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We report here the genome sequence of a Staphylococcus xylosus clinical isolate, strain SMA0341-04 (UGA5), which contains one chromosome and at least one plasmid. Notably, strain SMA0341-04 (UGA5) contains the tetracycline efflux major facilitator superfamily (MFS) transporter ( tetK ) gene.
Here, we report the sequence of a Staphylococcus pettenkoferi clinical isolate, strain SMA0010-04 (UGA20), which contains the PC1 beta-lactamase ( blaZ ) gene.
Plasmid-mediated horizontal gene transfer (HGT) is a major driver of genetic diversity in bacteria. We experimentally validated the function of a putative mercury resistance operon present on an abundant 8-kbp native plasmid found in groundwater samples without detectable levels of mercury. Phylogenetic analyses of the plasmid-encoded mercury reductases from the studied groundwater site show them to be distinct from those reported in proximal metal-contaminated sites. We synthesized the entire native plasmid and demonstrated that the plasmid was sufficient to confer functional mercury resistance in Escherichia coli . Given the possibility that natural transformation is a prevalent HGT mechanism in the low-cell-density environments of groundwaters, we also assayed bacterial strains from this environment for competence. We used the native plasmid-encoded metal resistance to design a screen and identified 17 strains positive for natural transformation. We selected 2 of the positive strains along with a model bacterium to fully confirm HGT via natural transformation. From an ecological perspective, the role of the native plasmid population in providing advantageous traits combined with the microbiome’s capacity to take up environmental DNA enables rapid adaptation to environmental stresses. Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identified 17 strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments.
A minority of HIV-1-infected patients produce broadly neutralizing antibodies (bNAbs). Identification of viral and host correlates of bNAb production may help develop vaccines. We aimed to characterize the neutralizing response and viral and host-associated factors in Angola, which has one of the oldest, most dynamic, and most diverse HIV-1 epidemics in the world. Three hundred twenty-two HIV-1-infected adults from Angola were included in this retrospective study. Phylogenetic analysis of C2V3C3 env gene sequences was used for virus subtyping. Env-binding antibody reactivity was tested against polypeptides comprising the C2, V3, and C3 regions. Neutralizing-antibody responses were determined against a reference panel of tier 2 Env pseudoviruses in TZM-bl cells; neutralizing epitope specificities were predicted using ClustVis. All subtypes were found, along with untypeable strains and recombinant forms. Notably, 56% of the patients developed cross neutralizing, broadly neutralizing, or elite neutralizing responses. Broad and elite neutralization was associated with longer infection time, subtype C, lower CD4 + T cell counts, higher age, and higher titer of C2V3C3-specific antibodies relative to failure to develop bNAbs. Neutralizing antibodies targeted the V3-glycan supersite in most patients. V3 and C3 regions were significantly less variable in elite neutralizers than in weak neutralizers and nonneutralizers, suggesting an active role of V3C3-directed bNAbs in controlling HIV-1 replication and diversification. In conclusion, prolonged and low-level envelope V3C3 stimulation by highly diverse and ancestral HIV-1 isolates promotes the frequent elicitation of bNAbs. These results provide important clues for the development of an effective HIV-1 vaccine. Studies on neutralization by antibodies and their determinants in HIV-1-infected individuals have mostly been conducted in relatively recent epidemics caused by subtype B and C viruses. Results have suggested that elicitation of broadly neutralizing antibodies (bNAbs) is uncommon. The mechanisms underlying the elicitation of bNAbs are still largely unknown. We performed the first characterization of the plasma neutralizing response in a cohort of HIV-1-infected patients from Angola. Angola is characterized by an old and dynamic epidemic caused by highly diverse HIV-1 variants. Remarkably, more than half of the patients produced bNAbs, mostly targeting the V3-glycan supersite in HIV-1. This was associated with higher age, longer infection time, lower CD4 + T cell counts, subtype C infection, or higher titer of C2V3C3-specific antibodies relative to patients that did not develop bNAbs. These results may help develop the next generation of vaccine candidates for HIV-1.
Despite the dominance of Rhodanobacter species in the subsurface of the contaminated Oak Ridge Reservation (ORR) site, very little is known about the mechanisms underlying their adaptions to the various stressors present at ORR. Recently, multiple Rhodanobacter strains have been isolated from the ORR groundwater samples from several wells with varying geochemical properties.
The production cross section of inclusive isolated photons has been measured by the ALICE experiment at the CERN LHC in pp collisions at a centre-of-momentum energy of √s= 7 TeV. The measurement is performed with the electromagnetic calorimeter EMCal and the central tracking detectors, covering a range of |η| < 0.27 in pseudorapidity and a transverse momentum range of 10< p γ T <60 GeV/c. The result extends the p T coverage of previously published results of the ATLAS and CMS experiments at the same collision energy to smaller p T . The measurement is compared to next-to-leading order perturbative QCD calculations and to the results from the ATLAS and CMS experiments. All measurements and theory predictions are in agreement with each other.
