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  1. Abstract Background The Aedes aegypti mosquito is a threat to human health across the globe. The A. aegypti genome was recently re-sequenced and re-assembled. Due to a combination of long-read PacBio and Hi-C sequencing, the AaegL5 assembly is chromosome complete and significantly improves the assembly in key areas such as the M/m sex-determining locus. Release of the updated genome assembly has precipitated the need to reprocess historical functional genomic data sets, including cis -regulatory element (CRE) maps that had previously been generated for A. aegypti. Results We re-processed and re-analyzed the A. aegypti whole embryo FAIRE seq data to createmore »an updated embryonic CRE map for the AaegL5 genome. We validated that the new CRE map recapitulates key features of the original AaegL3 CRE map. Further, we built on the improved assembly in the M/m locus to analyze overlaps of open chromatin regions with genes. To support the validation, we created a new method (PeakMatcher) for matching peaks from the same experimental data set across genome assemblies. Conclusion Use of PeakMatcher software, which is available publicly under an open-source license, facilitated the release of an updated and validated CRE map, which is available through the NIH GEO. These findings demonstrate that PeakMatcher software will be a useful resource for validation and transferring of previous annotations to updated genome assemblies.« less
    Free, publicly-accessible full text available December 1, 2022
  2. The increasing study of emerging wildlife pathogens and a lack of policy or legislation regulating their translocation and use has heightened concerns about laboratory escape, species spillover, and subsequent epizootics among animal populations. Responsible self-regulation by research laboratories, in conjunction with institutional-level safeguards, has an important role in mitigating pathogen transmission and spillover, as well as potential interspecies pathogenesis. A model system in disease ecology that highlights these concerns and related amelioration efforts is research focused on amphibian emerging infectious diseases. Whereas laboratory escape of amphibian pathogens has not been reported and may be rare compared with introduction events frommore »trade or human globalization, the threat that novel disease outbreaks with mass mortality effects pose to wild populations warrants thorough biosecurity measures to ensure containment and prevent spillover. Here, we present a case study of the laboratory biosecurity concerns for the emerging amphibian fungal pathogen Batrachochytrium salamandrivorans . We conclude that proactive biosecurity strategies are needed to integrate researcher and institutional oversight of aquatic wildlife pathogens generally, and we call for increased national and international policy and legislative enforcement. Furthermore, taking professional responsibility beyond current regulations is needed as development of legal guidance can be slow at national and international levels. We outline the need for annual laboratory risk assessments, comprehensive training for all laboratory personnel, and appropriate safeguards specific to pathogens under study. These strategies are critical for upholding the integrity and credibility of the scientific community and maintaining public support for research on wildlife diseases.« less
    Free, publicly-accessible full text available December 16, 2022
  3. Abstract Habits are inflexible behaviors that develop after extensive repetition, and overreliance on habits is a hallmark of many pathological states. The striatum is involved in the transition from flexible to inflexible responding, and interspersed throughout the striatum are patches, or striosomes, which make up ~15% of the volume of the striatum relative to the surrounding matrix compartment. Previous studies have suggested that patches are necessary for normal habit formation, but it remains unknown exactly how patches contribute to habit formation and expression. Here, using optogenetics, we stimulated striatal patches in Sepw1-NP67 mice during variable interval training (VI60), which is usedmore »to establish habitual responding. We found that activation of patches at reward retrieval resulted in elevated responding during VI60 training by modifying the pattern of head entry and pressing. Further, this optogenetic manipulation reduced subsequent responding following reinforcer devaluation, suggesting modified habit formation. However, patch stimulation did not generally increase extinction rates during a subsequent extinction probe, but did result in a small ‘extinction burst’, further suggesting goal-directed behavior. On the other hand, this manipulation had no effect in omission trials, where mice had to withhold responses to obtain rewards. Finally, we utilized fast-scan cyclic voltammetry to investigate how patch activation modifies evoked striatal dopamine release and found that optogenetic activation of patch projections to the substantia nigra pars compacta (SNc) is sufficient to suppress dopamine release in the dorsal striatum. Overall, this work provides novel insight into the role of the patch compartment in habit formation, and provides a potential mechanism for how patches modify habitual behavior by exerting control over dopamine signaling.« less
    Free, publicly-accessible full text available December 1, 2022
  4. ABSTRACT WD 0145+234 is a white dwarf that is accreting metals from a circumstellar disc of planetary material. It has exhibited a substantial and sustained increase in 3–5 $\mu$m flux since 2018. Follow-up Spitzer photometry reveals that emission from the disc had begun to decrease by late 2019. Stochastic brightening events superimposed on the decline in brightness suggest the liberation of dust during collisional evolution of the circumstellar solids. A simple model is used to show that the observations are indeed consistent with ongoing collisions. Rare emission lines from circumstellar gas have been detected at this system, supporting the emerging picture ofmore »white dwarf debris discs as sites of collisional gas and dust production.« less
    Free, publicly-accessible full text available July 7, 2022
  5. Free, publicly-accessible full text available June 1, 2022
  6. Taguchi, Y-h. (Ed.)
  7. Free, publicly-accessible full text available April 23, 2022
  8. Free, publicly-accessible full text available August 1, 2022
  9. Sinkhole collapse may result in significant property damage and even loss of life. Early detection of sinkhole attributes (buried voids, raveling zones) is critical to limit the cost of remediation. One of the most promising ways to obtain subsurface imaging is 3D seismic full-waveform inversion. For demonstration, a recently developed 3D Gauss-Newton full-waveform inversion (3D GN-FWI) method is used to detect buried voids, raveling soils, and characterize variable subsurface soil/rock layering. It is based on a finite-difference solution of 3D elastic wave equations and Gauss-Newton optimization. The method is tested first on a data set constructed from the numerical simulationmore »of a challenging synthetic model and subsequently on field data collected from two separate test sites in Florida. For the field tests, receivers and sources are placed in uniform 2D surface grids to acquire the seismic wavefields, which then are inverted to extract the 3D subsurface velocity structures. The inverted synthetic results suggest that the approach is viable for detecting voids and characterizing layering. The field seismic results reveal that the 3D waveform analysis identified a known manmade void (plastic culvert), unknown natural voids, raveling, as well as laterally variable soil/rock layering including rock pinnacles. The results are confirmed later by standard penetration tests, including depth to bedrock, two buried voids, and a raveling soil zone. Our study provides insight into the application of the 3D seismic FWI technique as a powerful tool in detecting shallow voids and other localized subsurface features.« less