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Abstract This article develops a novel decision-oriented framework that strategically deconstructs systems resilience in a way that focuses on systems’ design, capabilities, and management. The framework helps evaluate and compare how system design choices impact system resilience. First, we propose a resilience score based on a piecewise linear approximation to a resilience curve. Using multicriteria decision analysis principles, we score system design alternatives in terms of system-specific capabilities. We estimate the relevance of these capabilities to resilience curve parameters associated with resilience phases. Finally, we interpret the derivatives of resilience with respect to the curve parameter values as the leverage of these parameters. Using multiple levels of weighted sums of the scores, we calculate the first order impact of system design choices first on a proxy for the generic resilience parameters and then on resilience, which allows situational characteristics to be incorporated in their natural terminology while mapping their impact on resilience with a traceable logic. We illustrate the approach by using existing materials to develop an example comparing engineered designs for minimizing post-wildfire flood impacts.

Dercas nina Mell 1913 (Pieridae) is a little-studied butterfly species endemic to China that flies primarily in the forest canopy. Genome skimming by Illumina sequencing allowed assembly of 146,702 reads for complete 1471.3-fold mean coverage of the circular 15,264 bp mitogenome from D. nina consisting of 82.1% AT nucleotides. A gene order typical of butterflies was recovered consisting of 13 protein-coding genes, 22 tRNAs, two rRNAs, and a predicted control region. The Dercas nina COX1 open reading frame begins with atypical start codon CGA. Six protein-coding genes (COX1, COX2, ND2, ND3, ND4, ND5) with single-nucleotide (T) stop codons, and two protein-coding genes (ATP6, ATP8) with two-nucleotide (TA) stop codons encoded in the DNA were inferred to be completed by adenine nucleotides from the Poly-A tail of the mRNA. Bayesian’s phylogenetic reconstruction places the D. nina and D. lycorias mitogenomes as sister clades. Dercas mitogenomes were sister to those from genus Colias in the monophyletic subfamily Coliadinae. The mitogenome phylogeny is consistent with previous molecular phylogenetic hypotheses based on other markers, but differs somewhat from a morphology-based hypothesis that suggested that Dercas was more closely related to genus Gonepteryx. This may falsify the hypothesis or may instead reflect mitochondrial-nuclear phylogenetic discordance.

Societal Impact Statement Free‐air CO2 enrichment (FACE) experiments provide essential data on forest responses to increasing atmospheric CO2 for evaluations of climate change impacts on humanity. Understanding and reducing the uncertainty in the experimental results is critical to ensure scientific and public confidence in the models and policy initiatives that derive therefrom. One source of uncertainty is the estimation of tree biomass using mathematical relationships between biomass and easily obtained and non‐destructive measurements (allometry). We evaluated the robustness of the allometric relationships established at the beginning of a FACE experiment and discuss the challenges and opportunities for the new generation of FACE experiments. Summary Long‐term field experiments to elucidate forest responses to rising atmospheric CO2 concentration require allometric equations to estimate tree biomass from non‐destructive measurements of tree size. We analyzed whether the allometric equations established at the beginning of a free‐air CO2 enrichment (FACE) experiment in a Liquidambar styraciflua plantation were still valid at the end of the 12 year experiment. Aboveground woody biomass was initially predicted by an equation that included bole diameter, taper, and height, assuming that including taper and height as predictors would accommodate changes in tree structure that might occur over time and in response to elevated CO2. At the conclusion of the FACE experiment, we harvested 23 trees, measured dimensions and dry mass of boles and branches, and extracted and measured the woody root mass of 10 trees. Although 10 of the harvested trees were larger than the trees used to establish the allometric relationship, measured aboveground woody biomass was well predicted by the original allometry. The initial linear equation between bole basal area and woody root biomass underestimated final root biomass by 28%, but root biomass was just 21% of total wood mass, and errors in aboveground and belowground estimates were offsetting. The allometry established at the beginning of the experiment provided valid predictions of tree biomass throughout the experiment. New allometric approaches using terrestrial laser scanning should reduce an important source of uncertainty in decade‐long forest experiments and in assessments of centuries‐long forest biomass accretion used in evaluating carbon offsets and climate mitigation.

Abstract Spatially resolved molecular assays provide high dimensional genetic, transcriptomic, proteomic, and epigenetic information in situ and at various resolutions. Pairing these data across modalities with histological features enables powerful studies of tissue pathology in the context of an intact microenvironment and tissue structure. Increasing dimensions across molecular analytes and samples require new data science approaches to functionally annotate spatially resolved molecular data. A specific challenge is data-driven cross-sample domain detection that allows for analysis within and between consensus tissue compartments across high volumes of multiplex datasets stemming from tissue atlasing efforts. Here, we present MILWRM (multiplex image labeling with regional morphology)—a Python package for rapid, multi-scale tissue domain detection and annotation at the image- or spot-level. We demonstrate MILWRM’s utility in identifying histologically distinct compartments in human colonic polyps, lymph nodes, mouse kidney, and mouse brain slices through spatially-informed clustering in two different spatial data modalities from different platforms. We used tissue domains detected in human colonic polyps to elucidate the molecular distinction between polyp subtypes, and explored the ability of MILWRM to identify anatomical regions of the brain tissue and their respective distinct molecular profiles.

Abstract Hematological malignancies are associated with an increased risk of complications during SARS-CoV-2 infections. Primary series or monovalent booster vaccines reduce disease severity, hospitalization, and death among multiple myeloma patients. We characterized virus-neutralizing and spike-binding antibody profiles following monovalent (WA1) or bivalent (WA1/BA.5) SARS-CoV-2 booster vaccination in MM patients. Bivalent vaccination improved the breadth of binding antibodies but not neutralization activity against contemporary variants. Hybrid immunity and immune imprinting impact vaccine-elicited immunity.

