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Abstract Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other vertebrates. Also, extensive research is aimed at their potential to quantify biological aging rates and test longevity or rejuvenating interventions. Here, we discuss key challenges to understand clock mechanisms and biomarker utility. This requires dissecting the drivers and regulators of age-related changes in single-cell, tissue- and disease-specific models, as well as exploring other epigenomic marks, longitudinal and diverse population studies, and non-human models. We also highlight important ethical issues in forensic age determination and predicting the trajectory of biological aging in an individual.

Abstract Microbeam radiotherapy (MRT) is based on a spatial fractionation of synchrotron X-ray microbeams at the microscale level. Although the tissue-sparing effect (TSE) in response to non-uniform radiation fields was recognized more than one century ago, the TSE of MRT in the testes and its clinical importance for preventing male fertility remain to be determined. In this study, using the combination of MRT techniques and a unique ex vivo testes organ culture, we show, for the first time, the MRT-mediated TSE for the preservation of spermatogenesis. Furthermore, our high-precision microbeam analysis revealed that the survival and potential migration steps of the non-irradiated germ stem cells in the irradiated testes tissue would be needed for the effective TSE for spermatogenesis. Our findings indicated the distribution of dose irradiated in the testes at the microscale level is of clinical importance for delivering high doses of radiation to the tumor, while still preserving male fertility.

Abstract Background Exposure to the herbicide Agent Orange during the Vietnam War was widespread and is associated with numerous adverse health outcomes. A continuing concern of veterans is the possibility that exposure to the dioxin-containing herbicide might induce adverse reproductive outcomes. We sought to assess whether exposure to Agent Orange in Vietnam was associated with changes in DNA methylation in sperm in a subset of Vietnam veterans who participated in the Air Force Health Study (AFHS). Methods We studied 37 members of the AFHS chosen to have no, low, medium or high exposure to Agent Orange, based upon serum dioxin levels obtained during a series of examinations. DNA from stored semen was extracted and DNA methylation assessed on the Illumina 450 K platform. Results Initial epigenome-wide analysis returned no loci that survived control for false discovery. However, the TEAD3 gene had four different CpG sites that showed loss of DNA methylation associated with dioxin exposure. Analysis assessing regional DNA methylation changes revealed 36 gene regions, including the region of the imprinted gene H19 to have altered DNA methylation associated with high exposure compared to the low exposure group. Additional comparison of our data with sperm DNA methylation data from Russian boys exposed to dioxin found an additional 5 loci that were altered in both studies and exhibited a consistent direction of association. Conclusions Studying a small number of sperm samples from veterans enrolled in the AFHS, we did not find evidence of significant epigenome-wide alterations associated with exposure to Agent Orange. However, additional analysis showed that the H19 gene region is altered in the sperm of Agent Orange-exposed Ranch Hand veterans. Our study also replicated several findings of a prior study of dioxin-exposed Russian boys. These results provide additional candidate loci for further investigation and may have implications for the reproductive health of dioxin-exposed individuals.

Abstract Background Differentiated cells that arise from stem cells in early development contain DNA methylation features that provide a memory trace of their fetal cell origin (FCO). The FCO signature was developed to estimate the proportion of cells in a mixture of cell types that are of fetal origin and are reminiscent of embryonic stem cell lineage. Here we implemented the FCO signature estimation method to compare the fraction of cells with the FCO signature in tumor tissues and their corresponding nontumor normal tissues. Methods We applied our FCO algorithm to discovery data sets obtained from The Cancer Genome Atlas (TCGA) and replication data sets obtained from the Gene Expression Omnibus (GEO) data repository. Wilcoxon rank sum tests, linear regression models with adjustments for potential confounders and non-parametric randomization-based tests were used to test the association of FCO proportion between tumor tissues and nontumor normal tissues. P-values of

A field study was conducted for three consecutive seasons in the hot climate of central California to assess the performance of ‘Merlot’ grapevine (Vitis vinifera) grafted onto ‘Freedom’ [Fresno 1613-59 × Dog Ridge 5 (27% V. vinifera hybrid)] during training system conversion to facilitate mechanization. The traditional head-trained and cane-pruned (CP) system was either retained or converted either to a bilateral cordon-trained, spur-pruned California sprawl training system (HP), or to a bilateral cordon-trained, mechanically box-pruned single high-wire sprawling system (SHMP). After the conversion, SHMP sustained greater yield with more clusters per vine and smaller berries without affecting the canopy microclimate. This was due to a higher number of nodes retained after dormant pruning. The SHMP canopies, compared with CP and HP; filled allotted canopy space earlier based on photosynthetically active radiation (PAR) transmitted through the canopies, populating the space allotted per vine, favoring higher production efficiency. There were no adverse effects of training systems on berry composition or flavonoid concentration, during or after conversion to mechanical management. However, experimental year effect was obvious on anthocyanin composition of ‘Merlot’ berries, increasing trihydroxylated (i.e., delphinidin-based) anthocyanins in the latter years of the experiment. Our results also provided evidence that earlier canopy growth coupled with sufficient reproductive compensating responses allowed for increased yields while reaching commercial maturity without a decline in anthocyanin content with the SHMP. Converting CP to SHMP reduced labor operations costs by 90%. Furthermore, the SHMP had greater gross revenue and resulted in greater net income per acre even when the conversion year was taken into account. Therefore, SHMP is recommended for growers within the hot climate of the central San Joaquin Valley as a means to maintain productivity of vineyards while not sacrificing berry composition at the farm gate.