Measurements are presented of the triple-differential cross section for inclusive isolated-photon+jet events in pp collisions at $\sqrt{s} =$ 8 TeV as a function of photon transverse momentum ($p_\mathrm{T}^\gamma$), photon pseudorapidity ($\eta^\gamma$), and jet pseudorapidity ($\eta^\text{jet}$). The data correspond to an integrated luminosity of 19.7 fb$^{-1}$ that probe a broad range of the available phase space, for $|\eta^\gamma|<1.44$ and 1.57$<|\eta^\gamma|<$2.50, $|\eta^\text{jet}|<$2.5, 40$< p_\mathrm{T}^\gamma<$ 1000 GeV, and jet transverse momentum, $p_\mathrm{T}^\text{jet}$, $>$25 GeV. The measurements are compared to next-to-leading order perturbative quantum chromodynamics calculations, which reproduce the data within uncertainties.
Difficulty in using observations to isolate the impacts of aerosols from meteorology on deep convection often stems from inability to resolve the spatiotemporal variations in the environment serving as the storm’s inflow region. During the DOE TRacking Aerosol Convection interactions ExpeRiment (TRACER) in June-September 2022, a Texas A&M University (TAMU) team conducted a mobile field campaign to characterize the meteorological and aerosol variability in airmasses that serve as inflow to convection across the ubiquitous mesoscale boundaries associated with the sea- and bay-breezes in the Houston, Texas, region. These boundaries propagate inland over the fixed DOE Atmospheric Radiation Measurement (ARM) sites. However, convection occurs on either or both the continental or maritime sides or along the boundary. The maritime and continental airmasses serving as convection inflow may be quite distinct, with different meteorological and aerosol characteristics that fixed-site measurements cannot simultaneously sample. Thus, a primary objective of TAMU TRACER was to provide mobile measurements similar to those at the fixed sites, but in the opposite airmass across these moving mesoscale boundaries. TAMU TRACER collected radiosonde, lidar, aerosol, cloud condensation nuclei (CCN), and ice nucleating particle (INP) measurements on 29 enhanced operations days covering a variety of maritime, continental, outflow, and pre-frontal airmasses. This paper summarizes the TAMU TRACER deployment and measurement strategy, instruments, available datasets, and provides sample cases highlighting differences between these mobile measurements and those made at the ARM sites. We also highlight the exceptional TAMU TRACER undergraduate student participation in high impact learning activities through forecasting and field deployment opportunities.
The microphysical impacts of aerosol particles on scattered isolated deep convective cells near Houston, Texas, on 19 June 2013, are examined using multiple cloud-resolving model (CRM) simulations initialized with vertical profiles of low and high concentrations of cloud droplet–nucleating aerosols. These simulations formed part of the Model Intercomparison Project (MIP) conducted by the Deep Convective Working Group of the Aerosol, Cloud, Precipitation and Climate (ACPC) initiative. Each CRM generated a field of convective cells representing those observed during the case study with varying degrees of accuracy. The Tracking and Object-Based Analysis of Clouds (tobac) cell-tracking algorithm was applied to each MIP CRM simulation to track relatively long-lived convective cells (20–60 min). Most of the CRMs produced similar aerosol loading impacts on the warm phase of tracked cell properties with reduced autoconversion and accretion growth of rain, increased cloud water, reduced rainfall, and reduced near-surface evaporation of rain. The sign of aerosol impacts on the warm-phase properties of the convective cells was also quite consistent over cell lifetimes with the greatest magnitude of influence in the first half of the life cycle in most CRMs. In contrast, the ice-phase response to aerosol loading was highly variable among CRMs and included increases or decreases in ice amounts at inconsistent stages of the cell life cycle and midlevel versus upper-level changes in ice. This intermodel variability in ice is indicative both of the complex indirect interactions between aerosols and ice-phase processes in deep convection and their associated parameterizations.
Background: The optimal treatment for isolated local recurrence (ILR) of pancreatic adenocarcinoma (PDAC) after surgical resection remains unclear. This study aimed to evaluate the safety and efficacy of proton radiotherapy (PRT) for ILR of PDAC after surgery. Methods: The medical records of patients with ILR of PDAC after surgery who underwent proton beam therapy between 2011 and 2015 at Hyogo Ion Beam Medical Center were retrospectively studied. Results: The study analyzed 30 patients (14 women and 16 men) with a median age of 65 years (range 38–81 years) who had initially undergone pancreatoduodenectomy (n = 23) or distal pancreatectomy (n = 7) for their primary tumors. Upon ILR, PRT was administered with a median total cumulative dose of 67.5 gray equivalent (GyE) (range 50–67.5 GyE) using 19 to 25 fractions. For 25 patients, concurrent chemotherapy was administered using gemcitabine (n = 18) or S-1 (n = 7). Four patients (13.3%) experienced acute grade ≥ 3 gastrointestinal toxicities. After a median follow-up period of 17.6 months (range 2.1–50.4 months), 23 patients had experienced tumor progression and 10 had died. Nine patients (30%) experienced local tumor progression. The median overall, progression-free, and local progression-free survival rates were 26.1, 12.3, and 41.2 months, respectively. Pre-PRT serum levels of cancer antigen 19-9 higher than 100 U/mL and duke pancreatic monoclonal antigen type 2 higher than 150 U/mL were significantly associated with shorter progression-free survival rates. Conclusions: Proton radiotherapy for ILR of PDAC after surgery is well tolerated and produces good locoregional control and should be considered for eligible patients.
