We present the luminosity function and volumetric rate of a sample of Type IIP supernovae (SNe) from the Zwicky Transient Facility Census of the Local Universe survey (CLU). This is the largest sample of Type IIP SNe from a systematic volume-limited survey to-date. The final sample includes 330 Type IIP SNe and 36 low-luminosity Type II (LLIIP) SNe with M r ,peak > −16 mag, which triples the literature sample of LLIIP SNe. The fraction of LLIIP SNe is 1 9 − 4 + 3 % of the total CLU Type IIP SNe population ( 8 − 2 + 1 % of all core-collapse SNe). This implies that while LLIIP SNe likely represent the fate of core-collapse SNe of 8–12 M ⊙ progenitors, they alone cannot account for the fate of all massive stars in this mass range. To derive an absolute rate, we estimate the ZTF pipeline efficiency as a function of the apparent magnitude and the local surface brightness. We derive a volumetric rate of ( 3 . 9 − 0.4 + 0.4 ) × 1 0 4 Gpc − 3 yr − 1 for Type IIP SNe and ( 7 . 3 − 0.6 + 0.6 ) × 1 0 3 Gpc − 3 yr − 1 for LLIIP SNe. Now that the rate of LLIIP SNe is robustly derived, the unresolved discrepancy between core-collapse SN rates and star formation rates cannot be explained by LLIIP SNe alone.

Extrachromosomal DNAs (ecDNAs) are circular DNA molecules prevalent in human cancers that drive tumor evolution and drug resistance. Their circular topology, which disrupts topological domains and rewires regulatory circuits, has typically been studied via pairwise interactions. Here we develop ec3D, a computational method for reconstructing three-dimensional ecDNA structures from Hi-C data. Given a candidate ecDNA sequence and whole-genome Hi-C data, ec3D reconstructs spatial structures by maximizing the Poisson likelihood of observed interactions. We validate ec3D using simulated structures, previously characterized cancer cell lines, and microscopy imaging. Our reconstructions reveal that ecDNAs occupy spherical configurations and mediate unique long-range regulatory interactions involved in gene regulation. Through algorithmic innovations, ec3D can resolve complex structures with duplicated segments, identify multi-way interactions, and identify potential intermolecular (trans) interactions. Our findings provide insights into how ecDNA's spatial organization bypasses normal chromosomal constraints and contributes to increased oncogene expression.

Binaries containing compact objects, viewed nearly edge on, can produce periodic brightening events under certain conditions on the masses, radii, and binary separation. Such flares are caused by one object gravitationally lensing another, in what is known as self-lensing flares. We present a simulation tool that efficiently reproduces the main features of self-lensing flares and facilitates a detection sensitivity analysis for various sky surveys. We estimate the detection prospects for a handful of representative surveys when searching for systems of either two white dwarfs or a white dwarf with other compact objects, i.e., neutron stars and black holes. We find only a marginal ability to detect such systems in existing surveys. However, we estimate many such systems could be detectable by surveys in the near future, including the Vera Rubin Legacy Survey of Space and Time (LSST). We provide a quantitative analysis of the detectability of double-compact object self-lensing flares across the landscape of system parameters, and a qualitative discussion of survey and follow-up approaches to distinguish such flares from confounding events, such as stellar flares, satellite glints, and cosmic rays. We estimate 0.3, 3 and 247 double white dwarf systems could be detected by Transiting Exoplanet Survey Satellite, Zwicky Transient Facility, and LSST, respectively. A similar number of systems with a neutron star or black hole companion could be detected, but we caution that the number densities of such binaries is model dependent and so are our detection estimates. Such binaries can be used to constrain models of the end states of binary evolution.

Asteroid collisions are one of the main processes responsible for the evolution of bodies in the main belt. Using observations of the Dimorphos impact by the DART spacecraft, we estimate how asteroid collisions in the main belt may look in the first hours after the impact. If the DART event is representative of asteroid collisions with a ∼1 m sized impactor, then the light curves of these collisions will rise on timescales of about ≳100 s and will remain bright for about 1 hr. Next, the light curve will decay on a few hours' timescale to an intermediate luminosity level in which it will remain for several weeks, before slowly returning to its baseline magnitude. This estimate suffers from several uncertainties due to, e.g., the diversity of asteroid composition, their material strength, and spread in collision velocities. We estimate that the rate of collisions in the main belt with energy similar to or larger than the DART impact is of the order of 7000 yr ^−1 (±1 dex). The large range is due to the uncertainty in the abundance of ∼1 m sized asteroids. We estimate the magnitude distribution of such events in the main belt, and we show that ∼6% of these events may peak at magnitudes brighter than 21. The detection of these events requires a survey with ≲1 hr cadence and may contribute to our understanding of the asteroids’ size distribution, collisional physics, and dust production. With an adequate survey strategy, new survey telescopes may regularly detect asteroid collisions.