Background: Per- and polyfluoroalkyl substances (PFAS) may adversely influence cardiometabolic risk. However, few studies have examined if the timing of early life PFAS exposure modifies their relation to cardiometabolic risk. We examined the influence of gestational and childhood PFAS exposure on adolescents’ cardiometabolic risk. Methods: We quantified concentrations of four PFAS (perfluorooctanoate [PFOA], perfluorooctane sulfonate [PFOS], perfluorononanoate [PFNA], and perfluorohexane sulfonate [PFHxS]) in sera collected during pregnancy, at birth, and at ages 3, 8, and 12 years from 221 mother–child pairs in the HOME Study (enrolled 2003–06, Cincinnati, Ohio). We measured cardiometabolic risk factors using physical examinations, fasting serum biomarkers, and dual-energy X-ray absorptiometry scans at age 12 years. Cardiometabolic risk summary scores were calculated by summing age- and sex-standardized z-scores for individual cardiometabolic risk factors. We used multiple informant models to estimate covariate-adjusted associations of serum PFAS concentrations (log2-transformed) at each visit with cardiometabolic risk scores and their individual components, and tested for differences in associations across visits. Results: The associations of serum PFOA concentrations with cardiometabolic risk scores differed across visits (P for heterogeneity = 0.03). Gestational and cord serum PFOA concentrations were positively associated with cardiometabolic risk scores (βs and 95% confidence intervals [95% CIs]: gestational 0.8 [0.0, 1.6]; cord 0.9 [-0.1, 1.9] per interquartile range increase). These positive associations were primarily driven by homeostatic model assessment for insulin resistance index (β = 0.3 [0.1, 0.5]) and adiponectin to leptin ratio (β = -0.5 [-1.0, 0.0]). Other individual cardiometabolic risk factors associated with gestational PFOA included insulin and waist circumference. Gestational and cord PFHxS were also associated with higher cardiometabolic risk scores (βs: gestational 0.9 [0.2, 1.6]; cord 0.9 [0.1, 1.7]). Conclusion: In this cohort of children with higher gestational PFOA exposure, fetal exposure to PFOA and PFHxS was associated with unfavorable cardiometabolic risk in adolescence.

Background: Oral microbiota is believed to play important roles in systemic diseases, including cancer. Methods: We collected oral samples (tongue, buccal, supragingival, and saliva) and pancreatic tissue or intestinal samples from 52 subjects, and characterized 16S rRNA genes using high-throughput DNA sequencing. Results: Bray–Curtis plot showed clear separations between bacterial communities in the oral cavity and those in intestinal and pancreatic tissue samples. PERMANOVA tests indicated that bacterial communities from buccal samples were similar to supragingival and saliva samples, and pancreatic duct samples were similar to pancreatic tumor samples, but all other samples were significantly different from each other. A total of 73 unique Amplicon Sequence Variants (ASVs) were shared between oral and pancreatic or intestinal samples. Only four ASVs showed significant concordance, and two specific bacterial species (Gemella morbillorum and Fusobacterium nucleatum subsp. vincentii) showed consistent presence or absence patterns between oral and intestinal or pancreatic samples, after adjusting for within-subject correlation and disease status. Lastly, microbial co-abundance analyses showed distinct strain-level cluster patterns among microbiome members in buccal, saliva, duodenum, jejunum, and pancreatic tumor samples. Conclusions: Our findings indicate that oral, intestinal, and pancreatic bacterial microbiomes overlap but exhibit distinct co-abundance patterns in patients with pancreatic cancer and other gastrointestinal diseases.

Human cytomegalovirus (HCMV) is a highly prevalent herpes virus which persists as a latent infection and has been detected in several different tumor types. HCMV disease is rare but may occur in high-risk settings, often manifesting as a pulmonary infection. To date HCMV has not been investigated in malignant pleural mesothelioma (MPM). In a consecutive case series of 144 MPM patients we evaluated two biomarkers of HCMV: IgG serostatus (defined as positive and negative) and DNAemia (>100 copies/mL of cell free HCMV DNA in serum). Approximately half of the MPM patient population was HCMV IgG seropositive (51%). HCMV DNAemia was highly prevalent (79%) in MPM and independent of IgG serostatus. DNAemia levels consistent with high level current infection (>1000 copies/mL serum) were present in 41% of patients. Neither IgG serostatus nor DNAemia were associated with patient survival. In tissues, we observed that HCMV DNA was present in 48% of tumors (n = 40) and only 29% of normal pleural tissue obtained from individuals without malignancy (n = 21). Our results suggest nearly half of MPM patients have a high level current HCMV infection at the time of treatment and that pleural tissue may be a reservoir for latent HCMV infection. These findings warrant further investigation to determine the full spectrum of pulmonary infections in MPM patients, and whether treatment for high level current HCMV infection may improve patient outcomes.

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Accurate infectious disease forecasting can inform efforts to prevent outbreaks and mitigate adverse impacts. This study compares the performance of statistical, machine learning (ML), and deep learning (DL) approaches in forecasting infectious disease incidences across different countries and time intervals. We forecasted three diverse diseases: campylobacteriosis, typhoid, and Q-fever, using a wide variety of features (n = 46) from public datasets, e.g., landscape, climate, and socioeconomic factors. We compared autoregressive statistical models to two tree-based ML models (extreme gradient boosted trees [XGB] and random forest [RF]) and two DL models (multi-layer perceptron and encoder–decoder model). The disease models were trained on data from seven different countries at the region-level between 2009–2017. Forecasting performance of all models was assessed using mean absolute error, root mean square error, and Poisson deviance across Australia, Israel, and the United States for the months of January through August of 2018. The overall model results were compared across diseases as well as various data splits, including country, regions with highest and lowest cases, and the forecasted months out (i.e., nowcasting, short-term, and long-term forecasting). Overall, the XGB models performed the best for all diseases and, in general, tree-based ML models performed the best when looking at data splits. There were a few instances where the statistical or DL models had minutely smaller error metrics for specific subsets of typhoid, which is a disease with very low case counts. Feature importance per disease was measured by using four tree-based ML models (i.e., XGB and RF with and without region name as a feature). The most important feature groups included previous case counts, region name, population counts and density, mortality causes of neonatal to under 5 years of age, sanitation factors, and elevation. This study demonstrates the power of ML approaches to incorporate a wide range of factors to forecast various diseases, regardless of location, more accurately than traditional statistical approaches.

