A Tale of Two Narrow-Line Regions: Ionization, Kinematics, and Spectral Energy Distributions for a Local Pair of Merging Obscured Active Galaxies

We explore the gas ionization and kinematics, as well as the optical--IR spectral energy distributions for UGC 11185, a nearby pair of merging galaxies hosting obscured active galactic nuclei (AGNs), also known as SDSS J181611.72+423941.6 and J181609.37+423923.0 (J1816NE and J1816SW, $z \approx 0.04$). Due to the wide separation between these interacting galaxies ($\sim 23$ kpc), observations of these objects provide a rare glimpse of the concurrent growth of supermassive black holes at an early merger stage. We use BPT line diagnostics to show that the full extent of the narrow line emission in both galaxies is photoionized by an AGN and confirm the existence of a 10-kpc-scale ionization cone in J1816NE, while in J1816SW the AGN narrow-line region is much more compact (1--2 kpc) and relatively undisturbed. Our observations also reveal the presence of ionized gas that nearly spans the entire distance between the galaxies which is likely in a merger-induced tidal stream. In addition, we carry out a spectral analysis of the X-ray emission using data from {\em XMM-Newton}. These galaxies represent a useful pair to explore how the [\ion{O}{3}] luminosity of an AGN is dependent on the size of the region used to explore the extended emission. Given the growing evidence for AGN "flickering" over short timescales, we speculate that the appearances and impact of these AGNs may change multiple times over the course of the galaxy merger, which is especially important given that these objects are likely the progenitors of the types of systems commonly classified as "dual AGNs."Comment: 15 pages, 10 figures, accepted by the Astrophysical Journa

Fusion approach for remotely sensed mapping of agriculture (FARMA):A scalable open source method for land cover monitoring using data fusion

The increasing availability of very-high resolution (VHR; &lt;2 m) imagery has the potential to enable agricultural monitoring at increased resolution and cadence, particularly when used in combination with widely available moderate-resolution imagery. However, scaling limitations exist at the regional level due to big data volumes and processing constraints. Here, we demonstrate the Fusion Approach for Remotely Sensed Mapping of Agriculture (FARMA), using a suite of open source software capable of efficiently characterizing time-series field-scale statistics across large geographical areas at VHR resolution. We provide distinct implementation examples in Vietnam and Senegal to demonstrate the approach using WorldView VHR optical, Sentinel-1 Synthetic Aperture Radar, and Sentinel-2 and Sentinel-3 optical imagery. This distributed software is open source and entirely scalable, enabling large area mapping even with modest computing power. FARMA provides the ability to extract and monitor sub-hectare fields with multisensor raster signals, which previously could only be achieved at scale with large computational resources. Implementing FARMA could enhance predictive yield models by delineating boundaries and tracking productivity of smallholder fields, enabling more precise food security observations in low and lower-middle income countries.</p

Improving the LSST dithering pattern and cadence for dark energy studies

The Large Synoptic Survey Telescope (LSST) will explore the entire southern sky over 10 years starting in 2022 with unprecedented depth and time sampling in six filters, $ugrizy$. Artificial power on the scale of the 3.5 deg LSST field-of-view will contaminate measurements of baryonic acoustic oscillations (BAO), which fall at the same angular scale at redshift $z \sim 1$. Using the HEALPix framework, we demonstrate the impact of an "un-dithered" survey, in which $17\%$ of each LSST field-of-view is overlapped by neighboring observations, generating a honeycomb pattern of strongly varying survey depth and significant artificial power on BAO angular scales. We find that adopting large dithers (i.e., telescope pointing offsets) of amplitude close to the LSST field-of-view radius reduces artificial structure in the galaxy distribution by a factor of $\sim$10. We propose an observing strategy utilizing large dithers within the main survey and minimal dithers for the LSST Deep Drilling Fields. We show that applying various magnitude cutoffs can further increase survey uniformity. We find that a magnitude cut of $r < 27.3$ removes significant spurious power from the angular power spectrum with a minimal reduction in the total number of observed galaxies over the ten-year LSST run. We also determine the effectiveness of the observing strategy for Type Ia SNe and predict that the main survey will contribute $\sim$100,000 Type Ia SNe. We propose a concentrated survey where LSST observes one-third of its main survey area each year, increasing the number of main survey Type Ia SNe by a factor of $\sim$1.5, while still enabling the successful pursuit of other science drivers.Comment: 9 pages, 6 figures, published in SPIE proceedings; corrected typo in equation

Activated lymphocyte recruitment into the tumor microenvironment following preoperative sipuleucel-T for localized prostate cancer.

BackgroundSipuleucel-T is a US Food and Drug Administration-approved immunotherapy for asymptomatic or minimally symptomatic metastatic castration-resistant prostate cancer (mCRPC). Its mechanism of action is not fully understood. This prospective trial evaluated the direct immune effects of systemically administered sipuleucel-T on prostatic cancer tissue in the preoperative setting.MethodsPatients with untreated localized prostate cancer were treated on an open-label Phase II study of sipuleucel-T prior to planned radical prostatectomy (RP). Immune infiltrates in RP specimens (posttreatment) and in paired pretreatment biopsies were evaluated by immunohistochemistry (IHC). Correlations between circulating immune response and IHC were assessed using Spearman rank order.ResultsOf the 42 enrolled patients, 37 were evaluable. Adverse events were primarily transient, mild-to-moderate and infusion related. Patients developed T cell proliferation and interferon-γ responses detectable in the blood following treatment. Furthermore, a greater-than-three-fold increase in infiltrating CD3(+), CD4(+) FOXP3(-), and CD8(+) T cells was observed in the RP tissues compared with the pretreatment biopsy (binomial proportions: all P &lt; .001). This level of T cell infiltration was observed at the tumor interface, and was not seen in a control group consisting of 12 concurrent patients who did not receive any neoadjuvant treatment prior to RP. The majority of infiltrating T cells were PD-1(+) and Ki-67(+), consistent with activated T cells. Importantly, the magnitude of the circulating immune response did not directly correlate with T cell infiltration within the prostate based upon Spearman's rank order correlation.ConclusionsThis study is the first to demonstrate a local immune effect from the administration of sipuleucel-T. Neoadjuvant sipuleucel-T elicits both a systemic antigen-specific T cell response and the recruitment of activated effector T cells into the prostate tumor microenvironment

