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PREMISE Plants rely on pools of internal nonstructural carbohydrates (NSCs: soluble sugars plus starch) to support metabolism, growth, and regrowth of tissues damaged from disturbance such as foliage herbivory. However, impacts of foliage herbivory on the quantity and composition of NSC pools in long-lived woody plants are currently unclear. We implemented a controlled defoliation experiment on mature Tamarix spp.-a dominant riparian woody shrub/tree that has evolved with intense herbivory pressure-to test two interrelated hypotheses: (1) Repeated defoliation disproportionately impacts aboveground versus belowground NSC storage. (2) Defoliation disproportionately impacts starch versus soluble sugar storage. METHODS Hypotheses were tested by transplanting six Tamarix seedlings into each of eight cylinder mesocosms (2 m diameter, 1 m in depth). After 2.5 years, plants in four of the eight mesocosms were mechanically defoliated repeatedly over a single growing season, and all plants were harvested in the following spring. RESULTS Defoliation had no impact on either above- or belowground soluble sugar pools. However, starch in defoliated plants dropped to 55% and 26% in stems and roots, respectively, relative to control plants, resulting in an over 2-fold higher soluble sugar to starch ratio in defoliated plants. CONCLUSIONS The results suggest that defoliation occurring over a single growing season does not impact immediate plant functions such as osmoregulation, but depleted starch could limit future fitness, particularly where defoliation occurs over multiple years. These results improve our understanding of how woody plants cope with episodic defoliation caused by foliage herbivory and other disturbances.

Approximately 50% of patients with metastatic HER2-positive (HER2+) breast cancer develop brain metastases (BCBMs). We report that the tumor suppressor p16

ChIP-seq and ATAC-seq have become essential technologies used as effective methods of measuring protein-DNA interactions and chromatin accessibility. However, there is a need for a scalable and reproducible pipeline that incorporates correct normalization between samples, adjustment of copy number variations, and integration of new downstream analysis tools. Here we present CoBRA, a modularized computational workflow which quantifies ChIP and ATAC-seq peak regions and performs unsupervised and supervised analysis. CoBRA provides a comprehensive state-of-the-art ChIP and ATAC-seq analysis pipeline that is usable by scientists with limited computational experience. This enables researchers to gain rapid insight into protein-DNA interactions and chromatin accessibility through sample clustering, differential peak calling, motif enrichment, comparison of sites to a reference DB and pathway analysis.Code availability: https://bitbucket.org/cfce/cobra

PURPOSE: The virtual tumor board (VTB) is a multidisciplinary group of specialist physicians who remotely educate the treating physician on the development of an evidence-based cancer treatment plan that will enhance patient outcomes according to the available literature. The use of hypofractionated (HF) radiation therapy (RT) is a preferred approach according to National Comprehensive Cancer Network guidelines and is encouraged by the VTB, when appropriate. MATERIALS AND METHODS: An observational, cohort study using prior authorization and claims data were conducted to show how the relative use of HF and conventional fractionated (CF) RT changed after the implementation of the VTB. Orders and claims for qualifying patients from 1 year before launch (August 2016) to 1 year after launch (August 2018) of the VTB were extracted. Claims were examined to observe which patients received CF (28-35 fractions) versus HF (15-21 fractions) RT. χ2 tests were used to assess the association between time period and the ordering and use of HF RT. Logistic regressions were used to test the association, after adjusting for the patient’s age, urbanicity, local average income, and the RT modality used. RESULTS: After implementation, we observed a significantly higher percentage of orders for HF RT (60.3% [n = 1,254 of 2,079] v 53.2% [n = 1,010 of 1,899]; P < .001) and claims for HF RT (71.5% [n = 1,143 of 1,598] v 59.0% [n = 941 of 1,595]; P < .001). Relative to before implementation, the adjusted odds of an order for HF RT was 1.35 (CI, 1.19 to 1.54), and the adjusted odds of a claim for HF RT was 1.76 (CI, 1.52 to 2.04). CONCLUSION: After the VTB was implemented, there was a significant increase in HF RT orders and claims.

We report two methods to create zinc-sponge electrodes that suppress dendrite formation and shape change for rechargeable zinc batteries. Both methods are characterized by creating a paste made of zinc particles, organic porogen, and viscosity-enhancing agent that is heated under an inert gas and then air. During heating under the inert gas, the zinc particles anneal together, and the porogen decomposes; under air, the zinc fuses and residual organic burns out, yielding an open-cell metal foam or sponge. We tune the mechanical and electrochemical properties of the zinc sponges by varying zinc-to-porogen mass ratio, heating time under inert gas and air, and size and shape of the zinc and porogen particles. An advantage of the reported methods is their ability to finely tune zinc-sponge architecture. The selected size and shape of the zinc and porogen particles influence the morphology of the pore structure. A limitation is that resulting sponges have disordered pore structures that result in low mechanical strength at low volume fractions of zinc (

Neuroendocrine carcinomas (NEC) are tumors expressing markers of neuronal differentiation that can arise at different anatomic sites but have strong histological and clinical similarities. Here we report the chromatin landscapes of a range of human NECs and show convergence to the activation of a common epigenetic program. With a particular focus on treatment emergent neuroendocrine prostate cancer (NEPC), we analyzed cell lines, patient-derived xenograft (PDX) models and human clinical samples to show the existence of two distinct NEPC subtypes based on the expression of the neuronal transcription factors ASCL1 and NEUROD1. While in cell lines and PDX models these subtypes are mutually exclusive, single cell analysis of human clinical samples exhibit a more complex tumor structure with subtypes coexisting as separate sub-populations within the same tumor. These tumor sub-populations differ genetically and epigenetically contributing to intra- and inter-tumoral heterogeneity in human metastases. Overall our results provide a deeper understanding of the shared clinicopathological characteristics shown by NECs. Furthermore, the intratumoral heterogeneity of human NEPCs suggests the requirement of simultaneous targeting of coexisting tumor populations as a therapeutic strategy.