Assessing DNA methylation profiles in human blood has become a major focus of epidemiologic inquiry. Understanding variability in CpG-specific DNA methylation over moderate periods of time is a critical first step in identifying CpG sites that are candidates for DNA methylation-based etiologic, diagnostic and prognostic predictors of pathogenesis. Using the Illumina MethylationEPIC [850K] BeadArray, DNA methylation was profiled in paired whole blood samples collected approximately 1 year apart from 35 healthy women enrolled in the Nurses Study II cohort. The median intraclass correlation coefficient (ICC) across all CpG loci was 0.19 [Interquartile Range (IQR) 0.00–0.50]; 74.8% of ICCs were in the low range (0–0.5), 16.9% in the mid-range of ICCs (0.5–0.8), and 8.3% in the high-range of ICCs (0.8–1). ICCs were similar for CpG probes on the 450K Illumina array (median 0.17) and the new probes added to the 850K array (median 0.21). ICCs for CpG loci on the sex chromosomes and known metastable epialleles were high (median 0.71, 0.97, respectively), and ICCs among methylation quantitative trait loci (mQTL) CpGs were significantly higher as compared to non-mQTL CpGs (median 0.73, 0.16, respectively, P

Objective: To review the published evidence of links between radon exposure and central nervous system tumors through a systematic review of the scientific literature. Methods: We performed a thorough bibliographic search in Medline (PubMed) and EMBASE. We combined MeSH (Medical Subject Heading) terms and free text. We developed a purpose-designed scale to assess the quality of the included manuscripts. Results: We have included 18 studies, 8 performed on miners, 3 on the general population and 7 on children, and the results have been structured using this classification. The results are inconclusive. An association between radon exposure and central nervous system tumors has been observed in some studies on miners, but not in others. The results observed in the general adult population and in children are also mixed, with some research evincing a statistically significant association and others showing no effect. Conclusions: We cannot conclude that there is a relationship between radon exposure and central nervous system tumors. The available studies are extremely heterogeneous in terms of design and populations studied. Further research is needed in this topic, particularly in the general population residing in areas with high levels of radon. Resumen: Objetivo: Revisar la evidencia publicada entre la exposición al radón y los tumores del sistema nervioso central a través de una revisión sistemática de la literatura científica. Método: Se realiza una revisión sistemática exhaustiva de la literatura científica en Medline (PubMed) y EMBASE, combinando términos MeSH (Medical Subject Heading) y texto libre. Se desarrolla una escala específica para valorar la calidad de los estudios incluidos. Resultados: Se incluyeron 18 estudios (8 realizados en mineros, 3 en población general y 7 en niños) y los resultados se estructuraron siguiendo esa clasificación. Los resultados son inciertos. Algunos estudios en mineros han observado una asociación entre la exposición a radón y tumores del sistema nervioso central, pero otros no. Los resultados en población general adulta y en niños también son diversos, con algunas investigaciones que encuentran una asociación estadísticamente significativa y otras que no encuentran ningún efecto. Conclusiones: No puede concluirse que exista una asociación entre la exposición al radón y los tumores del sistema nervioso central. Los estudios disponibles son muy heterogéneos en cuanto al diseño y los sujetos incluidos. Es necesaria más investigación sobre este tema, en particular en población general residente en áreas con elevados niveles de radón. Keywords: Central nervous system neoplasms, Radon, Systematic review, Palabras clave: Sistema nervioso central, Radón, Revisión sistemática

Abstract Background Tobacco smoking is a risk factor for multiple diseases, including cardiovascular disease and diabetes. Many smoking-associated signals have been detected in the blood methylome, but the extent to which these changes are widespread to metabolically relevant tissues, and impact gene expression or metabolic health, remains unclear. Methods We investigated smoking-associated DNA methylation and gene expression variation in adipose tissue biopsies from 542 healthy female twins. Replication, tissue specificity, and longitudinal stability of the smoking-associated effects were explored in additional adipose, blood, skin, and lung samples. We characterized the impact of adipose tissue smoking methylation and expression signals on metabolic disease risk phenotypes, including visceral fat. Results We identified 42 smoking-methylation and 42 smoking-expression signals, where five genes (AHRR, CYP1A1, CYP1B1, CYTL1, F2RL3) were both hypo-methylated and upregulated in current smokers. CYP1A1 gene expression achieved 95% prediction performance of current smoking status. We validated and replicated a proportion of the signals in additional primary tissue samples, identifying tissue-shared effects. Smoking leaves systemic imprints on DNA methylation after smoking cessation, with stronger but shorter-lived effects on gene expression. Metabolic disease risk traits such as visceral fat and android-to-gynoid ratio showed association with methylation at smoking markers with functional impacts on expression, such as CYP1A1, and at tissue-shared smoking signals, such as NOTCH1. At smoking-signals, BHLHE40 and AHRR DNA methylation and gene expression levels in current smokers were predictive of future gain in visceral fat upon smoking cessation. Conclusions Our results provide the first comprehensive characterization of coordinated DNA methylation and gene expression markers of smoking in adipose tissue. The findings relate to human metabolic health and give insights into understanding the widespread health consequence of smoking outside of the lung.

Purpose: The aim of this article is to report an unusual case of postoperative graft loss into the vitreous cavity after Descemet membrane endothelial keratoplasty (DMEK) in a patient with an unstable iris-lens diaphragm (scleral-fixated intraocular lens [sf-IOL]) and its successful retrieval with a favourable outcome. Methods: This is a retrospective case report. Results: DMEK procedure was performed in a vitrectomized eye of an 80-year-old woman with pre-existing sf-IOL due to pseudophakic bullous keratopathy. In the setting of an inadvertently created oversized Ando iridectomy and unstable iris-lens diaphragm due to sf-IOL, repeated loss of an anterior chamber gas tamponade occurred. At the 3rd postoperative day, the patient noticed a change in visual perception, and we could detect a loss of the graft into the vitreous via B-scan ultrasound. A 23-G vitrectomy was performed promptly to recover the graft using a bimanual hand-over-hand technique. Six months after DMEK, the patient had a clear cornea without dehiscences with a central corneal thickness of 533 µm and endothelial cell count of 1,219 cells/mm2. Conclusions: This case demonstrates the possibility of graft recovery from the vitreous after DMEK and subsequent corneal clearing despite unstable iris-lens diaphragm and vitrectomized eye.