A Tale of Two Narrow-Line Regions: Ionization, Kinematics, and Spectral Energy Distributions for a Local Pair of Merging Obscured Active Galaxies

We explore the gas ionization and kinematics, as well as the optical-IR spectral energy distributions for UGC 11185, a nearby pair of merging galaxies hosting obscured active galactic nuclei (AGNs), also known as SDSS J181611.72+423941.6 and J181609.37+423923.0 (J1816NE and J1816SW, z ≈ 0.04). Due to the wide separation between these interacting galaxies (~23 kpc), observations of these objects provide a rare glimpse of the concurrent growth of supermassive black holes at an early merger stage. We use BPT line diagnostics to show that the full extent of the narrow-line emission in both galaxies is photoionized by an AGN, and confirm the existence of a 10 kpc-scale ionization cone in J1816NE, while in J1816SW the AGN narrow-line region is much more compact (1–2 kpc) and relatively undisturbed. Our observations also reveal the presence of ionized gas that nearly spans the entire distance between the galaxies, which is likely in a merger-induced tidal stream. In addition, we carry out a spectral analysis of the X-ray emission using data from XMM-Newton. These galaxies represent a useful pair to explore how the [O iii] luminosity of an AGN is dependent on the size of the region used to explore the extended emission. Given the growing evidence for AGN flickering over short timescales, we speculate that the appearances and impacts of these AGNs may change multiple times over the course of the galaxy merger, which is especially important given that these objects are likely the progenitors of the types of systems commonly classified as dual AGNs

The temporal relationship between local school closure and increased incidence of pediatric diabetic ketoacidosis

IMPORTANCE: The incidence of pediatric diabetic ketoacidosis (DKA) increased early in the COVID-19 pandemic, but the relative contribution of behavioral changes and viral-related pathophysiology are unknown. OBJECTIVE: To evaluate the relationship between school closure date and onset of increased DKA to help clarify the etiology of the increased incidence. DESIGN: A multi-center, quality-controlled Pediatric Intensive Care Unit (PICU) database was used to identify the number of admissions to a participating PICU with DKA on each calendar day from 60 days before local school closure to 90 days after, and compared to baseline data from the same periods in 2018-2019. Interrupted time series and multiple linear regression analyses were used to identify admission rates that differed significantly between 2020 and baseline. SETTING: Eighty-one PICUs in the United StatesParticipants: Children ages 29 days to 17 years admitted to a PICU with DKAExposures: Statewide school closureMain outcome/measure: Rate of admission to the PICU for DKA. RESULTS: There were 1936 admissions for children with DKA in 2020 and 1795 admissions/year to those same PICUs in 2018-2019. Demographics and clinical outcomes did not differ before school closure, but pandemic-era patients were less often white and had longer hospital length of stay in the post-school closure period. The difference between 2020 admissions and 2018-2019 admissions was not different than zero before school closure, and significantly higher than zero after school closure, but was significantly increased in 2020 at \u3e30 days after school closure ( CONCLUSIONS/RELEVANCE: An increase in pediatric DKA admissions began one month after school closures. Given that behavioral changes started near school closure dates and viral activity peaked weeks after, this suggests that behavioral factors may not be the primary etiology and it is possible that SARS-CoV-2 infection may have direct effects on pediatric DKA

The Role of Expectations What Have We Learned? Conclusions References

In Aristotle’s (350 BC) list of common human logical errors: Attributing characteristics of the whole to the parts Google search for examples yields: America is rich Chris Carroll is American Chris Carroll is rich! Clearly a fallacy

DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation.

BACKGROUND: Nanopore long-read sequencing technology greatly expands the capacity of long-range, single-molecule DNA-modification detection. A growing number of analytical tools have been developed to detect DNA methylation from nanopore sequencing reads. Here, we assess the performance of different methylation-calling tools to provide a systematic evaluation to guide researchers performing human epigenome-wide studies. RESULTS: We compare seven analytic tools for detecting DNA methylation from nanopore long-read sequencing data generated from human natural DNA at a whole-genome scale. We evaluate the per-read and per-site performance of CpG methylation prediction across different genomic contexts, CpG site coverage, and computational resources consumed by each tool. The seven tools exhibit different performances across the evaluation criteria. We show that the methylation prediction at regions with discordant DNA methylation patterns, intergenic regions, low CG density regions, and repetitive regions show room for improvement across all tools. Furthermore, we demonstrate that 5hmC levels at least partly contribute to the discrepancy between bisulfite and nanopore sequencing. Lastly, we provide an online DNA methylation database ( https://nanome.jax.org ) to display the DNA methylation levels detected by nanopore sequencing and bisulfite sequencing data across different genomic contexts. CONCLUSIONS: Our study is the first systematic benchmark of computational methods for detection of mammalian whole-genome DNA modifications in nanopore sequencing. We provide a broad foundation for cross-platform standardization and an evaluation of analytical tools designed for genome-scale modified base detection using nanopore sequencing