SummaryDrugs that block the activity of the methyltransferase EZH2 are in clinical development for the treatment of non-Hodgkin lymphomas harboring gain-of-function EZH2 mutations that enhance its polycomb repressive function. In contrast, in castration-resistant prostate cancer (CRPC) we have previously reported that EZH2 plays a non-canonical role as a transcriptional activator. In this setting, we now show that EZH2 inhibitors can also block the non-canonical activity of EZH2 and inhibit the growth of CRPC cells. Gene expression and epigenomic profiling of cells treated with EZH2 inhibitors demonstrated that rather than de-repressing tumor suppressor genes silenced by PRC2, EZH2 inhibitors downregulate a set of DNA repair genes that are directly regulated by EZH2. In addition, genome-wide CRISPR/Cas9-mediated loss-of-function screens in the presence of EZH2 inhibitors identified these DNA repair genes to underlie the growth-inhibitory function of these compounds. Interrogation of public data from diverse solid tumor types expressing wild-type EZH2 showed that expression of DNA damage repair genes is significantly correlated with cellular sensitivity to EZH2 inhibitors. Consistent with these findings, treatment of CRPC cells with EZH2 inhibitors dramatically enhanced their sensitivity to genotoxic stress. These studies reveal a previously unappreciated mechanism of action of EZH2 inhibitors and provide a mechanistic basis for potential new combination cancer therapies.

Quaking aspen is found in western forests of the United States and is currently at risk of loss due to conifer competition at within-stand scales. Wildfires in these forests are impactful owing to conifer infilling during prolonged fire suppression post-Euro-American settlement. Here, restoration cuttings seek to impact wildfire behavior and aspen growing conditions. In this study, we explored how actual and hypothetical cuttings with a range of conifer removal intensity altered surface fuel and overstory structure at stand and fine scales. We then simulated wildfires, examining fire behavior and effects on post-fire forest structures around aspen trees. We found that conifer removal constrained by lower upper diameter limits (&lt, 56 cm) had marginal effects on surface fuel and overstory structure, likely failing to enhance resource conditions sufficiently to sustain aspen. Increasing the diameter limit also led to a higher likelihood of fire spread and a higher rate of spread, owing to greater within-canopy wind speed, though crown fire activity decreased. Our simulations suggest heavier treatments could facilitate reintroduction of fire while also dampening the effects of wildfires on forest structure. Cutting specifications that relax diameter limits and remove a substantial portion of conifer overstory could better promote aspen restoration and mitigate fire hazard.

Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization. Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling method that negates the optimization step and is suited to a variety of mammalian cells and tissues. Addition of 5-methyldeoxycytidine triphosphate during accessible chromatin labeling and an on-bead library making step substantially improved the signal to noise ratio while protecting the accessible regions from repeated nicking in cell lines, mouse T cells, mouse kidney, and human frozen tissue sections. We also demonstrate one tube UniNicE-seq for the FFPE tissue section for direct NGS library preparation without sonication and DNA purification steps. These refinements allowed reliable mapping of accessible chromatin for high-resolution genomic feature studies.

High-grade T1 (HGT1) bladder cancer is the highest risk subtype of non–muscle-invasive bladder cancer with unpredictable outcome and poorly understood risk factors. Here, we examined the association of somatic mutation profiles with nonrecurrent disease (GO, good outcome), recurrence (R), or progression (PD) in a cohort of HGT1 patients. Exome sequencing was performed on 62 HGT1 and 15 matched normal tissue samples. Both tumor only (TO) and paired analyses were performed, focusing on 95 genes known to be mutated in bladder cancer. Somatic mutations, copy-number alterations, mutation load, and mutation signatures were studied. Thirty-three GO, 10 R, 18 PD, and 1 unknown outcome patients were analyzed. Tumor mutational burden (TMB) was similar to muscle-invasive disease and was highest in GO, intermediate in PD, and lowest in R patients (P = 0.017). DNA damage response gene mutations were associated with higher TMB (P < 0.0001) and GO (P = 0.003). ERCC2 and BRCA2 mutations were associated with GO. TP53, ATM, ARID1A, AHR, and SMARCB1 mutations were more frequent in PD. Focal copy-number gain in CCNE1 and CDKN2A deletion was enriched in PD or R (P = 0.047; P = 0.06). APOBEC (46%) and COSMIC5 (34%) signatures were most frequent. APOBEC-A and ERCC2 mutant tumors (COSMIC5) were associated with GO (P = 0.047; P = 0.0002). pT1b microstaging was associated with a genomic cluster (P = 0.05) with focal amplifications of E2F3/SOX4, PVRL4, CCNE1, and TP53 mutations. Findings were validated using external public datasets. These findings require confirmation but suggest that management of HGT1 bladder cancer may be improved via molecular characterization to predict outcome. Significance: Detailed genetic analyses of HGT1 bladder tumors identify features that correlate with outcome, e.g., high mutational burden, ERCC2 mutations, and high APOBEC-A/ERCC2 mutation signatures were associated with good outcome.