Abstract Modulating inflammation is critical to enhance nerve regeneration after injury. However, clinically applicable regenerative therapies that modulate inflammation have not yet been established. Here, we demonstrate synergistic effects of the combination of an HMG-CoA reductase inhibitor, statin/fluvastatin and critical components of the extracellular matrix, Matrix-Bound Nanovesicles (MBV) to enhance axon regeneration and neuroprotection after mouse optic nerve injury. Mechanistically, co-intravitreal injections of fluvastatin and MBV robustly promote infiltration of monocytes and neutrophils, which lead to RGC protection and axon regeneration. Furthermore, monocyte infiltration is triggered by elevated expression of CCL2, a chemokine, in the superficial layer of the retina after treatment with a combination of fluvastatin and MBV or IL-33, a cytokine contained within MBV. Finally, this therapy can be further combined with AAV-based gene therapy blocking anti-regenerative pathways in RGCs to extend regenerated axons. These data highlight novel molecular insights into the development of immunomodulatory regenerative therapy.

Abstract Mutations in SARS-CoV-2 variants of concern (VOCs) have expanded the viral host range beyond primates, and a few other mammals, to mice, affording the opportunity to exploit genetically diverse mouse panels to model the broad spectrum of responses to infection in patient populations. Here we surveyed responses to VOC infection in genetically diverse Collaborative Cross (CC) founder strains. Infection of wild-derived CC founder strains produced a broad range of viral burden, disease susceptibility and survival, whereas most other strains were resistant to disease despite measurable lung viral titers. In particular, CAST/EiJ, a wild-derived strain, developed high lung viral burdens, more severe lung pathology than seen in other CC strains, and a dysregulated cytokine profile resulting in morbidity and mortality. These inbred mouse strains may serve as a valuable platform to evaluate therapeutic countermeasures against severe COVID-19 and other coronavirus pandemics in the future.

Abstract Purpose The purpose of this case series is to describe the clinical course of patients receiving foscarnet eyedrops for the treatment of refractory herpetic keratitis. Observations Six patients diagnosed with herpetic keratitis were treated with foscarnet 24 mg/mL (2.4%) eyedrops with resulting improvement in keratitis. Conclusion Topical foscarnet may be a safe and effective treatment for herpetic keratitis in conjunction with, or as an alternative to, conventional antiviral therapy. This is an off-label use of foscarnet.

Abstract Enhancing the efficacy of immunotherapy in brain metastases (BrM) requires an improved understanding of the immune composition of BrM and how this is affected by radiation and dexamethasone. Our two-arm pilot study (NCT04895592) allocated 26 patients with BrM to either low (Arm A) or high (Arm B) dose peri-operative dexamethasone followed by pre-operative stereotactic radiosurgery (pSRS) and resection (n= 13 per arm). The primary endpoint, a safety analysis at 4 months, was met. The secondary clinical endpoints of overall survival, distant brain failure, leptomeningeal disease and local recurrence at 12-months were 66%, 37.3%, 6%, and 0% respectively and were not significantly different between arms (p= 0.7739, p= 0.3884, p= 0.3469). Immunological data from two large retrospective BrM datasets and confirmed by correlates from both arms of this pSRS prospective trial revealed that BrM CD8 T cells were composed of predominantly PD1+ TCF1+ stem-like and PD1+ TCF1-TIM3+ effector-like cells. Clustering of TCF1+ CD8 T cells with antigen presenting cells in immune niches was prognostic for local control, even without pSRS. Following pSRS, CD8 T cell and immune niche density were transiently reduced compared to untreated BrM, followed by a rebound 6+ days post pSRS with an increased frequency of TCF1- effector-like cells. In sum, pSRS is safe and therapeutically beneficial, and these data provide a framework for how pSRS may be leveraged to maximize intracranial CD8 T cell responses.

Abstract Inducing high levels of antigen-specific CD8α+ T cells in the tumor is beneficial for cancer immunotherapy, but achieving this in a safe and effective manner remains challenging. Here, we have developed a designer liposomal nanovaccine containing a sonosensitizer (LNVS) to efficiently program T cell immunity in mice. Following intravenous injection, LNVS accumulates in the spleen in a protein corona and fluidity-dependent manner, leading to greater frequencies of antigen-specific CD8α+ T cells than soluble vaccines (the mixture of antigens and adjuvants). Meanwhile, some LNVS passively accumulates in the tumor, where it responds to ultrasound (US) to increase the levels of chemokines and adhesion molecules that are beneficial for recruiting CD8α+ T cells to the tumor. LNVS + US induces higher levels of intratumoral antitumor T cells than traditional sonodynamic therapy, regresses established mouse MC38 tumors and orthotopic cervical cancer, and protects cured mice from relapse. Our platform sheds light on the importance of tuning the fluidity and protein corona of naovaccines to program T cell immunity in mice and may inspire new strategies for cancer immunotherapy.

Abstract Progressive gait impairment is common among aging adults. Remote phenotyping of gait during daily living has the potential to quantify gait alterations and evaluate the effects of interventions that may prevent disability in the aging population. Here, we developed ElderNet, a self-supervised learning model for gait detection from wrist-worn accelerometer data. Validation involved two diverse cohorts, including over 1000 participants without gait labels, as well as 83 participants with labeled data: older adults with Parkinson's disease, proximal femoral fracture, chronic obstructive pulmonary disease, congestive heart failure, and healthy adults. ElderNet presented high accuracy (96.43 ± 2.27), specificity (98.87 ± 2.15), recall (82.32 ± 11.37), precision (86.69 ± 17.61), and F1 score (82.92 ± 13.39). The suggested method yielded superior performance compared to two state-of-the-art gait detection algorithms, with improved accuracy and F1 score (p

Ampakines are a class of orally available positive allosteric modulators of the AMPA-glutamate receptor (AMPAR) and have therapeutic implications for neurological/neuropsychiatric disorders in which AMPAR signaling is compromised. Low-impact ampakines are a distinct subclass of drugs that only modestly offset receptor desensitization and do not alter agonist binding affinity and thus lack the neurotoxicity and epileptogenic effects associated with other AMPAR modulators. In these studies, we describe the pre-clinical pharmacology of ampakine 1-(benzofurazan-5-ylcarbonyl)morpholine (CX717). CX717 modestly offsets desensitization in hippocampal patches and augments synaptic transmission in vivo. CX717 also enhances long-term potentiation in rats, which is crucial for learning and memory. CX717 enhances performance in the eight-arm radial maze and abrogates amphetamine-induced locomotor activity while being devoid of cataleptic activity in rats. CX717 also ameliorates alfentanil-induced respiratory depression in rats and is not toxic to cultured rat neurons. CX717 is active at doses of 0.3–10 mg/kg and lacked serious adverse events in safety studies in mice up to 2000 mg/kg. CX717 was also previously shown to be safe in humans and effective in reversing opiate-induced respiratory depression and hyperactivity and inattentiveness in adults with ADHD. These findings support the continued clinical investigation of CX717 in the treatment of ADHD, dementia, and opiate-induced respiratory depression.

