Intersection Information based on Common Randomness

The introduction of the partial information decomposition generated a flurry of proposals for defining an intersection information that quantifies how much of "the same information" two or more random variables specify about a target random variable. As of yet, none is wholly satisfactory. A palatable measure of intersection information would provide a principled way to quantify slippery concepts, such as synergy. Here, we introduce an intersection information measure based on the G\'acs-K\"orner common random variable that is the first to satisfy the coveted target monotonicity property. Our measure is imperfect, too, and we suggest directions for improvement.Comment: 19 pages, 5 figure

Partial Reconstruction of the Ergot Alkaloid Pathway by Heterologous Gene Expression in Aspergillus nidulans

Ergot alkaloids are pharmaceutically and agriculturally important secondary metabolites produced by several species of fungi. Ergot alkaloid pathways vary among different fungal lineages, but the pathway intermediate chanoclavine-I is evolutionarily conserved among ergot alkaloid producers. At least four genes, dmaW, easF, easE, and easC, are necessary for pathway steps prior to chanoclavine-I; however, the sufficiency of these genes for chanoclavine-I synthesis has not been established. A fragment of genomic DNA containing dmaW, easF, easE, and easC was amplified from the human-pathogenic, ergot alkaloid-producing fungus Aspergillus fumigatus and transformed into Aspergillus nidulans, a model fungus that does not contain any of the ergot alkaloid synthesis genes. HPLC and LC-MS analyses demonstrated that transformed A. nidulans strains produced chanoclavine-I and an earlier pathway intermediate. Aspergillus nidulans transformants containing dmaW, easF, and either easE or easC did not produce chanoclavine-I but did produce an early pathway intermediate and, in the case of the easC transformant, an additional ergot alkaloid-like compound. We conclude that dmaW, easF, easE, and easC are sufficient for the synthesis of chanoclavine-I in A. nidulans and expressing ergot alkaloid pathway genes in A. nidulans provides a novel approach to understanding the early steps in ergot alkaloid synthesis

Nature\u27s Assembly Line Logic for Natural Products

Nature fashions a very large number of diverse products (molecular weights ranging from ca. 200 to 2000 daltons) from simple monomeric metabolites used in primary metabolism. These include polyketide scaffolds generated from the simple C₃ malonyl CoA and C₄ methylmalonyl CoA monomers and nonribosomal peptides made from both the 20 proteinogenic amino acids and dozens of nonpoteinogenic amino acids.¹ A large family of terpenoid skeletons are built from the Δ²- and Δ³-alkene isomers of the biological isoprene monomer, isoprenyl-pyrophosphate.

The Hurricane Exposure, Adversity, and Recovery Tool (HEART): Developing and Validating a Risk Screening Instrument for Youth Exposed to Hurricane Harvey

Given the increasing regularity with which severe (named) hurricanes arise, there is a need for valid, practically useful measures that facilitate child-centered post-hurricane situation analysis and needs assessment. Measures that accurately assess the most potent hurricane-related risk factors are essential to identifying youth at risk for developing posttraumatic stress reactions and providing them with effective post-disaster support. With feedback from community stakeholders (e.g., school personnel, physicians and hospital staff, community clinicians), we developed the Hurricane Exposure, Adversity, and Recovery Tool (HEART), a 29-item self-report measure of hurricane risk factors. Test development procedures included: (1) Reviewing the literature regarding hurricane exposure-related risk factors in youth; (2) Generating a developmentally-informed test item pool; (3) Conducting interviews with clinicians, as well as youth impacted by Hurricane Harvey, to evaluate the comprehensibility and acceptability of candidate items; and (4) evaluating endorsement rates for hurricane exposure-related risk factors among (N = 107) youth in an outpatient clinic specializing in the treatment of childhood trauma and loss. Disaster-related exposure, pre-existing indicators of risk, and ongoing post-disaster adversities were correlated with posttraumatic stress and depressive symptoms. These results provide support for an integrative approach to post-hurricane screening for both hurricane-specific (e.g., witnessing injuries) and non-specific (e.g., prior trauma) factors

TISCC: A Surface Code Compiler and Resource Estimator for Trapped-Ion Processors

We introduce the Trapped-Ion Surface Code Compiler (TISCC), a software tool that generates circuits for a universal set of surface code patch operations in terms of a native trapped-ion gate set. To accomplish this, TISCC manages an internal representation of a trapped-ion system where a repeating pattern of trapping zones and junctions is arranged in an arbitrarily large rectangular grid. Surface code operations are compiled by instantiating surface code patches on the grid and using methods to generate transversal operations over data qubits, rounds of error correction over stabilizer plaquettes, and/or lattice surgery operations between neighboring patches. Beyond the implementation of a basic surface code instruction set, TISCC contains corner movement functionality and a patch translation that is implemented using ion movement alone. Except in the latter case, all TISCC functionality is extensible to alternative grid-like hardware architectures. TISCC output has been verified using the Oak Ridge Quasi-Clifford Simulator (ORQCS).Comment: 10 pages, 5 figures. Software to be released at https://github.com/ORNL-QCI/TISC

Community-acquired pneumonia in children: cell-free plasma sequencing for diagnosis and management.

Community-acquired pneumonia (CAP) is a common cause of pediatric hospital admission. Empiric antibiotic therapy for hospitalized children with serious CAP now targets the most likely pathogen(s), including those that may demonstrate significant antibiotic resistance. Cell-free plasma next-generation sequencing (CFPNGS) was first made available for Pediatric Infectious Diseases physicians in June 1, 2017, to supplement standard-of-care diagnostic techniques. A retrospective chart review was performed for children hospitalized with CAP between June 1, 2017, and January 22, 2018, to evaluate the impact of CFPNGS. We identified 15 hospitalized children with CAP without other underlying medical conditions for whom CFPNGS was performed. CFPNGS identified a pathogen in 13 of 15 (86%) children compared with 47% for those using standard culture and PCR-based methods alone. Changes in antibiotic management were made in 7 of 15 (47%) of children as a result of CFPNGS

FIREBALL: Instrument pointing and aspect reconstruction

The Faint Intergalactic Redshifted Emission Balloon (FIREBALL) had its first scientific flight in June 2009. The instrument is a 1 meter class balloon-borne telescope equipped with a vacuum-ultraviolet integral field spectrograph intended to detect emission from the inter-galactic medium at redshifts 0.3 < z < 1.0. The scientific goals and the challenging environment place strict constraints on the pointing and tracking systems of the gondola. In this manuscript we briefly review our pointing requirements, discuss the methods and solutions used to meet those requirements, and present the aspect reconstruction results from the first successful scientific flight

An Unusual Case of Bony Styloid Processes That Extend to the Hyoid Bone

The embryological origin of the hyoid bone is a point of uncertainty, with controversy surrounding the relative contribution of the second pharyngeal arch to hyoid development. We encountered a 52-year-old male with bilateral bony styloid extension to the lesser cornu of the hyoid bone during the workup of a patient with laryngeal cancer. This embryological malformation clearly supports the hypothesis that the second pharyngeal arch gives rise to the lesser cornu and demonstrates an unusual clinical finding that may be encountered by otolaryngologists. We demonstrate the imaging findings and surgical management of this unusual anatomical variant and review the embryological basis for this rare malformation