Abstract Philadelphia-positive leukemia is characterized by the translocation t(9;22)(q34;q11), which results in the oncogene BCR-ABL1 and a chromosome called the Philadelphia (Ph) chromosome (chr). The Philadelphia chromosome is best characterized in Chronic Myeloid Leukemia (CML); however, the translocation is also found in Acute Lymphoblastic Leukemia (ALL). Philadelphia-positive ALL has been historically understudied, especially in minority populations. Genome organization is a highly complex process by which chromatin is segregated within the nucleus into specific domains, making stable translocations highly unfavorable. How translocations are stabilized has been historically understudied. Here, we aim to examine how the Ph chr is stabilized and be the first to visualize an entire abnormal chr with high spatial and genomic resolution at the single-cell level. Using OligoSTORM, a super-resolution microscopy technique, we aim to image the entirety of the Ph chr at a nanoscale resolution in both CML and ALL cell lines. In addition to the DNA super-resolution trace, we have designed an RNA library to image a series of RNAs from the Ph chr on the same sample as the DNA trace, allowing us to connect the transcriptional data to the chromatin structure. We have successfully traced the entirety of the Ph chr. We have preliminary data suggesting that chr9 and chr22 segregate close to each other in non-leukemia healthy cells. We have also proven that our library design and methodology work to achieve the primary 500kb resolution. Preliminary data suggests that chr9 and chr22 in cells, that don’t typically have a Ph chr, segregate within proximity to translocate successfully. This study aims to compare the 3D structure of CML, ALL and non-leukemia cell lines to potentially identify genome organization-based biomarkers for identify and targeting the Philadelphia chromosome. Citation Format: Gabrielle S. Dewson, Guy Nir. Unraveling the structure of the Philadelphia chromosome using super-resolution microscopy [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C015.

Multipeaked supernovae with precursors, dramatic light-curve rebrightenings, and spectral transformation are rare, but are being discovered in increasing numbers by modern night-sky transient surveys like the Zwicky Transient Facility. Here, we present the observations and analysis of SN 2023aew, which showed a dramatic increase in brightness following an initial luminous (−17.4 mag) and long (∼100 days) unusual first peak (possibly precursor). SN 2023aew was classified as a Type IIb supernova during the first peak but changed its type to resemble a stripped-envelope supernova (SESN) after the marked rebrightening. We present comparisons of SN 2023aew’s spectral evolution with SESN subtypes and argue that it is similar to SNe Ibc during its main peak. P-Cygni Balmer lines are present during the first peak, but vanish during the second peak’s photospheric phase, before H α resurfaces again during the nebular phase. The nebular lines ([O i ], [Ca ii ], Mg i ], H α ) exhibit a double-peaked structure that hints toward a clumpy or nonspherical ejecta. We analyze the second peak in the light curve of SN 2023aew and find it to be broader than that of normal SESNe as well as requiring a very high ^56 Ni mass to power the peak luminosity. We discuss the possible origins of SN 2023aew including an eruption scenario where a part of the envelope is ejected during the first peak and also powers the second peak of the light curve through interaction of the SN with the circumstellar medium.

Detection of moving sources over a complicated background is important for several reasons. First is measuring the astrophysical motion of the source. Second is that such motion resulting from atmospheric scintillation, color refraction, or astrophysical reasons is a major source of false alarms for image-subtraction methods. We extend the Zackay, Ofek, and Gal-Yam image-subtraction formalism to deal with moving sources. The new method, named the translient (translational transient) detector, applies hypothesis testing between the hypothesis that the source is stationary and that the source is moving. It can be used to detect source motion or to distinguish between stellar variability and motion. For moving source detection, we show the superiority of translient over the proper image subtraction, using the improvement in the receiver-operating characteristic curve. We show that in the small translation limit, translient is an optimal detector of point-source motion in any direction. Furthermore, it is numerically stable, fast to calculate, and presented in a closed form. Efficient transient detection requires both the proper image-subtraction statistics and the translient statistics: When the translient statistic is higher, then the subtraction residual is likely due to motion. We test our algorithm both on simulated data and on real images obtained by the Large Array Survey Telescope. We demonstrate the ability of translient to distinguish between motion and variability, which has the potential to reduce the number of false alarms in transients detection. We provide the translient implementation in Python and MATLAB.

