Pulsar Discoveries and their Exploitation

Pulsars are the rapidly-rotating, highly-magnetized, neutron star remnants of the supernova explosions of massive stars. Pulsars have been used in a wide variety of studies of astronomy and physics. Of the >2500 pulsars now known, most were found in blind, large-scale searches at radio frequencies. The PALFA survey at the Arecibo Observatory is an example of this type of search. I present details of the PALFA data analysis software that I designed, which has already been used to discover 40 pulsars, bringing the total number of discoveries in the survey to 144 pulsars. Additionally, I implemented a novel technique for reliably measuring the survey’s sensitivity in the presence of terrestrial interference and red noise. The sensitivity determined with my technique agrees with theoretical predictions for millisecond-period pulsars (MSPs), but is reduced for long-period (P ∼ > 100 ms) pulsars. Simulations suggest that this reduction in sensitivity should result in 33 ± 3% fewer detections than expected, which corresponds to 224 ± 16 pulsars detected, given the observations to date. This result is consistent with the 241 pulsars actually detected. In general, pulsar timing analyses based on long-term monitoring campaigns are extremely productive scientifically. My collaborators and I conducted such an analysis for PSR J1952+2630, a 20.7-ms pulsar in a binary system with a massive white dwarf companion, found in the PALFA survey. Our analysis made it possible to constrain the evolutionary history of the binary system and the composition of the pulsar’s companion. Furthermore, our simulations of future observations of PSR J1952+2630 indicate that this system will be useful in constraining theories of relativistic gravity in the next ∼10 years. To maximize the scientific potential of MSPs, Pulsar Timing Array (PTA) projects conduct long-term, large-scale observing campaigns with many of the world’s largest radio telescopes. For example, as part of the European Pulsar Timing Array (EPTA), the Effelsberg 100-m radio telescope regularly observes ∼50 MSPs with PSRIX, a new data recording instrument installed in 2011. The first four years of these data have been reduced with the automated software that I developed. By comparing the PSRIX data with results from the previous instrument, the Effelsberg-Berkeley Pulsar Proces- sor, I found that PSRIX provides significantly greater sensitivity. With this increased sensitivity, I estimated the improvement in our chances of detecting the low-frequency gravitational wave background (GWB) with MSPs, one of the main goals of PTAs. A major obstacle to this detection is the effect of interstellar medium variations. With this in mind, I conducted observations at 5 and 9 GHz with PSRIX and showed that by pushing PTA observations to higher frequencies, it may be possible to mitigate this source of noise and further enhance the sensitivity to the GWB. Observations from the EPTA have been combined with data from the International Pulsar Timing Array (IPTA) community to form the largest, most sensitive pulsar timing data set ever assembled. This unique data set has many diverse applications. For instance, I am using it to measure the masses of the Solar System planets. My on- going analysis already provides results consistent with previous studies, and thus can be used to verify the quality of the IPTA data set, a key first step towards exploiting its unrivalled sensitivity

Host-symbiont stability and fast evolutionary rates in an ant-bacterium association : cospeciation of Camponotus species and their endosymbionts, Candidatus Blochmannia

