The simulation experiment description markup language (SED-ML): language specification for level 1 version 5

Modern biological research is increasingly informed by computational simulation experiments, which necessitate the development of methods for annotating, archiving, sharing, and reproducing the conducted experiments. These simulations increasingly require extensive collaboration among modelers, experimentalists, and engineers. The Minimum Information About a Simulation Experiment (MIASE) guidelines outline the information needed to share simulation experiments. SED-ML is a computer-readable format for the information outlined by MIASE, created as a community project and supported by many investigators and software tools. Level 1 Version 5 of SED-ML expands the ability of modelers to define simulations in SED-ML using the Kinetic Simulation Algorithm Onotoloy (KiSAO). While it was possible in Version 4 to define a simulation entirely using KiSAO, Version 5 now allows users to define tasks, model changes, ranges, and outputs using the ontology as well. SED-ML is supported by a growing ecosystem of investigators, model languages, and software tools, including various languages for constraint-based, kinetic, qualitative, rule-based, and spatial models, and many simulation tools, visual editors, model repositories, and validators. Additional information about SED-ML is available at https://sed-ml.org/.

VSCode-Antimony: a source editor for building, analyzing, and translating antimony models

MOTIVATION

Developing biochemical models in systems biology is a complex, knowledge-intensive activity. Some modelers (especially novices) benefit from model development tools with a graphical user interface. However, as with the development of complex software, text-based representations of models provide many benefits for advanced model development. At present, the tools for text-based model development are limited, typically just a textual editor that provides features such as copy, paste, find, and replace. Since these tools are not "model aware," they do not provide features for: (i) model building such as autocompletion of species names; (ii) model analysis such as hover messages that provide information about chemical species; and (iii) model translation to convert between model representations. We refer to these as BAT features.

RESULTS

We present VSCode-Antimony, a tool for building, analyzing, and translating models written in the Antimony modeling language, a human readable representation of Systems Biology Markup Language (SBML) models. VSCode-Antimony is a source editor, a tool with language-aware features. For example, there is autocompletion of variable names to assist with model building, hover messages that aid in model analysis, and translation between XML and Antimony representations of SBML models. These features result from making VSCode-Antimony model-aware by incorporating several sophisticated capabilities: analysis of the Antimony grammar (e.g. to identify model symbols and their types); a query system for accessing knowledge sources for chemical species and reactions; and automatic conversion between different model representations (e.g. between Antimony and SBML).

AVAILABILITY AND IMPLEMENTATION

VSCode-Antimony is available as an open source extension in the VSCode Marketplace https://marketplace.visualstudio.com/items?itemName=stevem.vscode-antimony. Source code can be found at https://github.com/sys-bio/vscode-antimony.

MakeSBML: A tool for converting between Antimony and SBML

We describe a web-based tool, MakeSBML (https://sys-bio.github.io/makesbml/), that provides an installation-free application for creating, editing, and searching the Biomodels repository for SBML-based models. MakeSBML is a client-based web application that translates models expressed in human-readable Antimony to the System Biology Markup Language (SBML) and vice-versa. Since MakeSBML is a web-based application it requires no installation on the user's part. Currently, MakeSBML is hosted on a GitHub page where the client-based design makes it trivial to move to other hosts. This model for software deployment also reduces maintenance costs since an active server is not required. The SBML modeling language is often used in systems biology research to describe complex biochemical networks and makes reproducing models much easier. However, SBML is designed to be computer-readable, not human-readable. We therefore employ the human-readable Antimony language to make it easy to create and edit SBML models.

Adapting modeling and simulation credibility standards to computational systems biology

Computational models are increasingly used in high-impact decision making in science, engineering, and medicine. The National Aeronautics and Space Administration (NASA) uses computational models to perform complex experiments that are otherwise prohibitively expensive or require a microgravity environment. Similarly, the Food and Drug Administration (FDA) and European Medicines Agency (EMA) have began accepting models and simulations as forms of evidence for pharmaceutical and medical device approval. It is crucial that computational models meet a standard of credibility when using them in high-stakes decision making. For this reason, institutes including NASA, the FDA, and the EMA have developed standards to promote and assess the credibility of computational models and simulations. However, due to the breadth of models these institutes assess, these credibility standards are mostly qualitative and avoid making specific recommendations. On the other hand, modeling and simulation in systems biology is a narrower domain and several standards are already in place. As systems biology models increase in complexity and influence, the development of a credibility assessment system is crucial. Here we review existing standards in systems biology, credibility standards in other science, engineering, and medical fields, and propose the development of a credibility standard for systems biology models.