We present X-sifter, a software package designed for near-optimal detection of sources in X-ray images and other forms of photon images in the Poisson-noise regime. The code is based on the Poisson-noise-matched filter (Ofek Zackay), which provides an efficient method for calculating the delta log-likelihood function for source detection. The software accounts for several complexities inherent in real data, including variations in both the instrumental Point Spread Function (PSF) and background across the detector and as a function of energy. We validate the pipeline using real data with simulated source injections, as well as actual Chandra images. A comparison between the sources detected by our pipeline and those in the Chandra Source Catalog (CSC) suggests an approximate 30 (real) sources. Near the detection limit, the reported S/N of our pipeline is approximately 1.3x higher than that of the CSC. This corresponds to a factor of 1.8 increase in survey speed.

In this second paper on the DECam deep-drilling field (DDF) program, we release 2020 optical gri-band light curves for transients and variables in the extragalactic COSMOS and ELAIS fields based on time series observations with a 3-d cadence from semester 2021A through 2023A. In order to demonstrate the wide variety of time domain events detected by the program and encourage others to use the data set, we characterize the sample by presenting a brief analysis of the light-curve parameters such as time span, amplitude, and peak brightness. We also present preliminary light-curve categorizations, and identify potential stellar variables, active galactic nuclei, tidal disruption events, supernovae (SNe) (such as Type Ia, Type IIP, superluminous, and gravitationally lensed SNe), and fast transients. Where relevant, the number of identified transients is compared to the predictions of the original proposal. We also discuss the challenges of analyzing DDF data in the context of the upcoming Vera C. Rubin Observatory and its Legacy Survey of Space and Time, which will include DDFs. Images from the Dark Energy Camera DDF program are available without proprietary period and the light curves presented in this work are publicly available for analysis.

Salmonella can exist in a free-living planktonic state, or form sessile communities known as biofilms. In the virulent state, Salmonella survives in an acidic vacuole inside host cells and disseminates to the liver and spleen to cause infection. These competing lifestyles are regulated by the same transcription factor, SsrB, through relief of silencing by the nucleoid-associated protein H-NS, as well as by direct activation of transcription.1 Our laboratories are interested in how environmental stresses lead to changes in genomic structure that drives large changes in transcription and gene regulation associated with these alternative lifestyles.

The classification of variable objects provides insight into a wide variety of astrophysics ranging from stellar interiors to galactic nuclei. The Zwicky Transient Facility (ZTF) provides time series observations that record the variability of more than a billion sources. The scale of these data necessitates automated approaches to make a thorough analysis. Building on previous work, this paper reports the results of the ZTF Source Classification Project (SCoPe), which trains neural network and XGBoost machine learning (ML) algorithms to perform dichotomous classification of variable ZTF sources using a manually constructed training set containing 170,632 light curves. We find that several classifiers achieve high precision and recall scores, suggesting the reliability of their predictions for 112,476,749 light curves across 40 ZTF fields. We also identify the most important features for XGB classification and compare the performance of the two ML algorithms, finding a pattern of higher precision among XGB classifiers. The resulting classification catalog is available to the public, and the software developed for SCoPe is open-source and adaptable to future time-domain surveys.

Abstract Genome organization in humans is governed by two major mechanisms: loop extrusion by cohesin and CTCF and the spatial compartmentalization of the chromosomes. These folding mechanisms have been shown to regulate several genomic functions, including gene expression. However, how transcription might regulate the chromatin structure remains a subject of many ongoing investigations. In this study, we use the Integrator protein complex as a tool to understand the impact of aberrant transcription on the 3D structure of the genome. During transcription initiation, RNA Polymerase-II (Pol-II) often pauses proximally to the promoter before further elongating transcripts. The Integrator protein complex regulates this checkpoint by its endonuclease and phosphatase activity. This protein complex is essential in premature transcription termination in hundreds of protein-coding genes. It also facilitates the synthesis of non-coding (ncRNA), such as enhancer RNAs (eRNAs) and long non-coding RNAs (lncRNAs), which have been shown to support loop extrusion domains, and their absence may disrupt these domains. Using HiC sequencing, we found that depleting Integrator proteins can interfere with forming and maintaining loop domains. This study aims to be the first to decipher the relationship between chromosome structure and Integrator protein activity and address our very little knowledge of how misregulation of transcription termination may influence the folding of chromosomes. Citation Format: Naiju Thomas, Timothy E. Reznicek, Erez Lieberman Aiden, M. Jordan Rowley, Eric Wagner, Guy Nir. Defining the impact of aberrant transcription on the chromatin structure [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1699.

