A Distributed and Incremental SVD Algorithm for Agglomerative Data Analysis on Large Networks

In this paper, we show that the SVD of a matrix can be constructed efficiently in a hierarchical approach. Our algorithm is proven to recover the singular values and left singular vectors if the rank of the input matrix $A$ is known. Further, the hierarchical algorithm can be used to recover the $d$ largest singular values and left singular vectors with bounded error. We also show that the proposed method is stable with respect to roundoff errors or corruption of the original matrix entries. Numerical experiments validate the proposed algorithms and parallel cost analysis

Modewise Johnson-Lindenstrauss Embeddings for Nuclear Many-Body Theory

In this work, we explore modewise Johnson-Lindenstrauss embeddings (JLEs) as a tool to reduce the computational cost and memory requirements of nuclear many-body methods. JLEs are randomized projections of high-dimensional data tensors onto low-dimensional subspaces that preserve key structural features. Such embeddings allow for the oblivious and incremental compression of large tensors, e.g., the nuclear Hamiltonian, into significantly smaller random sketches that still allow for the accurate calculation of ground-state energies and other observables. Their oblivious character makes it possible to compress a tensor without knowing in advance exactly what observables one might want to approximate at a later time. This opens the door for the use of tensors that are much too large to store in memory, e.g., complete two-plus three-nucleon Hamiltonians in large, symmetry-unrestricted bases. Such compressed Hamiltonians can be stored and used later on with relative ease. As a first step, we analyze the JLE's impact on the second-order Many-Body Perturbation Theory (MBPT) corrections for nuclear ground-state observables. Numerical experiments for a wide range of closed-shell nuclei, model spaces and state-of-the-art nuclear interactions demonstrate the validity and potential of the proposed approach: We can compress nuclear Hamiltonians hundred- to thousand-fold while only incurring mean relative errors of 1\% or less in ground-state observables. Importantly, we show that JLEs capture the relevant physical information contained in the highly structured Hamiltonian tensor despite their random characteristics. In addition to the significant storage savings, the achieved compressions imply multiple order-of magnitude reductions in computational effort when the compressed Hamiltonians are used in higher-order MBPT or nonperturbative many-body methods.Comment: 23 pages, 14 figure

Functional redundancy of two C. elegans homologs of the histone chaperone Asf1 in germline DNA replication

AbstractEukaryotic genomes contain either one or two genes encoding homologs of the highly conserved histone chaperone Asf1, however, little is known of their in vivo roles in animal development. UNC-85 is one of the two Caenorhabditis elegans Asf1 homologs and functions in post-embryonic replication in neuroblasts. Although UNC-85 is broadly expressed in replicating cells, the specificity of the mutant phenotype suggested possible redundancy with the second C. elegans Asf1 homolog, ASFL-1. The asfl-1 mRNA is expressed in the meiotic region of the germline, and mutants in either Asf1 genes have reduced brood sizes and low penetrance defects in gametogenesis. The asfl-1, unc-85 double mutants are sterile, displaying defects in oogenesis and spermatogenesis, and analysis of DNA synthesis revealed that DNA replication in the germline is blocked. Analysis of somatic phenotypes previously observed in unc-85 mutants revealed that they are neither observed in asfl-1 mutants, nor enhanced in the double mutants, with the exception of enhanced male tail abnormalities in the double mutants. These results suggest that the two Asf1 homologs have partially overlapping functions in the germline, while UNC-85 is primarily responsible for several Asf1 functions in somatic cells, and is more generally involved in replication throughout development

Are we there yet? Laboratory preparedness for emerging infectious diseases

The West African Ebola virus epidemic of 2013–2016 was the most widespread epidemic of this disease in history; it is estimated that this occurrence contributed to more than 11000 deaths. During the epidemic, healthcare workers (HCW)8 (including laboratorians) were mobilized to care for individuals with suspected or confirmed Ebola virus disease (EVD). However, at the height of the epidemic, guidance on appropriate safety measures for laboratory workers manipulating specimens from EVD patients was sparse. This highlighted the need for data and guidelines for laboratories testing specimens not only for patients with EVD, but for any emerging infectious disease. During the Ebola epidemic, questions were raised about the roles and responsibilities of laboratories in responding to highly infectious diseases, and the burden of ongoing readiness for rare events. As the outbreak decelerates, laboratorians must regroup, gather data, and prepare for future outbreaks. We have asked 4 experts in this field to share their thoughts on contemporary challenges in laboratory preparedness for emerging infectious disease

New Insights into HTLV-1 Particle Structure, Assembly, and Gag-Gag Interactions in Living Cells

Human T-cell leukemia virus type 1 (HTLV-1) has a reputation for being extremely difficult to study in cell culture. The challenges in propagating HTLV-1 has prevented a rigorous analysis of how these viruses replicate in cells, including the detailed steps involved in virus assembly. The details for how retrovirus particle assembly occurs are poorly understood, even for other more tractable retroviral systems. Recent studies on HTLV-1 using state-of-the-art cryo-electron microscopy and fluorescence-based biophysical approaches explored questions related to HTLV-1 particle size, Gag stoichiometry in virions, and Gag-Gag interactions in living cells. These results provided new and exciting insights into fundamental aspects of HTLV-1 particle assembly—which are distinct from those of other retroviruses, including HIV-1. The application of these and other novel biophysical approaches promise to provide exciting new insights into HTLV-1 replication