SBML level 3 package: spatial processes, version 1, release 1

While many biological processes can be modeled by abstracting away the space in which those processes occur, some modeling (particularly at the cellular level) requires space itself to be modeled, with processes happening not in well-mixed compartments, but spatially-defined compartments. The SBML Level 3 Core specification does not include an explicit mechanism to encode geometries and spatial processes in a model, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactic constructs. The SBML Spatial Processes package for SBML Level 3 adds the necessary features to allow models to encode geometries and other spatial information about the elements and processes it describes.

BioSimulators: a central registry of simulation engines and services for recommending specific tools

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations.

Somatic whole genome dynamics of precancer in Barrett's esophagus reveals features associated with disease progression

While the genomes of normal tissues undergo dynamic changes over time, little is understood about the temporal-spatial dynamics of genomes in premalignant tissues that progress to cancer compared to those that remain cancer-free. Here we use whole genome sequencing to contrast genomic alterations in 427 longitudinal samples from 40 patients with stable Barrett’s esophagus compared to 40 Barrett’s patients who progressed to esophageal adenocarcinoma (ESAD). We show the same somatic mutational processes are active in Barrett’s tissue regardless of outcome, with high levels of mutation, ESAD gene and focal chromosomal alterations, and similar mutational signatures. The critical distinction between stable Barrett’s versus those who progress to cancer is acquisition and expansion of TP53−/− cell populations having complex structural variants and high-level amplifications, which are detectable up to six years prior to a cancer diagnosis. These findings reveal the timing of common somatic genome dynamics in stable Barrett’s esophagus and define key genomic features specific to progression to esophageal adenocarcinoma, both of which are critical for cancer prevention and early detection strategies.

Barrett’s esophagus is a pre-malignant condition that can progress to esophageal cancer. Here, the authors carry out whole genome sequencing of samples from patients who did or did not progress to cancer and find that mutations in many genes occur regardless of progression status, but also find features associated with progressive disease.

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4

Computational simulation experiments increasingly inform modern biological research, and bring with them the need to provide ways to annotate, archive, share and reproduce the experiments performed. These simulations increasingly require extensive collaboration among modelers, experimentalists, and engineers. The Minimum Information About a Simulation Experiment (MIASE) guidelines outline the information needed to share simulation experiments. SED-ML is a computer-readable format for the information outlined by MIASE, created as a community project and supported by many investigators and software tools. The first versions of SED-ML focused on deterministic and stochastic simulations of models. Level 1 Version 4 of SED-ML substantially expands these capabilities to cover additional types of models, model languages, parameter estimations, simulations and analyses of models, and analyses and visualizations of simulation results. To facilitate consistent practices across the community, Level 1 Version 4 also more clearly describes the use of SED-ML constructs, and includes numerous concrete validation rules. SED-ML is supported by a growing ecosystem of investigators, model languages, and software tools, including eight languages for constraint-based, kinetic, qualitative, rule-based, and spatial models, over 20 simulation tools, visual editors, model repositories, and validators. Additional information about SED-ML is available at https://sed-ml.org/.

Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs

Cancer genomes often harbor hundreds of somatic DNA rearrangement junctions, many of which cannot be easily classified into simple (e.g., deletion) or complex (e.g., chromothripsis) structural variant classes. Applying a novel genome graph computational paradigm to analyze the topology of junction copy number (JCN) across 2,778 tumor whole-genome sequences, we uncovered three novel complex rearrangement phenomena: pyrgo, rigma, and tyfonas. Pyrgo are "towers" of low-JCN duplications associated with early-replicating regions, superenhancers, and breast or ovarian cancers. Rigma comprise "chasms" of low-JCN deletions enriched in late-replicating fragile sites and gastrointestinal carcinomas. Tyfonas are "typhoons" of high-JCN junctions and fold-back inversions associated with expressed protein-coding fusions, breakend hypermutation, and acral, but not cutaneous, melanomas. Clustering of tumors according to genome graph-derived features identified subgroups associated with DNA repair defects and poor prognosis.

