Accelerated Nano-Optical Imaging through Sparse Sampling.

The integration time and signal-to-noise ratio are inextricably linked when performing scanning probe microscopy based on raster scanning. This often yields a large lower bound on the measurement time, for example, in nano-optical imaging experiments performed using a scanning near-field optical microscope (SNOM). Here, we utilize sparse scanning augmented with Gaussian process regression to bypass the time constraint. We apply this approach to image charge-transfer polaritons in graphene residing on ruthenium trichloride (α-RuCl3) and obtain key features such as polariton damping and dispersion. Critically, nano-optical SNOM imaging data obtained via sparse sampling are in good agreement with those extracted from traditional raster scans but require 11 times fewer sampled points. As a result, Gaussian process-aided sparse spiral scans offer a major decrease in scanning time.

Development of a Robust Consensus Modeling Approach for Identifying Cellular and Media Metabolites Predictive of Mesenchymal Stromal Cell Potency.

Mesenchymal stromal cells (MSCs) have shown promise in regenerative medicine applications due in part to their ability to modulate immune cells. However, MSCs demonstrate significant functional heterogeneity in terms of their immunomodulatory function because of differences in MSC donor/tissue source, as well as non-standardized manufacturing approaches. As MSC metabolism plays a critical role in their ability to expand to therapeutic numbers ex vivo, we comprehensively profiled intracellular and extracellular metabolites throughout the expansion process to identify predictors of immunomodulatory function (T-cell modulation and indoleamine-2,3-dehydrogenase (IDO) activity). Here, we profiled media metabolites in a non-destructive manner through daily sampling and nuclear magnetic resonance (NMR), as well as MSC intracellular metabolites at the end of expansion using mass spectrometry (MS). Using a robust consensus machine learning approach, we were able to identify panels of metabolites predictive of MSC immunomodulatory function for 10 independent MSC lines. This approach consisted of identifying metabolites in 2 or more machine learning models and then building consensus models based on these consensus metabolite panels. Consensus intracellular metabolites with high predictive value included multiple lipid classes (such as phosphatidylcholines, phosphatidylethanolamines, and sphingomyelins) while consensus media metabolites included proline, phenylalanine, and pyruvate. Pathway enrichment identified metabolic pathways significantly associated with MSC function such as sphingolipid signaling and metabolism, arginine and proline metabolism, and autophagy. Overall, this work establishes a generalizable framework for identifying consensus predictive metabolites that predict MSC function, as well as guiding future MSC manufacturing efforts through identification of high-potency MSC lines and metabolic engineering.

Discovery and Folding Dynamics of a Fused Bicyclic Cysteine Knot Undecapeptide from the Marine Sponge Halichondria bowerbanki.

We describe the discovery and structure of an undecapeptide natural product from a marine sponge, termed halichondamide A, that is morphed into a fused bicyclic ring topology via two disulfide bonds. Molecular dynamics simulations allow us to posit that the installation of one disulfide bond biases the intermediate peptide conformation and predisposes the formation of the second disulfide bond. The natural product was found to be mildly cytotoxic against liver and breast cancer cell lines.

Quenched Excitons in WSe2/α-RuCl3 Heterostructures Revealed by Multimessenger Nanoscopy.

We investigate heterostructures composed of monolayer WSe2 stacked on α-RuCl3 using a combination of Terahertz (THz) and infrared (IR) nanospectroscopy and imaging, scanning tunneling spectroscopy (STS), and photoluminescence (PL). Our observations reveal itinerant carriers in the heterostructure prompted by charge transfer across the WSe2/α-RuCl3 interface. Local STS measurements show the Fermi level is shifted to the valence band edge of WSe2 which is consistent with p-type doping and verified by density functional theory (DFT) calculations. We observe prominent resonances in near-IR nano-optical and PL spectra, which are associated with the A-exciton of WSe2. We identify a concomitant, near total, quenching of the A-exciton resonance in the WSe2/α-RuCl3 heterostructure. Our nano-optical measurements show that the charge-transfer doping vanishes while excitonic resonances exhibit near-total recovery in "nanobubbles", where WSe2 and α-RuCl3 are separated by nanometer distances. Our broadband nanoinfrared inquiry elucidates local electrodynamics of excitons and an electron-hole plasma in the WSe2/α-RuCl3 system.

