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At least 127 records · Page 7

A novel procedure on next generation sequencing data analysis using text mining algorithm

Background: Next-generation sequencing (NGS) technologies have provided researchers with vast possibilities in various biological and biomedical research areas. Efficient data mining strategies are in high demand for large scale comparative and evolutional studies to be performed on the large amounts of data derived from NGS projects. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining. Methods: We report a novel procedure to analyse NGS data using topic modeling. It consists of four major procedures: NGS data retrieval, preprocessing, topic modeling, and data mining using Latent Dirichlet Allocation (LDA) topic outputs. The NGS data set of the Salmonella enterica strains were used as a case study to show the workflow of this procedure. The perplexity measurement of the topic numbers and the convergence efficiencies of Gibbs sampling were calculated and discussed for achieving the best result from the proposed procedure. Results: The output topics by LDA algorithms could be treated as features of Salmonella strains to accurately describe the genetic diversity of fliC gene in various serotypes. The results of a two-way hierarchical clustering and data matrix analysis on LDA-derived matrices successfully classified Salmonella serotypes based on the NGS data. The implementation of topic modeling in NGS data analysis procedure provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data. Conclusion: The implementation of topic modeling in NGS data analysis provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data.

59 BASIC BIOLOGICAL SCIENCES↗

Understanding Brønsted-Acid Catalyzed Monomolecular Reactions of Alkanes in Zeolite Pores by Combining Insights from Experiment and Theory

The front cover artwork is provided by Bell and co-workers. The image shows a butane molecule adsorbed at a Brønsted acid site inside the pores of zeolite H-MFI, surrounded by the products of monomolecular cracking and dehydrogenation reactions catalyzed by these sites. Read the full text of the Minireview at 10.1002/cphc.201701084.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On the Rate Constant for NH 2 +HO 2 and Third-Body Collision Efficiencies for NH 2 +H(+M) and NH 2 +NH 2 (+M)

In low-temperature flash photolysis of NH 3 /O 2 /N 2 mixtures, the NH 2 consumption rate and the product distribution is controlled by the reactions NH 2 + HO 2 → products (R1), NH 2 + H (+M) → NH 3 (+M) (R2), and NH 2 + NH 2 (+M) → N 2 H 4 (+M) (R3). In the present work, published flash photolysis experiments by, among others, Cheskis and co-workers, are re-interpreted using recent direct measurements of NH 2 + H (+N 2 ) and NH 2 + NH 2 (+N 2 ) from Altinay and Macdonald. To facilitate analysis of the FP data, relative third-body collision efficiencies compared to N 2 for R2 and R3 were calculated for O 2 and NH 3 as well as for other selected molecules. We report results were in good agreement with the limited experimental data. Based on reported NH 2 decay rates in flash photolysis of NH 3 /O 2 /N 2 , a rate constant for NH 2 + HO 2 → NH 3 + O 2 (R1a) of $k_{1\text{a}}$ = 1.5(±0.5) × 10 14 cm 3 mol –1 s –1 at 295 K was derived. This value is higher than earlier determinations based on the FP results but in good agreement with recent theoretical work. Kinetic modeling of reported N 2 O yields indicates that NH 2 + HO 2 → H 2 NO + O (R1c) is competing with R1a, but perturbation experiments with addition of CH4 indicate that it is not a dominating channel. Measured HNO profiles indicate that this component is formed directly by NH 2 + HO 2 → HNO + H 2 O (R1b), but theoretical work indicates that R1b is only a minor channel. Based on this analysis, we estimate $k_{1\text{c}}$ = 2.5 × 10 13 cm 3 mol –1 s –1 and $k_{1\text{b}}$ = 2.5 × 10 12 cm 3 mol –1 s –1 at 295 K, with significant uncertainty margins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Radiant Heat Transfer Between Nongray Parallel Plates of Tungsten

