured questionnaires The diagnosis of EONS was made using the WHO Young Infant Integrated Management of Childhood Illnesses algorithm. Cases were consecutively recruited while controls were recruited by simple random sampling in a ratio of 1:2. We excluded newborns whose mothers were too ill to consent. We used multivariable logistic regression analysis to identify maternal factors associated with EONS. Results We enrolled 52 cases and 104 controls. The mean age for the mothers was 27 (± 5.5) years. Neonates born to referred mothers had higher odds of EONS than those born to non-referred mothers (AOR = 6.2, 95% CI: 1.8–21). Additionally, decision-to-delivery time > 1 h for emergency caesarean section (AOR = 16, 95% CI: 4.2–65), antepartum hemorrhage (AOR = 8.0, 95% CI: 1.6–40), primiparity (AOR = 4.8, 95% CI: 1.1–21), and > 3 vaginal examinations after membrane rupture (AOR = 4.3, 95% CI: 1.5–12) were associated with EONS. Conclusions Prime gravidity, antepartum hemorrhage, multiple vaginal examinations after membrane rupture, long decision-to-delivery time, and referral status were associated with EONS among term babies delivered by caesarean section at MRRH. To reduce EONS risk, clinicians should limit post-membrane rupture vaginal exams or consider prophylactic antibiotics if multiple exams are needed. Screening babies born to primiparous women, those referred, those with antepartum hemorrhage, multiple vaginal exams after membranes rupture, and long decision-to-delivery times, could aid prompt recognition of EONS and timely interventions. Implementing standard procedures to reduce caesarean decision-to-delivery time could reduce risk for EONS in this setting.

Abstract Background Several surgical options for degenerative lumbar spinal stenosis (LSS) are available, but current guidelines do not recommend which one should be prioritized. Although previous network meta-analyses (NMAs) have been performed on this topic, they have major methodological problems and could not provide the convincing evidence and clinical practical information required. Methods Randomized controlled trials (RCTs) comparing at least two surgical interventions were included by searching AMED, CINAHL, EMBASE, the Cochrane Library, and MEDLINE (inception to August 2023). A frequentist random-effects NMA was performed for physical function and adverse events due to any reason. For physical function, three follow-up time points were included: short-term (

Abstract The Four Core Genotypes (FCG) is a mouse model system used to disentangle the function of sex chromosomes and hormones. We report that a copy of a 3.2 MB region of the X chromosome has translocated to the Y Sry- chromosome and thus increased the expression of X-linked genes including the single-stranded RNA sensor and autoimmune disease mediator Tlr7. This previously-unreported X-Y translocation complicates the interpretation of studies reliant on C57BL/6J FCG mice.

Abstract Hyperemia in response to neural activity is essential for brain health. A hyperemic response delivers O2 and nutrients, clears metabolic waste, and concomitantly exposes cerebrovascular endothelial cells to hemodynamic forces. While neurovascular research has primarily centered on the front end of hyperemia—neuronal activity-to-vascular response—the mechanical consequences of hyperemia have gone largely unexplored. Piezo1 is an endothelial mechanosensor that senses hyperemia-associated forces. Using genetic mouse models and pharmacologic approaches to manipulate endothelial Piezo1 function, we evaluated its role in blood flow control and whether it impacts cognition. We provide evidence of a built-in brake system that sculpts hyperemia, and specifically show that Piezo1 activation triggers a mechano-feedback system that promotes blood flow recovery to baseline. Further, genetic Piezo1 modification led to deficits in complementary memory tasks. Collectively, our findings establish a role for endothelial Piezo1 in cerebral blood flow regulation and a role in its behavioral sequelae.

Abstract Many disease-causing proteins have multiple pathogenic mechanisms, and conventional inhibitors struggle to reliably disrupt more than one. Targeted protein degradation (TPD) can eliminate the protein, and thus all its functions, by directing a cell’s protein turnover machinery towards it. Two established strategies either engage catalytic E3 ligases or drive uptake towards the endolysosomal pathway. Here we describe CYpHER (CatalYtic pH-dependent Endolysosomal delivery with Recycling) technology with potency and durability from a catalytic mechanism that shares the specificity and straightforward modular design of endolysosomal uptake. By bestowing pH-dependent release on the target engager and using the rapid-cycling transferrin receptor as the uptake receptor, CYpHER induces endolysosomal delivery of surface and extracellular targets while re-using drug, potentially yielding increased potency and reduced off-target tissue exposure risks. The TfR-based approach allows targeting to tumors that overexpress this receptor and offers the potential for transport to the CNS. CYpHER function was demonstrated in vitro with EGFR and PD-L1, and in vivo with EGFR in a model of EGFR-driven non-small cell lung cancer.

Abstract In this work, we extend vcfdist to be the first variant call benchmarking tool to jointly evaluate phased single-nucleotide polymorphisms (SNPs), small insertions/deletions (INDELs), and structural variants (SVs) for the whole genome. First, we find that a joint evaluation of small and structural variants uniformly reduces measured errors for SNPs (− 28.9%), INDELs (− 19.3%), and SVs (− 52.4%) across three datasets. vcfdist also corrects a common flaw in phasing evaluations, reducing measured flip errors by over 50%. Lastly, we show that vcfdist is more accurate than previously published works and on par with the newest approaches while providing improved result interpretability.