Machine Learning Reveals Lipidome Remodeling Dynamics in a Mouse Model of Ovarian Cancer.

Ovarian cancer (OC) is one of the deadliest cancers affecting the female reproductive system. It may present little or no symptoms at the early stages and typically unspecific symptoms at later stages. High-grade serous ovarian cancer (HGSC) is the subtype responsible for most ovarian cancer deaths. However, very little is known about the metabolic course of this disease, particularly in its early stages. In this longitudinal study, we examined the temporal course of serum lipidome changes using a robust HGSC mouse model and machine learning data analysis. Early progression of HGSC was marked by increased levels of phosphatidylcholines and phosphatidylethanolamines. In contrast, later stages featured more diverse lipid alterations, including fatty acids and their derivatives, triglycerides, ceramides, hexosylceramides, sphingomyelins, lysophosphatidylcholines, and phosphatidylinositols. These alterations underscored unique perturbations in cell membrane stability, proliferation, and survival during cancer development and progression, offering potential targets for early detection and prognosis of human ovarian cancer.

Discovery and Biosynthesis of Ureidopeptide Natural Products Macrocyclized via Indole N-acylation in Marine Microbulbifer spp. Bacteria.

Commensal bacteria associated with marine invertebrates are underappreciated sources of chemically novel natural products. Using mass spectrometry, we had previously detected the presence of peptidic natural products in obligate marine bacteria of the genus Microbulbifer cultured from marine sponges. In this report, the isolation and structural characterization of a panel of ureidohexapeptide natural products, termed the bulbiferamides, from Microbulbifer strains is reported wherein the tryptophan side chain indole participates in a macrocyclizing peptide bond formation. Genome sequencing identifies biosynthetic gene clusters encoding production of the bulbiferamides and implicates the involvement of a thioesterase in the indolic macrocycle formation. The structural diversity and widespread presence of bulbiferamides in commensal microbiomes of marine invertebrates point toward a possible ecological role for these natural products.

Incidental coronary artery calcification on non-gated CT thorax correlates with risk of cardiovascular events and death.

OBJECTIVES: To assess coronary artery calcification (CAC) on non-contrast non-ECG-gated CT thorax (NC-NECG-CTT) and to evaluate its correlation with short-term risk of cardiovascular disease (CVD) events and death. METHODS: Single-institution retrospective study including all patients 40-70 years old who underwent NC-NECG-CTT over a period of 6 months. Individuals with known CVD were excluded. The presence of CAC was assessed and quantified by the Agatston score (CACS). CAC severity was defined as mild (< 100), moderate (100-400), or severe (> 400). CVD events (including CVD death, myocardial infarction, revascularisation procedures, ischaemic stroke, acute peripheral atherosclerotic ischaemia), and all-cause mortality over a median of 3.5 years were recorded. Cox proportional-hazards regression modelling was performed including CACS, age, gender and CVD risk factors (smoking, hypertension, diabetes mellitus, dyslipidaemia, and family history of CVD). RESULTS: Of the total 717 eligible cases, 325 (45%) had CAC. In patients without CAC, there was only one CVD event, compared to 26 CVD events including 5 deaths in patients with CAC. The presence and severity of CAC correlated with CVD events (p < 0.001). A CACS > 100 was significantly associated with both CVD events, hazard ratio (HR) 5.74, 95% confidence interval: 2.19-15.02; p < 0.001, and all-cause mortality, HR 1.7, 95% CI: 1.08-2.66; p = 0.02. Ever-smokers with CAC had a significantly higher risk for all-cause mortality compared to never-smokers (p = 0.03), but smoking status was not an independent predictor for CVD events in any subgroup category of CAC severity. CONCLUSIONS: The presence and severity of CAC assessed on NC-NECG-CTT correlates with short-term cardiovascular events and death. KEY POINTS: • Patients aged 40-70 years old without known CVD but with CAC on NC-NECG-CTT have a higher risk of CVD events compared to those without CAC. • CAC (Agatston) score above 100 confers a 5.7-fold increase in the risk of short-term CVD events in these patients. • The presence and severity of CAC on NC-NECG-CTT may have prognostic and therapeutic implications.