Abstract According to sexual selection theory, the sexes are faced with opposing evolutionary goals. Male fitness benefits from access to females, whereas female fitness is constrained by food resources and safety for themselves and their offspring. Particularly in large solitary carnivores, such as polar bears (Ursus maritimus), these divergent goals can potentially lead to conflict between the sexes. Outside the mating season, when polar bears are on the move across vast distances, the consequences of such conflict can become apparent when individuals arrive at the same food source. To investigate interrelationships between the sexes, we observed successive polar bears visiting a bird breeding colony to feed on clutches of eggs. We found that males succeeded females more frequently and more closely than expected by chance. Moreover, when males were closer to conspecifics, they walked faster, spent less time in the colony and ingested less food. In contrast, female foraging performance was not associated with proximity to other bears. Irrespective of proximity, females generally spent short periods in the colony and ingested fewer clutches than males. Our results suggest that in polar bears, there is a trade-off between the benefits of food intake and the opportunities (in males) and risks (in females) posed by encountering conspecifics.

Abstract Resistance to radiotherapy is a major barrier during cancer treatment. Here using genome-scale CRISPR/Cas9 screening, we identify CD274 gene, which encodes PD-L1, to confer lung cancer cell resistance to ionizing radiation (IR). Depletion of endogenous PD-L1 delays the repair of IR-induced DNA double-strand breaks (DSBs) and PD-L1 loss downregulates non-homologous end joining (NHEJ) while overexpression of PD-L1 upregulates NHEJ. IR induces translocation of PD-L1 from the membrane into nucleus dependent on deglycosylation of PD-L1 at N219 and CMTM6 and leads to PD-L1 recruitment to DSBs foci. PD-L1 interacts with Ku in the nucleus and enhances Ku binding to DSB DNA. The interaction between the IgC domain of PD-L1 and the core domain of Ku is required for PD-L1 to accelerate NHEJ-mediated DSB repair and produce radioresistance. Thus, PD-L1, in addition to its immune inhibitory activity, acts as mechanistic driver for NHEJ-mediated DSB repair in cancer.

High blood pressure (BP) and cerebral amyloid angiopathy (CAA) are two common risk factors for intracranial hemorrhage, potentially leading to cognitive impairment. Less is known about the relationship between BP and CAA, the examination of which was the objective of this study. We analyzed data from 2510 participants in the National Alzheimer’s Coordinating Center (NACC) who had information on longitudinal BP measurements before death and on CAA from autopsy. Using the average of four systolic BPs (SBPs) prior to death, SBP was categorized into three groups: n = 435), 120–139 mmHg (n = 1335), and ≥140 mmHg (n = 740). CAA was diagnosed using immunohistochemistry in 1580 participants and categorized as mild (n = 759), moderate (n = 529), or severe (n = 292). When adjusted for age at death, sex, APOE genotype, Braak, CERAD, antihypertensive medication use, and microinfarcts, the odds ratios (95% CIs) for CAA associated with SBPs of 120–139 and ≥140 mmHg were 0.91 (0.74–1.12) and 1.00 (0.80–1.26), respectively. Findings from predictor effect plots show no variation in the probability of CAA between the three SBP categories. Microbleeds had no association with CAA, but among those with SBP ≥ 130 mmHg, the proportion of those with microbleeds was numerically greater in those with more severe CAA (p for trend, 0.084). In conclusion, we found no evidence of an association between SBP and CAA. Future studies need to develop non-invasive laboratory tests to diagnose CAA and prospectively examine this association and its implication on the pathophysiology and outcome of Alzheimer’s disease.

Abstract Pervasive SARS-CoV-2 infections in humans have led to multiple transmission events to animals. While SARS-CoV-2 has a potential broad wildlife host range, most documented infections have been in captive animals and a single wildlife species, the white-tailed deer. The full extent of SARS-CoV-2 exposure among wildlife communities and the factors that influence wildlife transmission risk remain unknown. We sampled 23 species of wildlife for SARS-CoV-2 and examined the effects of urbanization and human use on seropositivity. Here, we document positive detections of SARS-CoV-2 RNA in six species, including the deer mouse, Virginia opossum, raccoon, groundhog, Eastern cottontail, and Eastern red bat between May 2022–September 2023 across Virginia and Washington, D.C., USA. In addition, we found that sites with high human activity had three times higher seroprevalence than low human-use areas. We obtained SARS-CoV-2 genomic sequences from nine individuals of six species which were assigned to seven Pango lineages of the Omicron variant. The close match to variants circulating in humans at the time suggests at least seven recent human-to-animal transmission events. Our data support that exposure to SARS-CoV-2 has been widespread in wildlife communities and suggests that areas with high human activity may serve as points of contact for cross-species transmission.

Abstract It has been proposed that, when processing a stream of events, humans divide their experiences in terms of inferred latent causes (LCs) to support context-dependent learning. However, when shared structure is present across contexts, it is still unclear how the “splitting” of LCs and learning of shared structure can be simultaneously achieved. Here, we present the Latent Cause Network (LCNet), a neural network model of LC inference. Through learning, it naturally stores structure that is shared across tasks in the network weights. Additionally, it represents context-specific structure using a context module, controlled by a Bayesian nonparametric inference algorithm, which assigns a unique context vector for each inferred LC. Across three simulations, we found that LCNet could (1) extract shared structure across LCs in a function learning task while avoiding catastrophic interference, (2) capture human data on curriculum effects in schema learning, and (3) infer the underlying event structure when processing naturalistic videos of daily events. Overall, these results demonstrate a computationally feasible approach to reconciling shared structure and context-specific structure in a model of LCs that is scalable from laboratory experiment settings to naturalistic settings.