Background: Globally, viral hepatitis is decreasing, but nonalcoholic fatty liver disease (NAFLD), now metabolic dysfunction-associated steatotic liver disease (MASLD), is increasing. We assessed the burden and trends of MASLD and viral hepatitis in Saudi Arabia. Methods: Prevalence, death, and disability data due to MASLD, hepatitis C virus (HCV), and hepatitis B virus (HBV) were obtained from 2019 Global Burden of Disease (GBD) database for Saudi Arabia. Time trends were assessed by annual percent change (APC) from joinpoint regression. Results: From 2012 through 2019, MASLD prevalence in children and adults increased from 28.02% (n = 8.34 million) to 33.11% (n = 11.83 million); APC +2.43% (95% confidence interval: 2.33% to 2.54%). HBV prevalence decreased from 1.83% (n = 0.54 million) to 1.53% (n = 0.55 million); APC −1.74% (−2.66% to −0.81%). HCV prevalence stabilized from 0.72% (n = 0.21 million) to 0.73% (n = 0.26 million): APC +0.32% (−0.13% to 0.78%). Among adults (>20 years), MASLD prevalence increased from 40.64% to 43.95% (APC = +1.15%, 1.12% to 1.18%), HBV prevalence decreased from 2.67% to 2.05% (APC = −2.96%, −3.90% to −2.01%), and HCV leveled from 0.88% to 0.86% (APC = −0.30%, −0.75% to 0.16%). MASLD liver mortality rate from liver cancer and cirrhosis increased: APC of +1.15% (0.82% to 1.48%) from 1.31 to 1.43 (per 100,000). HBV and HCV liver mortality increased at slower rates (APC = +0.78%, 0.38% to 1.19%): 2.07 to 2.20 (per 100,000) and (APC = +0.55%, 0.09% to 0.89%): 6.32 to 6.61 (per 100,000), respectively. Conclusions: MASLD burden is increasing, while HBV and HCV burden is decreasing/remaining stable. Early prevention and diagnosis health policies for MASLD are needed.

Copper Beryllium (C17200) has ideal physical and mechanical properties of high fatigue strength, thermal conductivity, and hardness, making the alloy ideal for various high-reliability applications in aerospace, producing inserts and tooling for hazardous environments. However, surface quality and productivity challenges are prominent when processing the alloy due to its properties. This study evaluates the surface quality and productivity in end-milling of Copper Beryllium by analyzing the effects of feed rate, minimum quantity lubrication (MQL) flow rate, and cutting depth on surface roughness (Ra) and material removal rate (MRR). The experiment was designed using the Box-Behnken design, and the samples were machined on a CNC milling machine. The results showed that the MQL flow rate was significant to surface roughness, while the cutting depth was significant to MRR. The optimum parameters were determined as a feed rate of – 60 mm/min, an MQL flow rate of – 80 ml/hr., and a cutting depth of – 0.511 mm, which yielded a surface roughness of 0.12 µm and MRR of 10.19 g/min. The study's novelty is that it considers MQL flow using vegetable oil-based cutting fluid (CF) as an input parameter in machining, offering insight into eco-friendly and cost-effective machining practices. Finally, the significance of the study lies in investigating the machinability of Cu-Be alloy material, addressing challenges related to surface quality and productivity during milling operation.

Five new species of Metapolybia are described, Metapolybia carpenteriana, Andena & Noll, sp. nov. (Ecuador, Peru), Metapolybia pseudodocilis Cortes, sp. nov. (Bolivia), Metapolybia richardsi Andena, sp. nov. (Ecuador), Metapolybia sulamerica Carpenter, sp. nov. (Colombia), Metapolybia zucchiana Andena & Carpenter, sp. nov. (Panama), in addition to the hitherto unknown males of M. bromelicola, M. encantata, M. mesoamerica, M. servilis and M. rufata plus two new species. Comparative remarks for the species are given.

Abstract BRCA2 is essential for DNA repair by homologous recombination in mitosis and meiosis. It interacts with recombinases RAD51 and DMC1 to facilitate the formation of nucleoprotein filaments on resected DNA ends that catalyse recombination-mediated repair. BRCA2’s BRC repeats bind and disrupt RAD51 and DMC1 filaments, whereas its PhePP motifs bind recombinases and stabilise their nucleoprotein filaments. However, the mechanism of filament stabilisation has hitherto remained unknown. Here, we report the crystal structure of a BRCA2-DMC1 complex, revealing how core interaction sites of PhePP motifs bind to recombinases. The interaction mode is conserved for RAD51 and DMC1, which selectively bind to BRCA2’s two distinct PhePP motifs via subtly divergent binding pockets. PhePP motif sequences surrounding their core interaction sites protect nucleoprotein filaments from BRC-mediated disruption. Hence, we report the structural basis of how BRCA2’s PhePP motifs stabilise RAD51 and DMC1 nucleoprotein filaments for their essential roles in mitotic and meiotic recombination.

Unprecedented rates of biodiversity loss and ecosystem function necessitate the use of rapid, efficacious, and cost-effective biomonitoring tools. The combination of autonomous samplers and high throughput sequencing (i.e., “metabarcoding”) of environmental DNA (eDNA) samples enables characterization of entire communities at high frequency and can be an important tool for conservation and management, allowing researchers to track fluctuations in biodiversity. We deployed two autonomous samplers at two U.S. Geological Survey streamgage sites in the upper Snake River (Wyoming and Idaho, USA) to collect eDNA samples from July-September 2021 and 2022 to characterize fish diversity. We used a probabilistic approach to evaluate the effects of water temperature, water discharge, filter pore size, water volume filtered, number of samples collected, timing, and primers on the probability of detecting eDNA from fish species known to be present. We detected eDNA from 13/15 species present in these areas of the Snake River. Overall, we did not find evidence that filter pore size, water volume filtered, water discharge, and water temperature affected the probability of detecting fish species’ eDNA. By contrast, primers and sampling day affected fish detection probabilities, indicating that primer choice and sampling day can either over- or under- estimate species diversity. These results indicate that users would ideally consider sampling on non-consecutive days and which primer set will maximize species detections.

Abstract Drug-induced gene expression profiles can identify potential mechanisms of toxicity. We focus on obtaining signatures for cardiotoxicity of FDA-approved tyrosine kinase inhibitors (TKIs) in human induced-pluripotent-stem-cell-derived cardiomyocytes, using bulk transcriptomic profiles. We use singular value decomposition to identify drug-selective patterns across cell lines obtained from multiple healthy human subjects. Cellular pathways affected by cardiotoxic TKIs include energy metabolism, contractile, and extracellular matrix dynamics. Projecting these pathways to published single cell expression profiles indicates that TKI responses can be evoked in both cardiomyocytes and fibroblasts. Integration of transcriptomic outlier analysis with whole genomic sequencing of our six cell lines enables us to correctly reidentify a genomic variant causally linked to anthracycline-induced cardiotoxicity and predict genomic variants potentially associated with TKI-induced cardiotoxicity. We conclude that mRNA expression profiles when integrated with publicly available genomic, pathway, and single cell transcriptomic datasets, provide multiscale signatures for cardiotoxicity that could be used for drug development and patient stratification.