We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow (http://github.com/liulab-dfci/MAESTRO) for the integrative analyses of single-cell RNA-seq (scRNA-seq) and ATAC-seq (scATAC-seq) data from multiple platforms. MAESTRO provides functions for pre-processing, alignment, quality control, expression and chromatin accessibility quantification, clustering, differential analysis, and annotation. By modeling gene regulatory potential from chromatin accessibilities at the single-cell level, MAESTRO outperforms the existing methods for integrating the cell clusters between scRNA-seq and scATAC-seq. Furthermore, MAESTRO supports automatic cell-type annotation using predefined cell type marker genes and identifies driver regulators from differential scRNA-seq genes and scATAC-seq peaks.

Epigenetic processes govern prostate cancer (PCa) biology, as evidenced by the dependency of PCa cells on the androgen receptor (AR), a prostate master transcription factor. We generated 268 epigenomic datasets spanning two state transitions—from normal prostate epithelium to localized PCa to metastases—in specimens derived from human tissue. We discovered that reprogrammed AR sites in metastatic PCa are not created de novo; rather, they are prepopulated by the transcription factors FOXA1 and HOXB13 in normal prostate epithelium. Reprogrammed regulatory elements commissioned in metastatic disease hijack latent developmental programs, accessing sites that are implicated in prostate organogenesis. Analysis of reactivated regulatory elements enabled the identification and functional validation of previously unknown metastasis-specific enhancers at HOXB13, FOXA1 and NKX3-1. Finally, we observed that prostate lineage-specific regulatory elements were strongly associated with PCa risk heritability and somatic mutation density. Examining prostate biology through an epigenomic lens is fundamental for understanding the mechanisms underlying tumor progression. Analyses of epigenomic datasets spanning transitions from normal prostate epithelium to localized prostate cancer to metastases show that latent developmental programs are reactivated in metastatic disease and that prostate lineage-specific regulatory elements are strongly enriched for prostate cancer risk heritability.

In this review, we discuss the demonstrated value of vitamin D in bone maintenance, fracture resistance, spinal health, and spine surgery outcomes. Despite this, the effect of vitamin D levels in spine surgery has not been well described. Through this review of literature, several conclusions were drawn. First, despite the fact that a high number of spine surgery patients are vitamin D deficient, screening is not commonly performed. Second, adequate vitamin D levels will not be achieved in a majority of these patients without supplementation. Last, inadequate vitamin D levels may increase the risk of pseudarthrosis. Given these findings, we suggest that many patients undergoing spinal surgery could be treated with vitamin D supplementation prior to surgery without the need for confirmatory testing for vitamin D deficiency. This is a more cost-effective method than screening all patients. However, future randomized trials and cost-effectiveness analyses are needed to determine the ultimate effects of vitamin D supplementation on clinical morbidity and surgical outcomes.

Post-fire managers throughout the world use predictive models to estimate potential erosion risks to aid in evaluating downstream impacts of increased runoff and erosion, and to target critical areas within a fire for applying mitigation practices. Erosion prediction can be complicated by forest road networks. Using GIS technology and a soil erosion model, this study evaluated the effect of roads on erosion and sediment yield following a wildfire, and whether the predictive models were providing reasonable results. The GeoWEPP model was used to simulate onsite erosion and offsite sediment delivery before and after fire disturbance. A 2-m resolution DEM was used as the terrain layer. Erosion rates in excess of 4 Mg ha-1 yr-1 were predicted mainly from the moderate and high severity burn areas. Roads influenced both flow path and sub-catchment delineations, affecting the spatial distribution of sediment detachment and transport. Through that influence, roads tended to reduce estimated erosion on slopes below the roads, but road fillslopes and steep channels were areas of significant increases in erosion risks. Measured deposition amounts along roads and in sediment basins were similar to predicted amounts. The results confirm that road prisms, culverts and road ditches greatly influence sedimentation processes after wildfire, and they present opportunities to detain eroded sediments before they reach downstream water bodies.

Tay et al. show that HDAC3 acts early during CD8 T cell activation to inhibit cytotoxicity and effector differentiation gene programs. This study identifies a novel role for HDAC3 as an epigenetic regulator of CD8 T cell cytotoxicity and persistence following activation., Cytotoxic T cells play a key role in adaptive immunity by killing infected or cancerous cells. While the transcriptional control of CD8 T cell differentiation and effector function following T cell activation has been extensively studied, little is known about epigenetic regulation of these processes. Here we show that the histone deacetylase HDAC3 inhibits CD8 T cell cytotoxicity early during activation and is required for persistence of activated CD8 T cells following resolution of an acute infection. Mechanistically, HDAC3 inhibits gene programs associated with cytotoxicity and effector differentiation of CD8 T cells including genes encoding essential cytotoxicity proteins and key transcription factors. These data identify HDAC3 as an epigenetic regulator of the CD8 T cell cytotoxicity program.

Although cell therapy-mediated cardiac repair offers promise for treatment/management of heart failure, lack of fundamental understanding of how cell therapy works limits its translational potential. In particular, whether reparative cells from failing hearts differ from cells derived from nonfailing hearts remains unexplored. Here, we assessed differences between cardiac mesenchymal cells (CMC) derived from failing (HF) versus nonfailing (Sham) hearts and whether the source of donor cells (i.e., from HF vs. Sham) limits reparative capacity, particularly when administered late after infarction. To determine the impact of the donor source of CMCs, we characterized the transcriptional profile of CMCs isolated from sham (Sham-CMC) and failing (HF-CMC) hearts. RNA-seq analysis revealed unique transcriptional signatures in Sham-CMC and HF-CMC, suggesting that the donor source impacts CMC. To determine whether the donor source affects reparative potential, C57BL6/J female mice were subjected to 60 min of regional myocardial ischemia and then reperfused for 35 days. In a randomized, controlled, and blinded fashion, vehicle, HF-CMC, or Sham-CMC were injected into the lumen of the left ventricle at 35 days post-MI. An additional 5 weeks later, cardiac function was assessed by echocardiography, which indicated that delayed administration of Sham-CMC and HF-CMC attenuated ventricular dilation. We also determined whether Sham-CMC and HF-CMC treatments affected ventricular histopathology. Our data indicate that the donor source (nonfailing vs. failing hearts) affects certain aspects of CMC, and these insights may have implications for future studies. Our data indicate that delayed administration of CMC limits ventricular dilation and that the source of CMC may influence their reparative actions. NEW & NOTEWORTHY Most preclinical studies have used only cells from healthy, nonfailing hearts. Whether donor condition (i.e., heart failure) impacts cells used for cell therapy is not known. We directly tested whether donor condition impacted the reparative effects of cardiac mesenchymal cells in a chronic model of myocardial infarction. Although cells from failing hearts differed in multiple aspects, they retained the potential to limit ventricular remodeling.

