Lab Fattening and Non-invasive Estimates of Body Composition in Deer Mice

Total body electrical conductivity measurements and lipid composition were determined for the deer mouse (Peromyscus maniculatus) to derive species specific calibration equations for use with EM-SCAN estimates of lean and fat tissue. For each individual, total body electrical conductivity was measured by EM-SCAN, and actual lipid content was determined by chemical extraction. Then, using estimated and actual lipid values, separate calibration equations were generated for freshly captured (lean) and laboratory maintained (fat) individuals, and a combined equation was derived for all individuals. These equations were variable in the accuracy of lipid estimates; the lowest relative error estimate (percent body fat) was obtained with the equation for fat individuals while the highest error (percent body fat) was associated with the lean condition. Although high average error rates for lipid might preclude the use of this approach when absolute accuracy is necessary with lean individuals, estimates of lean tissue were very accurate regardless of body composition condition. When removed from the field and maintained in the laboratory, body composition changed significantly and quite rapidly with relative body fat doubling in six weeks. Thus, maintenance under laboratory conditions might affect physiologic and behavioral parameters in such subjects

Community-powered urban stream restoration: A vision for sustainable and resilient urban ecosystems

Urban streams can provide amenities to people living in cities, but those benefits are reduced when streams become degraded, potentially even causing harm (disease, toxic compounds, etc.). Governments and institutions invest resources to improve the values and services provided by urban streams; however, the conception, development, and implementation of such projects may not include meaningful involvement of community members and other stakeholders. Consequently, project objectives may be misaligned with community desires and needs, and projects may fail to achieve their goals. In February 2020, the 5(th) Symposium on Urbanization and Stream Ecology, an interdisciplinary meeting held every 3 to 5 y, met in Austin, Texas, USA, to explore new approaches to urban stream projects, including ways to maximize the full range of potential benefits by better integrating community members into project identification and decision making. The symposium included in-depth discussion about 4 nearby field case studies, participation of multidisciplinary urban stream experts from 5 continents, and input from the Austin community. Institutional barriers to community inclusion were identified and analyzed using real-world examples, both from the case studies and from the literature, which clarified disparities in power, equity, and values. Outcomes of the symposium have been aggregated into a vision that challenges the present institutional approach to urban stream management and a set of strategies to systematically address these barriers to improve restoration solutions. Integrating community members and other stakeholders throughout the urban restoration process, and a transparent decision-making process to resolve divergent objectives, can help identify appropriate goals for realizing both the ecological and social benefits of stream restoration

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

A Systematic Search of Zwicky Transient Facility Data for Ultracompact Binary LISA-detectable Gravitational-wave Sources

Using photometry collected with the Zwicky Transient Facility, we are conducting an ongoing survey for binary systems with short orbital periods (P_b < 1 hr) with the goal of identifying new gravitational-wave sources detectable by the upcoming Laser Interferometer Space Antenna (LISA). We present a sample of 15 binary systems discovered thus far, with orbital periods ranging from 6.91 to 56.35 minutes. Of the 15 systems, seven are eclipsing systems that do not show signs of significant mass transfer. Additionally, we have discovered two AM Canum Venaticorum systems and six systems exhibiting primarily ellipsoidal variations in their lightcurves. We present follow-up spectroscopy and high-speed photometry confirming the nature of these systems, estimates of their LISA signal-to-noise ratios, and a discussion of their physical characteristics

Constraining the Kilonova Rate with Zwicky Transient Facility Searches Independent of Gravitational Wave and Short Gamma-ray Burst Triggers

The first binary neutron star merger, GW170817, was accompanied by a radioactivity-powered optical/infrared transient called a kilonova. To date, no compelling kilonova has been found during optical surveys of the sky, independent of gravitational-wave triggers. In this work, we searched the first 23 months of the Zwicky Transient Facility (ZTF) data stream for candidate kilonovae in the form of rapidly evolving transients. We combined ZTF alert queries with forced point-spread-function photometry and nightly flux stacking to increase our sensitivity to faint and fast transients. Automatic queries yielded $>11,200$ candidates, 24 of which passed quality checks and strict selection criteria based on a grid of kilonova models tailored for both binary neutron star and neutron star-black hole mergers. None of the candidates in our sample was deemed a possible kilonova after thorough vetting, catalog cross-matching, and study of their color evolution. The sources that passed our selection criteria are dominated by Galactic cataclysmic variables. In addition, we identified two fast transients at high Galactic latitude, one of which is the confirmed afterglow of long-duration GRB190106A, and the other is a possible cosmological afterglow. Using a survey simulation code, we constrained the kilonova rate for a range of models including top-hat and linearly decaying light curves and synthetic light curves obtained with radiative transfer simulations. For prototypical GW170817-like kilonovae, we constrain the rate to be $R < 1775$ Gpc$^{-3}$ yr$^{-1}$ at 95% confidence level by requiring at least 2 high-significance detections. By assuming a population of kilonovae with the same geometry and composition of GW170817 observed under a uniform viewing angle distribution, we obtained a constraint on the rate of $R < 4029$ Gpc$^{-3}$ yr$^{-1}$.Comment: Submitted for publication in Ap

Constraining the Kilonova Rate with Zwicky Transient Facility Searches Independent of Gravitational Wave and Short Gamma-Ray Burst Triggers

The first binary neutron star merger, GW170817, was accompanied by a radioactivity-powered optical/infrared transient called a kilonova. To date, no compelling kilonova has been found in all-sky optical surveys, independently of short gamma-ray burst and gravitational-wave triggers. In this work, we searched the first 23 months of the Zwicky Transient Facility (ZTF) data stream for candidate kilonovae in the form of rapidly evolving transients. We combined ZTF alert queries with forced point-spread-function photometry and nightly flux stacking to increase our sensitivity to faint and fast transients. Automatic queries yielded >11,200 candidates, 24 of which passed quality checks and selection criteria based on a grid of kilonova models tailored for both binary neutron star and neutron star–black hole mergers. None of the candidates in our sample was deemed a possible kilonova after thorough vetting. The sources that passed our selection criteria are dominated by Galactic cataclysmic variables. We identified two fast transients at high Galactic latitude, one of which is the confirmed afterglow of long-duration GRB 190106A, the other is a possible cosmological afterglow. Using a survey simulation code, we constrained the kilonova rate for a range of models including top-hat, linearly decaying light curves, and synthetic light curves obtained with radiative transfer simulations. For prototypical GW170817-like kilonovae, we constrain the rate to be R < 1775 Gpc⁻³ yr⁻¹ (95% confidence). By assuming a population of kilonovae with the same geometry and composition of GW170817 observed under a uniform viewing angle distribution, we obtained a constraint on the rate of R < 4029 Gpc⁻³ yr⁻¹