WHAT IS A RECESSION?: A REPRISE.

This paper draws its title from a paper written over 30 years ago by Geoffrey H. Moore (1967). Why the need for a reprise? First, there would appear currently to be somewhat diverging views – particularly in Australia – as to what properly constitutes a recession. Second, largely as a result of this, in Australia and many other countries other than the US, there is no single widely-accepted business cycle chronology for the country in question. This paper will argue that in addition to an output dimension, there are other important dimensions to aggregate economic activity which need to be taken into account in determining the business cycle, viz., income, sales and employment. As such, our perspective would seem to be at odds with the apparent position taken by other recent Australian commentators on this issue who argue that GDP is all that is needed to represent Australia’s business cycle. We will also argue strongly against using the currently popular ‘two negative quarterly growth rate’ rule in dating the onset of a recession.

SOPRA: Scaffolding algorithm for paired reads via statistical optimization

<p>Abstract</p> <p>Background</p> <p>High throughput sequencing (HTS) platforms produce gigabases of short read (<100 bp) data per run. While these short reads are adequate for resequencing applications, <it>de novo </it>assembly of moderate size genomes from such reads remains a significant challenge. These limitations could be partially overcome by utilizing mate pair technology, which provides pairs of short reads separated by a known distance along the genome.</p> <p>Results</p> <p>We have developed SOPRA, a tool designed to exploit the mate pair/paired-end information for assembly of short reads. The main focus of the algorithm is selecting a sufficiently large subset of simultaneously satisfiable mate pair constraints to achieve a balance between the size and the quality of the output scaffolds. Scaffold assembly is presented as an optimization problem for variables associated with vertices and with edges of the contig connectivity graph. Vertices of this graph are individual contigs with edges drawn between contigs connected by mate pairs. Similar graph problems have been invoked in the context of shotgun sequencing and scaffold building for previous generation of sequencing projects. However, given the error-prone nature of HTS data and the fundamental limitations from the shortness of the reads, the ad hoc greedy algorithms used in the earlier studies are likely to lead to poor quality results in the current context. SOPRA circumvents this problem by treating all the constraints on equal footing for solving the optimization problem, the solution itself indicating the problematic constraints (chimeric/repetitive contigs, etc.) to be removed. The process of solving and removing of constraints is iterated till one reaches a core set of consistent constraints. For SOLiD sequencer data, SOPRA uses a dynamic programming approach to robustly translate the color-space assembly to base-space. For assessing the quality of an assembly, we report the no-match/mismatch error rate as well as the rates of various rearrangement errors.</p> <p>Conclusions</p> <p>Applying SOPRA to real data from bacterial genomes, we were able to assemble contigs into scaffolds of significant length (N50 up to 200 Kb) with very few errors introduced in the process. In general, the methodology presented here will allow better scaffold assemblies of any type of mate pair sequencing data.</p

Liver injury in COVID-19: The hepatic aspect of the respiratory syndrome — what we know so far

© 2020. All Rights Reserved. The 2019 novel coronavirus disease (COVID-19) pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a serious threat to global public health. Although primarily, the infection causes lung injury, liver enzyme abnormalities have also been reported to occur during the course of the disease. We conducted an extensive literature review using the PubMed database on articles covering a broad range of issues related to COVID-19 and hepatic injury. The present review summarizes available information on the spectrum of liver involvement, the possible mechanisms and risk factors of liver injury due to SARS-CoV-2 infection, and the prognostic significance of the presence of liver injury. Hopefully, this review will enable clinicians, especially the hepatologists, to understand and manage the liver derangements they may encounter in these atients better and provide guidance for further studies on the liver injury of COVID-19