Rationale The beta-O-linkage of N-acetylglucosamine (i.e., O-GlcNAc) to proteins is a pro-adaptive response to cellular insults. To this end, increased protein O-GlcNAcylation improves short-term survival of cardiomyocytes subjected to acute injury. This observation has been repeated by multiple groups and in multiple models; however, whether increased protein O-GlcNAcylation plays a beneficial role in more chronic settings remains an open question. Objective Here, we queried whether increasing levels of cardiac protein O-GlcNAcylation would be beneficial during infarct-induced heart failure. Methods and results To achieve increased protein O-GlcNAcylation, we targeted Oga, the gene responsible for removing O-GlcNAc from proteins. Here, we generated mice with cardiomyocyte-restricted, tamoxifen-inducible haploinsufficient Oga gene. In the absence of infarction, we observed a slight reduction in ejection fraction in Oga deficient mice. Overall, Oga reduction had no major impact on ventricular function. In additional cohorts, mice of both sexes and both genotypes were subjected to infarct-induced heart failure and followed for up to four weeks, during which time cardiac function was assessed via echocardiography. Contrary to our prediction, the Oga deficient mice exhibited exacerbated—not improved—cardiac function at one week following infarction. When the observation was extended to 4 wk post-MI, this acute exacerbation was lost. Conclusions The present findings, coupled with our previous work, suggest that altering the ability of cardiomyocytes to either add or remove O-GlcNAc modifications to proteins exacerbates early infarct-induced heart failure. We speculate that more nuanced approaches to regulating O-GlcNAcylation are needed to understand its role—and, in particular, the possibility of cycling, in the pathophysiology of the failing heart.

Cytotoxic T cells play a key role in adaptive immunity by killing infected or cancerous cells. While the transcriptional control of CD8 T cell differentiation and effector function following T cell activation has been extensively studied, little is known about epigenetic regulation of these processes. Here we show that the histone deacetylase HDAC3 inhibits CD8 T cell cytotoxicity early during activation and is required for persistence of activated CD8 T cells following resolution of an acute infection. Mechanistically, HDAC3 inhibits gene programs associated with cytotoxicity and effector differentiation of CD8 T cells including genes encoding essential cytotoxicity proteins and key transcription factors. These data identify HDAC3 as an epigenetic regulator of the CD8 T cell cytotoxicity program.

BACKGROUND: Minimally invasive transforaminal lumbar interbody fusion (MIS TLIF) is a common surgical procedure for treatment of degenerative spondylolisthesis (DS) but remains controversial for treatment of isthmic spondylolisthesis (IS). Few studies have compared IS and DS outcomes after MIS TLIF. Therefore, the objective of the current study was to compare outcomes of patients with IS and DS after MIS TLIF. METHODS: A retrospective cohort analysis was performed on a prospectively maintained database of patients who underwent a primary, 1-level MIS TLIF for grade I or II IS or DS. Grade I and II DS and grade I IS patients were treated with MIS TLIF via a unilateral tubular approach, whereas the grade II IS patients were treated via a bilateral tubular approach. Differences in patient demographics and preoperative characteristics were assessed using independent sample t tests and χ(2) tests. The type of spondylolisthesis and its effect on postoperative outcomes was analyzed using Poisson regression with robust error variance (binary outcomes) or linear regression (continuous outcomes) adjusted for preoperative characteristics. Subgroup analysis comparing grade I IS versus DS and grade II IS versus DS was performed. RESULTS: A total of 223 patients were included (IS: 62 [27.8%]; DS: 161 [72.2%]). IS patients were younger (P < .001), had a lower comorbidity burden (P < .001), and a greater incidence of grade II spondylolisthesis (P < .001) at L5–S1 (P < .001) than the DS cohort. Patients with IS experienced longer operative times (P < .001) and lower, but not statistically significant, arthrodesis rates compared to the DS cohort. No differences were observed in the remaining preoperative patient characteristics, perioperative or postoperative outcomes. CONCLUSIONS: Despite being younger and having a lower comorbidity burden than the DS cohort, similar outcomes were observed after MIS TLIF for IS patients. LEVEL OF EVIDENCE: 3. CLINICAL RELEVANCE: These results suggest MIS TLIF is an appropriate treatment option for IS patients despite the increased instability inherent with IS.

Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization. Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling method that negate the optimization step and is suited to a variety of mammalian cells and tissues. Addition of 5-methyldeoxycytidine triphosphate during accessible chromatin labeling and an on-bead library making step substantially improved the signal to noise ratio while protecting the accessible regions from repeated nicking in cell lines, mouse T cells, mouse kidney, and human frozen tissue sections. We also demonstrate one tube UniNicE-seq for FFPE tissue section for direct NGS library preparation without sonication and DNA purification steps. These refinements allowed reliable mapping of accessible chromatin for high resolution genomic feature studies.