Vaccine hesitancy threatens to reverse the progress in tackling vaccine-preventable diseases. We used an $ SIS $ model with a game theory model for vaccination and parameters from the COVID-19 pandemic to study how vaccine hesitancy impacts epidemic dynamics. The system showed three asymptotic behaviors: total rejection of vaccinations, complete acceptance, and oscillations. With increasing fear of infection, stable endemic states become periodic oscillations. Our results suggest that managing fear of infection relative to vaccination is vital to successful mass vaccinations.

Abstract Background Veterans with substance use disorder (SUD) are at high risk for cognitive problems due to neurotoxic effects of chronic drug and alcohol use coupled in many cases with histories of traumatic brain injury (TBI). These problems may in turn result in proneness to SUD relapse and reduced adherence to medical self-care regimens and therefore reliance on health care systems. However, the direct relationship between cognitive function and utilization of Veterans Health Administration (VHA) SUD and other VHA health care services has not been evaluated. We sought initial evidence as to whether neurocognitive performance relates to repeated health care engagement in Veterans as indexed by estimated VHA care costs. Methods Neurocognitive performance in 76 Veterans being treated for SUD was assessed using CNS-Vital Signs, a commercial computerized cognitive testing battery, and related to histories of outpatient and inpatient/residential care costs as estimated by the VHA Health Economics Resource Center. Results After controlling for age, an aggregate metric of overall neurocognitive performance (Neurocognition Index) correlated negatively with total VHA health care costs, particularly with SUD-related outpatient care costs but also with non-mental health-related care costs. Barratt Impulsiveness Scale scores also correlated positively with total VHA care costs. Conclusions In Veterans receiving SUD care, higher impulsivity and lower cognitive performance were associated with greater health care utilization within the VHA system. This suggests that veterans with SUD who show lower neurocognitive performance are at greater risk for continued health problems that require healthcare engagement. Cognitive rehabilitation programs developed for brain injury and other neurological conditions could be tried in Veterans with SUD to improve their health outcomes.

Abstract During metastasis, cancer cells traverse the vasculature by squeezing through very small gaps in the endothelium. Thus, nuclei in metastatic cancer cells must become more malleable to move through these gaps. Our lab showed invasive breast cancer cells have 50% less emerin protein resulting in smaller, misshapen nuclei, and higher metastasis rates than non-cancerous controls. Thus, emerin deficiency was predicted to cause increased nuclear compliance, cell migration, and metastasis. We tested this hypothesis by downregulating emerin in noninvasive MCF7 cells and found emerin knockdown causes smaller, dysmorphic nuclei, resulting in increased impeded cell migration. Emerin reduction in invasive breast cancer cells showed similar results. Supporting the clinical relevance of emerin reduction in cancer progression, our analysis of 192 breast cancer patient samples showed emerin expression inversely correlates with cancer invasiveness. We conclude emerin loss is an important driver of invasive transformation and has utility as a biomarker for tumor progression.

Abstract Background Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context. Results We systematically developed a global ocean AMG catalog by integrating previously described and newly identified AMGs and then placed this catalog into ecological and metabolic contexts relevant to ocean biogeochemistry. From 7.6 terabases of Tara Oceans paired prokaryote- and virus-enriched metagenomic sequence data, we increased known ocean virus populations to 579,904 (up 16%). From these virus populations, we then conservatively identified 86,913 AMGs that grouped into 22,779 sequence-based gene clusters, 7248 (~ 32%) of which were not previously reported. Using our catalog and modeled data from mock communities, we estimate that ~ 19% of ocean virus populations carry at least one AMG. To understand AMGs in their metabolic context, we identified 340 metabolic pathways encoded by ocean microbes and showed that AMGs map to 128 of them. Furthermore, we identified metabolic “hot spots” targeted by virus AMGs, including nine pathways where most steps (≥ 0.75) were AMG-targeted (involved in carbohydrate, amino acid, fatty acid, and nucleotide metabolism), as well as other pathways where virus-encoded AMGs outnumbered cellular homologs (involved in lipid A phosphates, phosphatidylethanolamine, creatine biosynthesis, phosphoribosylamine-glycine ligase, and carbamoyl-phosphate synthase pathways). Conclusions Together, this systematically curated, global ocean AMG catalog and analyses provide a valuable resource and foundational observations to understand the role of viruses in modulating global ocean metabolisms and their biogeochemical implications. Video Abstract

Abstract Teachers play a significant societal role, yet many feel underappreciated, and commonly cite this as a reason for considering leaving the profession. This study investigated responses to the #ThankYourTeacher social media campaign, which was created to generate public expressions of gratitude towards teachers. Data were collected from Twitter, Instagram, a campaign website, and public events and thematically analysed. Orr’s (1992) Head, Heart, and Hands Model of Transformational Learning was used as a framework for understanding the qualities of teachers and their teaching that participants appreciated. Notably, more individuals expressed gratitude for teachers’ motivational and compassionate qualities (Heart) and their enthusiasm and leadership (Hands) than for their subject knowledge (Head). These findings underscore the importance of the teacher-student relationship and relational qualities over subject expertise. This study also highlights the potential for further research into the impacts of practicing gratitude towards teachers and increasing teachers’ sense of being valued and appreciated.

Abstract Restoring motor function after stroke necessitates involvement of numerous cognitive systems. However, the impact of damage to motor and cognitive network organization on recovery is not well understood. To discover correlates of successful recovery, we explored imaging characteristics in chronic stroke subjects by combining noninvasive brain stimulation and fMRI. Twenty stroke survivors (6 months or more after stroke) were randomly assigned to a single session of transcranial direct current stimulation (tDCS) or sham during image acquisition. Twenty healthy subjects were included as controls. tDCS was limited to 10 min at 2 mA to serve as a mode of network modulation rather than therapeutic delivery. Fugl-Meyer Assessments (FMA) revealed significant motor improvement in the chronic stroke group receiving active stimulation (p = 0.0005). Motor changes in this group were correlated in a data-driven fashion with imaging features, including functional connectivity (FC), surface-based morphometry, electric field modeling and network topology, focusing on relevant regions of interest. We observed stimulation-related changes in FC in supplementary motor (p = 0.0029), inferior frontal gyrus (p = 0.0058), and temporo-occipital (p = 0.0095) areas, though these were not directly related to motor improvement. The feature most strongly associated with FMA improvement in the chronic stroke cohort was graph topology of the dorsal attention network (DAN), one of the regions surveyed and one with direct connections to each of the areas with FC changes. Chronic stroke subjects with a greater degree of motor improvement had lower signal transmission cost through the DAN (p = 0.029). While the study was limited by a small stroke cohort with moderate severity and variable lesion location, these results nevertheless suggest a top-down role for higher order areas such as attention in helping to orchestrate the stroke recovery process.

