IBRD Operational Decision Framework

The IBRD Operational Decision Framework in this document is an expansion of an emerging general risk management framework under development by an interagency working group. It provides the level of detail necessary to develop a general Consequence Management Guidance Document for biological contamination remediation and restoration. It is the intent of this document to support both wide area and individual site remediation and restoration activities. This product was initiated as a portion of the IBRD Task 1 Systems Analysis to aid in identification of wide area remediation and restoration shortcomings and gaps. The draft interagency general risk management framework was used as the basis for the analysis. The initial Task 1 analysis document expanded the draft interagency framework to a higher level of resolution, building on both the logic structure and the accompanying text explanations. It was then employed in a qualitative manner to identify responsible agencies, data requirements, tool requirements, and current capabilities for each decision and task. This resulted in identifying shortcomings and gaps needing resolution. Several meetings of a joint LLNL/SNL working group reviewed and approved the initial content of this analysis. At the conclusion of Task 1, work continued on the expanded framework to generate this Operational Decision Framework which is consistent with the existing interagency general risk management framework. A large LLNL task group met repeatedly over a three-month period to develop the expanded framework, coordinate the framework with the biological remediation checklist, and synchronize the logic with the Consequence Management Plan table of contents. The expanded framework was briefed at a large table top exercise reviewing the interagency risk management framework. This exercise had representation from major US metropolitan areas as well as national agencies. This product received positive comments from the participants. Upon completion of the Operational Decision Framework, another joint LLNL/SNL working group conducted a day-long review. Identified modifications were made to the document, resulting in the included product

Brownian Motions on Metric Graphs

Brownian motions on a metric graph are defined. Their generators are characterized as Laplace operators subject to Wentzell boundary at every vertex. Conversely, given a set of Wentzell boundary conditions at the vertices of a metric graph, a Brownian motion is constructed pathwise on this graph so that its generator satisfies the given boundary conditions.Comment: 43 pages, 7 figures. 2nd revision of our article 1102.4937: The introduction has been modified, several references were added. This article will appear in the special issue of Journal of Mathematical Physics celebrating Elliott Lieb's 80th birthda

Discovery of a small molecule agonist of phosphatidylinositol 3-kinase p110α that reactivates latent HIV-1

Combination antiretroviral therapy (cART) can effectively suppress HIV-1 replication, but the latent viral reservoir in resting memory CD4+ T cells is impervious to cART and represents a major barrier to curing HIV-1 infection. Reactivation of latent HIV-1 represents a possible strategy for elimination of this reservoir. In this study we describe the discovery of 1,2,9,10-tetramethoxy-7H-dibenzo[de,g]quinolin-7-one (57704) which reactivates latent HIV-1 in several cell-line models of latency (J89GFP, U1 and ACH-2). 57704 also increased HIV-1 expression in 3 of 4 CD8+-depleted blood mononuclear cell preparations isolated from HIV-1-infected individuals on suppressive cART. In contrast, vorinostat increased HIV-1 expression in only 1 of the 4 donors tested. Importantly, 57704 does not induce global T cell activation. Mechanistic studies revealed that 57704 reactivates latent HIV-1 via the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) signaling pathway. 57704 was found to be an agonist of PI3K with specificity to the p110a isoform, but not the p110β, δ or γ isoforms. Taken together, our work suggests that 57704 could serve as a scaffold for the development of more potent activators of latent HIV-1. Furthermore, it highlights the involvement of the PI3K/Akt pathway in the maintenance of HIV-1 latency. © 2014 Doyon et al