Constitutively Synergistic Multiagent Drug Formulations Targeting MERTK, FLT3, and BCL-2 for Treatment of AML.

PURPOSE: Although high-dose, multiagent chemotherapy has improved leukemia survival rates, treatment outcomes remain poor in high-risk subsets, including acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) in infants. The development of new, more effective therapies for these patients is therefore an urgent, unmet clinical need. METHODS: The dual MERTK/FLT3 inhibitor MRX-2843 and BCL-2 family protein inhibitors were screened in high-throughput against a panel of AML and MLL-rearranged precursor B-cell ALL (infant ALL) cell lines. A neural network model was built to correlate ratiometric drug synergy and target gene expression. Drugs were loaded into liposomal nanocarriers to assess primary AML cell responses. RESULTS: MRX-2843 synergized with venetoclax to reduce AML cell density in vitro. A neural network classifier based on drug exposure and target gene expression predicted drug synergy and growth inhibition in AML with high accuracy. Combination monovalent liposomal drug formulations delivered defined drug ratios intracellularly and recapitulated synergistic drug activity. The magnitude and frequency of synergistic responses were both maintained and improved following drug formulation in a genotypically diverse set of primary AML bone marrow specimens. CONCLUSIONS: We developed a nanoscale combination drug formulation that exploits ectopic expression of MERTK tyrosine kinase and dependency on BCL-2 family proteins for leukemia cell survival in pediatric AML and infant ALL cells. We demonstrate ratiometric drug delivery and synergistic cell killing in AML, a result achieved by a systematic, generalizable approach of combination drug screening and nanoscale formulation that may be extended to other drug pairs or diseases in the future.

Common fear molecules induce defensive responses in marine prey across trophic levels.

Predator-prey interactions are a key feature of ecosystems and often chemically mediated, whereby individuals detect molecules in their environment that inform whether they should attack or defend. These molecules are largely unidentified, and their discovery is important for determining their ecological role in complex trophic systems. Homarine and trigonelline are two previously identified blue crab (Callinectes sapidus) urinary metabolites that cause mud crabs (Panopeus herbstii) to seek refuge, but it was unknown whether these molecules influence other species within this oyster reef system. In the current study, homarine, trigonelline, and blue crab urine were tested on juvenile oysters (Crassostrea virginica) to ascertain if the same molecules known to alter mud crab behavior also affect juvenile oyster morphology, thus mediating interactions between a generalist predator, a mesopredator, and a basal prey species. Oyster juveniles strengthened their shells in response to blue crab urine and when exposed to homarine and trigonelline in combination, especially at higher concentrations. This study builds upon previous work to pinpoint specific molecules from a generalist predator's urine that induce defensive responses in two marine prey from different taxa and trophic levels, supporting the hypothesis that common fear molecules exist in ecological systems.

Non-occupational physical activity and risk of cardiovascular disease, cancer and mortality outcomes: a dose-response meta-analysis of large prospective studies.

OBJECTIVE: To estimate the dose-response associations between non-occupational physical activity and several chronic disease and mortality outcomes in the general adult population. DESIGN: Systematic review and cohort-level dose-response meta-analysis. DATA SOURCES: PubMed, Scopus, Web of Science and reference lists of published studies. ELIGIBILITY CRITERIA: Prospective cohort studies with (1) general population samples >10 000 adults, (2) ≥3 physical activity categories, and (3) risk measures and CIs for all-cause mortality or incident total cardiovascular disease, coronary heart disease, stroke, heart failure, total cancer and site-specific cancers (head and neck, myeloid leukaemia, myeloma, gastric cardia, lung, liver, endometrium, colon, breast, bladder, rectum, oesophagus, prostate, kidney). RESULTS: 196 articles were included, covering 94 cohorts with >30 million participants. The evidence base was largest for all-cause mortality (50 separate results; 163 415 543 person-years, 811 616 events), and incidence of cardiovascular disease (37 results; 28 884 209 person-years, 74 757 events) and cancer (31 results; 35 500 867 person-years, 185 870 events). In general, higher activity levels were associated with lower risk of all outcomes. Differences in risk were greater between 0 and 8.75 marginal metabolic equivalent of task-hours per week (mMET-hours/week) (equivalent to the recommended 150 min/week of moderate-to-vigorous aerobic physical activity), with smaller marginal differences in risk above this level to 17.5 mMET-hours/week, beyond which additional differences were small and uncertain. Associations were stronger for all-cause (relative risk (RR) at 8.75 mMET-hours/week: 0.69, 95% CI 0.65 to 0.73) and cardiovascular disease (RR at 8.75 mMET-hours/week: 0.71, 95% CI 0.66 to 0.77) mortality than for cancer mortality (RR at 8.75 mMET-hours/week: 0.85, 95% CI 0.81 to 0.89). If all insufficiently active individuals had achieved 8.75 mMET-hours/week, 15.7% (95% CI 13.1 to 18.2) of all premature deaths would have been averted. CONCLUSIONS: Inverse non-linear dose-response associations suggest substantial protection against a range of chronic disease outcomes from small increases in non-occupational physical activity in inactive adults. PROSPERO registration number CRD42018095481.