Abstract Background Anti-HER2 therapies, including the HER2 antibody–drug conjugates (ADCs) trastuzumab emtansine (T-DM1) and trastuzumab deruxtecan (T-DXd), have led to improved survival outcomes in patients with HER2-overexpressing (HER2+) metastatic breast cancer. However, intrinsic or acquired resistance to anti-HER2–based therapies remains a clinical challenge in these patients, as there is no standard of care following disease progression. The purpose of this study was to elucidate the mechanisms of resistance to T-DM1 and T-DXd in HER2+ BC patients and preclinical models and identify targets whose inhibition enhances the antitumor activity of T-DXd in HER2-directed ADC-resistant HER2+ breast cancer in vitro and in vivo. Methods Targeted DNA and whole transcriptome sequencing were performed in breast cancer patient tissue samples to investigate genetic aberrations that arose after anti-HER2 therapy. We generated T-DM1 and T-DXd–resistant HER2+ breast cancer cell lines. To elucidate their resistance mechanisms and to identify potential synergistic kinase targets for enhancing the efficacy of T-DXd, we used fluorescence in situ hybridization, droplet digital PCR, Western blotting, whole-genome sequencing, cDNA microarray, and synthetic lethal kinome RNA interference screening. In addition, cell viability, colony formation, and xenograft assays were used to determine the synergistic antitumor effect of T-DXd combinations. Results We found reduced HER2 expression in patients and amplified DNA repair–related genes in patients after anti-HER2 therapy. Reduced ERBB2 gene amplification in HER2-directed ADC–resistant HER2+ breast cancer cell lines was through DNA damage and epigenetic mechanisms. In HER2-directed ADC–resistant HER2+ breast cancer cell lines, our non-biased RNA interference screening identified the DNA repair pathway as a potential target within the canonical pathways to enhance the efficacy of T-DXd. We validated that the combination of T-DXd with ataxia telangiectasia and Rad3-related inhibitor, elimusertib, led to significant breast cancer cell death in vitro (P

Abstract A major and irreversible complication of diabetes is diabetic peripheral neuropathy (DPN), which can lead to significant disability and decreased quality of life. Prior work demonstrates the peptide hormone Angiotensin II (Ang II) is released locally in neuropathy and drives inflammation and impaired endoneurial blood flow. Therefore, we proposed that by utilizing a local thermoresponsive hydrogel injection, we could deliver inhibitors of angiotensin-converting enzyme (ACE) to suppress Ang II production and reduce nerve dysfunction in DPN through local drug release. The ACE inhibitor captopril was encapsulated into a micelle, which was then embedded into a reversibly thermoresponsive pluronics-based hydrogel matrix. Drug-free and captopril-loaded hydrogels demonstrated excellent product stability and sterility. Rheology testing confirmed sol properties with low viscosity at ambient temperature and increased viscosity and gelation at 37 °C. Captopril-loaded hydrogels significantly inhibited Ang II production in comparison to drug-free hydrogels. DPN mice treated with captopril-loaded hydrogels displayed normalized mechanical sensitivity and reduced inflammation, without side-effects associated with systemic exposure. Our data demonstrate the feasibility of repurposing ACE inhibitors as locally delivered anti-inflammatories for the treatment of sensory deficits in DPN. To the best of our knowledge, this is the first example of a locally delivered ACE inhibitor for the treatment of DPN.

Abstract Deployment of ultracold atom interferometers (AI) into space will capitalize on quantum advantages and the extended freefall of persistent microgravity to provide high-precision measurement capabilities for gravitational, Earth, and planetary sciences, and to enable searches for subtle forces signifying physics beyond General Relativity and the Standard Model. NASA’s Cold Atom Lab (CAL) operates onboard the International Space Station as a multi-user facility for fundamental studies of ultracold atoms and to mature space-based quantum technologies. We report on pathfinding experiments utilizing ultracold 87Rb atoms in the CAL AI. A three-pulse Mach–Zehnder interferometer was studied to understand the influence of ISS vibrations. Additionally, Ramsey shear-wave interferometry was used to manifest interference patterns in a single run that were observable for over 150 ms free-expansion time. Finally, the CAL AI was used to remotely measure the Bragg laser photon recoil as a demonstration of the first quantum sensor using matter-wave interferometry in space.

Abstract The evolutionary expansion of sensory neuron populations detecting important environmental cues is widespread, but functionally enigmatic. We investigated this phenomenon through comparison of homologous olfactory pathways of Drosophila melanogaster and its close relative Drosophila sechellia, an extreme specialist for Morinda citrifolia noni fruit. D. sechellia has evolved species-specific expansions in select, noni-detecting olfactory sensory neuron (OSN) populations, through multigenic changes. Activation and inhibition of defined proportions of neurons demonstrate that OSN number increases contribute to stronger, more persistent, noni-odour tracking behaviour. These expansions result in increased synaptic connections of sensory neurons with their projection neuron (PN) partners, which are conserved in number between species. Surprisingly, having more OSNs does not lead to greater odour-evoked PN sensitivity or reliability. Rather, pathways with increased sensory pooling exhibit reduced PN adaptation, likely through weakened lateral inhibition. Our work reveals an unexpected functional impact of sensory neuron population expansions to explain ecologically-relevant, species-specific behaviour.