This is a presentation on the Zonal Isolation Solution for Geothermal Wells by PetroQuip Energy Services, presented by Robert Coon. This video slide presentation discusses the proposed design and development of a multi-stage system consisting of an Open-Hole Packer (OHP), a Locking Bridge Plug (LBP), and a corresponding Locating Profile (LP). This presentation was featured in the Utah FORGE R&D Annual Workshop on August 14, 2024.
The dynamics of isolated-photon plus two-jet production in pp collisions at a centre-of-mass energy of 13 TeV are studied with the ATLAS detector at the LHC using a dataset corresponding to an integrated luminosity of 36.1 fb−1. Cross sections are measured as functions of a variety of observables, including angular correlations and invariant masses of the objects in the final state, γ+jet+jet. Measurements are also performed in phase-space regions enriched in each of the two underlying physical mechanisms, namely direct and fragmentation processes. The measurements cover the range of photon (jet) transverse momenta from 150 GeV (100 GeV) to 2 TeV. The tree-level plus parton-shower predictions from SHERPA and PYTHIA as well as the next-to-leading-order QCD predictions from SHERPA are compared with the measurements. The next-to-leading-order QCD predictions describe the data adequately in shape and normalisation except for regions of phase space such as those with high values of the invariant mass or rapidity separation of the two jets, where the predictions overestimate the data.
CERN-LHC. Measurement of the ratio of cross sections for inclusive isolated-photon production in proton-proton collisions at a centre-of-mass energy of 13 TeV over 8 TeV. Measurement is also presented of the double ratio of the ratio above to the ratio of the fiducial cross sections for Z boson production at 13 TeV and 8 TeV using the decay channels Z into an electron-positron pair and Z into a muon-antimuon pair.
CERN-LHC. Measurement of the cross section for inclusive isolated-photon production in proton-proton collisions at a centre-of-mass energy of 13 TeV with 36/fb of data collected in 2015 and 2016.
The Waste Isolation Pilot Plant (WIPP) is an operating geologic repository in southeastern New Mexico for transuranic (TRU) waste from nuclear defense activities. Past nuclear criticality concerns have generally been low at the WIPP due to the low initial concentration of fissile material and the natural tendency of fissile solute to disperse during fluid transport in porous media (Rechard et al. 2000). On the other hand, the list of acceptable WIPP waste types has expanded over the years to include Criticality Control Overpack (CCO) containers and Pipe Overpack (POP) containers. Containers bound for WIPP are bundled together in hexagon shaped 7-packs (six containers surround one container in the center). Two 7-packs are often combined into a TRUPACT-II package for a total of 14 containers. Most TRUPACT-II packages are restricted to a maximum fissile mass equivalent to plutonium (FMEP) between 0.1 and 0.38 kg, but a CCO TRUPACT-II package and a POP TRUPACT-II package are respectively permitted to have 5.32 kg and 2.80 kg FMEP (see Section 3 of US DOE (2013)). Consequently, CCO container criticality after emplacement at the WIPP was evaluated in Saylor and Scaglione (2018), and Oak Ridge National Laboratories is currently at work on POP container criticality analyses.
This report presents an unreliability evaluation of the isolation condenser (ISO) system at four U.S. boiling water reactors. Demand, run hours, and failure data from calendar year 1998 through 2018 for selected components were obtained from the Institute of Nuclear Power Operations (INPO) Industry Reporting and Information System (IRIS), formerly the INPO Consolidated Events Database (ICES). The unreliability results are trended for the most recent 10 year period while yearly estimates for system unreliability are provided for the entire active period. No statistically significant increasing or decreasing trends were identified in the ISO results.
This report presents an unreliability evaluation of the reactor core isolation cooling (RCIC) system at 31 U.S. commercial boiling water reactors. Demand, run hours, and failure data from calendar years 1998 through 2018 for selected components were obtained from the Institute of Nuclear Power Operations (INPO) Industry Reporting and Information System (IRIS), formerly the INPO Consolidated Events Database (ICES). The unreliability results are trended for the most recent 10 year period while yearly estimates for system unreliability are provided for the entire active period. No statistically significant increasing or decreasing trends were identified in the RCIC results.
Final report for UW effort on project Automated Isolation of Astatine-211 and chemistry evaluation