Curvature-Induced One-Dimensional Phonon Polaritons at Edges of Folded Boron Nitride Sheets.

Generation and manipulation of phonon polaritons are of paramount importance for understanding the interaction between an electromagnetic field and dielectric materials and furthering their application in mid-infrared optical communication. However, the formation of tunable one-dimensional phonon polaritons has been rarely realized in van der Waals layered structures. Here we report the discovery of curvature-induced phonon polaritons localized at the crease of folded hexagonal boron nitrides (h-BNs) with a few atomic layers using monochromated electron energy-loss spectroscopy. Compared to bulk regions, the creased-localized signals undergo an abnormal blue-shift of 1.4 meV. First-principles calculations reveal that the energy shift arises from the optical phonon hardening in the curled region. Interestingly, the curvature-induced phonon polariton can also be controllably achieved via an electron-beam etching approach. This work opens an avenue of tailoring local electromagnetic response and creating unique phonon polariton modes in van der Waals layered materials for diverse applications.

Long-Lived Phonon Polaritons in Hyperbolic Materials.

Natural hyperbolic materials with dielectric permittivities of opposite signs along different principal axes can confine long-wavelength electromagnetic waves down to the nanoscale, well below the diffraction limit. Confined electromagnetic waves coupled to phonons in hyperbolic dielectrics including hexagonal boron nitride (hBN) and α-MoO3 are referred to as hyperbolic phonon polaritons (HPPs). HPP dissipation at ambient conditions is substantial, and its fundamental limits remain unexplored. Here, we exploit cryogenic nanoinfrared imaging to investigate propagating HPPs in isotopically pure hBN and naturally abundant α-MoO3 crystals. Close to liquid-nitrogen temperatures, losses for HPPs in isotopic hBN drop significantly, resulting in propagation lengths in excess of 8 µm, with lifetimes exceeding 5 ps, thereby surpassing prior reports on such highly confined polaritonic modes. Our nanoscale, temperature-dependent imaging reveals the relevance of acoustic phonons in HPP damping and will be instrumental in mitigating such losses for miniaturized mid-infrared technologies operating at liquid-nitrogen temperatures.

Enzymatic Synthesis Assisted Discovery of Proline-Rich Macrocyclic Peptides in Marine Sponges.

Proline-rich macrocyclic peptides (PRMPs) are natural products present in geographically and phylogenetically dispersed marine sponges. The large diversity and low abundance of PRMPs in sponge metabolomes precludes isolation and structure elucidation of each individual PRMP congener. Here, using standards developed via biomimetic enzymatic synthesis of PRMPs, a mass spectrometry-based workflow to sequence PRMPs was developed and validated to reveal that the diversity of PRMPs in marine sponges is much greater than that has been realized by natural product isolation-based strategies. Findings are placed in the context of diversity-oriented transamidative macrocyclization of peptide substrates in sponge holobionts.

Influence of External Heating Rate on the Structure and Porosity of Thermally Exfoliated Graphite Oxide.