IBRD Operational Decision Framework

The IBRD Operational Decision Framework in this document is an expansion of an emerging general risk management framework under development by an interagency working group. It provides the level of detail necessary to develop a general Consequence Management Guidance Document for biological contamination remediation and restoration. It is the intent of this document to support both wide area and individual site remediation and restoration activities. This product was initiated as a portion of the IBRD Task 1 Systems Analysis to aid in identification of wide area remediation and restoration shortcomings and gaps. The draft interagency general risk management framework was used as the basis for the analysis. The initial Task 1 analysis document expanded the draft interagency framework to a higher level of resolution, building on both the logic structure and the accompanying text explanations. It was then employed in a qualitative manner to identify responsible agencies, data requirements, tool requirements, and current capabilities for each decision and task. This resulted in identifying shortcomings and gaps needing resolution. Several meetings of a joint LLNL/SNL working group reviewed and approved the initial content of this analysis. At the conclusion of Task 1, work continued on the expanded framework to generate this Operational Decision Framework which is consistent with the existing interagency general risk management framework. A large LLNL task group met repeatedly over a three-month period to develop the expanded framework, coordinate the framework with the biological remediation checklist, and synchronize the logic with the Consequence Management Plan table of contents. The expanded framework was briefed at a large table top exercise reviewing the interagency risk management framework. This exercise had representation from major US metropolitan areas as well as national agencies. This product received positive comments from the participants. Upon completion of the Operational Decision Framework, another joint LLNL/SNL working group conducted a day-long review. Identified modifications were made to the document, resulting in the included product

A Sensitive Branched DNA HIV-1 Signal Amplification Viral Load Assay with Single Day Turnaround

Branched DNA (bDNA) is a signal amplification technology used in clinical and research laboratories to quantitatively detect nucleic acids. An overnight incubation is a significant drawback of highly sensitive bDNA assays. The VERSANT® HIV-1 RNA 3.0 Assay (bDNA) (“Versant Assay”) currently used in clinical laboratories was modified to allow shorter target incubation, enabling the viral load assay to be run in a single day. To dramatically reduce the target incubation from 16–18 h to 2.5 h, composition of only the “Lysis Diluent” solution was modified. Nucleic acid probes in the assay were unchanged. Performance of the modified assay (assay in development; not commercially available) was evaluated and compared to the Versant Assay. Dilution series replicates (>950 results) were used to demonstrate that analytical sensitivity, linearity, accuracy, and precision for the shorter modified assay are comparable to the Versant Assay. HIV RNA-positive clinical specimens (n = 135) showed no significant difference in quantification between the modified assay and the Versant Assay. Equivalent relative quantification of samples of eight genotypes was demonstrated for the two assays. Elevated levels of several potentially interfering endogenous substances had no effect on quantification or specificity of the modified assay. The modified assay with drastically improved turnaround time demonstrates the viability of signal-amplifying technology, such as bDNA, as an alternative to the PCR-based assays dominating viral load monitoring in clinical laboratories. Highly sensitive bDNA assays with a single day turnaround may be ideal for laboratories with especially stringent cost, contamination, or reliability requirements

Draft Guidance: Response, Restoration, and Recovery Checklist for Biologically Contaminated Facilities

The Checklist for Facility Response, Restoration, and Recovery presented in this document is principally focused on the Consequence Management Phase of a biothreat agent (i.e., Bacillus anthracis) release at a large facility, such as an airport or subway. Information in this document conforms to the National Response Plan (NRP) (DHS 2004) and the National Incident Management System (NIMS 2004). Under these two guidance documents, the personnel responsible for managing biological response and recovery efforts--that is, the decision-makers--are members of an Incident Command (IC), which is likely to transition to a Unified Command (UC) in the event of a biological warfare agent attack. A UC is used when more than one agency has incident jurisdiction or when incidents cross political jurisdictions. The location for primary, tactical-level command and management is referred to as the Incident Command Post (ICP), as described in the NRP. Thus, regardless of whether an IC or an UC is used, the responsible entities are located at an ICP. Agencies work together through designated members of the UC to establish their designated Incident Commanders at a single ICP and to establish a common set of objectives and strategies and a single Incident Action Plan. Initially during the Crisis Management Phase, the Incident Commander is likely to be the Chief of the fire department that serves the affected facility. As life-safety issues are resolved and the Crisis Management Phase shifts to the Consequence Management Phase, the work of characterization, decontamination, and facility clearance begins. There will likely be a coincident transition in organizational structure as well, and new restoration-focused groups, units, and personnel will be added as restoration needs are anticipated. Depending on the specific facility and type of incident, the responsible individual (Incident Commander or Unified Commander) within the UC during the Consequence Management Phase could be the Facility Manager, the Facility Emergency Operations Manager, or their designee. In an incident involving large-scale biological contamination, the Governor of the state would typically request, and the President of the United States would likely declare, an emergency under the Stafford Act (1974; amended 2002). The Secretary of Homeland Security would likely determine that the event is an Incident of National Significance on the basis of criteria established in Homeland Security Presidential Directive 5 (HSPD-5), ''Management of Domestic Incidents''. Incidents of National Significance are those high-impact events that require a coordinated and effective response by an appropriate combination of Federal, state, local, tribal, private-sector, and nongovernmental entities to save lives, minimize damage, and provide the basis for long-term community recovery and mitigation activities. If facility authorities request outside assistance, or if an emergency is declared under the Stafford Act, then other members of the UC could include local and state agencies as well as Federal agencies, such as the Federal Emergency Management Agency (FEMA) and the U.S. Environmental Protection Agency (USEPA). If an Incident of National Significance is declared, a Principal Federal Official will be appointed by the Department of Homeland Security (DHS) to facilitate Federal support to the UC structure. The following Checklist for Facility Response, Restoration, and Recovery presents the critical steps that would be taken by organizations involved in responding to a biological incident. It is intended for use by key decision-makers in the event that an incident occurs and steps must be taken immediately and systematically. The organizations would follow the Incident Command System (ICS). See Appendix A for more information on the ICS and how the responsible personnel identified in the checklist map into the consequence management organizational structure. The Notification and First-Response Phases are cursorily addressed in the checklist, whereas the main focus is on consequence management actions. The order of actions is generally sequential. However, depending on the specifics of an event and how the response is implemented, actions may be reordered. For example, preparing a Remediation Action Plan (RAP) is identified in the checklist as a critical step of the Remediation Phase. However, it is likely that preparation of the RAP would begin before completing all actions identified in the Characterization Phase. In addition to the actions recommended in the checklist, any emergency response conducted at a major metropolitan facility should comply with notification and response procedures established by the facility, as well as applicable procedures established by the jurisdictional responding agencies