Background: Atrial fibrillation (AF) adversely impacts health-related quality of life (hrQoL). While some patients demonstrate improvements in hrQoL, the factors associated with large improvements in hrQoL are not well described. Methods: We assessed factors associated with a 1-year increase in the Atrial Fibrillation Effect on Quality-of-Life score of 1 SD (≥18 points; 3× clinically important difference), among outpatients in the Outcomes Registry for Better Informed Treatment of Atrial Fibrillation I registry. Results: Overall, 28% (181/636) of patients had such a hrQoL improvement. Compared with patients not showing large hrQoL improvement, they were of similar age (median 73 versus 74, P =0.3), equally likely to be female (44% versus 48%, P =0.3), but more likely to have newly diagnosed AF at baseline (18% versus 8%; P =0.0004), prior antiarrhythmic drug use (52% versus 40%, P =0.005), baseline antiarrhythmic drug use (34.8% versus 26.8%, P =0.045), and more likely to undergo AF-related procedures during follow-up (AF ablation: 6.6% versus 2.0%, P =0.003; cardioversion: 12.2% versus 5.9%, P =0.008). In multivariable analysis, a history of alcohol abuse (adjusted OR, 2.41; P =0.01) and increased baseline diastolic blood pressure (adjusted OR, 1.23 per 10-point increase and >65 mm Hg; P =0.04) were associated with large improvements in hrQoL at 1 year, whereas patients with prior stroke/transient ischemic attack, chronic obstructive pulmonary disease, and peripheral arterial disease were less likely to improve ( P Conclusions: In this national registry of patients with AF, potentially treatable AF risk factors are associated with large hrQoL improvement, whereas less reversible conditions appeared negatively associated with hrQoL improvement. Understanding which patients are most likely to have large hrQoL improvement may facilitate targeting interventions for high-value care that optimizes patient-reported outcomes in AF. Registration: URL: http://www.clinicaltrials.gov . Unique identifier: NCT01165710.

Electrochemical energy storage arises from processes that are broadly categorized as capacitive, pseudocapacitive, or battery-like. Advanced charge-storing materials that are designed to deliver high capacity at a high rate often exhibit a multiplicity of such mechanisms, which complicates the understanding of their charge-storage behavior. Herein, we apply a "3D Bode analysis" technique to identify key descriptors for fast Li-ion storage processes, where AC impedance data, such as the real capacitance (C') or phase angle (ϕ), are represented versus the frequency (f) and a third independent variable, the applied DC cell voltage. For double-layer processes, a near-constant C' or ϕ is supported across the entire voltage range, and the decrease in these values shows a near-linear decrease at higher f. For pseudocapacitance, an increase in C' is delivered, accompanied by high C' retention at higher f compared to double-layer processes. Interestingly, the lower ϕ values, where C' is highest, suggest that this is a key descriptor for pseudocapacitance, where high-rate charge storage is still facilitated within a kinetically limited regime. For battery-like processes, a high C' is only observed at the voltage at which the material stores charge, while outside that voltage, C' is negligible. The three-dimensional (3D) Bode analysis allows charge-storage dynamics to be mapped out in great detail with more delineation between mechanisms compared to the more frequently deployed kinetic analyses derived from cyclic voltammetry.

BackgroundImmune checkpoint blockade (ICB) therapy has improved patient survival in a variety of cancers, but only a minority of cancer patients respond. Multiple studies have sought to identify general biomarkers of ICB response, but elucidating the molecular and cellular drivers of resistance for individual tumors remains challenging. We sought to determine whether a tumor with defined genetic background exhibits a stereotypic or heterogeneous response to ICB treatment.ResultsWe establish a unique mouse system that utilizes clonal tracing and mathematical modeling to monitor the growth of each cancer clone, as well as the bulk tumor, in response to ICB. We find that tumors derived from the same clonal populations showed heterogeneous ICB response and diverse response patterns. Primary response is associated with higher immune infiltration and leads to enrichment of pre-existing ICB-resistant cancer clones. We further identify several cancer cell-intrinsic gene expression signatures associated with ICB resistance, including increased interferon response genes and glucocorticoid response genes. These findings are supported by clinical data from ICB treatment cohorts.ConclusionsOur study demonstrates diverse response patterns from the same ancestor cancer cells in response to ICB. This suggests the value of monitoring clonal constitution and tumor microenvironment over time to optimize ICB response and to design new combination therapies. Furthermore, as ICB response may enrich for cancer cell-intrinsic resistance signatures, this can affect interpretations of tumor RNA-seq data for response-signature association studies.

This paper considers non-classical continuum theory for thermoviscous fluids without memory incorporating internal rotation rates resulting from the antisymmetric part of the velocity gradient tensor to derive ordered rate constitutive theories for the Cauchy stress and the Cauchy moment tensor based on entropy inequality and representation theorem. Using the generalization of the conjugate pairs in the entropy inequality, the ordered rate constitutive theory for Cauchy stress tensor considers convected time derivatives of the Green&rsquo, s strain tensor (or Almansi strain tensor) of up to orders n &epsilon, as its argument tensors and the ordered rate constitutive theory for the Cauchy moment tensor considers convected time derivatives of the symmetric part of the rotation gradient tensor up to orders n &Theta, While the convected time derivatives of the strain tensors are well known the convected time derivatives of higher orders of the symmetric part of the rotation gradient tensor need to be derived and are presented in this paper. Complete and general constitutive theories based on integrity using conjugate pairs in the entropy inequality and the generalization of the argument tensors of the constitutive variables and the representation theorem are derived and the material coefficients are established. It is shown that for the type of non-classical thermofluids considered in this paper the dissipation mechanism is an ordered rate mechanism due to convected time derivatives of the strain tensor as well as the convected time derivatives of the symmetric part of the rotation gradient tensor. The derivations of the constitutive theories presented in the paper is basis independent but can be made basis specific depending upon the choice of the specific basis for the constitutive variables and the argument tensors. Simplified linear theories are also presented as subset of the general constitutive theories and are compared with published works.