Prolamins are hydrophobic proteins extracted using water-ethanol mixtures, useful for texturing meat and cheese alternatives at low temperatures due to their self-aggregating properties. This study explored the rheological and structural properties of the corn prolamin zein under varying temperature and pH conditions and compared its rheological behavior to the barley prolamin hordein. Zein showed plasticization when heated, with plasticization temperatures ranging from 41.3 °C at pH 4 to 46.7 °C at pH 6. Texture maps indicated that zein formed brittle gels within the linear viscoelastic range and tougher structures at crossover, unlike hordein, which was more elastic and lacked a clear plasticization behavior (softening) during heating. These differences were linked to zein's hydrophobicity. Coarse-grained molecular dynamics simulations showed zein self-aligning into anisotropic protein structures during heating, with its radius of gyration increasing from Rg = 21 Å to Rg = 34 Å by heating. This study provided insights into the structuring of prolamins and highlighted the need to understand plasticization mechanisms to improve zein's functionality in food applications.

Summary: Kaposi sarcoma (KS) punch biopsies present unique challenges for extracting nucleic acids, which can be exacerbated by their long-term stabilization in RNAlater. Here, we present a protocol for simultaneously isolating DNA, RNA, and miRNA from a single KS punch biopsy. We detail the steps for preparing reagents and supplies, disrupting KS tissue using manual and mechanical methods, isolating DNA and total RNA, evaluating nucleic acid quality, and storing nucleic acids long-term. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

The interaction between redox-active species and dissolved organic carbon (DOC) is crucial in driving lacustrine benthic microbial processes. In lacustrine porewaters, many redox-active species exist in their reduced form, while DOC acts as a substrate and an electron acceptor. Understanding the types and abundance of redox-active species in porewaters along with their complementary DOC substrate is pivotal for gaining insights into benthic processes, particularly in regions susceptible to climate change. We report the in-situ measurement of redox-active species in sediment porewaters, alongside the ex-situ measurement of DOC extracted from cores collected from two Arctic lakes (Toolik and Fog 1). Fe2+ was abundantly detected below 4 cm of the sediment-water interface in all cores and was inversely related to dissolved O2. Additionally, two distinct Fe(III)-complexes were identified. DOC ranged in the order of 10s of mg/L and either remained stable or increased with depth. A comparison between Toolik and Fog 1 lakes revealed a higher accumulation of Fe2+ and DOC in the latter. This study marks the first of its kind to assess spatial distributions of redox-active species and DOC as a function of depth from multiple sites in Arctic lacustrine porewaters.

Infinium Methylation BeadChip arrays remain one of the most popular platforms for epigenome-wide association studies, but tools for downstream pathway analysis have their limitations. Functional class scoring (FCS) is a group of pathway enrichment techniques that involve the ranking of genes and evaluation of their collective regulation in biological systems, but the implementations described for Infinium methylation array data do not retain direction information, which is important for mechanistic understanding of genomic regulation. Here, we evaluate several candidate FCS methods that retain directional information. According to simulation results, the best-performing method involves the mean aggregation of probe limma t-statistics by gene followed by a rank-ANOVA enrichment test using the mitch package. This method, which we call ‘LAM,’ outperformed an existing over-representation analysis method in simulations, and showed higher sensitivity and robustness in an analysis of real lung tumour-normal paired datasets. Using matched RNA-seq data, we examine the relationship of methylation differences at promoters and gene bodies with RNA expression at the level of pathways in lung cancer. To demonstrate the utility of our approach, we apply it to three other contexts where public data were available. First, we examine the differential pathway methylation associated with chronological age. Second, we investigate pathway methylation differences in infants conceived with in vitro fertilization. Lastly, we analyse differential pathway methylation in 19 disease states, identifying hundreds of novel associations. These results show LAM is a powerful method for the detection of differential pathway methylation complementing existing methods. A reproducible vignette is provided to illustrate how to implement this method.

ABSTRACTTo date, an affordable, effective treatment for an HIV-1 cure remains only a concept with most “latency reversal” agents (LRAs) lacking specificity for the latent HIV-1 reservoir and failing in early clinical trials. We assessed HIV-1 latency reversal using a multivalent HIV-1-derived virus-like particle (HLP) to treat samples from 32 people living with HIV-1 (PLWH) in Uganda, US and Canada who initiated combined antiretroviral therapy (cART) during chronic infection. Even after 5–20 years on stable cART, HLP could target CD4+ T cells harbouring latent HIV-1 reservoir resulting in 100-fold more HIV-1 release into culture supernatant than by common recall antigens, and 1000-fold more than by chemotherapeutic LRAs. HLP induced release of a divergent and replication-competent HIV-1 population from PLWH on cART. These findings suggest HLP provides a targeted approach to reactivate the majority of latent HIV-1 proviruses among individuals infected with HIV-1.

ABSTRACT Iron (Fe) is a trace nutrient required by nearly all organisms. As a result of the demand for Fe and the toxicity of non-chelated cytosolic ionic Fe, regulatory systems have evolved to tightly balance Fe acquisition and usage while limiting overload. In most bacteria, including the mammalian pathogen Staphylococcus aureus, the ferric uptake regulator (Fur) is the primary transcriptional regulator controlling the transcription of genes that code for Fe uptake and utilization proteins. Fpa (formerly YlaN) was demonstrated to be essential in Bacillus subtilis unless excess Fe is added to the growth medium, suggesting a role in Fe homeostasis. Here, we demonstrate that Fpa is essential in S. aureus upon Fe deprivation. Null fur alleles bypassed the essentiality of Fpa. The absence of Fpa abolished the derepression of Fur-regulated genes during Fe limitation. Bioinformatic analyses suggest that fpa was recruited to Gram-positive bacteria and, once acquired, was maintained in the genome as it co-evolved with Fur. Consistent with a role for Fpa in alleviating Fur-dependent repression, Fpa and Fur interacted in vivo, and Fpa decreased the DNA-binding ability of Fur in vitro. Fpa bound Fe(II) in vitro using oxygen or nitrogen ligands with an association constant that is consistent with a physiological role in Fe homeostasis. These findings have led to a model wherein Fpa is an Fe(II) binding protein that influences Fur-dependent regulation through direct interaction.IMPORTANCEIron (Fe) is an essential nutrient for nearly all organisms. If Fe homeostasis is not maintained, Fe may accumulate in the cytosol, which can be toxic. Questions remain about how cells efficiently balance Fe uptake and usage to prevent overload. Iron uptake and proper metalation of proteins are essential processes in the mammalian bacterial pathogen Staphylococcus aureus. Understanding the gene products involved in the genetic regulation of Fe uptake and usage and the physiological adaptations that S. aureus uses to survive in Fe-depleted conditions provides insight into pathogenesis. Herein, we demonstrate that the DNA-binding activity of the ferric uptake regulator transcriptional repressor is alleviated under Fe limitation, but uniquely, in S. aureus, alleviation requires the presence of Fpa.