Abstract Genome-wide methylation arrays are powerful tools for assessing cell composition of complex mixtures. We compare three approaches to select reference libraries for deconvoluting neutrophil, monocyte, B-lymphocyte, natural killer, and CD4+ and CD8+ T-cell fractions based on blood-derived DNA methylation signatures assayed using the Illumina HumanMethylationEPIC array. The IDOL algorithm identifies a library of 450 CpGs, resulting in an average R2 = 99.2 across cell types when applied to EPIC methylation data collected on artificial mixtures constructed from the above cell types. Of the 450 CpGs, 69% are unique to EPIC. This library has the potential to reduce unintended technical differences across array platforms.

Abstract Background Preclinical radiation biology has become increasingly sophisticated due to the implementation of advanced small animal image guided radiation platforms into laboratory investigation. These small animal radiotherapy devices enable state-of-the-art image guided therapy (IGRT) research to be performed by combining high-resolution cone beam computed tomography (CBCT) imaging with an isocentric irradiation system. Such platforms are capable of replicating modern clinical systems similar to those that integrate a linear accelerator with on-board CBCT image guidance. Methods In this study, we present a dosimetric evaluation of the small animal radiotherapy research platform (SARRP, Xstrahl Inc.) focusing on small field dosimetry. Physical dosimetry was assessed using ion chamber for calibration and radiochromic film, investigating the impact of beam focus size on the dose rate output as well as beam characteristics (beam shape and penumbra). Two film analysis tools) have been used to assess the dose output using the 0.5 mm diameter aperture. Results Good agreement (between 1.7–3%) was found between the measured physical doses and the data provided by Xstrahl for all apertures used. Furthermore, all small field dosimetry data are in good agreement for both film reading methods and with our Monte Carlo simulations for both focal spot sizes. Furthermore, the small focal spot has been shown to produce a more homogenous beam with more stable penumbra over time. Conclusions FilmQA Pro is a suitable tool for small field dosimetry, with a sufficiently small sampling area (0.1 mm) to ensure an accurate measurement. The electron beam focus should be chosen with care as this can potentially impact on beam stability and reproducibility.

Electrification to reduce or eliminate greenhouse gas emissions is essential to mitigate climate change. However, a substantial portion of our manufacturing and transportation infrastructure will be difficult to electrify and/or will continue to use carbon as a key component, including areas in aviation, heavy-duty and marine transportation, and the chemical industry. In this Roadmap, we explore how multidisciplinary approaches will enable us to close the carbon cycle and create a circular economy by defossilizing these difficult-to-electrify areas and those that will continue to need carbon. We discuss two approaches for this: developing carbon alternatives and improving our ability to reuse carbon, enabled by separations. Furthermore, we posit that co-design and use-driven fundamental science are essential to reach aggressive greenhouse gas reduction targets.

Extracellular matrix bioscaffolds can influence the cardiac microenvironment and modulate endogenous cellular mechanisms. These materials can optimize cardiac surgery for repair and reconstruction. We investigated the biocompatibility and bioinductivity of bovine pericardium fixed via dye-mediated photo-oxidation on human cardiac fibroblast activity. We compared a dye-mediated photo-oxidation fixed bioscaffold to glutaraldehyde-fixed and non-fixed bioscaffolds reported in contemporary literature in cardiac surgery. Human cardiac fibroblasts from consenting patients were seeded on to bioscaffold materials to assess the biocompatibility and bioinductivity. Human cardiac fibroblast gene expression, secretome, morphology and viability were studied. Dye-mediated photo-oxidation fixed acellular bovine pericardium preserves human cardiac fibroblast phenotype and viability; and potentiates a pro-vasculogenic paracrine response. Material tensile properties were compared with biomechanical testing. Dye-mediated photo-oxidation fixed acellular bovine pericardium had higher compliance compared to glutaraldehyde-fixed bioscaffold in response to tensile force. The biocompatibility, bioinductivity, and biomechanical properties of dye-mediated photo-oxidation fixed bovine pericardium demonstrate its feasibility as a bioscaffold for use in cardiac surgery. As a fixed yet bioinductive solution, this bioscaffold demonstrates enhanced compliance and retains bioinductive properties that may leverage endogenous reparative pathways. Dye-mediated photo-oxidation fixed bioscaffold warrants further investigation as a viable tool for cardiac repair and reconstruction.

We investigated the effectiveness of severe plastic deformation by equal channel angular extrusion (ECAE) for consolidation of metal powders into metal matrix composites. Equal volumes of copper (Cu) and tantalum (Ta) powders were consolidated at ambient temperature via different ECAE routes. Composites processed by ECAE routes 4E and 4Bc were also processed at 300 °C. The resulting materials were characterized by scanning electron microscopy (SEM) and compression testing. Processing by route 4Bc at 300 °C resulted in the highest compressive strength, lowest anisotropy, and least strain rate sensitivity. We conclude that the superior properties achieved by this route arise from mechanical bonding due to interlocking Cu and Ta phases as well as enhanced metallurgical bonds from contact of pristine metal surfaces when the material is sheared along orthogonal planes.

Herein, we correlate the prior austenite grain (PAG) microstructure to deformation and fracture mechanisms of an ultra-high strength martensitic steel. To this end, a low-carbon martensitic steel is subjected to five heat-treatments and the PAG microstructure in the material is reconstructed from the EBSD inverse pole figure maps of the martensitic microstructure. The deformation and fracture response of all heat-treated materials are characterized by in situ tension tests of dog-bone and single-edge notch specimens that allow us to capture both the macroscopic mechanical response and the evolution of microscopic strains via microscale digital image correlation. The experimental results, together with microstructure-based finite element analysis, are then used to elucidate the effect of the PAG microstructure on the mechanical response of the material. Our results show that the interaction between the heterogeneous deformation fields induced by the notch and the bimodal PAG size distribution leads to an increase in the propensity of shear deformation and degradation in the fracture response of the material with increasing heat-treatment temperature and time. Our results also suggest that achieving a unform distribution of fine grains is an effective way to enhance both the strength and fracture properties of this class of materials.