The Oort cloud is presumably a pristine relic of the solar system formation. Detection of the Oort cloud may provide information regarding the stellar environment in which the Sun was born and on the planetesimal population during the outer planets’ formation phase. The best suggested approach for detecting Oort cloud objects in situ, is by searching for subsecond occultations of distant stars by these objects. Following Brown & Webster, we discuss the possibility of detecting Oort cloud objects by observing near the quadrature direction. Due to the Earth’s projected velocity, the occultations are longer near the quadrature direction and are therefore easier to detect, but have lower rate. We show that, for ≲1 m size telescopes, the increased exposure time will result in about one to 3 orders of magnitude increase in the number of detectable stars that have an angular size smaller than the Fresnel scale and are therefore suitable for an occultation search. We discuss the ability of this method to detect Oort cloud objects using existing survey telescopes, and we estimate the detection rate as a function of the power-law index of the size distribution of the Oort cloud objects and their distance from the Sun. We show that occultations detected using ≈1 s integration by ≲1 m telescopes at the optimal region near the quadrature points will be marginally dominated by Oort cloud objects rather than Kuiper belt objects.

The rise of time-domain astronomy including electromagnetic counterparts to gravitational waves, gravitational microlensing, explosive phenomena, and even astrometry with Gaia, are showing the power and need for surveys with high-cadence, large area, and long time baselines to study the transient universe. A constellation of SmallSats or CubeSats providing wide, instantaneous sky coverage down to 21 Vega mag at optical wavelengths would be ideal for addressing this need. We are assembling CuRIOS-ED (CubeSats for Rapid Infrared and Optical Survey-Exploration Demo), an optical telescope payload which will act as a technology demonstrator for a larger constellation of several hundred 16U CubeSats known as CuRIOS. The full CuRIOS constellation will study the death and afterlife of stars by providing all-sky, all-the-time observations to a depth of 21 Vega magnitudes in the optical bandpass. In preparation for CuRIOS, CuRIOS-ED will launch in late 2025 as part of the 12U Starspec InspireSat MVP payload funded through the Canadian Space Agency. CuRIOS-ED will be used to demonstrate the <1" pointing capabilities of the StarSpec ADCS system and to space-qualify a commercial camera package for use on the full CuRIOS payload. The CuRIOS-ED camera system will utilize a Sony IMX455 CMOS detector delivered in an off-the-shelf Atik apx60 package which has no previous space heritage. We deconstructed and repackaged the apx60 camera to make it compatible with operations in vacuum environments as well as the CubeSat form factor, power, and thermal constraints. By qualifying this commercial camera solution, the cost of each CuRIOS satellite will be greatly decreased (similar to 100x) when compared with current space-qualified cameras with IMX455 detectors. Therefore, the results from this work have great implications on the CuRIOS mission as well as other Cube or SmallSat missions. We discuss the CuRIOS-ED mission design with an emphasis on the disassembly, repackaging, and testing of the Atik apx60 for space-based missions. The testing results include characterization of the Sony IMX455 detector and Atik electronics performance. We find a read noise of 2.43 +/- 0.05 e- at a gain of 1 electron/ADU and detector temperatures ranging from -10 C to 25 C. The apx60's dark current is well below an electron per second at the temperatures and exposure times tested. The apx60 camera also exhibits patterned noise in the form of horizontal striping and an asymmetric signal gradient which increases across the detector's columns. We will also comment on preliminary environmental testing results.

We study a magnitude-limited sample of 36 broad-lined type Ic supernovae (SNe Ic-BL) from the Zwicky Transient Facility Bright Transient Survey (detected between 2018 March and 2021 August), which is the largest systematic study of SNe Ic-BL done in literature thus far. We present the light curves (LCs) for each of the SNe and analyze the shape of the LCs to derive empirical parameters, along with the explosion epochs for every event. The sample has an average absolute peak magnitude in the r band of Mr,max=-18.51 +/- 0.15 mag. Using spectra obtained around peak light, we compute expansion velocities from the Fe ii 5169 & Aring; line for each event with high enough signal-to-noise ratio spectra, and find an average value of vph=16,100 +/- 1100 km s-1. We also compute bolometric LCs, study the blackbody temperature and radii evolution over time, and derive the explosion properties of the SNe. The explosion properties of the sample have average values of MNi=0.37-0.06+0.08M circle dot , Mej=2.45-0.41+0.47M circle dot , and EK=(4.02-1.00+1.37)x1051 erg. Thirteen events have radio observations from the Very Large Array, with eight detections and five non-detections. We find that the populations that have radio detections and radio non-detections are indistinct from one another with respect to their optically inferred explosion properties, and there are no statistically significant correlations present between the events' radio luminosities and optically inferred explosion properties. This provides evidence that the explosion properties derived from optical data alone cannot give inferences about the radio properties of SNe Ic-BL and likely their relativistic jet formation mechanisms.