AimWe aim to compare different operational definitions of medication adherence as well as examine the within-patient variability among these measures among patients treated for multiple comorbid conditions.MethodsElectronically monitored adherence data from a study on comorbid conditions were examined using three different calculation methods. DAILY adherence calculated the number of administrations divided by the number prescribed, without considering inter-dose interval. TIMING used predefined inter-dose intervals. Measures were aggregated to six 30-day periods. A PILLCOUNT approach counted the total administrations divided by the expected number in each 30-day period. Within-patient variability was computed based on DAILY and TIMING results for each 30-day period.ResultsResults varied by adherence calculation method. PILLCOUNT demonstrated the largest adherence rates (89%–92%); DAILY rates were lower (79%–85%); and TIMING was the lowest (62%–68%) over the 6-month period. TIMING within-patient variability (29%–35%) was larger than DAILY (20%–25%).DiscussionDifferences among the three methods confirm the importance of the adherence definition. TIMING may underestimate medicinal effects because patients may take medication as instructed (e.g., with meals) rather than at fixed intervals. PILLCOUNT may overestimate adherence by not accounting for inconsistent use. DAILY may best provide daily estimates of correct administration. Higher variability for TIMING may indicate patients are more likely to vary time between doses. Adherence calculation methods are important in interpreting results. Variability measures provide a more complete picture of adherence and may raise the likelihood of effects on biological outcomes. We propose studies of adherence include calculation method in the definition of adherence.

Objective: Although the metabolic state of an organism affects olfactory function, the precise mechanisms and their impact on behavior and metabolism remain unknown. Here, we assess whether ghrelin receptors (GHSRs) in the olfactory bulb (OB) increase olfactory function and influence foraging behaviors and metabolism. Methods: We performed a detailed behavioural and metabolic analysis in mice lacking GHSRs in the OB (OBGHSR deletion). We also analsyed OB scRNA-seq and spatial transcriptomic datasets to assess GHSR+ cells in the main and accessory olfactory bulbs, as well as the anterior olfactory nucleus. Results: OBGHSR deletion affected olfactory discrimination and habituation to both food and non-food odors. Anxiety-like and depression-like behaviors were significantly greater after OBGHSR deletion, whereas exploratory behavior was reduced, with the greatest effect under fasted conditions. OBGHSR deletion impacted feeding behavior as evidenced by altered bout number and duration, as well as buried food-seeking. OBGHSR deletion increased body weight and fat mass, spared fat utilisation on a chow diet and impaired glucose metabolism indicating metabolic dysfunction. Cross referenced analysis of OB scRNA-seq and spatial transcriptomic datasets revealed GHSR+ glutamate neurons in the main and accessory olfactory bulbs, as well as the anterior olfactory nucleus. Ablation of glutamate neurons in the OB reduced ghrelin-induced food finding and phenocopied results seen after OBGHSR deletion. Conclusions: OBGHSRs help to maintain olfactory function, particularly during hunger, and facilitate behavioral adaptations that optimise food-seeking in anxiogenic environments, priming metabolic pathways in preparation for food consumption.

Most people in the United States have been exposed to per- and polyfluoroalkyl substances (PFAS) which have been linked to a wide array of adverse health conditions in adults and children. The consumption of contaminated drinking water is an important human exposure pathway to PFAS. Residential sources also contribute to PFAS exposure through dermal contact and ingestion of house dust, which acts as an aggregate of chemicals from sources like furnishing materials and consumer products. The U.S. Department of Housing and Urban Development (HUD) conducted the first nationwide survey of residential hazards called the American Healthy Homes Survey (AHHS) in 2005, followed by a second survey (AHHS II) in 2017. The U.S. Environmental Protection Agency (EPA) collaborated with HUD on both efforts and subsequently analyzed PFAS in household tap water and house dust collected from the same homes during the AHHS II study. This study leverages these paired samples to investigate potentially important exposure sources and pathways in the residential environment. Here we report results for paired household tap water and house dust samples from 241 homes for 13 and 16 PFAS chemicals, respectively. All 13 targeted chemicals were detected in the household tap water samples with detections ranging from 100 % for PFBS to 1 % for PFNS, and all 16 targeted chemicals were detected in the house dust samples with detections ranging from 97 % for PFOA to 9 % for PFNS. Four chemicals (PFOA, PFOS, PFHxS, and PFHpA) were measured above the limit of detection in at least 50 % of the samples in both media. All households had at least one of the targeted PFAS detected in both their tap water and house dust. Results provided evidence that geographical factors, such as proximity to ambient contamination sources, were main drivers of PFAS contamination in tap water, while PFAS contamination in house dust was driven mainly by within-home sources. Exposure estimates calculated from the measured PFAS concentrations highlight the importance of addressing potential sources of exposure to PFAS within homes in addition to ambient sources affecting communities’ drinking water, particularly to reduce children’s exposure to these chemicals.