Net radiant heat flow between two infinite, parallel, tungsten plates was computed by summing the monochromatic energy exchange; the results are graphically presented as a function of the temperatures of the two surfaces. In general these fluxes range from approximately a to 25 percent greater than the results of gray-body computations based on the same emissivity data. The selection of spectral emissivity data and the computational procedure are discussed. The present analytical procedure is so arranged that, as spectral emissivity data for a material become available, these data can be readily introduced into the NASA data-reduction equipment, which has been programmed to compute the net heat flux for the particular geometry and basic assumptions cited in the text. Nongray-body computational techniques for determining radiant heat flux appear practical provided the combination of select spectral emissivity data and the proper mechanized data-reduction equipment are brought to bear on the problem.

Branstetter, J. Robert↗

Inelastic response of metal matrix composites under biaxial loading

Elements of the analytical/experimental program to characterize the response of silicon carbide titanium (SCS-6/Ti-15-3) composite tubes under biaxial loading are outlined. The analytical program comprises prediction of initial yielding and subsequent inelastic response of unidirectional and angle-ply silicon carbide titanium tubes using a combined micromechanics approach and laminate analysis. The micromechanics approach is based on the method of cells model and has the capability of generating the effective thermomechanical response of metal matrix composites in the linear and inelastic region in the presence of temperature and time-dependent properties of the individual constituents and imperfect bonding on the initial yield surfaces and inelastic response of (0) and (+ or - 45)sub s SCS-6/Ti-15-3 laminates loaded by different combinations of stresses. The generated analytical predictions will be compared with the experimental results. The experimental program comprises generation of initial yield surfaces, subsequent stress-strain curves and determination of failure loads of the SCS-6/Ti-15-3 tubes under selected loading conditions. The results of the analytical investigation are employed to define the actual loading paths for the experimental program. A brief overview of the experimental methodology is given. This includes the test capabilities of the Composite Mechanics Laboratory at the University of Virginia, the SCS-6/Ti-15-3 composite tubes secured from McDonnell Douglas Corporation, a text fixture specifically developed for combined axial-torsional loading, and the MTS combined axial-torsion loader that will be employed in the actual testing.

Mirzadeh, F.↗

SchemaOnRead: A Package for Schema-on-Read in R

Schema-on-read is an agile approach to data storage and retrieval that defers investments in data organization until production queries need to be run by working with data directly in native form. Schema-on-read functions have been implemented in a wide range of analytical systems, most notably Hadoop. SchemaOnRead is a CRAN package that uses R’s flexible data representations to provide transparent and convenient support for the schema-on-read paradigm in R. The schema-on- read tools within the package include a single function call that recursively reads folders with text, comma separated value, raster image, R data, HDF5, NetCDF, spreadsheet, Weka, Epi Info, Pajek network, R network, HTML, SPSS, Systat, and Stata files. The provided tools can be used as-is or easily adapted to implement customized schema-on-read tool chains in R. This paper’s contribution is that it introduces and describes SchemaOnRead, the first R package specifically focused on providing explicit schema-on-read support in R.

Data Science↗

SchemaOnRead: A Package for Schema-on-Read in R

Schema-on-read is an agile approach to data storage and retrieval that defers investments in data organization until production queries need to be run by working with data directly in native form. Schema-on-read functions have been implemented in a wide range of analytical systems, most notably Hadoop. SchemaOnRead is a CRAN package that uses R’s flexible data representations to provide transparent and convenient support for the schema-on-read paradigm in R. The schema-on- read tools within the package include a single function call that recursively reads folders with text, comma separated value, raster image, R data, HDF5, NetCDF, spreadsheet, Weka, Epi Info, Pajek network, R network, HTML, SPSS, Systat, and Stata files. The provided tools can be used as-is or easily adapted to implement customized schema-on-read tool chains in R. This paper’s contribution is that it introduces and describes SchemaOnRead, the first R package specifically focused on providing explicit schema-on-read support in R.