Nuclear organization impacts gene expression activity and cell phenotype. Our current understanding is mainly derived from ensemble-level sequencing studies that reflect the 3D genome structure of millions of cells. These approaches have provided invaluable details on the 3D organizations of the genome and their relation to other nuclear landmarks. However, they mostly lack the ability to provide multimodal information simultaneously at the single-cell level. In recent years, cutting-edge imaging technologies have risen to the challenge of simultaneously describing multiple components of the nuclear space at the single-cell level, paving the way for a deeper understanding of the genome structure-function relationship. This review will focus on the development and utilization of such technologies to gain a multi-component view of the nucleus at single-cell resolution, dissecting the complexity and heterogeneity of nuclear organization.

Mosquito transmission of dengue viruses to humans starts with infection of skin resident cells at the biting site. There is great interest in identifying transmission-enhancing factors in mosquito saliva in order to counteract them. Here we report the discovery of high levels of the anti-immune subgenomic flaviviral RNA (sfRNA) in dengue virus 2-infected mosquito saliva. We established that sfRNA is present in saliva using three different methods: northern blot, RT-qPCR and RNA sequencing. We next show that salivary sfRNA is protected in detergent-sensitive compartments, likely extracellular vesicles. In support of this hypothesis, we visualized viral RNAs in vesicles in mosquito saliva and noted a marked enrichment of signal from 3’UTR sequences, which is consistent with the presence of sfRNA. Furthermore, we show that incubation with mosquito saliva containing higher sfRNA levels results in higher virus infectivity in a human hepatoma cell line and human primary dermal fibroblasts. Transfection of 3’UTR RNA prior to DENV2 infection inhibited type I and III interferon induction and signaling, and enhanced viral replication. Therefore, we posit that sfRNA present in salivary extracellular vesicles is delivered to cells at the biting site to inhibit innate immunity and enhance dengue virus transmission.

SkyPortal is an open-source software package designed to efficiently discover interesting transients, manage follow-up, perform characterization, and visualize the results. By enabling fast access to archival and catalog data, cross-matching heterogeneous data streams, and the triggering and monitoring of on-demand observations for further characterization, a SkyPortal-based platform has been operating at scale for 2 yr for the Zwicky Transient Facility Phase II community, with hundreds of users, containing tens of millions of time-domain sources, interacting with dozens of telescopes, and enabling community reporting. While SkyPortal emphasizes rich user experiences (UX) across common frontend workflows, recognizing that scientific inquiry is increasingly performed programmatically, SkyPortal also surfaces an extensive and well-documented API system. From backend and frontend software to data science analysis tools and visualization frameworks, the SkyPortal design emphasizes the re-use and leveraging of best-in-class approaches, with a strong extensibility ethos. For instance, SkyPortal now leverages ChatGPT large-language models (LLMs) to automatically generate and surface source-level human-readable summaries. With the imminent re-start of the next-generation of gravitational wave detectors, SkyPortal now also includes dedicated multi-messenger features addressing the requirements of rapid multi-messenger follow-up: multi-telescope management, team/group organizing interfaces, and cross-matching of multi-messenger data streams with time-domain optical surveys, with interfaces sufficiently intuitive for the newcomers to the field. (abridged)

Kuiper belt objects smaller than a few kilometers are difficult to observe directly. They can be detected when they randomly occult a background star. Close to the ecliptic plane, each star is occulted once every tens of thousands of hours, and occultations typically last for less than a second. We present an algorithm, and companion pipeline, for detection of diffractive occultation events. Our approach includes: cleaning the data; an efficient and optimal matched filtering of the light-curves with a template bank of diffractive occultations; treating the red-noise in the light-curves; injection of simulated events for efficiency estimation; and applying data quality cuts. We discuss human vetting of the candidate events in a blinded way to reduce bias caused by the human-in-the-loop. We present Markov Chain Monte Carlo tools to estimate the parameters of candidate occultations, and test them on simulated events. This pipeline is used by the W-FAST. The methods discussed here can be applied to searches for other Trans-Neptunian objects, albeit with larger radii that correspond to a larger diffraction length scale.

Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF's RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted.