An Improved Annual Chronology of U.S. Business Cycles since the 1790's

The NBER's pre-WWI chronology of annual peaks and troughs has the remarkable implication that the U.S. economy spent nearly every other year in recession, although previous research has argued that the post-Civil War dates are flawed. This paper extends that research by redating annual peaks and troughs for the entire 1796-1914 period using a single metric: Davis' (2004) annual industrial production index. The new pre-WWI chronology alters more than 40% of the peak and troughs, and removes cycles long considered the most questionable. An important implication of the new chronology is the lack of discernible differences in the frequency and duration of industrial cycles among the pre-Civil War, Civil War to WWI, and post-WWII periods. Of course, my comparison between pre-WWI and post-WWII cycles is limited by its reliance on a single annual index (as opposed to many monthly series) that is less comprehensive than GDP.

Glow in the Dark Matter: Observing galactic halos with scattered light

We consider the observation of diffuse halos of light around the discs of spiral galaxies, as a probe of the interaction cross section between Dark Matter and photons. Using the galaxy M101 as an example, we show that for a scattering cross section at the level of 10^(-23) x (m/GeV) cm^2 or greater Dark Matter in the halo will scatter light out from the more luminous centre of the disc to larger radii, contributing to an effective increased surface brightness at the edges of the observed area on the sky. This allows us to set an upper limit on the DM-photon cross section using data from the Dragonfly instrument. We then show how to improve this constraint, and the potential for discovery, by combining the radial profile of DM-photon scattering with measurements at multiple wavelengths. Observation of diffuse light presents a new and potentially powerful way to probe the interactions of Dark Matter with photons, which is complimentary to existing searches.Comment: 6 pages, 3 figures: v2 matches version accepted to PRL, with an extended discussion of potential background

The Antebellum U.S. Iron Industry: Domestic Production and Foreign Competition

This paper presents new annual estimates of U.S. production of pig iron and imports of pig iron products dating back to 1827. These estimates are used to assess the vulnerability of the antebellum iron industry to foreign competition and the role of the tariff in fostering the industry's early development. Domestic pig iron production is found to be highly sensitive to changes in import prices. Although import price fluctuations had a much greater impact on U.S. production than changes in import duties, our estimates suggest that the tariff permitted domestic output to be about thirty to forty percent larger than it would have been without protection.

Shocking Signals of Dark Matter Annihilation

We examine whether charged particles injected by self-annihilating Dark Matter into regions undergoing Diffuse Shock Acceleration (DSA) can be accelerated to high energies. We consider three astrophysical sites where shock acceleration is supposed to occur, namely the Galactic Centre, galaxy clusters and Active Galactic Nuclei (AGN). For the Milky Way, we find that the acceleration of cosmic rays injected by dark matter could lead to a bump in the cosmic ray spectrum provided that the product of the efficiency of the acceleration mechanism and the concentration of DM particles is high enough. Among the various acceleration sources that we consider (namely supernova remnants (SNRs), Fermi bubbles and AGN jets), we find that the Fermi bubbles are a potentially more efficient accelerator than SNRs. However both could in principle accelerate electrons and protons injected by dark matter to very high energies. At the extragalactic level, the acceleration of dark matter annihilation products could be responsible for enhanced radio emission from colliding clusters and prediction of an increase of the anti-deuteron flux generated near AGNs.Comment: 9 pages, 4 figure

Pax3/7 genes reveal conservation and divergence in the arthropod segmentation hierarchy

AbstractSeveral features of Pax3/7 gene expression are shared among distantly related insects, including pair-rule, segment polarity, and neural patterns. Recent data from arachnids imply that roles in segmentation and neurogenesis are likely to be played by Pax3/7 genes in all arthropods. To further investigate Pax3/7 genes in non-insect arthropods, we isolated two monoclonal antibodies that recognize the products of Pax3/7 genes in a wide range of taxa, allowing us to quickly survey Pax3/7 expression in all four major arthropod groups. Epitope analysis reveals that these antibodies react to a small subset of Paired-class homeodomains, which includes the products of all known Pax3/7 genes. Using these antibodies, we find that Pax3/7 genes in crustaceans are expressed in an early broad and, in one case, dynamic domain followed by segmental stripes, while myriapods and chelicerates exhibit segmental stripes that form early in the posterior-most part of the germ band. This suggests that Pax3/7 genes acquired their role in segmentation deep within, or perhaps prior to, the arthropod lineage. However, we do not detect evidence of pair-rule patterning in either myriapods or chelicerates, suggesting that the early pair-rule expression pattern of Pax3/7 genes in insects may have been acquired within the crustacean–hexapod lineage

Understanding and harnessing energy-dependent proteolysis for controlled protein degradation in bacteria