Data Science↗

Kinetics and Energetics of Electron Transfer to Dimer Radical Cations

In this work, spectra of the dimer cations naphthalene (Nap 2 •+ ) and ethene (Ethene 2 •+ ) were measured in liquid dichloromethane (DCM). The spectra peak at very different energies, 1.2 and 3.3 eV. In DCM dimerization stabilizes Nap 2 •+ by Δ$G_\text{d}°$(Nap 2 •+ ) = -218 meV relative to the monomer Nap •+ as determined from the dimerization equilibrium constant. Both dimers can transfer a positive charge to hole acceptor molecules, but for both the rate constants rise more gradually with reaction energetics than do many charge transfer reactions previously studied. A striking observation finds that the rate constant for hole transfer from the Nap 2 •+ dimer to phenanthrene is smaller by two decades than that from biphenyl•+ monomer to Nap, although both reactions have the same –Δ$\textit{G}°$=0.05 eV. A plausible interpretation for these observations is the presence of an energy of reorganization, λ(M 2 ), for the dimer that involves movement apart of the two partners in the dimer. While the dimerization equilibrium cannot be measured for Ethene 2 •+ the charge transfer data imply that both Δ$G_\text{d}°$(Ethene 2 •+ ) and λ(Ethene 2 •+ ), are considerably larger, perhaps by factors of 2-4 than for Nap 2 •+ .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding the effect of resonant magnetic perturbations on tearing mode dynamics

Numerical understandings of the effect of resonant magnetic perturbations (RMPs) on 2/1 tearing mode (TM) dynamics observed on J-TEXT tokamak (Hu et al. Nucl. Fusion 52, 083011 (2012)) are presented in this paper. The non-uniform mode rotation frequency, modulated by electromagnetic force (F{sub em}) and viscous force (F{sub vs}), results in the applied RMPs contributing both net stabilizing and braking effect on TM. Numerical evaluation based on analytical theory shows the applied RMP contributes a dominant stabilizing effect, which is responsible for the suppression of TM. The dynamics of the first discovered small locked island are investigated. It is found that the island is locked at the stabilizing phase and the saturated island width is less than the linear layer width. The simulated Mirnov signal indicates the small locked island is likely to be the complete suppression case observed in experiments. Associated with the application of RMP, the shape of Mirnov signal deviates from sinusoidal before mode locking, which is explained by numerical modeling. The comparisons between the numerical and experimental results are in good agreement phenomenally.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Convective carbon dioxide dissolution in a closed porous medium at low pressure

Motivated by the persistence of natural carbon dioxide ( $\text{CO}_{2}$ ) fields, we investigate the convective dissolution of $\text{CO}_{2}$ at low pressure (below 1 MPa) in a closed system, where the pressure in the gas declines as convection proceeds. This introduces a negative feedback that reduces the convective dissolution rate even before the brine becomes saturated. We analyse the case of an ideal gas with a solubility given by Henry’s law, in the limits of very low and very high Rayleigh numbers. The equilibrium state in this system is determined by the dimensionless dissolution capacity, $\unicode[STIX]{x1D6F1}$ , which gives the fraction of the gas that can be dissolved into the underlying brine. Analytic approximations of the pure diffusion problem with $\unicode[STIX]{x1D6F1}>0$ show that the diffusive base state is no longer self-similar and that diffusive mass transfer declines rapidly with time. Direct numerical simulations at high Rayleigh numbers show that no constant flux regime exists for $\unicode[STIX]{x1D6F1}>0$ ; nevertheless, the quantity $F/C_{s}^{2}$ remains constant, where $F$ is the dissolution flux and $C_{s}$ is the dissolved concentration at the top of the domain. Simple mathematical models are developed to predict the evolution of $C_{s}$ and $F$ for high-Rayleigh-number convection in a closed system. The negative feedback that limits convection in closed systems may explain the persistence of natural $\text{CO}_{2}$ accumulations over millennial time scales.

Mechanics↗

Diving into a holographic superconductor

Charged black holes in anti-de Sitter space become unstable to forming charged scalar hair at low temperatures T < T_\text{c} T < T c . This phenomenon is a holographic realization of superconductivity. We look inside the horizon of these holographic superconductors and find intricate dynamical behavior. The spacetime ends at a spacelike Kasner singularity, and there is no Cauchy horizon. Before reaching the singularity, there are several intermediate regimes which we study both analytically and numerically. These include strong Josephson oscillations in the condensate and possible `Kasner inversions’ in which after many e-folds of expansion, the Einstein-Rosen bridge contracts towards the singularity. Due to the Josephson oscillations, the number of Kasner inversions depends very sensitively on T T , and diverges at a discrete set of temperatures \{T_n\} { T n } that accumulate at T_c T c . Near these T_n T n , the final Kasner exponent exhibits fractal-like behavior.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A Model Based Approach to Extract Health Information from Textual Data

In current nuclear power plants (NPPs) a large amount of condition-based data is being generated and stored to assess and monitor component health and performance. The format of this data can be either numeric (e.g., pump vibration data) or textual (e.g., condition report which assess component health). While assessing component health from numeric data can be performed with a large variety of methods, the extraction of information from textual data still remains a challenge. Natural language processing (NLP) methods are starting to be deployed in current NPPs mainly to filter out incident reports (IRs) that are not safety related by employing supervised machine learning methods. However, these methods do not really provide the quantitative information that might be contained in IRs. This paper presents an approach to extract information from textual data (e.g., from IRs, maintenance reports) that is based on NLP data analytics methods coupled with model-based system engineer (MBSE) models. NLP methods are employed to perform syntactic and semantic analyses. Syntactic analysis analyzes the grammatical structure of a sentence; such analysis includes: part of speech (POS) tagging (i.e., identification of grammatic elements of each string - e.g., nouns, verbs), named entity recognition (i.e., identification of text entities - e.g., names, dates, events), and relation extraction (e.g., coreference resolution). On the other hand, semantic analysis is designed to analyze the logic structure of a sentence. Through a specific set of rules, our methods can identify whether a sentence contains health information of a component (e.g., degraded performance, anomaly behavior) or the causal relationship between two events (i.e., a cause-effect pair). An innovative element of our approach is that semantic analysis relies on MBSE models to identify links between textual elements. MBSE are diagrams designed to represent system and component dependencies (from both a form and functional point of view). In our approach, MBSE models emulate system engineer knowledge about component/system architecture. This paper presents in detail how the integration of NLP methods and MBSE models is performed. Few analysis examples focusing on centrifugal pumps are presented.

97 - MATHEMATICS AND COMPUTING↗

MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets

Abstract Our knowledge of viral sequence space has exploded with advancing sequencing technologies and large-scale sampling and analytical efforts. Though archaea are important and abundant prokaryotes in many systems, our knowledge of archaeal viruses outside of extreme environments is limited. This largely stems from the lack of a robust, high-throughput, and systematic way to distinguish between bacterial and archaeal viruses in datasets of curated viruses. Here we upgrade our prior text-based tool (MArVD) via training and testing a random forest machine learning algorithm against a newly curated dataset of archaeal viruses. After optimization, MArVD2 presented a significant improvement over its predecessor in terms of scalability, usability, and flexibility, and will allow user-defined custom training datasets as archaeal virus discovery progresses. Benchmarking showed that a model trained with viral sequences from the hypersaline, marine, and hot spring environments correctly classified 85% of the archaeal viruses with a false detection rate below 2% using a random forest prediction threshold of 80% in a separate benchmarking dataset from the same habitats.

Vik, Dean (ORCID:000000027546899X)↗

Towards a Heterogeneous, Polystore-like Data Architecture for the US Department of Veteran Affairs (VA) Enterprise Analytics

The Polystore architecture revisits the federated approach to access and querying of the standalone, independent databases in the uniform and optimized fashion, but this time in the context of heterogeneous data and specialized analyses. In the light of this architectural philosophy, and in the light of the major data architecture development efforts at the US Department of Veterans Administration (VA), we discuss the need for the heterogeneous data store consisting of the large relational data warehouse, an image and text datastore, and a peta-scale genomic repository. The VA's heterogeneous datastore would, to a larger or smaller degree, follow the architectural blueprint proposed by the polystore architecture. To this end, we discuss the current state of the data architecture at VA, architectural alternatives for development of the heterogeneous datastore, the anticipated challenges, and the drawbacks and benefits of adopting the polystore architecture.

Federated Databases↗

A low-luminosity core-collapse supernova very similar to SN 2005cs

ABSTRACT We present observations and analysis of PSN J17292918+7542390, a low-luminosity Type II-P supernova (LL SN IIP). The observed sample of such events is still low, and their nature is still under debate. Such SNe are similar to SN 2005cs, a well-observed LL Type II-P event, having low expansion velocities, and small ejected 56Ni mass. We have developed a robust and relatively fast Monte Carlo code that fits semi-analytic models to light curves of core-collapse SNe. This allows the estimation of the most important physical parameters, like the radius of the progenitor star, the mass of the ejected envelope, the mass of the radioactive nickel synthesized during the explosion, among others. PSN J17292918+7542390 has $R_0 = 91_{-70}^{+119} \times 10^{11} \, \text{cm}$, $M_\text{ej} = 9.89_{-1.00}^{+2.10} \, \mathrm{ M}_{\odot }$, $E_{\mbox{kin}} = 0.65_{-0.18}^{+0.19} \, \text{foe}$, and $v_{\mbox{exp}} = 3332_{-347}^{+216}$ km s−1, for its progenitor radius, ejecta mass, kinetic energy, and expansion velocity, respectively. The initial nickel mass of the PSN J17292918+7542390 turned out to be $1.55_{-0.70}^{+0.75} \times 10^{-3} \, \mathrm{M}_{\odot }$. The measured photospheric velocity at the earliest observed phase is 7000 km s−1. As far as we can tell based on the small population of observed LL SNe IIP, the determined values are typical for these events.

Jäger, Jr, Zoltán↗

The expressivity of classical and quantum neural networks on entanglement entropy

Abstract Analytically continuing the von Neumann entropy from Rényi entropies is a challenging task in quantum field theory. While then-th Rényi entropy can be computed using the replica method in the path integral representation of quantum field theory, the analytic continuation can only be achieved for some simple systems on a case-by-case basis. In this work, we propose a general framework to tackle this problem using classical and quantum neural networks with supervised learning. We begin by studying several examples with known von Neumann entropy, where the input data is generated by representing$${\text {Tr}}\rho _A^n$$ Tr ρ A n with a generating function. We adopt KerasTuner to determine the optimal network architecture and hyperparameters with limited data. In addition, we frame a similar problem in terms of quantum machine learning models, where the expressivity of the quantum models for the entanglement entropy as a partial Fourier series is established. Our proposed methods can accurately predict the von Neumann and Rényi entropies numerically, highlighting the potential of deep learning techniques for solving problems in quantum information theory.

Physics↗

Remediation Guidance for Major Airports after a Bioterrorist Attack

This document provides general guidelines for airport managers, local officials, and other stakeholders for developing a response and recovery plan for a major airport following the release of a biological warfare agent, with specific guidance for remediation. San Francisco International Airport was selected as the example airport during development of the guidance to illustrate specific details. The spore-forming bacterium Bacillus anthracis was selected as the biological agent of primary concern because it is the most difficult of known bioterrorism agents to inactivate and is considered to be one of the agents most likely to be used as a biological weapon. The focus of the guidance is on cleanup and disposal activities associated with the Characterization, Decontamination, and Clearance Phases that are defined herein. Activities associated with the Notification and First-Response Phases are brieÀy discussed in Appendixes A and B, respectively. In addition to the main text of this Remediation Guidance document and associated appendixes, a data supplement was developed specifically for San Francisco International Airport. Requests for the data supplement must be made directly to the Emergency Planning Operations Division of San Francisco International Airport. This document does not describe public health responses to release of a biological warfare agent. If laboratory analytical results confirm the presence of a biological agent, the responsible public health agency involved in the response will commence appropriate public health actions, such as treatment (CDC 2004) and decontamination of potentially contaminated individuals, distribution of prophylaxis, and medical examinations. See the Centers for Disease Control and Prevention web site for more information on emergency public health responses (http://www.bt.cdc.gov/). Effective communication with the media and the public is an essential component of airport remediation and recovery. Whereas such communication is beyond the scope of this document, many helpful resources are available. (See Section 1.1 for more information.) The concept of operations described in this document for cleanup of a Bacillus anthracis release at a major airport conforms to the National Response Framework (NRF) (DHS 2008) and implementation of the National Incident Management System (NIMS 2004). In most cases, a Unified Command would be formed to direct the cleanup process jointly and to take ultimate responsibility for all cleanup decisions. The Unified Command would likely include the Airport Manager or Airport Emergency Operations Manager, representatives from state and local public health and emergency management agencies, and Federal agencies, such as the U.S. Environmental Protection Agency. The Unified Command and Incident Command Staff would ideally be co-located in an Incident Command Post in an uncontaminated area of the airport. If a release is large or complex, co-location of all key players may not be possible. If a major incident is declared, a Principal Federal Official may be appointed by the Department of Homeland Security to facilitate Federal support to the Unified Command. In some facilities and jurisdictions, additional response plans or procedures (such as BioWatch or other emergency response plans, procedures, or protocols) may govern notification and first response. Facility personnel, responders, and emergency management coordinators should be aware of all applicable plans and procedures and how to implement them. Cleanups following the anthrax attacks of 2001 in the U.S. pre-dated the NRF and NIMS and did not make use of a NIMS Incident Command System as we know it today. Most Incident Commanders for the larger of those cleanups chose to convene a Technical Working Group (TWG) of multi-agency, multi-disciplinary, outside experts to advise in developing sampling and decontamination plans. Most of the Incident Commanders also convened a separate Environmental Clearance Committee (ECC) to independently review pre- and post decontamination sampling data as well as data on decontamination parameters, to evaluate whether the decontamination was effective, and to add credibility regarding a decision that decontaminated areas may be reoccupied. Use of such specialized technical expertise is strongly recommended, although it would now operate within the construct of the NIMS Incident Command System. The TWG, if convened, would act in an advisory capacity to the Environmental Unit within the Planning Section. Likewise, the ECC, if convened, would provide independent peer review of products and recommendations by the Environmental Unit. For maximum impartiality, the ECC could also provide recommendations directly to the Unified Command. Cleanup activities commence with site characterization. The principal goal of characterization is to define the extent of contamination and to gather information needed to design the decontamination approach. Initial sampling data collected by first responders are assessed to approximate the location(s) of contamination. Confirmation of the agent type and viability is obtained from a Laboratory Response Network laboratory. Additional characterization data are collected to determine the extent of contamination and where decontamination actions are needed. Areas suspected of being contaminated are contained and isolated to the degree possible to prevent further movement of an agent to uncontaminated areas or the environment, and to reduce the potential for future exposure from the agent or fumigant, if fumigation is needed. Agent air monitoring in areas adjacent to the contained contamination zones is done to ensure the protection of remediation personnel and to monitor any release from the contained zones. Various sampling approaches are considered. For example, wipe samples can be used to sample hard, nonporous surfaces. Swab samples can be