Abstract We aimed to know if radon concentration is associated with municipal mortality due to brain cancer in Galicia, Spain. We designed an ecological study taking as study unit Galician municipalities. To be included, municipalities had to have at least three radon measurements. We correlated radon concentrations with municipal mortality due to these malignant tumors during the period 1999–2008. We calculated the relative risk of dying of brain cancers for each municipality and correlated this value with municipal radon concentration using Spearman’s Rho. 251 municipalities were included, with close to 3,500 radon measurements and an average of 14 radon measurements at each municipality. We observed a significant correlation between residential radon with brain cancer mortality for males and females and the intensity of the correlation was higher for females. These results were reinforced when the analysis was restricted to municipalities with more than 5 radon measurements: Spearman’s Rho 0.286 (p-value

Abstract Background The androgen receptor (AR) is a major driver of prostate cancer, and increased AR levels and co-activators of the receptor promote the development of prostate cancer. INhibitor of Growth (ING) proteins target lysine acetyltransferase or lysine deacetylase complexes to the histone H3K4Me3 mark of active transcription, to affect chromatin structure and gene expression. ING3 is a stoichiometric member of the TIP60 lysine acetyltransferase complex implicated in prostate cancer development. Methods Biopsies of 265 patients with prostate cancer were stained for ING3, pan-cytokeratin, and DNA. LNCaP and C4-2 androgen-responsive cells were used for in vitro assays including immunoprecipitation, western blotting, Luciferase reporter assay and quantitative polymerase chain reaction. Cell viability and migration assays were performed in prostate cancer cell lines using scrambled siRNA or siRNA targeting ING3. Results We find that ING3 levels and AR activity positively correlate in prostate cancer. ING3 potentiates androgen effects, increasing expression of androgen-regulated genes and androgen response element-driven reporters to promote growth and anchorage-independent growth. Conversely, ING3 knockdown inhibits prostate cancer cell growth and invasion. ING3 activates the AR by serving as a scaffold to increase interaction between TIP60 and the AR in the cytoplasm, enhancing receptor acetylation and translocation to the nucleus. Activation is independent of ING3's ability to target the TIP60 complex to H3K4Me3, identifying a previously unknown chromatin-independent cytoplasmic activity for ING3. In agreement with in vitro observations, analysis of The Cancer Genome Atlas (TCGA) data (n = 498) and a prostate cancer tissue microarray (n = 256) show that ING3 levels are higher in aggressive prostate cancers, with high levels of ING3 predicting shorter patient survival in a low AR subgroup. Including ING3 levels with currently used indicators such as the Gleason score provides more accurate prognosis in primary prostate cancer. Conclusions In contrast to the majority of previous reports suggesting tumor suppressive functions in other cancers, our observations identify a clear oncogenic role for ING3, which acts as a co-activator of AR in prostate cancer. Data from TCGA and our previous and current tissue microarrays suggest that ING3 levels correlate with AR levels and that in patients with low levels of the receptor, ING3 level could serve as a useful prognostic biomarker.

[This corrects the article DOI: 10.1371/journal.pone.0057408.].

BackgroundVariations in survival among patients with oligodendroglioma are unexplained by known prognostic factors. To assess the impact of peripheral immune profiles on prognosis, we applied immunomethylomics analyses-DNA methylation of archived whole blood samples, to characterize immune cells.MethodsWe compared the proportions of immune cells from patients with oligodendroglioma to other glioma subtypes and controls. We used recursive partitioning analysis (RPA) within the oligodendrogliomas to correlate with survival.ResultsPatients with oligodendrogliomas (141) were median age at diagnosis of 44 years; 57% male; 75% White; 60% prior chemotherapy; and 25% on dexamethasone at sample collection. Patients with oligodendrogliomas had immune profiles more similar to controls than other glioma subtypes, though with notably lower B-cells. RPA of patients with oligodendrogliomas delineated 2 survival groups based on an interaction between age and B-naïve cells. Patients with longer survival (median 24.2 years) were ≤42 years of age with higher B-naïve cells versus worse survival (median 16.9 years) who were ≤42 years of age with lower B-naïve cells or >42 years of age (P = .00032). Patients with worse survival also had lower CD4- and CD8-naïve T-cells. Similar immune profiles were observed in an independent cohort of oligodendroglioma patients prior to surgery.ConclusionsPeripheral blood immune profiles in oligodendroglioma suggested that younger patients with lower B-naïve cells experienced shorter survival. Though our findings lack of validation cohort and use a heterogenous patient population, they suggest peripheral blood immune profiles may be prognostic for patients with glioma and warrant further investigation.

Background: Bladder cancer and therapy responses hinge on immune profiles in the tumor microenvironment (TME) and blood, yet studies linking tumor-infiltrating immune cells to peripheral immune profiles are limited. Methods: DNA methylation cytometry quantified TME and matched peripheral blood immune cell proportions. With tumor immune profile data as the input, subjects were grouped by immune infiltration status and consensus clustering. Results: Immune hot and cold groups had different immune compositions in the TME but not in circulating blood. Two clusters of patients identified with consensus clustering had different immune compositions not only in the TME but also in blood. Conclusion: Detailed immune profiling via methylation cytometry reveals the significance of understanding tumor and systemic immune relationships in cancer patients.