Clinical management of non-small cell lung cancer (NSCLC) requires accurate identification of tumor-specific genetic alterations to inform treatment options. Historically, providers have relied on single-gene testing (SGT) for actionable variants due to a perception of cost-effectiveness and/or efficient turnaround time compared to next-generation sequencing (NGS). However, not all actionable variants may be evaluated through SGT modalities, and an SGT approach can exhaust valuable tissue needed for more comprehensive analyses. In contrast, comprehensive genomic profiling (CGP) tests employ NGS to sequence megabases of DNA and RNA to evaluate all relevant molecular alterations, providing a broader genetic profile to identify actionable alterations that SGT may not accurately or efficiently assess. Here, we briefly describe four cases from a large reference laboratory in which actionable alterations were identified by CGP but not SGT. The discussion highlights the utility and advantages of using CGP to provide complete and timely treatment options and clinical trial opportunities for patients with NSCLC.

Abstract Sphingolipids play vital roles in metabolism and regulation. Previously, the aryl hydrocarbon receptor (AHR), a ligand‐activated transcription factor, was reported to directly regulate ceramide synthesis genes by binding to their promoters. Herein, sphingosine kinase 2 (SPHK2), responsible for producing sphingosine‐1‐phosphate (S1P), was found to interact with AHR through LXXLL motifs, influencing AHR nuclear localization. Through mutagenesis and co‐transfection studies, AHR activation and subsequent nuclear translocation was hindered by SPHK2 LXXLL mutants or SPHK2 lacking a nuclear localization signal (NLS). Similarly, an NLS‐deficient AHR mutant impaired SPHK2 nuclear translocation. Silencing SPHK2 reduced AHR expression and its target gene CYP1A1, while SPHK2 overexpression enhanced AHR activity. SPHK2 was found enriched on the CYP1A1 promoter, underscoring its role in AHR target gene activation. Additionally, S1P rapidly increased AHR expression at both the mRNA and protein levels and promoted AHR recruitment to the CYP1A1 promoter. Using mouse models, AHR deficiency compromised SPHK2 nuclear translocation, illustrating a critical interaction where SPHK2 facilitates AHR nuclear localization and supports a positive feedback loop between AHR and sphingolipid enzyme activity in the nucleus. These findings highlight a novel function of SPHK2 in regulating AHR activity and gene expression.

Summary: Background: With increasing recognition of the value of incorporating prognostic markers into amyotrophic lateral sclerosis (ALS) trial design and analysis plans, there is a pressing need to understand which among the prevailing clinical and biochemical markers have real value, and how they can be optimally used. Methods: A subset of patients with ALS recruited through the multi-center Phenotype-Genotype-Biomarker study (clinicaltrials.gov: NCT02327845) was identified as “trial-like” based on meeting common trial eligibility criteria. Clinical phenotyping was performed by evaluators trained in relevant assessments. Serum neurofilament light (NfL) and phosphorylated neurofilament heavy (pNfH), urinary p75ECD, plasma microRNA-181, and an array of biochemical and clinical measures were evaluated for their prognostic value. Associations with functional progression were estimated by random-slopes mixed models of ALS functional rating scale-revised (ALSFRS-R) score. Associations with survival were estimated by log-rank test and Cox proportional hazards regression. Potential sample size savings from adjusting for given biomarkers in a hypothetical trial were estimated. Findings: Baseline serum NfL is a powerful prognostic biomarker, predicting survival and ALSFRS-R rate of decline. Serum NfL 100 pg/mL correspond to future ALSFRS-R slopes of ∼0.5 and ∼1.5 points/month, respectively. Serum NfL also adds value to the best available clinical predictors, encapsulated by the European Network to Cure ALS (ENCALS) predictor score. In models of functional decline, the addition of NfL yields ∼25% sample size saving above those achieved by inclusion of either clinical predictors or ENCALS score alone. The prognostic value of serum pNfH, urinary p75ECD, and plasma miR-181ab is more limited. Interpretation: Among the multitude of biomarkers considered, only blood NfL adds value to the ENCALS prediction model and should be incorporated into analysis plans for all ongoing and future ALS trials. Defined thresholds of NfL might also be used in trial design, for enrichment or stratified randomisation, to improve trial efficiency. Funding: NIH (U01-NS107027, U54-NS092091). ALSA (16-TACL-242).

Traumatic brain injury (TBI) has reached epidemic proportions worldwide. The consequences of TBI can be severe even with repetitive mild trauma. If death and coma are avoided, the consequences of TBI in the long term typically involve dizziness, sleep disturbances, headache, seizures, cognitive impairment, focal deficits, depression, and anxiety. The severity of brain injury is a significant predictor of outcome. However, the heterogenous nature of the injury makes prognosis difficult. The present review of the literature focuses on the genetics of TBI including genome wide (GWAS) data and candidate gene associations, among them brain-derived neurotrophic factor (BDNF) with TBI and development of post-traumatic epilepsy (PTE). Molecular biomarkers of TBI are also discussed with a focus on proteins and the inflammatory protein IL1-β. The secondary medical sequela to TBI of cognitive impairment, PTE, headache and risk for neurodegenerative disorders is also discussed. This overview of TBI concludes with a review and discussion of the medical management of TBI and the medicines used for and being developed at the preclinical and clinical stages for the treatment of TBI and its host of life-debilitating symptoms.

The organophosphate chlorpyrifos is a commonly used pesticide for fruits and vegetables despite its association with neurotoxicity in humans. While some studies suggest that organophosphates may impact the gut microbiota, no studies to date have investigated the direct effect of chlorpyrifos on the gut microbiota with doses that approximate environmentally relevant dietary concentrations (EPA chronic reference dose: 0.3 µg/kg/day in humans and EPA acute reference dose: 5 µg/kg/day in humans). Thus, we examined the influence of chlorpyrifos on the gut microbiota by assessment of bacterial physiology and metabolism using flow cytometry, 1H NMR-based metabolomics, and changes in the cecal microbiota community with 16S rRNA amplicon sequencing and analysis. Chlorpyrifos did not directly damage bacteria but rather perturbed bacterial metabolism. Chlorpyrifos exposure to bacteria increased the concentration of amino acids, carbohydrates, and nucleic acids. The relative abundances of Lactobacillus, Allobaculum, Roseburia, and Butyricicoccus increased after exposure to chlorpyrifos. Analyses of the 16S rRNA gene amplicon data predicted decreased amino acid biosynthesis and nucleic acid degradation and increased glycolysis which was supported by 1H NMR-based metabolomics. Collectively, these results demonstrate that environmentally relevant doses of chlorpyrifos can impact the metabolic activity of isolated gut microbes which may result in an imbalance in overall gut metabolic activity.