No consensus currently exist on the optimal treatment of patients with high-risk nonmuscle invasive (HGT1) micropapillary variant of bladder cancer (MPBC). Transcripsome analysis may allow stratification of MPBC-HGT1 enabling prediction of recurrence and guide therapeutic management for individual patients. Whole transcriptome RNA-Sequencing of tumors from 23 patients with MPBC-HGT1 and 64 conventional urothelial carcinomas (cUC) (reference set) was performed. Differentially expressed genes between MPBC-HGT1 and cUC-HGT1 were explored. Cox proportional hazard models and Kapplan–Meier methods were used to assess the relation between time to progression (TTP) and individual gene expression adjusting for clinical covariates. Over 3000 genes were differentially expressed in MPBC-HGT1 as compared with cUC-HGT1 and a 26-gene signature is characteristic of MPBC within HGT1. A set of three genes; CD36, FAPB3 and RAETE1; were significantly associated with TTP. High expression of FABP3 and CD36 were associated with shorter TTP (p = 0.045 and p = 0.08) as was low expression of RAET1E (p = 0.01). Our study suggest that a 26-gene signature can define MPBC-HGT1 within conventional urothelial carcinomas. A prognostic risk index of three genes (FABP3, CD36 and RAET1E) was found to be associated with shorter TTP and may help classify a group of patients with MPBC-HGT1 with high-risk of early progression. These observations might have implications in terms of radical cystectomy recommendation in MPBC patients.

In diploid cells, maternal and paternal copies of genes usually have similar transcriptional activity. Mammalian allele-specific epigenetic mechanisms such as X-chromosome inactivation (XCI) and imprinting were historically viewed as rare exceptions to this rule. The discovery of mitotically stable monoallelic autosomal expression (MAE) a decade ago revealed an additional allele-specific mode regulating thousands of mammalian genes. However, despite its prevalence, the mechanistic basis of MAE remains unknown. To uncover the mechanism of MAE maintenance, we devised a small-molecule screen for reactivation of silenced alleles across multiple loci using targeted RNA sequencing. Contrary to previous reports, we identified DNA methylation as a key mechanism of MAE mitotic maintenance. In contrast with the binary choice of the active allele in XCI, stringent transcriptome-wide analysis revealed MAE as a regulatory mode with tunable control of allele-specific expression, dependent on the extent of DNA methylation. In a subset of MAE genes, allelic imbalance was insensitive to changes in DNA methylation, implicating additional mechanisms in MAE maintenance in these loci. Our findings identify a key mechanism of MAE maintenance, reveal tunability of this mode of gene regulation, and provide the essential platform for probing the biological role of MAE in development and disease.

This study aimed to research the effect of miR-202-5p-mediated ATG7 on autophagy and apoptosis of degenerative nucleus pulposus cells.The intervertebral disc nucleus pulposus (NP) tissue of patients with intervertebral disc degenerative disease and normal intervertebral disc nucleus pulposus (NP) tissue of patients with spinal fractures was collected as the research object. Normal NP cells and degenerative NP cells were isolated. Low expression of miR-202-5p and overexpression of ATG7 were carried out in degenerative NP cells. The expression of miR-202-5p and ATG7 mRNA was detected by RT-PCR. The expression of ATG7, LC3-II, Bax, and Bcl-2 proteins was detected by Western blot. The autophagy of cells was detected by MDC staining. The apoptosis of NP cells was detected by flow cytometry. The targeting relationship between miR-202-5p and ATG7 was detected by Dual-Luciferase reporter.In the degenerative NP tissues, miR-202-5p was highly expressed and ATG7 was low expressed. The inhibition of miR-202-5p expression can effectively promote autophagy of NP cells, increase the expression of ATG7 and LC3-II, inhibit the apoptosis of NP cells, inhibit the expression of pro-apoptotic proteins Bax, and promote the expression of pro-apoptotic proteins Bcl-2 proteins. The upregulation of ATG7 expression in degenerative NP cells alone had the same effect as the downregulation of miR-202-5p. The assay of the Dual-Luciferase reporter confirmed the targeting relationship between miR-202-5p and ATG7.MiR-202-5p can affect the autophagy and apoptosis of degenerative nucleus pulposus cells through targeted adjustment of ATG7, which may be a new therapeutic target for intervertebral disc degenerative diseases.

Introduction The objectives were to describe pharmacy students' perceptions of professionalism and to compare students and faculty/staff perceptions of professionalism during the didactic years at Touro University California College of Pharmacy in California (TUC COP). Methods A two-part online survey was administered to the TUC COP faculty/staff and first-year (P1) and second-professional year (P2) students in May 2016. The first part of the survey collected demographic information, assessment of faculty/staff and students' overall opinions on behavior and conduct displayed by P1 and P2 students, students' responses about the average of missed lectures per month, and the average number of days of late arrival to lecture per week. The second part assessed professionalism perceptions responses to 20 scenarios using a 4-point Likert rating. Results The study included 37 (88.4%) faculty/staff and 181 (96.4%) P1 and P2 students, for a 98% response rate. Of the faculty/staff, 59.5% perceived the students' overall behaviors and conduct as acceptable whereas 35.3% of students perceived the overall behavior of P1 and P2 students as acceptable, with the majority of students self-reporting missing on average fewer than five lectures per month (65.2%) and arriving late to lecture fewer than one day each week (71.8%). There were statistically significant differences between faculty/staff and students' responses in 9 of the 20 scenarios. Conclusions Differences in responses between faculty/staff and students regarding what is considered professional suggest that there is a gap in professionalism perceptions that should be addressed during didactic years.