Failure to Detect the Novel Retrovirus XMRV in Chronic Fatigue Syndrome

BACKGROUND:In October 2009 it was reported that 68 of 101 patients with chronic fatigue syndrome (CFS) in the US were infected with a novel gamma retrovirus, xenotropic murine leukaemia virus-related virus (XMRV), a virus previously linked to prostate cancer. This finding, if confirmed, would have a profound effect on the understanding and treatment of an incapacitating disease affecting millions worldwide. We have investigated CFS sufferers in the UK to determine if they are carriers of XMRV. METHODOLOGY:Patients in our CFS cohort had undergone medical screening to exclude detectable organic illness and met the CDC criteria for CFS. DNA extracted from blood samples of 186 CFS patients were screened for XMRV provirus and for the closely related murine leukaemia virus by nested PCR using specific oligonucleotide primers. To control for the integrity of the DNA, the cellular beta-globin gene was amplified. Negative controls (water) and a positive control (XMRV infectious molecular clone DNA) were included. While the beta-globin gene was amplified in all 186 samples, neither XMRV nor MLV sequences were detected. CONCLUSION:XMRV or MLV sequences were not amplified from DNA originating from CFS patients in the UK. Although we found no evidence that XMRV is associated with CFS in the UK, this may be a result of population differences between North America and Europe regarding the general prevalence of XMRV infection, and might also explain the fact that two US groups found XMRV in prostate cancer tissue, while two European studies did not

The HIV-1 Nef protein binds argonaute-2 and functions as a viral suppressor of RNA interference

The HIV-1 accessory protein Nef is an important virulence factor. It associates with cellular membranes and modulates the endocytic machinery and signaling pathways. Nef also increases the proliferation of multivesicular bodies (MVBs), which are sites for virus assembly and budding in macrophages. The RNA interference (RNAi) pathway proteins Ago2 and GW182 localize to MVBs, suggesting these to be sites for assembly and turnover of the miRNA-induced silencing complex (miRISC). While RNAi affects HIV replication, it is not clear if the virus encodes a suppressor activity to overcome this innate host response. Here we show that Nef colocalizes with MVBs and binds Ago2 through two highly conserved Glycine-Tryptophan (GW) motifs, mutations in which abolish Nef binding to Ago2 and reduce virus yield and infectivity. Nef also inhibits the slicing activity of Ago2 and disturbs the sorting of GW182 into exosomes resulting in the suppression of miRNA-induced silencing. Thus, besides its other activities, the HIV-1 Nef protein is also proposed to function as a viral suppressor of RNAi (VSR)