Abstract We present the open-source SIMUnet code, designed to fit Standard Model Effective Field Theory (SMEFT) Wilson coefficient alongside Parton Distribution Functions (PDFs) of the proton. SIMUnet can perform SMEFT global fits, as well as simultaneous fits of the PDFs and of an arbitrarily large number of SMEFT degrees of freedom, by including both PDF-dependent and PDF-independent observables. SIMUnet can also be used to determine whether the effects of any New Physics models can be fitted away in a global fit of PDFs. SIMUnet is built upon the open-source NNPDF code and is released together with documentation, and tutorials. To illustrate the functionalities of the new tool, we present a new global analysis of the SMEFT Wilson coefficients accounting for their interplay with the PDFs. We increment our previous analysis of the LHC Run II top quark data with both (i) the Higgs production and decay rates data from the LHC, and (ii) the precision electroweak and diboson measurements from LEP and the LHC.

Abstract Preclinical studies suggest that simultaneous HER2/VEGF blockade may have cooperative effects in gastroesophageal adenocarcinomas. In a single-arm investigator initiated clinical trial for patients with untreated advanced HER2+ gastroesophageal adenocarcinoma, bevacizumab was added to standard of care capecitabine, oxaliplatin, and trastuzumab in 36 patients (NCT01191697). Primary endpoint was objective response rate and secondary endpoints included safety, duration of response, progression free survival, and overall survival. The study met its primary endpoint with an objective response rate of 81% (95% CI 65–92%). Median progression free and overall survival were 14.0 (95% CI, 11.3–36.4) and 23.2 months (95% CI, 16.6–36.4), respectively. The median duration of response was 14.9 months. The regimen was well tolerated without unexpected or severe toxicities. In post-hoc ctDNA analysis, baseline ctDNA features were prognostic: Higher tumor fraction and alternative MAPK drivers portended worse outcomes. ctDNA at resistance identified oncogenic mutations and these were detectable 2–8 cycles prior to radiographic progression. Capecitabine, oxaliplatin, trastuzumab and bevacizumab shows robust clinical activity in HER2+ gastroesophageal adenocarcinoma. Combination of VEGF inhibitors with chemoimmunotherapy and anti-PD1 regimens is warranted.

Abstract Background Understanding the complex interactions between genes and their causal effects on diseases is crucial for developing targeted treatments and gaining insight into biological mechanisms. However, the analysis of molecular networks, especially in the context of high-dimensional data, presents significant challenges. Methods This study introduces MRdualPC, a computationally tractable algorithm based on the MRPC approach, to infer large-scale causal molecular networks. We apply MRdualPC to investigate the upstream causal transcriptomics influencing hypertension using a comprehensive dataset of kidney genome and transcriptome data. Results Our algorithm proves to be 100 times faster than MRPC on average in identifying transcriptomics drivers of hypertension. Through clustering, we identify 63 modules with causal driver genes, including 17 modules with extensive causal networks. Notably, we find that genes within one of the causal networks are associated with the electron transport chain and oxidative phosphorylation, previously linked to hypertension. Moreover, the identified causal ancestor genes show an over-representation of blood pressure-related genes. Conclusions MRdualPC has the potential for broader applications beyond gene expression data, including multi-omics integration. While there are limitations, such as the need for clustering in large gene expression datasets, our study represents a significant advancement in building causal molecular networks, offering researchers a valuable tool for analyzing big data and investigating complex diseases.

Abstract Background Biliary tract cancers (BTC) are rare and aggressive malignancies originating from intrahepatic and extrahepatic bile ducts and the gallbladder. Surgery is the only curative option, but due to late-stage diagnosis, is frequently not feasible, leaving chemotherapy as the primary treatment. Radiotherapy (RT) can be an effective alternative for patients with unresectable, non-metastatic BTC despite the generally poor prognosis and significant variability. To help manage patients with unresectable BTC who receive RT, we aimed to identify prognostic markers that could aid in predicting overall survival (OS). Methods A retrospective cohort study was conducted at the University of Pennsylvania, involving seventy-eight patients with unresectable BTC treated with definitive intent RT. Comprehensive demographic, clinical, and treatment-related data were extracted from the electronic medical records. Univariate and multivariate Cox regressions were employed to identify predictors of OS after RT. A biomarker model was developed for refined survival prediction. Results The cohort primarily comprised patients with good performance status without significant hepatic dysfunction at presentation. The predominant treatment approach involved hypofractionated RT or concurrent 5FU-based chemoRT. Median OS after RT was 12.3 months, and 20 patients (15.6%) experienced local progression with a median time of 30.1 months. Univariate and multivariate analyses identified CA19-9 (above median) and higher albumin-bilirubin (ALBI) grades at presentation as significant predictors of poor OS. Median OS after RT was 24 months for patients with no risk factors and 6.3 months for those with both. Conclusions Our study demonstrates generally poor but significantly heterogeneous OS in patients with unresectable BTC treated with RT. We have developed a biomarker model based on CA19-9 and ALBI grade at presentation that can distinguish sub-populations with markedly diverse prognoses. This model can aid the clinical management of this challenging disease.

Abstract Background Understanding connections between biodiversity and ecosystem services can be enhanced by shifting focus from species richness to functional trait-based approaches, that when paired with comparative phylogenetic methods can provide even deeper insights. We investigated the functional ecology and phylogenetic diversity of pollination services provided by hymenopteran insects visiting apple flowers in orchards surrounded by either ‘natural’ or ‘disturbed’ landscapes in New South Wales, Australia. We assessed whether morphological and behavioural traits (hairiness, body size, glossa length, pollen load purity, and probability of loose pollen) exhibited non-random phylogenetic patterns. Then, explored whether bees, the primary pollinators in this system, filled unique or overlapping functional entities (FEs). For each landscape, we calculated phylogenetic diversity and used FEs to assess functional richness, evenness, and diversion. Results A phylogenomic matrix based on ultraconserved elements (UCEs; 1,382,620 bp from 1,969 loci) was used to infer a fully-resolved and well-supported maximum likelihood phylogeny for 48 hymenopteran morphospecies. There was no significant difference in species richness between landscape categories. Pollinator communities at natural sites had higher phylogenetic complexity (X = 2.37) and functional divergence (x̄ = 0.74 ± 0.02 s.e.) than disturbed sites (X = 1.65 and x̄ = 0.6 ± 0.01 s.e.). Hairiness showed significant phylogenetic clustering (K = 0.94), whereas body size, glossa length, and loose pollen showed weaker non-random phylogenetic patterns (K between 0.3–0.5). Pollen load purity showed no association with phylogeny. The assemblage of 17 bee morphospecies comprised nine FEs: eight FEs consisted of native bees with three containing 65% of all native bee taxa. The introduced honey bee (Apis mellifera) occupied a unique FE, likely due to its different evolutionary history. Both landscape types supported six FEs each with three overlapping: two native bee FEs and the honey bee FE. Conclusions Bee hairiness was the only functional trait to exhibit demonstrable phylogenetic signal. Despite differences in species richness, and functional and phylogenetic diversity between orchard landscape types, both maintained equal bee FE numbers. While no native bee taxon was analogous to the honey bee FE, four native bee FEs shared the same hairiness level as honey bees. Health threats to honey bee populations in Australia will likely disrupt pollination services to apple, and other pollination-dependent food crops, given the low level of functional redundancy within the investigated pollinator assemblages.