Kinematics of flows on curved, deformable media

In this article, we first investigate the kinematics of specific geodesic flows on two dimensional media with constant curvature, by explicitly solving the evolution (Raychaudhuri) equations for the expansion, shear and rotation along the flows. We point out the existence of singular (within a finite value of the time parameter) and non-singular solutions and illustrate our results through a `phase' diagram. This diagram demonstrates under which initial conditions (or combinations thereof) we end up with a singularity in the congruence and when, if at all, we encounter non--singular solutions for the kinematic variables. Our analysis illustrates the differences which arise due to a positive or negative value of the curvature. Subsequently, we move on to geodesic flows on two dimensional spaces with varying curvature. As an example, we discuss flows on a torus, where interesting oscillatory features of the expansion, shear and rotation emerge, which are found to depend on the ratio of the radii of the torus. The singular (within a finite time)/non--singular nature of the solutions are also discussed. Finally, we arrive at some general statements and point out similarities or dissimilarities that arise in comparison to our earlier work on media in flat space.Comment: Corrections in some equations and in one figure

Epigenetic Chromatin Silencing: Bistability and Front Propagation

The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms. We formulate a coarse-grained model of chromatin silencing in yeast and study the conditions under which the system becomes bistable, allowing for different epigenetic states. We also study the dynamics of the boundary between the two locally stable states of chromatin: silenced and unsilenced. The model could be of use in guiding the discussion on chromatin silencing in general. In the context of silencing in budding yeast, it helps us understand the phenotype of various mutants, some of which may be non-trivial to see without the help of a mathematical model. One such example is a mutation that reduces the rate of background acetylation of particular histone side-chains that competes with the deacetylation by Sir2p. The resulting negative feedback due to a Sir protein depletion effect gives rise to interesting counter-intuitive consequences. Our mathematical analysis brings forth the different dynamical behaviors possible within the same molecular model and guides the formulation of more refined hypotheses that could be addressed experimentally.Comment: 19 pages, 5 figure

Discussion of a spin-cluster model for the low temperature phase of NaV_2O_5

We discuss magnetic excitations of a spin-cluster model which has been suggested to describe the low temperature phase of alpha'-NaV_2O_5. This model fulfills all symmetry criteria proposed by recent x-ray investigations. We find that this model is not able to describe the occurence of two well separated magnon lines perpendicular to the ladder direction as observed in INS experiments. We suggest further experimental analysis to generally distinguish between models with double reflection or inversion symmetry.Comment: 4 pages, 4 figures, added a calculation of level repulsio

Statistical mechanics of transcription-factor binding site discovery using Hidden Markov Models

Hidden Markov Models (HMMs) are a commonly used tool for inference of transcription factor (TF) binding sites from DNA sequence data. We exploit the mathematical equivalence between HMMs for TF binding and the "inverse" statistical mechanics of hard rods in a one-dimensional disordered potential to investigate learning in HMMs. We derive analytic expressions for the Fisher information, a commonly employed measure of confidence in learned parameters, in the biologically relevant limit where the density of binding sites is low. We then use techniques from statistical mechanics to derive a scaling principle relating the specificity (binding energy) of a TF to the minimum amount of training data necessary to learn it.Comment: 25 pages, 2 figures, 1 table V2 - typos fixed and new references adde

Overscreened Single Channel Kondo Problem

We consider the single channel Kondo problem with the Kondo coupling between a spin $S$ impurity and conduction electrons with spin $j$. These problems arise as multicritical points in the parameter spaces of two- and higher-level tunneling systems, and some impurity models of heavy fermion compounds. In contrast to the previous Bethe-anstaz conjectures, it turns out that the dynamics of the spin sector is the same as that of a spin $S$ impurity coupled to $k(j)$ channels of spin $1/2$ electrons with $k(j) = 2j(j+1)(2j+1)/3$. As a result, for $2S < k(j)$, the system shows non-Fermi liquid behavior with the same exponents for the thermodynamic quantities as those of $k(j)$ channel Kondo problem. However, both the finite-size spectrum and the operator content are different due to the presence of the other sectors and can be obtained by conformal field theory techniques.Comment: 4 pages, revtex, no figures. Revised Versio