Author Posting. © Society of Systematic Biologists, 2004. This article is posted here by permission of Taylor and Francis for personal use, not for redistribution. The definitive version was published in Systematic Biology 53 (2004): 95-110, doi:10.1080/10635150490264842.Bacterial endosymbionts are widespread across several insect orders and are involved in interactions ranging from obligate mutualism to reproductive parasitism. Candidatus Blochmannia gen. nov. (Blochmannia) is an obligate bacterial associate of Camponotus and related ant genera (Hymenoptera: Formicidae). The occurrence of Blochmannia in all Camponotus species sampled from field populations and its maternal transmission to host offspring suggest that this bacterium is engaged in a long-term, stable association with its ant hosts. However, evidence for cospeciation in this system is equivocal because previous phylogenetic studies were based on limited gene sampling, lacked statistical analysis of congruence, and have even suggested host switching. We compared phylogenies of host genes (the nuclear EF-1alphaF2 and mitochondrial COI/II) and Blochmannia genes (16S ribosomal DNA [rDNA], groEL, gidA, and rpsB), totaling more than 7 kilobases for each of 16 Camponotus species. Each data set was analyzed using maximum likelihood and Bayesian phylogenetic reconstruction methods. We found minimal conflict among host and symbiont phylogenies, and the few areas of discordance occurred at deep nodes that were poorly supported by individual data sets. Concatenated protein-coding genes produced a very well-resolved tree that, based on the Shimodaira-Hasegawa test, did not conflict with any host or symbiont data set. Correlated rates of synonymous substitution (dS) along corresponding branches of host and symbiont phylogenies further supported the hypothesis of cospeciation. These findings indicate that Blochmannia-Camponotus symbiosis has been evolutionarily stable throughout tens of millions of years. Based on inferred divergence times among the ant hosts, we estimated rates of sequence evolution of Blochmannia to be sim0.0024 substitutions per site per million years (s/s/MY) for the 16S rDNA gene and sim0.1094 s/s/MY at synonymous positions of the genes sampled. These rates are several-fold higher than those for related bacteria Buchnera aphidicola and Escherichia coli. Phylogenetic congruence among Blochmannia genes indicates genome stability that typifies primary endosymbionts of insects.Funding for this research was provided by the NIH (R01 GM62626-01), the NSF (DEB 0089455 and associated REU supplement award), the NASA Astrobiology Institute (NCC2-1054), and the Josephine Bay Paul and C. Michael Paul Foundation

In pursuit of happiness : Creation of an academic hospitalist wellness committee and well-being survey

Physician burnout poses a critical threat to the delivery of healthcare. A solution to this problem is a leadership imperative. Managing demands on physicians can prevent burnout and foster engagement. This study assesses stress and burnout within an academic hospitalist group and identifies areas to focus interventions on both personal and systemic levels.Includes bibliographical reference

Genetic Activation, Inactivation, and Deletion Reveal a Limited And Nuanced Role for Somatostatin-Containing Basal Forebrain Neurons in Behavioral State Control

Recent studies have identified an especially important role for basal forebrain GABAergic (BF(VGAT)) neurons in the regulation of behavioral waking and fast cortical rhythms associated with cognition. However, BF(VGAT) neurons comprise several neurochemically and anatomically distinct subpopulations, including parvalbumin-containing BF(VGAT) neurons and somatostatin-containing BF(VGAT) neurons (BF(SOM) neurons), and it was recently reported that optogenetic activation of BF(SOM) neurons increases the probability of a wakefulness to non-rapid-eye movement (NREM) sleep transition when stimulated during the rest period of the animal. This finding was unexpected given that most BF(SOM) neurons are not NREM sleep active and that central administration of the synthetic somatostatin analog, octreotide, suppresses NREM sleep or increases REM sleep. Here we used a combination of genetically driven chemogenetic and optogenetic activation, chemogenetic inhibition, and ablation approaches to further explore the in vivo role of BF(SOM) neurons in arousal control. Our findings indicate that acute activation or inhibition of BF(SOM) neurons is neither wakefulness nor NREM sleep promoting and is without significant effect on the EEG, and that chronic loss of these neurons is without effect on total 24 h sleep amounts, although a small but significant increase in waking was observed in the lesioned mice during the early active period. Our in vitro cell recordings further reveal electrophysiological heterogeneity in BF(SOM) neurons, specifically suggesting at least two distinct subpopulations. Together, our data support the more nuanced view that BF(SOM) neurons are electrically heterogeneous and are not NREM sleep or wake promoting per se, but may exert, in particular during the early active period, a modest inhibitory influence on arousal circuitry.SIGNIFICANCE STATEMENT The cellular basal forebrain (BF) is a highly complex area of the brain that is implicated in a wide range of higher-level neurobiological processes, including regulating and maintaining normal levels of electrocortical and behavioral arousal. The respective in vivo roles of BF cell populations and their neurotransmitter systems in the regulation of electrocortical and behavioral arousal remains incompletely understood. Here we seek to define the neurobiological contribution of GABAergic somatostatin-containing BF neurons to arousal control. Understanding the respective contribution of BF cell populations to arousal control may provide critical insight into the pathogenesis of a host of neuropsychiatric and neurodegenerative disorders, including Alzheimer\u27s disease, Parkinson\u27s disease, schizophrenia, and the cognitive impairments of normal aging