Abstract Objective We attempted to conduct a randomized controlled trial of three different informed consent training formats to evaluate their effectiveness. We recruited 503 clinical research professionals, who received $50 for participation. Incidental findings showed unexpectedly low rates of compliance with completing the study training protocols, resulting in insufficient statistical power to test our original hypotheses. In this report, we conducted a secondary analysis of the data in which we characterize and evaluate the observed low compliance. This involved using literature on average reading times, speed-reading times, and video play speeds to calculate the timeframes required to complete the three training formats. Results Only 13% of participants completed the training in a reasonable timeframe. Furthermore, only 46% of participants completed the training in the minimum possible timeframe. These findings lead us to ask whether online research training is effective, since no training can be effective if participants do not actually complete the training. Given extensive requirements for educational training among clinical research professionals, we feel the burden of proof is on training programs to demonstrate that they have positive effects.

The use of thermal energy storage (TES) contributes to the ongoing process of integrating various types of energy resources in order to achieve cleaner, more flexible, and more sustainable energy use. Numerical modelling of hot storage packed bed storage systems has been conducted in this paper in order to investigate the optimum design of the hot storage system. In this paper, the effect of varying design parameters, including the diameter of the packed bed, the storage material, the void fraction, and the aspect ratio of the packed bed, on storage performance was investigated. COMSOL Multiphysics 5.6 software has been used to design, simulate, and validate an axisymmetric model, which was then applied to evaluate the performance of the storage system based on the total energy stored, the heat transfer efficiency, and the capacity factor. In this paper, a novel-packed bed was proposed based on the parametric analysis. This involved a 0.2 void fraction, 4 mm porous media particle diameter, and Magnesia as the optimum storage material with air as the heat transfer fluid.

Abstract Determining movement parameters for pest insects such as tephritid fruit flies is critical to developing models which can be used to increase the effectiveness of surveillance and control strategies. In this study, harmonic radar was used to track wild-caught male Queensland fruit flies (Qflies), Bactrocera tryoni, in papaya fields. Experiment 1 continuously tracked single flies which were prodded to induce movement. Qfly movements from this experiment showed greater mean squared displacement than predicted by both a simple random walk (RW) or a correlated random walk (CRW) model, suggesting that movement parameters derived from the entire data set do not adequately describe the movement of individual Qfly at all spatial scales or for all behavioral states. This conclusion is supported by both fractal and hidden Markov model (HMM) analysis. Lower fractal dimensions (straighter movement paths) were observed at larger spatial scales (> 2.5 m) suggesting that Qflies have qualitatively distinct movement at different scales. Further, a two-state HMM fit the observed movement data better than the CRW or RW models. Experiment 2 identified individual landing locations, twice a day, for groups of released Qflies, demonstrating that flies could be tracked over longer periods of time.

Abstract Objective The endophytic mycobiome is present in all studied plant compartments, including fruits and seeds. Here, we studied the mycobiome of seed wings as they are transferred with seeds in common ash and tested whether the mycobiome differs among trees. To achieve this, we used ITS1-based amplicon sequencing and two genotypes of F. excelsior as a model to compare the mycobiome of mother trees and their wings. Results We compared the mycobiome of 57 seed wings to the seed stalks (57) collected from two genotypes of F. excelsior using three ramets of each genotype. Alpha diversity indices (ACE, Fisher and Observed OTUs) suggested a higher richness of the mycobiome associated with the seed wing than the seed stalk within each genotype. However, there were neither significant differences in Shannon diversity between the mycobiomes from the two tissue types nor the two genotypes. PERMANOVA revealed significant differences in the mycobiome composition between tissue types (P

Abstract Engineering metabolism to efficiently produce chemicals from multi-step pathways requires optimizing multi-gene expression programs to achieve enzyme balance. CRISPR-Cas transcriptional control systems are emerging as important tools for programming multi-gene expression, but poor predictability of guide RNA folding can disrupt expression control. Here, we correlate efficacy of modified guide RNAs (scRNAs) for CRISPR activation (CRISPRa) in E. coli with a computational kinetic parameter describing scRNA folding rate into the active structure (r S = 0.8). This parameter also enables forward design of scRNAs, allowing us to design a system of three synthetic CRISPRa promoters that can orthogonally activate (>35-fold) expression of chosen outputs. Through combinatorial activation tuning, we profile a three-dimensional design space expressing two different biosynthetic pathways, demonstrating variable production of pteridine and human milk oligosaccharide products. This RNA design approach aids combinatorial optimization of metabolic pathways and may accelerate routine design of effective multi-gene regulation programs in bacterial hosts.

Abstract Engineering stabilized proteins is a fundamental challenge in the development of industrial and pharmaceutical biotechnologies. We present Stability Oracle: a structure-based graph-transformer framework that achieves SOTA performance on accurately identifying thermodynamically stabilizing mutations. Our framework introduces several innovations to overcome well-known challenges in data scarcity and bias, generalization, and computation time, such as: Thermodynamic Permutations for data augmentation, structural amino acid embeddings to model a mutation with a single structure, a protein structure-specific attention-bias mechanism that makes transformers a viable alternative to graph neural networks. We provide training/test splits that mitigate data leakage and ensure proper model evaluation. Furthermore, to examine our data engineering contributions, we fine-tune ESM2 representations (Prostata-IFML) and achieve SOTA for sequence-based models. Notably, Stability Oracle outperforms Prostata-IFML even though it was pretrained on 2000X less proteins and has 548X less parameters. Our framework establishes a path for fine-tuning structure-based transformers to virtually any phenotype, a necessary task for accelerating the development of protein-based biotechnologies.