Within-patient phylogenetic reconstruction reveals early events in Barrett's Esophagus

Barrett's Esophagus is a neoplastic condition which progresses to esophageal adenocarcinoma in 5% of cases. Key events affecting the outcome likely occur before diagnosis of Barrett's and cannot be directly observed; we use phylogenetic analysis to infer such past events. We performed whole-genome sequencing on 4-6 samples from 40 cancer outcome and 40 noncancer outcome patients with Barrett's Esophagus, and inferred within-patient phylogenies of deconvoluted clonal lineages. Spatially proximate lineages clustered in the phylogenies, but temporally proximate ones did not. Lineages with inferred loss-of-function mutations in both copies of TP53 and CDKN2A showed enhanced spatial spread, whereas lineages with loss-of-function mutations in other frequently mutated loci did not. We propose a two-phase model with expansions of TP53 and CKDN2A mutant lineages during initial growth of the segment, followed by relative stasis. Subsequent to initial expansion, mutations in these loci as well as ARID1A and SMARCA4 may show a local selective advantage but do not expand far: The spatial structure of the Barrett's segment remains stable during surveillance even in patients who go on to cancer. We conclude that the cancer/noncancer outcome is strongly affected by early steps in formation of the Barrett's segment.

SBML Level 3: an extensible format for the exchange and reuse of biological models

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.

Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1

Biological models often contain elements that have inexact numerical values, since they are based on values that are stochastic in nature or data that contains uncertainty. The Systems Biology Markup Language (SBML) Level 3 Core specification does not include an explicit mechanism to include inexact or stochastic values in a model, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactic constructs. The SBML Distributions package for SBML Level 3 adds the necessary features to allow models to encode information about the distribution and uncertainty of values underlying a quantity.

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

Rule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains and the states and binding status of the involved components. Conceptually, fine-grained spatial information such as locations can also be provided. Through “wildcards” representing component states, entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states, and multiple compartments. The systems biology markup language (SBML) Level 3 Multi Package Version 1 extends the SBML Level 3 Version 1 core with the “type” concept in the Species and Compartment classes. Therefore, reaction rules may contain species that can be patterns and exist in multiple locations. Multiple software tools such as Simmune and BioNetGen support this standard that thus also becomes a medium for exchanging rule-based models. This document provides the specification for Release 2 of Version 1 of the SBML Level 3 Multi package. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the correction of errata and the addition of clarifications.

CNValidator: validating somatic copy-number inference

Motivation

CNValidator assesses the quality of somatic copy-number calls based on coherency of haplotypes across multiple samples from the same individual. It is applicable to any copy-number calling algorithm, which makes calls independently for each sample. This test is useful in assessing the accuracy of copy-number calls, as well as choosing among alternative copy-number algorithms or tuning parameter values.

Results

On a dataset of somatic samples from individuals with Barrett’s Esophagus, CNValidator provided feedback on the correctness of sample ploidy calls and also detected data quality issues.

Availability and implementation

CNValidator is available on GitHub at https://github.com/kuhnerlab/CNValidator.

Supplementary information

Supplementary data are available at Bioinformatics online.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. Release 2 corrects some errors and clarifies some ambiguities discovered in Release 1. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project website at http://sbml.org/.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the format of annotations, the correction of errata and the addition of clarifications. Other materials and software are available from the SBML project website at http://sbml.org/.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

phraSED-ML: A paraphrased, human-readable adaptation of SED-ML

MOTIVATION

Model simulation exchange has been standardized with the Simulation Experiment Description Markup Language (SED-ML), but specialized software is needed to generate simulations in this format. Text-based languages allow researchers to create and modify experimental protocols quickly and easily, and export them to a common machine-readable format.

RESULTS

phraSED-ML language allows modelers to use simple text commands to encode various elements of SED-ML (models, tasks, simulations, and results) in a format easy to read and modify. The library can translate this script to SED-ML for use in other softwares.

AVAILABILITY

phraSED-ML language specification, libphrasedml library, and source code are available under BSD license from http://phrasedml.sourceforge.net/ .

SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3

Constructing a model in a hierarchical fashion is a natural approach to managing model complexity, and offers additional opportunities such as the potential to re-use model components. The SBML Level 3 Version 1 Core specification does not directly provide a mechanism for defining hierarchical models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Hierarchical Model Composition package for SBML Level 3 adds the necessary features to SBML to support hierarchical modeling. The package enables a modeler to include submodels within an enclosing SBML model, delete unneeded or redundant elements of that submodel, replace elements of that submodel with element of the containing model, and replace elements of the containing model with elements of the submodel. In addition, the package defines an optional "port" construct, allowing a model to be defined with suggested interfaces between hierarchical components; modelers can chose to use these interfaces, but they are not required to do so and can still interact directly with model elements if they so chose. Finally, the SBML Hierarchical Model Composition package is defined in such a way that a hierarchical model can be "flattened" to an equivalent, non-hierarchical version that uses only plain SBML constructs, thus enabling software tools that do not yet support hierarchy to nevertheless work with SBML hierarchical models.

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

Apoglobin Stability Is the Major Factor Governing both Cell-free and in Vivo Expression of Holomyoglobin

Expression levels in animal muscle tissues and in Escherichia coli vary widely for naturally occurring mammalian myoglobins (Mb). To explore this variation, we developed an in vitro transcription and wheat germ extract-based translation assay to examine quantitatively the factors that govern expression of holoMb. We constructed a library of naturally occurring Mbs from two terrestrial and four deep-diving aquatic mammals and three distal histidine mutants designed to enhance apoglobin stability but decrease hemin affinity. A strong linear correlation is observed between cell-free expression levels of holo-metMb variants and their corresponding apoglobin stabilities, which were measured independently by guanidine HCl-induced unfolding titrations using purified proteins. In contrast, there is little dependence of expression on hemin affinity. Our results confirm quantitatively that deep diving mammals have highly stable Mbs that express to higher levels in animal myocytes, E. coli, and the wheat germ cell-free system than Mbs from terrestrial mammals. Our theoretical analyses show that the rate of aggregation of unfolded apoMb is very large, and as a result, the key factor for high level expression of holoMb, and presumably other heme proteins, is an ultra high fraction of folded, native apoglobin that is capable of rapidly binding hemin. This fraction is determined by the overall equilibrium folding constant and not hemin affinity. These results also demonstrate that the cell-free transcription/translation system can be used as a high throughput platform to screen for apoglobin stability without the need to generate large amounts of protein for in vitro unfolding measurements.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

Balkan (endemic) nephropathy

The clinical and pathological features of Balkan (endemic) nephropathy are discussed and correlations of incidence with excess late summer and autumn rainfall outlined. Cultures of a strain of Penicillium verrucosum var. cyclopium isolated from maize collected in an endemic area were fed to rats and lesions were produced in the straight third segment of the proximal kidney tubules. Extensive degeneration and nuclear changes were seen and on prolonged feeding further nuclear enlargement (to greater than 6n) and the formation of multinucleate cells occurred. The relevance of these findings to the clinical disease in man, especially the occurrence of urinary tract tumours, and the evidence supporting mycotoxin involvement, are discussed.

Multidose Medication Vial Sterility: An In-Use Study and a Review of the Literature

Contaminated multiple-dose medication vials (MDV) have been implicated in transmission of bacterial infections. It has been suggested that MDV be discarded after 24 hours or even after a single use. At our hospital, we cultured 1,223 weekly samples from 864 MDV in-use over a three-month period. Medications included xylocaine, insulin, heparin, immunizations, and miscellaneous agents. None of the samples was culture-positive. The duration of use was 9.5d (median), 18d (mean), and 1-402d (range) with 13% of vials in-use for more than 30 days. The mean duration of use was significantly shorter for medicine wards, emergency room, and outpatient clinics than for surgery and obgyn wards (p<0.05). Heparin and insulin MDV were in-use for significantly less time than xylocaine and miscellaneous agents (p<0.05), and insulin MDV were more regularly dated (p=0.001). The percentage of undated MDV declined significantly by month during die study (p=0.003). These results lend support to our current guideline that MDV should be dated upon opening and that, unless visible or suspected contamination occurs, vials are discarded either when empty or at the manufacturer's expiration date.

SBML and CellML translation in antimony and JSim

MOTIVATION

The creation and exchange of biologically relevant models is of great interest to many researchers. When multiple standards are in use, models are more readily used and re-used if there exist robust translators between the various accepted formats.

SUMMARY

Antimony 2.4 and JSim 2.10 provide translation capabilities from their own formats to SBML and CellML. All provided unique challenges, stemming from differences in each format's inherent design, in addition to differences in functionality.

AVAILABILITY AND IMPLEMENTATION

Both programs are available under BSD licenses; Antimony from http://antimony.sourceforge.net/and JSim from http://physiome.org/jsim/.

CONTACT

lpsmith@u.washington.edu.

Early replication in pulmonary B cells after infection with Marek's disease herpesvirus by the respiratory route

Abstract Natural infection with Marek's disease virus occurs through the respiratory mucosa after chickens inhale dander shed from infected chickens. The early events in the lung following exposure to the feather and squamous epithelial cell debris containing the viral particles remain unclear. In order to elucidate the virological and immunological consequences of MDV infection for the respiratory tract, chickens were infected by intratracheal administration of infective dander. Differences between susceptible and resistant chickens were immediately apparent, with delayed viral replication and earlier onset of interferon (IFN)-gamma production in the latter. CD4(+) and CD8(+) T cells surrounded infected cells in the lung. Although viral replication was evident in macrophages, pulmonary B cells were the main target cell type in susceptible chickens following intratracheal infection with MDV. In accordance, depletion of B cells curtailed viremia and substantially affected pathogenesis in susceptible chickens. Together the data described here demonstrate the role of pulmonary B cells as the primary and predominant target cells and their importance for MDV pathogenesis.

The limits of fine-scale mapping

When a novel genetic trait arises in a population, it introduces a signal in the haplotype distribution of that population. Through recombination that signal's history becomes differentiated from the DNA distant to it, but remains similar to the DNA close by. Fine-scale mapping techniques rely on this differentiation to pinpoint trait loci. In this study, we analyzed the differentiation itself to better understand how much information is available to these techniques. Simulated alleles on known recombinant coalescent trees show the upper limit for fine-scale mapping. Varying characteristics of the population being studied increase or decrease this limit. The initial uncertainty in map position has the most direct influence on the final precision of the estimate, with wider initial areas resulting in wider final estimates, though the increase is sigmoidal rather than linear. The Theta of the trait (4Nmu) is also important, with lower values for Theta resulting in greater precision of trait placement up to a point--the increase is sigmoidal as Theta decreases. Collecting data from more individuals can increase precision, though only logarithmically with the total number of individuals, so that each added individual contributes less to the final precision. However, a case/control analysis has the potential to greatly increase the effective number of individuals, as the bulk of the information lies in the differential between affected and unaffected genotypes. If haplotypes are unknown due to incomplete penetrance, much information is lost, with more information lost the less indicative phenotype is of the underlying genotype.

Antimony: a modular model definition language

MOTIVATION

Model exchange in systems and synthetic biology has been standardized for computers with the Systems Biology Markup Language (SBML) and CellML, but specialized software is needed for the generation of models in these formats. Text-based model definition languages allow researchers to create models simply, and then export them to a common exchange format. Modular languages allow researchers to create and combine complex models more easily. We saw a use for a modular text-based language, together with a translation library to allow other programs to read the models as well.

SUMMARY

The Antimony language provides a way for a researcher to use simple text statements to create, import, and combine biological models, allowing complex models to be built from simpler models, and provides a special syntax for the creation of modular genetic networks. The libAntimony library allows other software packages to import these models and convert them either to SBML or their own internal format.

AVAILABILITY

The Antimony language specification and the libAntimony library are available under a BSD license from http://antimony.sourceforge.net/.

Comparing likelihood and Bayesian coalescent estimation of population parameters

We have developed a Bayesian version of our likelihood-based Markov chain Monte Carlo genealogy sampler LAMARC and compared the two versions for estimation of theta = 4N(e)mu, exponential growth rate, and recombination rate. We used simulated DNA data to assess accuracy of means and support or credibility intervals. In all cases the two methods had very similar results. Some parameter combinations led to overly narrow support or credibility intervals, excluding the truth more often than the desired percentage, for both methods. However, the Bayesian approach rejected the generative parameter values significantly less often than the likelihood approach, both in cases where the level of rejection was normal and in cases where it was too high.

Liberalized screening for blunt carotid and vertebral artery injuries is justified

BACKGROUND

Current literature suggests that blunt carotid injuries (BCIs) and vertebral artery injuries (BVIs) are more common than once appreciated. Screening criteria have been suggested, but only one previous study has attempted to identify factors that predict the presence of BCI/BVI. This current study was conducted for two reasons. First, we wanted to determine the incidence of BCI/BVI in our institution. Second, we wanted to determine the incidence of abnormal four-vessel cerebral angiograms ordered for injuries and signs believed to be associated with BCI/BVI and thus to determine whether the screening protocol developed was appropriate.

METHODS

From August 1998, we used liberalized screening criteria for patients who were prospectively identified and suspected to be at high risk for BCI/BVI if any of the following were present: anisocoria, unexplained mono-/hemiparesis, unexplained neurologic exam, basilar skull fracture through or near the carotid canal, fracture through the foramen transversarium, cerebrovascular accident or transient ischemic attack, massive epistaxis, severe flexion or extension cervical spine fracture, massive facial fractures, or neck hematoma. Four-vessel cerebral angiograms were used for screening for BCI/BVI.

RESULTS

Over the 18-month study period, 48 patients were angiographically screened, with 21 patients (44%) being identified as having a total of 19 BCIs and 10 BVIs. Nine patients had unilateral carotid artery injuries and three patients had bilateral carotid artery injuries. Vertebral artery injuries were unilateral in six patients. One patient had bilateral carotid artery injuries and a unilateral vertebral artery injury. One patient had a unilateral carotid artery injury and a unilateral vertebral artery injury, and one patient had a unilateral carotid artery injury and bilateral vertebral artery injuries. During the same study period, 2,331 trauma patients were admitted, with 1,941 (83%) secondary to blunt trauma. The overall incidence of BCI/BVI was 1.1%. The frequency of abnormal angiograms ordered for cerebrovascular accident or transient ischemic attack, massive epistaxis, or severe cervical spine fractures was 100%. The frequency of abnormal angiograms ordered for the other indications was as follows: fracture through foramen transversarium, 60%; unexplained mono- or hemiparesis, 44%; basilar skull fracture, 42%; unexplained neurologic examination, 38%; anisocoria, 33%; and severe facial fractures, 0%.

CONCLUSION

The liberalized screening criteria used in this study were appropriate to identify patients with BCI/BVI. This study suggests BCI/BVI to be more common than previously believed and justifies that screening should be liberalized.

Expression of bone morphogenetic proteins during membranous bone healing

For the reconstructive plastic surgeon, knowledge of the molecular biology underlying membranous fracture healing is becoming increasingly vital. Understanding the complex patterns of gene expression manifested during the course of membranous fracture repair will be crucial to designing therapies that augment poor fracture healing or that expedite normal osseous repair by strategic manipulation of the normal course of gene expression. In the current study, we present a rat model of membranous bone repair. This model has great utility because of its technical simplicity, reproducibility, and relatively low cost. Furthermore, it is a powerful tool for analysis of the molecular regulation of membranous bone repair by immunolocalization and/or in situ hybridization techniques. In this study, an osteotomy was made within the caudal half of the hemimandible, thus producing a stable bone defect without the need for external or internal fixation. The healing process was then catalogued histologically in 28 Sprague-Dawley rats that were serially killed at 1, 2, 3, 4, 5, 6, and 8 weeks after operation. Furthermore, using this novel model, we analyzed, within the context of membranous bone healing, the temporal and spatial expression patterns of several members of the bone morphogenetic protein (BMP) family, known to be critical regulators of cells of osteoblast lineage. Our data suggest that BMP-2/-4 and BMP-7, also known as osteogenic protein-1 (OP-1), are expressed by osteoblasts, osteoclasts, and other more primitive mesenchymal cells within the fracture callus during the early stages of membranous fracture healing. These proteins continue to be expressed during the process of bone remodeling, albeit less prominently. The return of BMP-2/-4 and OP-1 immunostaining to baseline intensity coincides with the histological appearance of mature lamellar bone. Taken together, these data underscore the potentially important regulatory role played by the bone morphogenetic proteins in the process of membranous bone repair.

Osteoblast expression of vascular endothelial growth factor is modulated by the extracellular microenvironment

Angiogenesis, the formation of new blood vessels, is crucial to the process of fracture healing. Vascular disruption after osseous injury results in an acidic, hypoxic wound environment. We have previously shown that osteoblasts can produce vascular endothelial growth factor (VEGF) in response to a variety of stimuli. In this study we examined pH and lactate concentration, two components of the putative fracture extracellular microenvironment, and determined their relative contribution to regulation of rat calvarial osteoblast VEGF production under both normoxic and hypoxic conditions. Our results demonstrate that pH and lactate concentration do independently affect osteoblast VEGF mRNA and protein production. Acidic pH (7.0) significantly decreased VEGF production, under normoxic and hypoxic conditions (P < 0.05), compared with neutral pH (7.4). This decrease was primarily transcriptionally regulated, because the rate of VEGF mRNA degradation was unchanged at pH 7.0 vs. 7.4. Similarly, an elevated lactate concentration (22 mM) also depressed osteoblast elaboration of VEGF at both neutral and acidic pH (P < 0.001). Furthermore, the effects of increasing acidity and elevated lactate appeared to be additive.

A molecular analysis of the isolated rat posterior frontal and sagittal sutures: differences in gene expression

Although it is one of the most commonly occurring craniofacial congenital disabilities, craniosynostosis (the premature fusion of cranial sutures) is nearly impossible to prevent because the molecular mechanisms that regulate the process of cranial suture fusion remain largely unknown. Recent studies have implicated the dura mater in determining the fate of the overlying cranial suture; however, the molecular biology within the suture itself has not been sufficiently investigated. In the murine model of cranial suture fusion, the posterior frontal suture is programmed to begin fusing by postnatal day 12 in rats (day 25 in mice), reliably completing bony union by postnatal day 22 (day 45 in mice). In contrast, the sagittal suture remains patent throughout the life of the animal. Using this model, this study sought to examine for the first time what differences in gene expression--if any--exist between the two sutures with opposite fates. For each series of experiments, 35 to 40 posterior frontal and sagittal suture complexes were isolated from 6-day-old Sprague-Dawley rat pups. Suture-derived cell cultures were established, and ribonuicleic acid was derived from snap-frozen, isolated suture tissue. Results demonstrated that molecular differences between the posterior frontal and sagittal suture complexes were readily identified in vivo, although these distinctions were lost once the cells comprising the suture complex were cultured in vitro. Hypothetically, this change in gene expression resulted from the loss of the influence of the underlying dura mater. Significant differences in the expression of genes encoding extracellular matrix proteins existed in vivo between the posterior frontal and sagittal sutures. However, the production of the critical, regulatory cytokine transforming growth factor beta-1 was equal between the two suture complexes, lending further support to the hypothesis that dura mater regulates the fate of the overlying cranial suture.

The effect of wind speed and direction on the distribution of sewage-associated bacteria

A study of the relationship between wind and the distribution of sewage-associated bacteria was undertaken at a location where the sewage was discharged into the sea adjacent to the mouth of a river. The numbers of presumptive Escherichia coli were determined in 149 sea-water samples taken from three locations at distances of 1.9, 2.4 and 4.3 km from the outfall. On each sampling occasion, data on the wind speed and direction in the 3 h prior to collection of the samples were also collected. Analysis of these data demonstrated a significant role for wind speed and direction. With respect to wind direction, the numbers of presumptive E. coli present in a sample were significantly higher when the sample site lay downwind of the outfall. Wind speed was shown to have an influence on the numbers of presumptive E. coli only when the sample site was downwind of the outfall. In an analysis of 61 samples, an inverse correlation (r2 = 0.73) between salinity and log presumptive E. coli numbers was demonstrated. These data demonstrate that wind speed and direction at the time of sampling significantly influence the numbers of presumptive E. coli detected in any sea-water sample. It is argued that failure to pay sufficient attention to these parameters in the design of monitoring programmes may result in the generation of data that could provide a seriously distorted picture of the microbiological status of a water body.

Protein engineering strategies for designing more stable hemoglobin-based blood substitutes

Over the past five years our laboratory has been using rational, comparative, and random combinatorial mutagenesis strategies to optimize the alpha and beta subunits of recombinant human hemoglobin (Hb) for efficient O2 transport, greater stability, and minimum interference with vascular activity. In each approach, mammalian myoglobin (Mb) has been used as a prototype to develop experimental methodologies and to study the stereochemical mechanisms that govern O2 affinity, discrimination against CO, rates of ligand binding, auto- and chemically induced oxidation, resistance to hemin loss, and stability to globin denaturation. Multiple replacements in the distal portion of the heme pocket have been designed rationally to lower oxygen affinity and at the same time inhibit oxidative side reactions. The P50 values are adjusted by altering electrostatic and steric interactions between the bound ligand and residues at the Leu(B10), His(E7), and Va(E11) positions. Large apolar residues (Leu, Phe, Trp) at the B10 and E11 positions inhibit NO-induced and autooxidation in both myoglobin and hemoglobin by excluding oxidants and proton donors from the immediate vicinity of the bound ligand. Similar strategies appear to have evolved in a number of animal myoglobins and hemoglobins which have unusual amino acids at the E7, B10, and E11 positions. Random combinatorial mutagenesis techniques have been developed to insert new amino acid combinations near the bound ligand in sperm whale Mb. The objective is to obtain "unnatural" distal pocket structures that enhance O2 transport and resistance to oxidation by alternative mechanisms.

Information system for labor and delivery surveillance

An on-line information system has been developed and implemented at St. Mary Medical Center in Long Beach, California, to support a ten-bed labor and delivery suite. A Digital Equipment Corporation VAX 750 was programmed to provide on-line multi-terminal clinical surveillance. The reports implemented include an obstetrical summary report, labor record, obstetrical clinical record, and the birth certificate. Computer terminals and monitors are placed at the nursing station and other work areas, such as the anesthesia on-call room, obstetrical supervisor's office, on-call room, neonatal ICU, O.R., admission room, and M.D. conference room. The system includes computer databases used to store information for medical quality assurance, management reports, obligatory statutory reports, and research, and to provide comparison of patient data with data from other hospitals.