Despite remarkable clinical efficacies of immune checkpoint blockade (ICB) in cancer treatment, ICB benefits in triple-negative breast cancer (TNBC) remain limited. Through pooled in vivo CRISPR knockout (KO) screens in syngeneic TNBC mouse models, we found that inhibition of the E3 ubiquitin ligase Cop1 in cancer cells decreases the secretion of macrophage-associated chemokines, reduces tumor macrophage infiltration, and shows synergy in anti-tumor immunity with ICB. Transcriptomics, epigenomics, and proteomics analyses revealed Cop1 functions through proteasomal degradation of the C/ebpδ protein. Cop1 substrate Trib2 functions as a scaffold linking Cop1 and C/ebpδ, which leads to polyubiquitination of C/ebpδ. Cop1 inhibition stabilizes C/ebpδ to suppress the expression of macrophage chemoattractant genes. Our integrated approach implicates Cop1 as a target for improving cancer immunotherapy efficacy by regulating chemokine secretion and macrophage levels in the TNBC tumor microenvironment.

Electrochemical ion insertion into transition metal oxides forms the foundation of several energy technologies. Transition metal oxides can exhibit sluggish ion transport and/or phase-transformation kinetics during ion insertion that can limit their performance at high rates (+ insertion using staircase potentiostatic electrochemical impedance spectroscopy (SPEIS) and electrochemical quartz crystal microbalance (EQCM) analysis of WO3·H2O and WO3 thin-film electrodes. Overall, the presence of structural water in WO3·H2O improves Li+ insertion kinetics compared to WO3 and leads to a less potential-dependent insertion process. Operando electrogravimetry and 3D Bode impedance analyses of nanostructured films reveal that the presence of structural water promotes charge accommodation without significant co-insertion of solvent, leading to our hypothesis that the electrochemically induced structural transitions of WO3 hinder the electrode response at faster timescales (

The transcriptional co-activator YAP1 oncogene is the downstream effector of the Hippo pathway, which regulates tissue homeostasis, organ size, regeneration, and tumorigenesis. Multiple cancers are dependent on sustained expression of YAP1 for cell proliferation, survival, and tumorigenesis, but the molecular basis of this oncogene dependency is not well understood. To identify genes that can functionally substitute for YAP1, we performed a genome-scale genetic rescue screen in YAP1-dependent colon cancer cells expressing an inducible YAP1-specific shRNA. We found that the transcription factor PRDM14 rescued cell proliferation and tumorigenesis upon YAP1 suppression in YAP1-dependent cells, xenografts, and colon cancer organoids. YAP1 and PRDM14 individually activated the transcription of calmodulin 2 (CALM2) and a glucose transporter SLC2A1 upon YAP1 suppression, and CALM2 or SLC2A1 expression was required for the rescue of YAP1 suppression. Together, these findings implicate PRDM14-mediated transcriptional upregulation of CALM2 and SLC2A1 as key components of oncogenic YAP1 signaling and dependency.

This study evaluated the incidence and long-term outcomes of postoperative type 1a endoleak (PT1a) following endovascular aortic aneurysm repair (EVAR).A retrospective review of consecutive aortoiliac EVARs performed at a single institution from June 2006 to June 2012 was conducted. Patients with PT1a were identified by postoperative imaging and compared with those who did not develop a PT1a. Late outcomes were also studied of a subset of patients with PT1a who had persistent intraoperative type 1a endoleak (iT1a) on completion angiogram during EVAR that had resolved on initial follow-up imaging.Three hundred eighty-nine patients underwent EVAR with median follow-up of 87 months (interquartile range, 64-111 months). The incidence of PT1a was 8.2% (n = 32) with a median follow-up of 74 months (interquartile range, 52-138 months). Compared with the total cohort, those who developed PT1a were statistically more likely to be female (32% vs 17%; P = .03) and have a higher all-cause mortality (71% vs 40%; P .01) and aneurysm-related mortality (15.6% vs 1.7%; P .01). Median time to presentation was 52 months. Of the 32 patients with PT1a, five (15.6%) presented with aortic rupture, of which three underwent extension cuff placement, one had open graft explant, and one declined intervention. Six patients in total (18.7%) declined intervention; five of these died of nonaneurysmal causes and one remains alive. Of the 26 patients with PT1a who had intervention, 21 (80.7%) showed resolution of PT1a, and five (19.2%) had recurrence. For patients with recurrent PT1a, two had resulting aneurysm-related mortality, two endoleaks resolved after relining with an endograft, and one patient declined intervention but remains alive. Patients with PT1a who had intervention with resolution showed no significant difference in median survival estimates (140.0 months) compared with the remaining EVAR cohort (120.0 months; P = .80). Within the PT1a cohort, 6 (18.7%) had also experienced iT1a with a mean time to presentation of the late PT1a of 45 months. iT1a was associated with a significantly increased likelihood of developing a PT1a (P .01) and decreased median survival (P .01), but there was no known aneurysm-related mortality.Development of PT1a following elective EVAR is associated with increased all-cause and aneurysm-related mortality and presents an average of 52 months postoperatively. This underscores the importance of long-term surveillance. Patients with PT1a who had a successful intervention showed no significant difference in median survival. Those with iT1a had a higher risk for PT1a compared with the EVAR cohort overall and had decreased median survival, without increased aneurysm-related mortality.