Fast external heating rates in graphite oxide thermal exfoliation have been reported to be advantageous for generating high surface area graphene-based materials for a variety of applications. The study yields the surprising result that the surface area and porosity developed in reduced graphite oxide under some conditions are independent of instrument-set external heating rates. The true "total" heating rate experienced by the sample is shown to be the sum of the external rate and the local self-heating rate associated with the exothermicity of graphite oxide exfoliation, and under many conditions, the local self-heating contribution dominates. In these instances, increasing external heating rate does not increase the total rate, improve exfoliation degree or enhance surface area. These results are important for optimizing the conditions for fabrication of reduced graphene oxide with tailored properties.

Manufacture Dependent Differential Biodegradation of 3D Printed Shape Memory Polymers.

In the field of tissue engineering, 3D printed shape memory polymers (SMPs) are drawing increased interest. Understanding how these 3D printed SMPs degrade is critical for their use in the clinic, as small changes in material properties can significantly change how they behave after in vivo implantation. Degradation of 3D printed acrylated poly(glycerol-dodecanedioate) (APGD) was examined via in vitro hydrolytic, enzymatic, and in vivo subcutaneous implantation assays. Three APGD manufacturing modalities were assessed to determine differences in degradation. Material extrusion samples showed significantly larger mass and volume loss at 2 months, compared to lasercut and vat photopolymerization samples, under both enzymatic and in vivo degradation. Critically, melt transition temperatures of degraded PGD increased over time in vitro, but not in vivo. Histology of tissue surrounding APGD implants showed no significant signs of inflammation compared to controls, providing a promising outlook for use of 3D printed APGD devices in the clinic.

Integrative Analysis of Cytokine and Lipidomics Datasets Following Mild Traumatic Brain Injury in Rats.

Traumatic brain injury (TBI) is a significant source of disability in the United States and around the world and may lead to long-lasting cognitive deficits and a decreased quality of life for patients across injury severities. Following the primary injury phase, TBI is characterized by complex secondary cascades that involve altered homeostasis and metabolism, faulty signaling, neuroinflammation, and lipid dysfunction. The objectives of the present study were to (1) assess potential correlations between lipidome and cytokine changes after closed-head mild TBI (mTBI), and (2) examine the reproducibility of our acute lipidomic profiles following TBI. Cortices from 54 Sprague Dawley male and female rats were analyzed by ultra-high-performance liquid chromatography mass spectrometry (LC-MS) in both positive and negative ionization modes and multiplex cytokine analysis after single (smTBI) or repetitive (rmTBI) closed-head impacts, or sham conditions. Tissue age was a variable, given that two cohorts (n = 26 and n = 28) were initially run a year-and-a-half apart, creating inter-batch variations. We annotated the lipidome datasets using an in-house data dictionary based on exact masses of precursor and fragment ions and removed features with statistically significant differences between sham control batches. Our results indicate that lipids with high-fold change between injury groups moderately correlate with the cytokines eotaxin, IP-10, and TNF-α. Additionally, we show a significant decrease in the pro-inflammatory markers IL-1ß and IP-10, TNF-α, and RANTES in the rmTBI samples relative to the sham control. We discuss the major challenges in correlating high dimensional lipidomic data with functional cytokine profiles and the implications for understanding the biological significance of two related but disparate analysis modes in the study of TBI, an inherently heterogeneous neurological disorder.

Comparing Brain and Blood Lipidome Changes following Single and Repetitive Mild Traumatic Brain Injury in Rats.

Traumatic brain injury (TBI) is a major health concern in the United States and globally, contributing to disability and long-term neurological problems. Lipid dysregulation after TBI is underexplored, and a better understanding of lipid turnover and degradation could point to novel biomarker candidates and therapeutic targets. Here, we investigated overlapping lipidome changes in the brain and blood using a data-driven discovery approach to understand lipid alterations in the brain and serum compartments acutely following mild TBI (mTBI) and the potential efflux of brain lipids to peripheral blood. The cortices and sera from male and female Sprague-Dawley rats were analyzed via ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) in both positive and negative ion modes following single and repetitive closed head impacts. The overlapping lipids in the data sets were identified with an in-house data dictionary for investigating lipid class changes. MS-based lipid profiling revealed overall increased changes in the serum compartment, while the brain lipids primarily showed decreased changes. Interestingly, there were prominent alterations in the sphingolipid class in the brain and blood compartments after single and repetitive injury, which may suggest efflux of brain sphingolipids into the blood after TBI. Genetic algorithms were used for predictive panel selection to classify injured and control samples with high sensitivity and specificity. These overlapping lipid panels primarily mapped to the glycerophospholipid metabolism pathway with Benjamini-Hochberg adjusted q-values less than 0.05. Collectively, these results detail overlapping lipidome changes following mTBI in the brain and blood compartments, increasing our understanding of TBI-related lipid dysregulation while identifying novel biomarker candidates.

