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We report the genome sequence of Dysgonomonas hofstadii DSM 104969T, a type strain isolated from a human surgical wound. The genome has 5.03 Mbp and a guanine-cytosine content of 39.27%. The complete genome sequence will facilitate studies of D. hofstadii and its pathogenic potential, particularly in relation to multidrug resistance.
This study describes the whole genome sequence of Dolosicoccus paucivorans 2991-95 (DSM 15742) isolated from human blood in Cleveland, Ohio. The genome length is approximately 1.8 Mbp with 107 contigs and a G + C content of 37.91%. Annotation identified 1,752 coding genes and multiple virulence factors.
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.
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.
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
The goal of this transportation analysis (TA) is to update the 2008 TA in order to evaluate the impacts associated with the transportation of transuranic (TRU) waste from waste generator sites to the Waste Isolation Pilot Plant (WIPP) facility and from waste generator sites to the Idaho National Laboratory (INL).
Detailed simulations of the Atmospheric boundary layer (ABL) provides information on wind velocity, direction and turbulence for optimizing the design of wind turbines and wind farms and their operations. Distributed wind turbines have been considered for use in urban or suburban areas for covering energy needs using a sustainable energy solution. Simulations of high Reynolds number turbulent ABL flows past obstacles can be used for the prediction of the velocity deficit and turbulence characteristics in the leeward side of building-like obstacles, allowing for the estimation of power losses and fatigue loads in wind turbines. However, fully three-dimensional simulations of high Reynolds number ABL flows using Large Eddy Simulation (LES) or Reynolds Average Navier-Stokes Simulations (RANS) continue to require large computational/ execution times. As a result, these 3D simulations may not be ideal tools for the rapid assessment of wind energy potential. In the present study, 3D numerical results from wall resolved RANS simulations were used for the development of a low order model that allows the rapid assessment of wind velocity and turbulence in the leeward side of an isolated building.
Experimental measurements of room closure in salt repositories are valuable for understanding the evolution of the underground and for validating geomechanical models. Room closure was measured during a number of experiments at the Waste Isolation Pilot Plant (WIPP) during the 1980's and 1990's. Most rooms were excavated using a multi-pass mining sequence, where each pass necessarily destroyed some of the mining sequence closure measurement points. These destroyed points were promptly reinstalled to capture the closure after the mining pass. After the room was complete, the mining sequence closure measurement stations were supplemented with remotely read closure measurement stations. Although many aspects of these experiments were thoroughly documented, the digital copies of the closure data were inadvertently destroyed, the non-trivial process of zeroing and shifting the raw closure measurements after each mining pass was not precisely described, the various closure measurements within a given room were not directly compared on the same plot, and the measurements were collected for several years longer than previously reported. Consequently, the hand-written mining sequence closure measurements for Rooms D, B, G, and Q were located in the WIPP archives, digitized, and reanalyzed for this report. The process of reconstructing the mining sequence closure histories was documented in detail and the raw data can be found in the appendices. Within the mid-section of a given room, the reconstructed closure histories were largely consistent with other mining sequence and remotely read closure histories, which builds confidence in the experiments and suggests that plane strain is an appropriate modeling assumption. The reconstructed closure histories were also reasonably consistent with previously published results, except in one notable case: the reconstructed Room Q closure histories 30 days after excavation were about 45 % less than the corresponding closures reported in Munson's 1997 capstone paper.