Understanding how structural and functional alterations of individual tissues impact on whole-joint function is challenging, particularly in humans where direct invasive experimentation is difficult. Finite element (FE) computational models produce quantitative predictions of the mechanical and physiological behaviour of multiple tissues simultaneously, thereby providing a means to study changes that occur through healthy ageing and disease such as osteoarthritis (OA). As a result, significant research investment has been placed in developing such models of the human knee. Previous work has highlighted that model predictions are highly sensitive to the various inputs used to build them, particularly the mathematical definition of material properties of biological tissues. The goal of this systematic review is two-fold. First, we provide a comprehensive summation and evaluation of existing linear elastic material property data for human tibiofemoral joint tissues, tabulating numerical values as a reference resource for future studies. Second, we review efforts to model tibiofemoral joint mechanical behaviour through FE modelling with particular focus on how studies have sourced tissue material properties. The last decade has seen a renaissance in material testing fuelled by development of a variety of new engineering techniques that allow the mechanical behaviour of both soft and hard tissues to be characterised at a spectrum of scales from nano- to bulk tissue level. As a result, there now exists an extremely broad range of published values for human tibiofemoral joint tissues. However, our systematic review highlights gaps and ambiguities that mean quantitative understanding of how tissue material properties alter with age and OA is limited. It is therefore currently challenging to construct FE models of the knee that are truly representative of a specific age or disease-state. Consequently, recent tibiofemoral joint FE models have been highly generic in terms of material properties even relying on non-human data from multiple species. We highlight this by critically evaluating current ability to quantitatively compare and model (1) young and old and (2) healthy and OA human tibiofemoral joints. We suggest that future research into both healthy and diseased knee function will benefit greatly from a subject- or cohort-specific approach in which FE models are constructed using material properties, medical imagery and loading data from cohorts with consistent demographics and/or disease states.

The power of quantum chemistry to predict the ground and excited state properties of complex chemical systems has driven the development of computational quantum chemistry software, integrating advances in theory, applied mathematics, and computer science. The emergence of new computational paradigms associated with exascale technologies also poses significant challenges that require a flexible forward strategy to take full advantage of existing and forthcoming computational resources. In this context, the sustainability and interoperability of computational chemistry software development are among the most pressing issues. In this perspective, we discuss software infrastructure needs and investments with an eye to fully utilize exascale resources and provide unique computational tools for next-generation science problems and scientific discoveries.

BackgroundImmune profiles have been associated with bladder cancer outcomes and may have clinical applications for prognosis. However, associations of detailed immune cell subtypes with patient outcomes remain underexplored and may contribute crucial prognostic information for better managing bladder cancer recurrence and survival.MethodsBladder cancer case peripheral blood DNA methylation was measured using the Illumina HumanMethylationEPIC array. Extended cell-type deconvolution quantified 12 immune cell-type proportions, including memory, naïve T and B cells, and granulocyte subtypes. DNA methylation clocks determined biological age. Cox proportional hazards models tested associations of immune cell profiles and age acceleration with bladder cancer outcomes. The partDSA algorithm discriminated 10-year overall survival groups from clinical variables and immune cell profiles, and a semi-supervised recursively partitioned mixture model (SS-RPMM) with DNA methylation data was applied to identify a classifier for 10-year overall survival.ResultsHigher CD8T memory cell proportions were associated with better overall survival [HR = 0.95, 95% confidence interval (CI) = 0.93-0.98], while higher neutrophil-to-lymphocyte ratio (HR = 1.36, 95% CI = 1.23-1.50), CD8T naïve (HR = 1.21, 95% CI = 1.04-1.41), neutrophil (HR = 1.04, 95% CI = 1.03-1.06) proportions, and age acceleration (HR = 1.06, 95% CI = 1.03-1.08) were associated with worse overall survival in patient with bladder cancer. partDSA and SS-RPMM classified five groups of subjects with significant differences in overall survival.ConclusionsWe identified associations between immune cell subtypes and age acceleration with bladder cancer outcomes.ImpactThe findings of this study suggest that bladder cancer outcomes are associated with specific methylation-derived immune cell-type proportions and age acceleration, and these factors could be potential prognostic biomarkers.

The running ability of Tyrannosaurus rex has been intensively studied due to its relevance to interpretations of feeding behaviour and the biomechanics of scaling in giant predatory dinosaurs. Different studies using differing methodologies have produced a very wide range of top speed estimates and there is therefore a need to develop techniques that can improve these predictions. Here we present a new approach that combines two separate biomechanical techniques (multibody dynamic analysis and skeletal stress analysis) to demonstrate that true running gaits would probably lead to unacceptably high skeletal loads in T. rex. Combining these two approaches reduces the high-level of uncertainty in previous predictions associated with unknown soft tissue parameters in dinosaurs, and demonstrates that the relatively long limb segments of T. rex—long argued to indicate competent running ability—would actually have mechanically limited this species to walking gaits. Being limited to walking speeds contradicts arguments of high-speed pursuit predation for the largest bipedal dinosaurs like T. rex, and demonstrates the power of multiphysics approaches for locomotor reconstructions of extinct animals.

Grape Phylloxera, Daktulosphaira vitifoliae, is a gall-forming insect that feeds on the leaves and roots of many Vitis species. The roots of the cultivated V. vinifera cultivars and hybrids are highly susceptible to grape phylloxera feeding damage. The native range of this insect covers most of North America, and it is particularly abundant in the eastern and central United States. Phylloxera was introduced from North America to almost all grape-growing regions across five of the temperate zone continents. It devastated vineyards in each of these regions causing large-scale disruptions to grape growers, wine makers and national economies. In order to understand the population diversity of grape phylloxera in its native range, more than 500 samples from 19 States and 34 samples from the introduced range (northern California, Europe and South America) were genotyped with 32 simple sequence repeat markers. STRUCTURE, a model based clustering method identified five populations within these samples. The five populations were confirmed by a neighbor-joining tree and principal coordinate analysis (PCoA). These populations were distinguished by their Vitis species hosts and their geographic locations. Samples collected from California, Europe and South America traced back to phylloxera sampled in the northeastern United States on V. riparia, with some influence from phylloxera collected along the Atlantic Coast and Central Plains on V. vulpina. Reproductive statistics conclusively confirmed that sexual reproduction is common in the native range and is combined with cyclical parthenogenesis. Native grape phylloxera populations were identified to be under Hardy-Weinberg equilibrium. The identification of admixed samples between many of these populations indicates that shared environments facilitate sexual reproduction between different host associated populations to create new genotypes of phylloxera. This study also found that assortative mating might occur across the sympatric range of the V. vulpina west and V. cinerea populations.