Indications of a positive feedback between coastal development and beach nourishment

Beach nourishment, a method for mitigating coastal storm damage or chronic erosion by deliberately replacing sand on an eroded beach, has been the leading form of coastal protection in the United States for four decades. However, investment in hazard protection can have the unintended consequence of encouraging development in places especially vulnerable to damage. In a comprehensive, parcel-scale analysis of all shorefront single-family homes in the state of Florida, we find that houses in nourishing zones are significantly larger and more numerous than in non-nourishing zones. The predominance of larger homes in nourishing zones suggests a positive feedback between nourishment and development that is compounding coastal risk in zones already characterized by high vulnerability

SARS-CoV-2 elimination, not mitigation, creates best outcomes for health, the economy, and civil liberties

International audienc

Raritas: a program for counting high diversity categorical data with highly unequal abundances

Acquiring data on the occurrences of many types of difficult to identify objects are often still made by human observation, for example, in biodiversity and paleontologic research. Existing computer counting programs used to record such data have various limitations, including inflexibility and cost. We describe a new open-source program for this purpose—Raritas. Raritas is written in Python and can be run as a standalone app for recent versions of either MacOS or Windows, or from the command line as easily customized source code. The program explicitly supports a rare category count mode which makes it easier to collect quantitative data on rare categories, for example, rare species which are important in biodiversity surveys. Lastly, we describe the file format used by Raritas and propose it as a standard for storing geologic biodiversity data. ‘Stratigraphic occurrence data’ file format combines extensive sample metadata and a flexible structure for recording occurrence data of species or other categories in a series of samples

Small genome of Candidatus Blochmannia, the bacterial endosymbiont of Camponotus, implies irreversible specialization to an intracellular lifestyle

Blochmannia (Candidatus Blochmannia gen. nov.) is the primary bacterial endosymbiont of the ant genus Camponotus. Like other obligate endosymbionts of insects, Blochmannia occurs exclusively within eukaryotic cells and has experienced long-term vertical transmission through host lineages. In this study, PFGE was used to estimate the genome size of Blochmannia as approximately 800 kb, which is significantly smaller than its free-living relatives in the enterobacteria. This small genome implies that Blochmannia has deleted most of the genetic machinery of related free-living bacteria. Due to restricted gene exchange in obligate endosymbionts, the substantial gene loss in Blochmannia and other insect mutualists may reflect irreversible specialization to a host cellular environment

Indications of a positive feedback between coastal development and beach nourishment: COASTAL DEVELOPMENT BEACH NOURISHMENT

Beach nourishment, a method for mitigating coastal storm damage or chronic erosion by deliberately replacing sand on an eroded beach, has been the leading form of coastal protection in the United States for four decades. However, investment in hazard protection can have the unintended consequence of encouraging development in places especially vulnerable to damage. In a comprehensive, parcel‐scale analysis of all shorefront single‐family homes in the state of Florida, we find that houses in nourishing zones are significantly larger and more numerous than in non‐nourishing zones. The predominance of larger homes in nourishing zones suggests a positive feedback between nourishment and development that is compounding coastal risk in zones already characterized by high vulnerability

Identification and manipulation of the pleuromutilin gene cluster from Clitopilus passeckerianus for increased rapid antibiotic production

Semi-synthetic derivatives of the tricyclic diterpene antibiotic pleuromutilin from the basidiomycete Clitopilus passeckerianus are important in combatting bacterial infections in human and veterinary medicine. These compounds belong to the only new class of antibiotics for human applications, with novel mode of action and lack of cross-resistance, representing a class with great potential. Basidiomycete fungi, being dikaryotic, are not generally amenable to strain improvement. We report identification of the seven-gene pleuromutilin gene cluster and verify that using various targeted approaches aimed at increasing antibiotic production in C. passeckerianus, no improvement in yield was achieved. The seven-gene pleuromutilin cluster was reconstructed within Aspergillus oryzae giving production of pleuromutilin in an ascomycete, with a significant increase (2106%) in production. This is the first gene cluster from a basidiomycete to be successfully expressed in an ascomycete, and paves the way for the exploitation of a metabolically rich but traditionally overlooked group of fungi