198 research outputs found
Multi-Locus Variable-Number Tandem Repeat Profiling of Salmonella enterica Serovar Typhi Isolates from Blood Cultures and Gallbladder Specimens from Makassar, South-Sulawesi, Indonesia
Multi-locus variable-number tandem repeat analysis differentiated 297 Salmonella enterica serovar Typhi blood culture isolates from Makassar in 76 genotypes and a single unique S. Typhi genotype was isolated from the cholecystectomy specimens of four patients with cholelithiasis. The high diversity in S. Typhi genotypes circulating in Makassar indicates that the number of carriers could be very large, which may complicate disease prevention and control
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 -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
Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas
Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R2>0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region
Virulence of 32 Salmonella Strains in Mice
Virulence and persistence in the BALB/c mouse gut was tested for 32 strains of Salmonella enterica for which genome sequencing is complete or underway, including 17 serovars within subspecies I (enterica), and two representatives of each of the other five subspecies. Only serovar Paratyphi C strain BAA1715 and serovar Typhimurium strain 14028 were fully virulent in mice. Three divergent atypical Enteritidis strains were not virulent in BALB/c, but two efficiently persisted. Most of the other strains in all six subspecies persisted in the mouse intestinal tract for several weeks in multiple repeat experiments although the frequency and level of persistence varied considerably. Strains with heavily degraded genomes persisted very poorly, if at all. None of the strains tested provided immunity to Typhimurium infection. These data greatly expand on the known significant strain-to-strain variation in mouse virulence and highlight the need for comparative genomic and phenotypic studies
Galactic Gamma-Ray Diffuse Emission at TeV energies with HAWC Data
The Galactic gamma-ray diffuse emission (GDE) is emitted by cosmic rays
(CRs), ultra-relativistic protons and electrons, interacting with gas and
electromagnetic radiation fields in the interstellar medium. Here we present
the analysis of TeV diffuse emission from a region of the Galactic Plane over
the range in longitude of , using data collected with
the High Altitude Water Cherenkov (HAWC) detector. Spectral, longitudinal and
latitudinal distributions of the TeV diffuse emission are shown. The radiation
spectrum is compatible with the spectrum of the emission arising from a CR
population with an "index" similar to that of the observed CRs. When comparing
with the \texttt{DRAGON} \textit{base model}, the HAWC GDE flux is higher by
about a factor of two. Unresolved sources such as pulsar wind nebulae and TeV
halos could explain the excess emission. Finally, deviations of the Galactic CR
flux from the locally measured CR flux may additionally explain the difference
between the predicted and measured diffuse fluxes
Horizontal muon track identification with neural networks in HAWC
Nowadays the implementation of artificial neural networks in high-energyphysics has obtained excellent results on improving signal detection. In thiswork we propose to use neural networks (NNs) for event discrimination in HAWC.This observatory is a water Cherenkov gamma-ray detector that in recent yearshas implemented algorithms to identify horizontal muon tracks. However, thesealgorithms are not very efficient. In this work we describe the implementationof three NNs: two based on image classification and one based on objectdetection. Using these algorithms we obtain an increase in the number ofidentified tracks. The results of this study could be used in the future toimprove the performance of the Earth-skimming technique for the indirectmeasurement of neutrinos with HAWC.<br
The TeV Sun Rises: Discovery of Gamma rays from the Quiescent Sun with HAWC
We report the first detection of a TeV gamma-ray flux from the solar disk
(6.3), based on 6.1 years of data from the High Altitude Water
Cherenkov (HAWC) observatory. The 0.5--2.6 TeV spectrum is well fit by a power
law, dN/dE = , with TeV cm s and . The flux
shows a strong indication of anticorrelation with solar activity. These results
extend the bright, hard GeV emission from the disk observed with Fermi-LAT,
seemingly due to hadronic Galactic cosmic rays showering on nuclei in the solar
atmosphere. However, current theoretical models are unable to explain the
details of how solar magnetic fields shape these interactions. HAWC's TeV
detection thus deepens the mysteries of the solar-disk emission.Comment: 15 pages, 8 figures including supplementary material. Accepted for
publication in Physical Review Letter
A Contribution of the HAWC Observatory to the TeV era in the High Energy Gamma-Ray Astrophysics: The case of the TeV-Halos
We present a short overview of the TeV-Halos objects as a discovery and a
relevant contribution of the High Altitude Water \v{C}erenkov (HAWC)
observatory to TeV astrophysics. We discuss history, discovery, knowledge, and
the next step through a new and more detailed analysis than the original study
in 2017. TeV-Halos will contribute to resolving the problem of the local
positron excess observed on the Earth. To clarify the latter, understanding the
diffusion process is mandatory.Comment: Work presented in the 21st International Symposium on Very High
Energy Cosmic Ray Interactions(ISVHECRI 2022) as part of the Ph. D. Thesis of
Ramiro Torres-Escobedo (SJTU, Shanghai, China). Accepted for publication in
SciPost Physics Proceedings (ISSN 2666-4003). 11 pages, 3 Figures. Short
overview of HAWC and TeV Halos objects until 202
Adaptation and Preadaptation of Salmonella enterica to Bile
Bile possesses antibacterial activity because bile salts disrupt membranes, denature proteins, and damage DNA. This study describes mechanisms employed by the bacterium Salmonella enterica to survive bile. Sublethal concentrations of the bile salt sodium deoxycholate (DOC) adapt Salmonella to survive lethal concentrations of bile. Adaptation seems to be associated to multiple changes in gene expression, which include upregulation of the RpoS-dependent general stress response and other stress responses. The crucial role of the general stress response in adaptation to bile is supported by the observation that RpoS− mutants are bile-sensitive. While adaptation to bile involves a response by the bacterial population, individual cells can become bile-resistant without adaptation: plating of a non-adapted S. enterica culture on medium containing a lethal concentration of bile yields bile-resistant colonies at frequencies between 10−6 and 10−7 per cell and generation. Fluctuation analysis indicates that such colonies derive from bile-resistant cells present in the previous culture. A fraction of such isolates are stable, indicating that bile resistance can be acquired by mutation. Full genome sequencing of bile-resistant mutants shows that alteration of the lipopolysaccharide transport machinery is a frequent cause of mutational bile resistance. However, selection on lethal concentrations of bile also provides bile-resistant isolates that are not mutants. We propose that such isolates derive from rare cells whose physiological state permitted survival upon encountering bile. This view is supported by single cell analysis of gene expression using a microscope fluidic system: batch cultures of Salmonella contain cells that activate stress response genes in the absence of DOC. This phenomenon underscores the existence of phenotypic heterogeneity in clonal populations of bacteria and may illustrate the adaptive value of gene expression fluctuations
Selenophene and thiophene-core estrogen receptor ligands that inhibit motility and development of parasitic stages of Haemonchus contortus
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