Mitochondria are complex organelles that play critical roles in diverse aspects of cellular function. Heart disease and a number of other pathologies are associated with perturbations in the molecular machinery of the mitochondria. Therefore, comprehensive, unbiased examination of the mitochondrial proteome represents a powerful approach toward system-level insights into disease mechanisms. A crucial aspect in proteomics studies is design of bioanalytical strategies that maximize coverage of the complex repertoire of mitochondrial proteins. In this study, we evaluated the performance of gel-based and gel-free multidimensional platforms for profiling of the proteome in subsarcolemmal mitochondria harvested from rat heart. We compared three different multidimensional proteome fractionation platforms: polymeric reversed-phase liquid chromatography at high pH (PLRP), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and isoelectric focusing (IEF) separations combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS), and bioinformatics for protein identification. Across all three platforms, a total of 1043 proteins were identified. Among the three bioanalytical strategies, SDS-PAGE followed by LC-MS/MS provided the best coverage of the mitochondrial proteome. With this platform, 890 proteins with diverse physicochemical characteristics were identified; the mitochondrial protein panel encompassed proteins with various functional roles including bioenergetics, protein import, and mitochondrial fusion. Taken together, results of this study provide a large-scale view of the proteome in subsarcolemmal mitochondria from the rat heart, and aid in the selection of optimal bioanalytical platforms for differential protein expression profiling of mitochondria in health and disease.

During walking, variability in step parameters allows the body to adapt to changes in substrate or unexpected perturbations that may occur as the feet interface with the environment. Despite a rich literature describing biomechanical variability in step parameters, there are as yet no studies that consider variability at the body–environment interface. Here, we used pedobarographic statistical parametric mapping (pSPM) and two standard measures of variability, mean square error (m.s.e.) and the coefficient of variation (CV), to assess the magnitude and spatial variability in plantar pressure across a range of controlled walking speeds. Results by reduced major axis, and pSPM regression, revealed no consistent linear relationship between m.s.e. and speed or m.s.e. and Froude number. A positive linear relationship, however, was found between CV and walking speed and CV and Froude number. The spatial distribution of variability was highly disparate when assessed by m.s.e. and CV: relatively high variability was consistently confined to the medial and lateral forefoot when measured by m.s.e., while the forefoot and heel show high variability when measured by CV. In absolute terms, variability by CV was universally low (less than 2.5%). From these results, we determined that variability as assessed by m.s.e. is independent of speed, but dependent on speed when assessed by CV.

The colossal size and body plan of sauropod dinosaurs are unparalleled in terrestrial vertebrates. However, to date, there have been only limited attempts to examine temporal and phylogenetic patterns in the sauropod bauplan. Here, we combine three-dimensional computational models with phylogenetic reconstructions to quantify the evolution of whole-body shape and body segment properties across the sauropod radiation. Limitations associated with the absence of soft tissue preservation in fossils result in large error bars about mean absolute body shape predictions. However, applying any consistent skeleton : body volume ratio to all taxa does yield changes in body shape that appear concurrent with major macroevolutionary events in sauropod history. A caudad shift in centre-of-mass (CoM) in Middle Triassic Saurischia, associated with the evolution of bipedalism in various dinosaur lineages, was reversed in Late Triassic sauropodomorphs. A craniad CoM shift coincided with the evolution of quadrupedalism in the Late Triassic, followed by a more striking craniad shift in Late Jurassic–Cretaceous titanosauriforms, which included the largest sauropods. These craniad CoM shifts are strongly correlated with neck enlargement, a key innovation in sauropod evolution and pivotal to their gigantism. By creating a much larger feeding envelope, neck elongation is thought to have increased feeding efficiency and opened up trophic niches that were inaccessible to other herbivores. However, we find that relative neck size and CoM position are not strongly correlated with inferred feeding habits. Instead the craniad CoM positions of titanosauriforms appear closely linked with locomotion and environmental distributions, potentially contributing to the continued success of this group until the end-Cretaceous, with all other sauropods having gone extinct by the early Late Cretaceous.

DNA methylation (DNAm)-based cell mixture deconvolution (CMD) has become a quintessential part of epigenome-wide association studies where DNAm is profiled in heterogeneous tissue types. Despite being introduced over a decade ago, detection limits, which represent the smallest fraction of a cell type in a mixed biospecimen that can be reliably detected, have yet to be determined in the context of DNAm-based CMD. Moreover, there has been little attention given to approaches for quantifying the uncertainty associated with DNAm-based CMD. Here, analytical frameworks for determining both cell-specific limits of detection and quantification of uncertainty associated with DNAm-based CMD are described. This work may contribute to improved rigor, reproducibility and replicability of epigenome-wide association studies involving CMD.

The development of the process and electrochemical materials for conversion of H2S in a fuel cell to co-generate electrical power and benign products is outlined. While the thermodynamic basis for the process was clear, it was necessary to perform extensive research into the development of materials as catalysts and electrolytes, and to determine the optimal process and operating conditions. Through the use of composite anode catalysts and compatible new protonic electrolytes that are both chemically and thermally stable in the operating environment, we have achieved good and sustainable power densities. The only products are power, elemental sulfur and steam.