Coronary-pulmonary artery fistulas (CPAFs) are rare entities that can cause significant left-to-right shunting and complicate routine coronary artery bypass grafting. There are no best practice guidelines and a scarcity of reports regarding concomitant treatment of CPAF with coronary artery disease. We present a case of bilateral CPAFs in a 60-year-old man with symptomatic coronary artery disease treated successfully with coronary artery bypass, epicardial ligation, and transpulmonary closure of CPAF with patch reconstruction. This case highlights the importance of optimal myocardial protection and complete closure of the fistula to prevent risk of coronary steal.

Borrelia miyamotoi is an emerging tickborne pathogen that has been associated with central nervous system infections in immunocompromised patients, albeit infrequently. We describe a case-patient in Minnesota, USA, who had meningeal symptoms of 1 month duration. B. miyamotoi infection was diagnosed by Gram staining on cerebrospinal fluid and confirmed by sequencing.

Spinal arachnoid web (AW) is a rare condition causing spinal cord-related issues. Its cause is often idiopathic but can be linked to past trauma or spine surgery. We describe two cases of AWs that developed after subarachnoid hemorrhage (SAH). Case #1 is a 71-year-old male with nonaneurysmal SAH who developed myelopathy 1 year later. Magnetic resonance imaging revealed upper thoracic cord edema and an AW. Case #2 is a 57-year-old female who underwent coiling of a ruptured basilar artery aneurysm and ventriculoperitoneal shunting for hydrocephalus. Twenty months later, she developed mid-thoracic AW requiring surgical resection. Both patients showed symptom improvement postresection avoiding further reoperation. History of SAH is emerging as a risk factor for AW development, emphasizing the importance of monitoring delayed-onset myelopathy and back pain in recent SAH patients.

Abstract Freezing of gait (FOG) is a debilitating problem that markedly impairs the mobility and independence of 38-65% of people with Parkinson’s disease. During a FOG episode, patients report that their feet are suddenly and inexplicably “glued” to the floor. The lack of a widely applicable, objective FOG detection method obstructs research and treatment. To address this problem, we organized a 3-month machine-learning contest, inviting experts from around the world to develop wearable sensor-based FOG detection algorithms. 1,379 teams from 83 countries submitted 24,862 solutions. The winning solutions demonstrated high accuracy, high specificity, and good precision in FOG detection, with strong correlations to gold-standard references. When applied to continuous 24/7 data, the solutions revealed previously unobserved patterns in daily living FOG occurrences. This successful endeavor underscores the potential of machine learning contests to rapidly engage AI experts in addressing critical medical challenges and provides a promising means for objective FOG quantification.

Since 2011, massive new strandings of holopelagic Sargassum have been reported on the coasts of the Caribbean, northern Brazil, Guiana, and West Africa, causing severe economic and ecological damage. Three common morphotypes (S. fluitans III, S. natans I, and S. natans VIII) were identified as responsible for these catastrophic events, with dominance shifts between them over time. However, the taxonomic status of these holopelagic Sargassum morphotypes remains unclear. Using an integrative taxonomy framework, combining a morphological study and molecular analyses, this study aimed to clarify their taxonomic status. Morphological analyses of 54 characters revealed no intermediate form between the three morphotypes, with the overall shape, nature of the axis, and size and shape of blades and vesicles being the most discriminating. An analysis of mitochondrial (IGS, cox2, cox3, mt16S rRNA, and nad6) and plastid (rbcL) markers confirmed the genetic divergence among the three morphotypes, with a lower level of divergence between the two S. natans morphotypes. Without additional molecular characterization, these morphotypes cannot be classified as three distinct species. However, due to their distinct morphological characteristics and sympatry within drifting aggregations, a revision of holopelagic species names is proposed, with Sargassum fluitans var. fluitans (for S. fluitans III), Sargassum natans var. natans (for S. natans I), and S. natans var. wingei (for S. natans VIII). This revision provides necessary clarity on the species involved in inundations of the tropical Atlantic.

Abstract Triazoles, the most widely used class of antifungal drugs, inhibit the biosynthesis of ergosterol, a crucial component of the fungal plasma membrane. Inhibition of a separate ergosterol biosynthetic step, catalyzed by the sterol C-24 methyltransferase Erg6, reduces the virulence of pathogenic yeasts, but its effects on filamentous fungal pathogens like Aspergillus fumigatus remain unexplored. Here, we show that the lipid droplet-associated enzyme Erg6 is essential for the viability of A. fumigatus and other Aspergillus species, including A. lentulus, A. terreus, and A. nidulans. Downregulation of erg6 causes loss of sterol-rich membrane domains required for apical extension of hyphae, as well as altered sterol profiles consistent with the Erg6 enzyme functioning upstream of the triazole drug target, Cyp51A/Cyp51B. Unexpectedly, erg6-repressed strains display wild-type susceptibility against the ergosterol-active triazole and polyene antifungals. Finally, we show that erg6 repression results in significant reduction in mortality in a murine model of invasive aspergillosis. Taken together with recent studies, our work supports Erg6 as a potentially pan-fungal drug target.

Abstract Step length is an important diagnostic and prognostic measure of health and disease. Wearable devices can estimate step length continuously (e.g., in clinic or real-world settings), however, the accuracy of current estimation methods is not yet optimal. We developed machine-learning models to estimate step length based on data derived from a single lower-back inertial measurement unit worn by 472 young and older adults with different neurological conditions, including Parkinson’s disease and healthy controls. Studying more than 80,000 steps, the best model showed high accuracy for a single step (root mean square error, RMSE = 6.08 cm, ICC(2,1) = 0.89) and higher accuracy when averaged over ten consecutive steps (RMSE = 4.79 cm, ICC(2,1) = 0.93), successfully reaching the predefined goal of an RMSE below 5 cm (often considered the minimal-clinically-important-difference). Combining machine-learning with a single, wearable sensor generates accurate step length measures, even in patients with neurologic disease. Additional research may be needed to further reduce the errors in certain conditions.