We previously demonstrated that a redesign of the form factor for zinc (Zn) anodes to a monolithic, porous 3D-wired sponge sets a new benchmark for rechargeable alkaline Zn batteries. By engineerin...

Summary Zinc-based batteries are experiencing a resurgence in interest owing to their promising energy and power metrics, and inherent safety advantages compared with lithium-ion batteries. As scientists worldwide address the remaining obstacles to realizing competitive performance across the family of zinc batteries, the enthusiasm to report new “breakthroughs” at the materials or small-device level must be tempered by a realistic understanding of how such improvements will translate to practical energy-storage devices. Framing early-stage results in such a context will advance the prospects of next-generation Zn batteries while avoiding the “hype cycle” that has plagued research and development for other energy-storage technologies. Herein, we present guidelines by which to evaluate and report data derived from new electrode formulations and cell components such that the results will directly inform which breakthroughs are technologically relevant to scale up.

Protocols that express functional materials in a way that amplifies their surface-to-volume ratio offer a means to probe the structural ambiguity and surface-mediated reactivity of technologically important materials. We previously reported that three-dimensional (3D) ultraporous scaffolds, such as silica aerogels, silica fiber paper, and carbon nanofoam paper (CNF), provide a form factor that expresses energy-storing, catalytic ruthenium oxide (RuOx) as essentially all-surface—and a highly disordered one at that. To track the chemical state and solid-state structure of the 3D-expressed RuOx nanoskins as a function of thermal processing, we use X-ray near-edge structure (XANES), extended X-ray fine structure (EXAFS), and differential pair-distribution function (DPDF) analyses. We find that a Ru-centered ∼2.4 A correlation present in the as-deposited oxide, also observed in PDF analysis of RuO2·nH2O but previously unassigned, fits the metastable corundum-like Ru2O3 structure. This corundum-like feature dim...

Evaluation of left ventricular devices is becoming increasingly important as the implantation of these devices increases. Cardiac computed tomography angiography (CCTA) has many potential advantages compared with plain radiographs and echocardiography to troubleshoot these devices and potentially help guide therapy. Heart failure (HF) remains a deadly, progressive disease with substantive and increasing morbidity, mortality, cost, and prevalence. Use of left ventricular assist devices (LVAD) as treatment for refractory HF has been steadily rising during the last decade. Seventy-four LVAD recipients who met an indication for CCTA were referred for scanning at our center for a total of 94 studies. All recipients had received a Heart Mate II (Thoratec, Pleasanton, CA) LVAD at a previous time. All patients underwent gated CCTA on a 320 row multidetector scanner (Aquilion ONE, Toshiba Medical Systems, Irvine, California, USA). Images were then reconstructed and analysis was performed using multiple oblique views. All 94 studies had technically good images. In survival analysis, 43 of the 74 LVAD patients had normal CCTA findings while 31 had abnormal CCTA results. The 6, 12, and 18 months survival was 93%, 79%, and 77% in those with normal results and 71%, 61%, and 61%, respectively, in the abnormal CCTA findings. Overall survival was statistically significant in when comparing the two groups (p = 0.003). Cardiac computed tomography angiography may be used as an aid for risk stratification and a potential indicator of short- and long-term prognosis in LVAD patients.

BACKGROUND Despite the critical role of educators as gatekeepers for school mental health services, they receive limited training to support student mental health. We report findings from a trial of an online mental health role-play simulation for elementary school teachers on changes in attitudes and self-reported helping behaviors for students experiencing psychological distress. METHODS We randomly assigned 18,896 elementary school teachers to wait-list control or intervention conditions in which they received the 45- to 90-minute online role-play simulation. We administered a version of the validated Gatekeeper Behavior Scale at baseline and postintervention, which measures attitudinal dimensions shown to predict teacher helping behavior change. Self-reported helping behaviors were collected at baseline and 3-month follow-up. Outcomes were compared between the intervention follow-up and control group baseline measures. RESULTS The intervention group posttraining scores were significantly higher (p < .001) than the control group for all the preparedness, likelihood, and self-efficacy Gatekeeper Behavior subscales. All 5 helping behaviors were significantly higher among the intervention group at follow-up compared to the control group at baseline. CONCLUSIONS We found that a brief online role-play simulation was an effective strategy for improving teacher attitudes and behaviors needed to perform a positive mental health gatekeeper role in schools.

Methods for investigating the vulnerability of existing or proposed coastal features to storm impacts often rely on simplified parametric models or one-dimensional process-based modeling studies that focus on changes to a profile across a dune or barrier island. These simple studies tend to neglect the impacts to curvilinear or alongshore varying island planforms, influence of non-uniform nearshore hydrodynamics and sediment transport, irregular morphology of the offshore bathymetry, and impacts from low magnitude wave events (e.g. cold fronts). Presented here is a framework for simulating regionally specific, low and high magnitude scenario-based storm impacts to assess the alongshore variable vulnerabilities of a coastal feature. Storm scenarios based on historic hydrodynamic conditions were derived and simulated using the process-based morphologic evolution model XBeach. Model results show that the scenarios predicted similar patterns of erosion and overwash when compared to observed qualitative morphologic changes from recent storm events that were not included in the dataset used to build the scenarios. The framework model simulations were capable of predicting specific areas of vulnerability in the existing feature and the results illustrate how this storm vulnerability simulation framework could be used as a tool to help inform the decision-making process for scientists, engineers, and stakeholders involved in coastal zone management or restoration projects.