Abstract Effective recycling of end-of-life Li-ion batteries (LIBs) is essential due to continuous accumulation of battery waste and gradual depletion of battery metal resources. The present closed-loop solutions include destructive conversion to metal compounds, by destroying the entire three-dimensional morphology of the cathode through continuous thermal treatment or harsh wet extraction methods, and direct regeneration by lithium replenishment. Here, we report a solvent- and water-free flash Joule heating (FJH) method combined with magnetic separation to restore fresh cathodes from waste cathodes, followed by solid-state relithiation. The entire process is called flash recycling. This FJH method exhibits the merits of milliseconds of duration and high battery metal recovery yields of ~98%. After FJH, the cathodes reveal intact core structures with hierarchical features, implying the feasibility of their reconstituting into new cathodes. Relithiated cathodes are further used in LIBs, and show good electrochemical performance, comparable to new commercial counterparts. Life-cycle-analysis highlights that flash recycling has higher environmental and economic benefits over traditional destructive recycling processes.

The Eocene-Oligocene Transition is one of the major stages of the Cenozoic reshaping of the world oceans with associated changes in climate, of ocean coastlines and circulation patterns. This altogether created challenging environments for fossilization and preservation of native biota. Consequently, well preserved Oligocene fossils are infrequent worldwide and just as rare in the Central Paratethys. The well-preserved Rupelian (Early Oligocene) diatomites from the Skole Nappe, the external unit of the Outer Carpathians in southeastern Poland were deposited in the Central Paratethys. In some samples, in addition to diatoms, sediments also contain a great diversity of other silicified micro- and nannofossils. Here we report our findings of silicoflagellates (fifteen taxa from five genera), two rotosphaeridians, and several morphotypes of fossil scales, some of uncertain taxonomic affinity. Among silicoflagellates, the most common are species from genera Corbisema ( C. triacantha , C. hastata , and C. apiculata ) and Dictyocha ( D. clinata and D. fibula ). We also recovered scales of rotosphaeridians ( Pinaciophora and possibly Rabdiophrys ) and remains of organisms of uncertain affinity ( Clathropyxidella and Macrora ) often reported together with silicoflagellates. All of these taxa are the first reports for the Central Paratethys. Silicoflagellate species composition is consistent with the datums derived from other fossils. Silicoflagellates, marine diatoms and archaeomonads suggest a neritic depositional environment.

Abstract Per- and polyfluoroalkyl substances (PFAS) are persistent and bioaccumulative pollutants that can easily accumulate in soil, posing a threat to environment and human health. Current PFAS degradation processes often suffer from low efficiency, high energy and water consumption, or lack of generality. Here, we develop a rapid electrothermal mineralization (REM) process to remediate PFAS-contaminated soil. With environmentally compatible biochar as the conductive additive, the soil temperature increases to >1000 °C within seconds by current pulse input, converting PFAS to calcium fluoride with inherent calcium compounds in soil. This process is applicable for remediating various PFAS contaminants in soil, with high removal efficiencies ( >99%) and mineralization ratios ( >90%). While retaining soil particle size, composition, water infiltration rate, and cation exchange capacity, REM facilitates an increase of exchangeable nutrient supply and arthropod survival in soil, rendering it superior to the time-consuming calcination approach that severely degrades soil properties. REM is scaled up to remediate soil at two kilograms per batch and promising for large-scale, on-site soil remediation. Life-cycle assessment and techno-economic analysis demonstrate REM as an environmentally friendly and economic process, with a significant reduction of energy consumption, greenhouse gas emission, water consumption, and operation cost, when compared to existing soil remediation practices.

Abstract Background Chronic exposure to microorganisms inside homes can impact respiratory health. Few studies have used advanced sequencing methods to examine adult respiratory outcomes, especially continuous measures. We aimed to identify metagenomic profiles in house dust related to the quantitative traits of pulmonary function and airway inflammation in adults. Microbial communities, 1264 species (389 genera), in vacuumed bedroom dust from 779 homes in a US cohort were characterized by whole metagenome shotgun sequencing. We examined two overall microbial diversity measures: richness (the number of individual microbial species) and Shannon index (reflecting both richness and relative abundance). To identify specific differentially abundant genera, we applied the Lasso estimator with high-dimensional inference methods, a novel framework for analyzing microbiome data in relation to continuous traits after accounting for all taxa examined together. Results Pulmonary function measures (forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio) were not associated with overall dust microbial diversity. However, many individual microbial genera were differentially abundant (p-value < 0.05 controlling for all other microbial taxa examined) in relation to FEV1, FVC, or FEV1/FVC. Similarly, fractional exhaled nitric oxide (FeNO), a marker of airway inflammation, was unrelated to overall microbial diversity but associated with differential abundance for many individual genera. Several genera, including Limosilactobacillus, were associated with a pulmonary function measure and FeNO, while others, including Moraxella to FEV1/FVC and Stenotrophomonas to FeNO, were associated with a single trait. Conclusions Using state-of-the-art metagenomic sequencing, we identified specific microorganisms in indoor dust related to pulmonary function and airway inflammation. Some were previously associated with respiratory conditions; others were novel, suggesting specific environmental microbial components contribute to various respiratory outcomes. The methods used are applicable to studying microbiome in relation to other continuous outcomes. Video Abstract

Abstract Background Oesophageal adenocarcinoma (OAC) is a highly heterogeneous cancer with poor survival. Standard curative treatment is chemotherapy with or without radiotherapy followed by oesophagectomy. Genomic heterogeneity is a feature of OAC and has been linked to treatment resistance. Methods Whole-genome sequencing data from 59 treatment-naïve and 18 post-treatment samples from 29 OAC patients was analysed. Twenty-seven of these were enrolled in the DOCTOR trial, sponsored by the Australasian Gastro-Intestinal Trials Group. Two biopsies from each treatment-naïve tumour were assessed to define ‘shared’ (between both samples) and ‘private’ (present in one sample) mutations. Results Mutational signatures SBS2/13 (APOBEC) and SBS3 (BRCA) were almost exclusively detected in private mutation populations of treatment-naïve tumours. Patients presenting these signatures had significantly worse disease specific survival. Furthermore, mutational signatures associated with platinum-based chemotherapy treatment as well as high platinum enrichment scores were only detected in post-treatment samples. Additionally, clones with high putative neoantigen binding scores were detected in some treatment-naïve samples suggesting immunoediting of clones. Conclusions This study demonstrates the high intra-tumour heterogeneity in OAC, as well as indicators for treatment-induced changes during tumour evolution. Intra-tumour heterogeneity remains a problem for successful treatment strategies in OAC.