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2010.Cataloged from PDF version of thesis.Includes bibliographical references.Regulated intracellular protein degradation is critical for cellular viability. In many organisms, degradation controls cell-cycle progression, executes responses to stress-inducing environmental changes, and enables the rapid depletion of unwanted or deleterious proteins. In bacteria, most processive protein degradation is carried out by a family of AAA+ compartmentalized proteases. These molecular machines convert the chemical energy of ATP binding and hydrolysis into mechanical work, forcefully unfolding their substrates as a prelude to proteolysis. The AAA+ ClpXP protease, recognizes short peptide tags (degrons) in substrate proteins either directly or with the aid of dedicated specificity factors (adaptors). The prior identification and detailed biochemical characterization of an efficient ClpXP degron (the ssrA tag) and cognate adaptor (SspB) serve as powerful tools and enable the mechanistic studies presented here. In Chapter 2, I describe a collaborative investigation of substrate denaturation and degradation by ClpXP with single-molecule resolution. Detailed kinetic analysis of these experiments revealed homogenous protease activity across the population of enzymes with comparable levels of microscopic and macroscopic ClpXP activity. These experiments required the development of methods to attach ClpXP to surfaces and stabilize the multimeric enzyme at sub-nanomolar concentrations, advances that should be applicable to future single-molecule studies of complex protein machines. Subsequent chapters describe the development of molecular tools that harness our understanding of targeted proteolysis and enable small-molecule control of degradation. By engineering synthetic substrates, adaptors and proteases, I directly test models previously proposed to explain adaptor function and identify the minimal requirements for adaptor-mediated substrate delivery. Many different configurations of protease and adaptor domains lead to efficient, predictable substrate degradation and demonstrate the highly modular nature of this system. These tools allow for facile, small-molecule controlled protein degradation in vivo and should be valuable in basic research and biotechnology. I also describe a family of synthetic insulated promoters that allow predictable, context-independent levels of protein synthesis.by Joseph H. Davis.Ph.D

Harvests and Business Cycles in Nineteenth-Century America

Most major American industrial business cycles from around 1880 to the First World War were caused by fluctuations in the size of the cotton harvest due to economically exogenous factors such as weather. Wheat and corn harvests did not affect industrial production; nor did the cotton harvest before the late 1870s. The unique effect of the cotton harvest in this period can be explained as an essentially monetary phenomenon, the result of interactions between harvests, international gold flows and high-powered money demand under America's gold-standard regime of 1879-1914.

3‐Deaza‐Adenosine Inhibition of Stimulus‐Response Coupling in Human Polymorphonuclear Leukocytes

In an effort to define better the functional role of S‐adenosyl‐methionine‐mediated methylation reactions in modulating polymorphonuclear (PMN) functional responses to chemotactic stimuli, we investigated the effects of 3‐deaza‐adenosine (3‐DZA), a known inhibitor of methylation reactions in phagocytic cells, on formyl methionyl‐leucyl‐phenylalanine (FMLP)‐induced responses in human PMN leukocytes. Using the fluorescent cyanine dye 3,3’‐dipropylthiocarbocyanine (di‐S‐C3‐(5)) as an optical probe of membrane potential we observed that 3‐DZA at concentrations that inhibit FMLP‐induced O2− production does not significantly alter FMLP‐induced changes in transmembrane potential. Additional studies showed an inhibitory effect of 3‐DZA on FMLP‐induced PMN pinocytosis and to a lesser degree on FMLP‐induced degranulation. However, pretreatment of PMNs with 3‐DZA did not alter FMLP‐induced changes in Quin‐2 fluorescence, an indicator of changes in intracellular calcium levels. These findings demonstrate a dissociation between chemotactic factor‐induced cell membrane depolarization, changes in intracellular calcium, and specific neutrophil functional responses and suggest that chemotactic factor‐induced changes in transmembrane potential and intracellular calcium are independent of chemotactic factor‐induced methylation reactions. Furthermore, 3‐DZA did not alter phorbol myristate acetate induced O2− production or fluid pinocytosis indicating a stimulus specificity for the inhibitory effects of this agent on O2− production.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141044/1/jlb0121.pd

Reconstructing continuous distributions of 3D protein structure from cryo-EM images

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of proteins and other macromolecular complexes at near-atomic resolution. In single particle cryo-EM, the central problem is to reconstruct the three-dimensional structure of a macromolecule from $10^{4-7}$ noisy and randomly oriented two-dimensional projections. However, the imaged protein complexes may exhibit structural variability, which complicates reconstruction and is typically addressed using discrete clustering approaches that fail to capture the full range of protein dynamics. Here, we introduce a novel method for cryo-EM reconstruction that extends naturally to modeling continuous generative factors of structural heterogeneity. This method encodes structures in Fourier space using coordinate-based deep neural networks, and trains these networks from unlabeled 2D cryo-EM images by combining exact inference over image orientation with variational inference for structural heterogeneity. We demonstrate that the proposed method, termed cryoDRGN, can perform ab initio reconstruction of 3D protein complexes from simulated and real 2D cryo-EM image data. To our knowledge, cryoDRGN is the first neural network-based approach for cryo-EM reconstruction and the first end-to-end method for directly reconstructing continuous ensembles of protein structures from cryo-EM images