HPV infection is a causal agent in many epithelial cancers, yet our understanding of genetic susceptibility to HPV infection and resultant cancer risk is limited. Epidermodysplasia Verruciformis is a rare condition of extreme susceptibility to cutaneous HPV infection primarily attributable to mutations in TMC6 and TMC8. Genetic variation in the TMC6/TMC8 region has been linked to beta-type HPV infection and squamous cell carcinoma of the skin, cervical cancer, HPV persistence and progression to cervical cancer. Here, we have tested the hypothesis that the common TMC8 SNP rs7208422 is associated with high-risk HPV infection and risk of head and neck squamous cell carcinoma (HNSCC). Seropositivity to the HPV L1 protein (HPV16, 18, 11, 31, 33, 35, 45, 52, 58) was measured in 514 cases and 452 population-based controls. Genotype was significantly associated with seropositivity to HPV18 L1 (OR TT vs AA = 0.48, 95% CI = 0.22-0.99) and borderline significantly associated with HPV16 L1 (OR TT vs AA = 0.58, 95% CI = 0.22-1.17). There was a consistent inverse association between TMC8 genotype and infection with other HPV types, including statistically significant associations for HPV31 and HPV52. Consistent with these results, the variant T genotype was associated with a reduced risk of HNSCC (ORAT: 0.63, 95% CI 0.45-0.89, ORTT: 0.54, 95% CI 0.36-0.81), even among subjects seronegative for all HPV types (ORAT: 0.71, 95% CI 0.45-1.11, ORTT: 0.54, 95% CI 0.31-0.93). Our data indicate that common genetic variation in TMC8 is associated with high-risk HPV infection and HNSCC etiology.

Introduction: Despite the wide availability of clinical decision rules for imaging of the cervical spine after a traumatic injury (eg, NEXUS C-spine rule and Canadian C-spine rule), there is significant overutilization of computed tomography (CT) imaging in patients who are deemed to be at low risk for a clinically significant cervical spine injury by these clinical decision rules. The purpose of this study was to identify the major factors associated with the overuse of CT cervical spine imaging using a logistic regression model.Methods: This was a retrospective review of all adult patients who underwent CT cervical spine imaging for evaluation of a traumatic injury at a tertiary academic emergency department (ED) and three affiliate community EDs in January and February 2019. We performed multivariable logistic regression to identify factors associated with obtaining CT cervical spine imaging despite low-risk classification by the NEXUS C-spine Rule.Results: A total of 1,051 patients underwent CT cervical spine imaging for traumatic indications during the study period, and 889 patients were included in the analysis. Of these patients, 376 (42.3%) were negative by the NEXUS C-spine rule. Variables that were associated with increased likelihood of unnecessary imaging included age over 65, Emergency Severity Index (ESI) score 2 and 3, arrival as a walk-in, and anticoagulation status. Patients who presented to the tertiary academic ED had a significantly lower likelihood of unnecessary imaging. Twenty-one patients (2.4%) were found to have cervical spine fractures on imaging, two of whom were negative by the NEXUS C-spine rule, but neither had a clinically significant fracture.Conclusion: Cervical spine imaging is vastly overused in patients presenting to the ED with traumatic injuries, as adjudicated using the NEXUS C-spine rule as a reference standard. Older age, ESI level, arrival as a walk-in, and taking anticoagulation drugs were associated with overutilization of CT imaging. Conversely, presenting to the tertiary academic ED was associated with a lower likelihood of undergoing unnecessary imaging. This model can guide future interventions to optimize ED CT utilization and minimize unnecessary testing.

BackgroundOver the past decade, DNA methylation (DNAm)-based deconvolution methods that leverage cell-specific DNAm markers of immune cell types have been developed to provide accurate estimates of the proportions of leukocytes in peripheral blood. Immune cell phenotyping using DNAm markers, termed immunomethylomics or methylation cytometry, offers a solution for determining the body's immune cell landscape that does not require fresh blood and is scalable to large sample sizes. Despite significant advances in DNAm-based deconvolution, references at the population level are needed for clinical and research interpretation of these additional immune layers. Here we aim to provide some references for immune populations in a group of multi-ethnic post-menopausal American women.ResultsWe applied DNAm-based deconvolution to a large sample of post-menopausal women enrolled in the Women's Health Initiative (baseline, N = 58) or the ancillary Long Life Study (WHI-LLS, N = 1237) to determine the reference ranges of 58 immune parameters, including proportions and absolute counts for 19 leukocyte subsets and 20 derived cell ratios. Participants were 50-94 years old at the time of blood draw, and N = 898 (69.3%) self-identified as White. Using linear regression models, we observed significant associations between age at blood draw and absolute counts and proportions of naïve B, memory CD4+, naïve CD4+, naïve CD8+, memory CD8+ memory, neutrophils, and natural killer cells. We also assessed the same immune profiles in a subset of paired longitudinal samples collected 14-18 years apart across N = 52 participants. Our results demonstrate high inter-individual variability in rates of change of leukocyte subsets over this time. And, when conducting paired t tests to test the difference in counts and proportions between the baseline visit and LLS visit, there were significant changes in naïve B, memory CD4+, naïve CD4+, naïve CD8+, memory CD8+ cells and neutrophils, similar to the results seen when analyzing the association with age in the entire cohort.ConclusionsHere, we show that derived cell counts largely reflect the immune profile associated with proportions and that these novel methods replicate the known immune profiles associated with age. Further, we demonstrate the value this methylation cytometry approach can add as a potential application in epidemiological studies.

IntroductionThe human brain comprises heterogeneous cell types whose composition can be altered with physiological and pathological conditions. New approaches to discern the diversity and distribution of brain cells associated with neurological conditions would significantly advance the study of brain-related pathophysiology and neuroscience. Unlike single-nuclei approaches, DNA methylation-based deconvolution does not require special sample handling or processing, is cost-effective, and easily scales to large study designs. Existing DNA methylation-based methods for brain cell deconvolution are limited in the number of cell types deconvolved.MethodsUsing DNA methylation profiles of the top cell-type-specific differentially methylated CpGs, we employed a hierarchical modeling approach to deconvolve GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells.ResultsWe demonstrate the utility of our method by applying it to data on normal tissues from various brain regions and in aging and diseased tissues, including Alzheimer's disease, autism, Huntington's disease, epilepsy, and schizophrenia.DiscussionWe expect that the ability to determine the cellular composition in the brain using only DNA from bulk samples will accelerate understanding brain cell type composition and cell-type-specific epigenetic states in normal and diseased brain tissues.