Abstract When somatic cells acquire complex karyotypes, they often are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human neurons harbors idiosyncratic copy number variants (CNVs, “CNV neurons”), but previous analyses of CNV neurons are limited by relatively small sample sizes. Here, we develop an allele-based validation approach, SCOVAL, to corroborate or reject read-depth based CNV calls in single human neurons. We apply this approach to 2,125 frontal cortical neurons from a neurotypical human brain. SCOVAL identifies 226 CNV neurons, which include a subclass of 65 CNV neurons with highly aberrant karyotypes containing whole or substantial losses on multiple chromosomes. Moreover, we find that CNV location appears to be nonrandom. Recurrent regions of neuronal genome rearrangement contain fewer, but longer, genes.

We describe the detection of Paranannizziopsis sp. fungus in a wild population of vipers in Europe. Fungal infections were severe, and 1 animal likely died from infection. Surveillance efforts are needed to better understand the threat of this pathogen to snake conservation.

Introduction: Intradetrusor onabotulinumtoxinA (Botox) injections, to treat idiopathic overactive bladder (OAB), can be performed in the office setting under local analgesia alone or in the operating room (OR) under local and/or sedation. The objective of this study was to compare the symptomatic improvement in patients with OAB who underwent treatment with intradetrusor onabotulinumtoxinA injections in an in-office versus the OR setting. Methods: We performed a multicenter retrospective cohort study of women with the diagnosis of refractory non-neurogenic OAB who elected to undergo treatment with intradetrusor onabotulinumtoxinA injections between January 2015 and December 2020. The electronic medical records were queried for all the demographic and peri-procedural data, including the report of subjective improvement post procedure. Patients were categorized as either “in-office” versus “OR” based on the setting in which they underwent their procedure. Results: Five hundred and thirty-nine patients met the inclusion criteria: 297 (55%) in the in-office group and 242 (45%) in the OR group. A total of 30 (5.6%) patients reported retention after their procedure and it was more common in the in-office group (8.1%) versus the OR group (2.5%), (P = 0.003). The rate of urinary tract infection within 6 months of the procedure was higher in the OR group (26.0% vs. 16.8%, P = 0.009). The overall subjective improvement rate was 77% (95% confidence interval: 73%–80%). Patients in the OR group had a higher reported improvement as compared to the in-office group (81.4% vs. 73.3%, P = 0.03). Conclusions: In this cohort study of patients with OAB undergoing intradetrusor onabotulinumtoxinA injections, post procedural subjective improvement was high regardless of the setting in which the procedure was performed.

Abstract Triazole antifungals function as ergosterol biosynthesis inhibitors and are frontline therapy for invasive fungal infections, such as invasive aspergillosis. The primary mechanism of action of triazoles is through the specific inhibition of a cytochrome P450 14-α-sterol demethylase enzyme, Cyp51A/B, resulting in depletion of cellular ergosterol. Here, we uncover a clinically relevant secondary mechanism of action for triazoles within the ergosterol biosynthesis pathway. We provide evidence that triazole-mediated inhibition of Cyp51A/B activity generates sterol intermediate perturbations that are likely decoded by the sterol sensing functions of HMG-CoA reductase and Insulin-Induced Gene orthologs as increased pathway activity. This, in turn, results in negative feedback regulation of HMG-CoA reductase, the rate-limiting step of sterol biosynthesis. We also provide evidence that HMG-CoA reductase sterol sensing domain mutations previously identified as generating resistance in clinical isolates of Aspergillus fumigatus partially disrupt this triazole-induced feedback. Therefore, our data point to a secondary mechanism of action for the triazoles: induction of HMG-CoA reductase negative feedback for downregulation of ergosterol biosynthesis pathway activity. Abrogation of this feedback through acquired mutations in the HMG-CoA reductase sterol sensing domain diminishes triazole antifungal activity against fungal pathogens and underpins HMG-CoA reductase-mediated resistance.

Abstract Infectious diseases are influenced by interactions between host and pathogen, and the number of infected hosts is rarely homogenous across the landscape. Areas with elevated pathogen prevalence can maintain a high force of infection and may indicate areas with disease impacts on host populations. However, isolating the ecological processes that result in increases in infection prevalence and intensity remains a challenge. Here we elucidate the contribution of pathogen clade and host species in disease hotspots caused by Ophidiomyces ophidiicola, the pathogen responsible for snake fungal disease, in 21 species of snakes infected with multiple pathogen strains across 10 countries in Europe. We found isolated areas of disease hotspots in a landscape where infections were otherwise low. O. ophidiicola clade had important effects on transmission, and areas with multiple pathogen clades had higher host infection prevalence. Snake species further influenced infection, with most positive detections coming from species within the Natrix genus. Our results suggest that both host and pathogen identity are essential components contributing to increased pathogen prevalence.

Abstract Aims This study aimed to evaluate the bidirectional relationship between kidney and cardiovascular (CV) events in trial participants with type 2 diabetes and CV disease. Methods and results Post hoc analyses of EMPA‐REG OUTCOME using Cox regression models were performed to assess the association of baseline factors with risk of a kidney event and bidirectional associations of incident kidney events and CV events. Among placebo‐treated participants, baseline factors significantly associated with greater kidney event risk included lower baseline estimated glomerular filtration rate, albuminuria, higher uric acid, low‐density lipoprotein cholesterol levels, and prior heart failure (HF). Coronary artery disease was not associated with increased risk. In placebo‐treated participants, occurrence of an incident non‐fatal kidney event increased the subsequent risk of hospitalization for HF (HHF) but not 3‐point major adverse CV events (non‐fatal stroke, non‐fatal myocardial infarction, and CV death). Vice versa, HHF (but not myocardial infarction/stroke) increased the risk of subsequent kidney events. These associations were generally also seen in empagliflozin‐treated participants and in the overall population. Interestingly, the risk of kidney events following HHF was not significantly increased in the relatively small number of placebo‐treated participants already diagnosed with HF at baseline. Conclusions These findings demonstrate a bidirectional inter‐relationship between HHF and kidney events. Further exploration of this relationship and strategies to optimize the use of therapies to reduce both kidney and HF outcomes is warranted.