Heavy quarkonium: progress, puzzles, and opportunities

A golden age for heavy quarkonium physics dawned a decade ago, initiated by the confluence of exciting advances in quantum chromodynamics (QCD) and an explosion of related experimental activity. The early years of this period were chronicled in the Quarkonium Working Group (QWG) CERN Yellow Report (YR) in 2004, which presented a comprehensive review of the status of the field at that time and provided specific recommendations for further progress. However, the broad spectrum of subsequent breakthroughs, surprises, and continuing puzzles could only be partially anticipated. Since the release of the YR, the BESII program concluded only to give birth to BESIII; the $B$-factories and CLEO-c flourished; quarkonium production and polarization measurements at HERA and the Tevatron matured; and heavy-ion collisions at RHIC have opened a window on the deconfinement regime. All these experiments leave legacies of quality, precision, and unsolved mysteries for quarkonium physics, and therefore beg for continuing investigations. The plethora of newly-found quarkonium-like states unleashed a flood of theoretical investigations into new forms of matter such as quark-gluon hybrids, mesonic molecules, and tetraquarks. Measurements of the spectroscopy, decays, production, and in-medium behavior of c\bar{c}, b\bar{b}, and b\bar{c} bound states have been shown to validate some theoretical approaches to QCD and highlight lack of quantitative success for others. The intriguing details of quarkonium suppression in heavy-ion collisions that have emerged from RHIC have elevated the importance of separating hot- and cold-nuclear-matter effects in quark-gluon plasma studies. This review systematically addresses all these matters and concludes by prioritizing directions for ongoing and future efforts.Comment: 182 pages, 112 figures. Editors: N. Brambilla, S. Eidelman, B. K. Heltsley, R. Vogt. Section Coordinators: G. T. Bodwin, E. Eichten, A. D. Frawley, A. B. Meyer, R. E. Mitchell, V. Papadimitriou, P. Petreczky, A. A. Petrov, P. Robbe, A. Vair

First report of potato blackleg caused by a biovar 3 Dickeya sp. in Georgia

In Western and Northern Europe, Dickeya species are causing increasingly severe economic losses in potato (Solanum tuberosum) crops. The costs of seed potato production resulting from Dickeya spp. infection are high due to rejection and declassification of seed tubers (Slawiak et al., 2009). Potato blackleg caused by Dickeya spp. is primarily a seed tuber-borne disease (Tsror et al., 2009). Symptoms including blackening of the stem base, wilting of plants and rotten seed tubers are observed. Recently, outbreaks of potato blackleg were recorded in Georgia on three cultivars, in Samtskhe-Javakheti region, Akhalkalaki district, in an area in excess of 100 hectare

Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans

A small proportion of human immunodeficiency virus-1 (HIV-1) infected individuals, termed HIV-1 controllers, suppress viral replication to very low levels in the absence of therapy. Genetic investigations of this phenotype have strongly implicated variation in the class I major histocompatibility complex (MHC) region as key to HIV-1 control. We collected sequence-based classical class I HLA genotypes at 4-digit resolution in HIV-1-infected African American controllers and progressors (n = 1107), and tested them for association with host control using genome-wide single nucleotide polymorphism data to account for population structure. Several classical alleles at HLA-B were associated with host control, including B*57:03 [odds ratio (OR) = 5.1; P= 3.4 × 10(-18)] and B*81:01 (OR = 4.8; P= 1.3 × 10(-9)). Analysis of variable amino acid positions demonstrates that HLA-B position 97 is the most significant association with host control in African Americans (omnibus P = 1.2 × 10(-21)) and explains the signal of several HLA-B alleles, including B*57:03. Within HLA-B, we also identified independent effects at position 116 (omnibus P= 2.8 × 10(-15)) in the canonical F pocket, position 63 in the B pocket (P= 1.5 × 10(-3)) and the non-pocket position 245 (P= 8.8 × 10(-10)), which is thought to influence CD8-binding kinetics. Adjusting for these HLA-B effects, there is evidence for residual association in the MHC region. These results underscore the key role of HLA-B in affecting HIV-1 replication, likely through the molecular interaction between HLA-B and viral peptides presented by infected cells, and suggest that sites outside the peptide-binding pocket also influence HIV-1 control

eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data

The recent advances in high-throughput sequencing technologies bring the potential of a better characterization of the genetic variation in humans and other organisms. In many occasions, either by design or by necessity, the sequencing procedure is performed on a pool of DNA samples with different abundances, where the abundance of each sample is unknown. Such a scenario is naturally occurring in the case of metagenomics analysis where a pool of bacteria is sequenced, or in the case of population studies involving DNA pools by design. Particularly, various pooling designs were recently suggested that can identify carriers of rare alleles in large cohorts, dramatically reducing the cost of such large-scale sequencing projects. A fundamental problem with such approaches for population studies is that the uncertainly of DNA proportions from different individuals in the pools might lead to spurious associations. Fortunately, it is often the case that the genotype data of at least some of the individuals in the pool is known. Here, we propose a method (eALPS) that uses the genotype data in conjunction with the pooled sequence data in order to accurately estimate the proportions of the samples in the pool, even in cases where not all individuals in the pool were genotyped (eALPS-LD). Using real data from a sequencing pooling study of Non-Hodgkin's Lymphoma, we demonstrate that the estimation of the proportions is crucial, since otherwise there is a risk for false discoveries. Additionally, we demonstrate that our approach is also applicable to the problem of quantification of species in metagenomics samples (eALPS-BCR), and is particularly suitable for metagenomic quantification of closely-related species. © 2013 Springer-Verlag

Biostratigraphy, Depositional Environments, and Diagenesis of the Tamana Formation, Trinidad: a Tectonic Marker Horizon

The Tamana Formation of the Central Range of Trinidad was studied in order to determine its importance in the stratigraphical and structural development of north‐eastern South America. Biostratigraphical, petrological and mineralogical data, combined with field mapping show that the Tamana sediments are composed of five distinct lithofacies: inner to outer shelf, burrowed shaley mudstone; outer shelf, Fe‐rich sandy limestone; submarine channel, conglomeratic mudstone; middle shelf to nearshore, algal‐foram packstone/grainstone; and intertidal to nearshore, algal‐stromatolite‐coral boundstone with coral bioherms. Maximum thickness of the Tamana Formation is 244 m. Deposition of the Tamana limestones occurred between the Praeorbulina glomerosa (latest early Miocene) and Globorotalia fohsi robusta (middle part of the middle Miocene) planktonic foraminiferal zones, and in a more continuous trend than is seen in the current outcrop belt. Detailed biostratigraphy shows that the Tamana Formation is a facies equivalent of the shallow‐ and deep‐water shales of the Brasso Formation, and the deep water turbidites of the Herrera Member of the Cipero Formation. The early diagenetic history of the Tamana limestones was dominated by the precipitation of authigenic glauconitic smectite, and the dissolution of skeletal grains and carbonate matrix. Late burial diagenesis was dominated by the precipitation of illite and illite/smectite. Comparative mineralogy and textural analyses indicate a minimum range of burial depth for the Tamana Formation at 800–1500m, with a maximum of 2400 m. Alteration of Fe‐bearing minerals to geothite and late fracturing occurred during post‐Pliocene tectonic uplift and unroofing of the Central Range. The Tamana Formation sediments can be used as a structural and stratigraphical event marker within the Late Tertiary geological history of Trinidad. These units record a phase of the tectonic interaction between the Caribbean and South American plates in the south‐eastern Caribbean, and reflect the onset of contractile deformation in the Central Range