Divergent Skeletal Muscle Metabolomic Signatures of Different Exercise Training Modes Independently Predict Cardiometabolic Risk Factors.

We investigated the link between enhancement of SI (by hyperinsulinemic-euglycemic clamp) and muscle metabolites after 12 weeks of aerobic (high-intensity interval training [HIIT]), resistance training (RT), or combined training (CT) exercise in 52 lean healthy individuals. Muscle RNA sequencing revealed a significant association between SI after both HIIT and RT and the branched-chain amino acid (BCAA) metabolic pathway. Concurrently with increased expression and activity of branched-chain ketoacid dehydrogenase enzyme, many muscle amino metabolites, including BCAAs, glutamate, phenylalanine, aspartate, asparagine, methionine, and γ-aminobutyric acid, increased with HIIT, supporting the substantial impact of HIIT on amino acid metabolism. Short-chain C3 and C5 acylcarnitines were reduced in muscle with all three training modes, but unlike RT, both HIIT and CT increased tricarboxylic acid metabolites and cardiolipins, supporting greater mitochondrial activity with aerobic training. Conversely, RT and CT increased more plasma membrane phospholipids than HIIT, suggesting a resistance exercise effect on cellular membrane protection against environmental damage. Sex and age contributed modestly to the exercise-induced changes in metabolites and their association with cardiometabolic parameters. Integrated transcriptomic and metabolomic analyses suggest various clusters of genes and metabolites are involved in distinct effects of HIIT, RT, and CT. These distinct metabolic signatures of different exercise modes independently link each type of exercise training to improved SI and cardiometabolic risk. ARTICLE HIGHLIGHTS: We aimed to understand the link between skeletal muscle metabolites and cardiometabolic health after exercise training. Although aerobic, resistance, and combined exercise training each enhance muscle insulin sensitivity as well as other cardiometabolic parameters, they disparately alter amino and citric acid metabolites as well as the lipidome, linking these metabolomic changes independently to the improvement of cardiometabolic risks with each exercise training mode. These findings reveal an important layer of the unique exercise mode-dependent changes in muscle metabolism, which may eventually lead to more informed exercise prescription for improving SI.

Serum Lipidome Profiling Reveals a Distinct Signature of Ovarian Cancer in Korean Women.

BACKGROUND: Distinguishing ovarian cancer from other gynecological malignancies is crucial for patient survival yet hindered by non-specific symptoms and limited understanding of ovarian cancer pathogenesis. Accumulating evidence suggests a link between ovarian cancer and deregulated lipid metabolism. Most studies have small sample sizes, especially for early-stage cases, and lack racial/ethnic diversity, necessitating more inclusive research for improved ovarian cancer diagnosis and prevention. METHODS: Here, we profiled the serum lipidome of 208 ovarian cancer, including 93 early-stage patients with ovarian cancer and 117 nonovarian cancer (other gynecological malignancies) patients of Korean descent. Serum samples were analyzed with a high-coverage liquid chromatography high-resolution mass spectrometry platform, and lipidome alterations were investigated via statistical and machine learning (ML) approaches. RESULTS: We found that lipidome alterations unique to ovarian cancer were present in Korean women as early as when the cancer is localized, and those changes increase in magnitude as the diseases progresses. Analysis of relative lipid abundances revealed specific patterns for various lipid classes, with most classes showing decreased abundance in ovarian cancer in comparison with other gynecological diseases. ML methods selected a panel of 17 lipids that discriminated ovarian cancer from nonovarian cancer cases with an AUC value of 0.85 for an independent test set. CONCLUSIONS: This study provides a systemic analysis of lipidome alterations in human ovarian cancer, specifically in Korean women. IMPACT: Here, we show the potential of circulating lipids in distinguishing ovarian cancer from nonovarian cancer conditions.