Abstract Air pollution has the potential to disrupt ecologically- and economically-beneficial services provided by invertebrates, including pollination and natural pest regulation. To effectively predict and mitigate this disruption requires an understanding of how the impacts of air pollution vary between invertebrate groups. Here we conduct a global meta-analysis of 120 publications comparing the performance of different invertebrate functional groups in unpolluted and polluted atmospheres. We focus on the pollutants ozone, nitrogen oxides, sulfur dioxide and particulate matter. We show that beneficial invertebrate performance is reduced by air pollution, whereas the performance of plant pest invertebrates is not significantly affected. Ozone pollution has the most detrimental impacts, and these occur at concentrations below national and international air quality standards. Changes in invertebrate performance are not dependent on air pollutant concentrations, indicating that even low levels of pollution are damaging. Predicted increases in tropospheric ozone could result in unintended consequences to global invertebrate populations and their valuable ecological services.

Abstract Background Lack of physical activity is a concern for children across diverse backgrounds, particularly affecting those in rural areas who face distinct challenges compared to their urban counterparts. Community-derived interventions are needed that consider the unique context and additional physical activity barriers in under-resourced rural settings. Therefore, a prospective pre-post pilot/feasibility study of Hoosier Sport was conducted over 8-weeks with 6th and 7th grade children in a low-socioeconomic rural middle school setting. The primary objective of the present study was to assess trial- and intervention-related feasibility indicators; and the secondary objective was to collect preliminary assessment data for physical activity levels, fitness, psychological needs satisfaction, and knowledge of physical activity and nutrition among participating youth. Methods This prospective 8-week pilot/feasibility study took place in the rural Midwestern United States where twenty-four middle school students participated in a mixed-methods pre-post intervention during physical education classes. The intervention included elements like sport-based youth development, individualized goal setting, physical activity monitoring, pedometer usage, and health education. Data were collected at baseline (T1) and post-intervention (T3), with intermediate measures during the intervention (T2). Qualitative data were integrated through semi-structured interviews. Analytical methods encompassed descriptive statistics, correlations, repeated measures ANOVA, and thematic analysis. Results Key findings indicate robust feasibility, with intervention-related scores (FIM, AIM, and IAM) consistently surpassing the “good” threshold and 100% retention and recruitment success. Additionally, participants showed significant physical performance improvement, shifting from the 25th to the 50th percentile in the 6-minute walk test (p

Abstract Microporous organic polymers that have three-dimensional connectivity stemming from monomers with tetrahedral or tetrahedron-like geometry can have high surface areas and strong fluorescence. There are however few examples of such polymers based on hindered biaryls, and their fluorescence has not been studied. Hypothesizing that the contortion in a hindered biphenyl moiety would modulate the optical properties of a polymer built from it, we synthesized a meta-enchained polyphenylene from a 2,2ʹ,6,6ʹ-tetramethylbiphenyl-based monomer, in which the two phenyl rings are nearly mutually perpendicular. The polymer was microporous with S BET = 495 m2 g−1. The polymer absorbed near-UV light and emitted blue fluorescence despite the meta-enchainment that would have been expected to break the conjugation. A related copolymer, synthesized from 2,2ʹ,6,6ʹ-tetramethylbiphenyl-based and unsubstituted biphenyl-based monomers, was microporous but not fluorescent.

Abstract Functional impairments contribute to poor quality of life in schizophrenia spectrum disorders (SSD). We sought to (Objective I) define the main functional phenotypes in SSD, then (Objective II) identify key biopsychosocial correlates, emphasizing interpretable data-driven methods. Objective I was tested on independent samples: Dataset I (N = 282) and Dataset II (N = 317), with SSD participants who underwent assessment of multiple functioning areas. Participants were clustered based on functioning. Objective II was evaluated in Dataset I by identifying key features for classifying functional phenotype clusters from among 65 sociodemographic, psychological, clinical, cognitive, and brain volume measures. Findings were replicated across latent discriminant analyses (LDA) and one-vs.-rest binomial regularized regressions to identify key predictors. We identified three clusters of participants in each dataset, demonstrating replicable functional phenotypes: Cluster 1—poor functioning across domains; Cluster 2—impaired Role Functioning, but partially preserved Independent and Social Functioning; Cluster 3—good functioning across domains. Key correlates were Avolition, anhedonia, left hippocampal volume, and measures of emotional intelligence and subjective social experience. Avolition appeared more closely tied to role functioning, and anhedonia to independent and social functioning. Thus, we found three replicable functional phenotypes with evidence that recovery may not be uniform across domains. Avolition and anhedonia were both critical but played different roles for different functional domains. It may be important to identify critical functional areas for individual patients and target interventions accordingly.

Abstract The potato cyst nematode Globodera rostochiensis originates from the Andean Mountain region in South America and has unintentionally been introduced to all inhabited continents. Several studies have examined the population genetic structure of this pest in various countries by using microsatellite markers. However, merging microsatellite data produced from different laboratories is challenging and can introduce uncertainty when interpreting the results. To overcome this challenge and to explore invasion routes of this pest, we have genotyped 22 G. rostochiensis populations from all continents. Within populations, the highest genetic diversity was observed in the South American populations, the European populations showed an intermediate level of genetic diversity and the remaining populations were the less diverse. This confirmed pre-existing knowledge such as a first introduction event from South America to Europe, but the less diverse populations could originate either from South America or from Europe. At the continental scale, STRUCTURE genetic clustering output indicated that North America and Asia have experienced at least two introduction events. Comparing different evolutionary scenarios, the Approximate Bayesian Computation analysis showed that Europe served as a secondary distribution centre for the invasion of G. rostochiensis into all other continents (North America, Africa, Asia and Oceania).