used to sample nooks, crannies, joints, and seams. Appendix I is a template for preparing an incident-specific, operational characterization plan. Upon completion of the characterization plan, an internal review is initiated. Upon approval of the plan by the Unified Command, characterization commences. The Site Safety Officer develops a Health and Safety Plan to ensure that coordinated health and safety measures are in place for all responding personnel. This plan describes physical, chemical, and biological hazards at the site, personal protective equipment, personal decontamination procedures, and emergency procedures to be used by sampling and remediation personnel. An incident-specific Remediation Action Plan is developed, which describes the decontamination methods to be used and other details, including waste disposal. Under NIMS, this overall plan, as well as other plans described below, are implemented through a series of standardized, shorter-term Incident Action Plans, which describe specific activities that will take place during a shift or a day. The template in Appendix J is designed to facilitate preparation of the Remediation Action Plan. If fumigation will be done, a Sampling and Analysis Plan will be needed, as well as an Ambient Air Monitoring Plan, which can be a component of the Remediation Action Plan. These three plans are needed to obtain a crisis exemption from the U.S. Environmental Protection Agency for authorized use of an unregistered sterilant or pesticide during cleanup. If pesticide products become registered for inactivation of B. anthracis in the future, the three plans will likely be required by the product’s labeling, but the plans would no longer be submitted to the U.S. Environmental Protection Agency for approval; rather, the Incident Commander would approve them. If fumigation is used, an Emergency Response Plan is also recommended, although such a plan is not required for a crisis exemption. For some nonpersistent biological warfare agents, natural attenuation may be an adequate decontamination option. In cases where contamination is not extensive or an agent is not persistent, application of surface decontaminants or other methods of medical infection control may be effective. For extensive contamination by persistent agents, such as Bacillus anthracis, fumigation may be necessary. In those cases, the Decontamination Phase commences with source reduction, such as pre-cleaning surfaces to reduce the contaminant load. To expedite cleanup and prevent costs from escalating unnecessarily, a cost–benefit analysis should be incorporated in the decision process related to retention versus disposal of facility items and materials. Certain materials and structural components can be decontaminated for reuse, but it may not be feasible or cost-effective to decontaminate other items. Those items must be pre-treated, packaged (with the package decontaminated externally), and removed for disposal as waste. Site preparation includes sealing openings to prevent leaks and setting up equipment. Decontamination reagents and delivery systems are selected, and pre-testing all systems is done before carrying out chemical treatment(s). The important choice of decontamination technologies depends on characteristics of the agent, the nature and extent of contamination, and other site parameters identified during characterization. Decontamination-related decisions can have a major impact on waste-disposal costs, and it is necessary to develop a disposal plan that identifies a means of disposal, necessary approvals, transportation, and other details. A clearance strategy is developed to ensure that after decontamination, the risk of exposure to residual contamination is negligible. A clearance sampling plan is developed, which sets clearance criteria, specifies how to determine whether the criteria have been met, and describes how and where to collect clearance samples after decontamination. In most cases, clearance sampling includes both surface and aggressive air samples. Appendix K is a clearance plan template that identifies the types of required information. To determine whether the decontaminated area may be reoccupied, the Environmental Unit (and the ECC separately, if one is convened) evaluates the results of clearance samples. For the anthrax incidents to date, and given methods that have been used, cleanup was considered successful only when there was no growth of B. anthracis cultured from any environmental samples taken after decontamination. Other factors that will be considered include the decontamination process parameters (e.g., temperature, relative humidity, decontaminant concentration, and contact time) and the results from post-decontamination culture of biological indicators that may have been used during fumigation or sterilization processes. From such an evaluation the Environmental Unit or ECC, or both, recommend whether the area may be reoccupied, or whether further decontamination is necessary. The UC makes the final decision that a facility is appropriately decontaminated for reoccupancy. The facility owner or responsible public health agency makes the final decision to reopen a decontaminated facility. A theme that is emphasized throughout this document is that many activities can greatly reduce the time required to restore airport operations if those activities are conducted prior to an actual release of biological warfare agent. A summary of specific resources (such as Federal, state, and local agency contacts; contractors; prospective team members; subject-matter experts; laboratory facilities; and other entities) that should be identified in advance by airport officials is provided in each pertinent section of this document, and summary contact lists of such resources are provided in Appendix L. A summary of overall pre-planning actions that should be completed by airport officials is presented at the end of this document.

59 BASIC BIOLOGICAL SCIENCES↗