Rapid detection of group B streptococcal antigen in human amniotic fluid

Infants exposed in utero to group B streptococcus (GBS)-infected human amniotic fluid (HAF) are at high risk for serious infection. Latex particle agglutination (LPA) tests are not approved for detection of GBS in HAF. Two LPA systems, Patho-Dx Strep B and Wellcogen Strep B, were used to test unfiltered sterile HAF and filtered HAF containing concentrations of GBS carbohydrate from 0.2 to 100 micrograms/ml. Four different processing techniques were used to prevent nonspecific LPA: EDTA, nitrous acid, enzyme, and nitrous acid-heat. GBS (10(2) CFU/ml) was inoculated into filtered HAF, incubated, sampled serially, processed with enzyme, and tested by LPA. Unprocessed, unfiltered HAF showed 33% nonspecific agglutination when tested by LPA. Processing of HAF removed nonspecific agglutination and improved GBS antigen detection. Without processing, LPA could not detect less than 100 micrograms of GBS carbohydrate per ml. With nitrous acid or enzyme processing, as little as 0.2 microgram/ml could be detected. Results were easier to read after enzyme processing than after nitrous acid processing. Although both LPA systems were equally efficient, testing was easier with the Patho-Dx system. After enzyme processing, LPA could detect as few as 10(4) CFU/ml when agglutination was read with a 4 X hand lens. Substances in HAF induce false-positive reactions during LPA testing. Processing removes the interference and improves the detection of GBS. LPA testing of HAF may allow earlier identification and treatment of infants at risk for serious GBS infection.

Temporal variation in rates of cesarean section for dystocia: does "convenience" play a role?

The purpose of this study is to test the hypothesis that convenience for the physician plays a role in the rate of cesarean section performed because of dystocia. Three time periods were defined (night, 12 midnight to 7:59 AM; day, 8 AM to 5:59 PM; evening, 6 PM to 11:59 PM) based on the work commitments and daily routines of the obstetrician. Rates of cesarean section for dystocia were determined for each of the three time periods. An evening peak in the cesarean section rate is partially but not entirely explained by an evening increase in the proportion of patients in prolonged labor. When patients were stratified according to labor duration (less than 12, 12 to 15, and greater than 16 hours), a persistent evening excess in the rate of cesarean section for dystocia was observed for patients whose labor duration was less than 16 hours. Although this is interpreted as being consistent with the hypothesis of physician convenience, the magnitude of this effect on the overall rate of cesarean section for dystocia is small.

Ultrasonography and computed tomography in severe urinary tract infection

A prospective study evaluated the utility of renal computed tomography (CT) and ultrasonography in 35 patients hospitalized for treatment of urinary tract infection. Renal computed tomograms were abnormal in 18 of 28 patients with acute pyelonephritis and three of four patients with urosepsis, showing findings consistent with pyelonephritis in 17 patients and intrarenal abscess or focal bacterial nephritis in four patients. Renal sonograms were abnormal in only eight patients, showing findings compatible with pyelonephritis in four and intrarenal abscess or focal bacterial nephritis in the other four. Flank tenderness was absent in only four patients with CT findings of pyelonephritis, of whom three were diabetic. We therefore found that (1) renal CT is a sensitive test for acute upper urinary tract infection, (2) ultrasonography detects focal bacterial nephritis and abscesses but is insensitive to uncomplicated upper urinary tract infection, and (3) painless pyelonephritis may be more common in patients with diabetes mellitus.

Multiple-dose vials: persistence of bacterial contaminants and infection control implications

Due to sporadic infections attributed to contaminated multiple-dose medication vials (MDV), some authorities have suggested discarding all MDV within 24 hours. We inoculated 11 commonly used medications with suspensions of 10 bacterial species previously associated with contaminated parenteral solutions and determined microbial persistence at both room and refrigerator temperature. At 22 degrees C, atropine, curare, folic acid, NPH insulin and triamcinolone did not allow microbial persistence beyond 4 hours. Lidocaine and heparin were sterile by 24 hours. Regular insulin, immune serum globulin, and myochrysine allowed persistence for up to 7 days. At 4 degrees C, bacterial persistence was significantly prolonged for all medications including those MDV requiring refrigeration. No organisms proliferated; however, F. meningosepticum and P. maltophilia were particularly persistent at both temperatures. The risk of persistent MDV contamination appears to be dependent upon specific pharmaceutical, microbe and storage temperature interactions. Recommendations for the refrigeration of MDV medications may require reevaluation on a product-by-product basis.

Comparison of single-dose tetracycline hydrochloride to conventional therapy of urinary tract infections

Sixty-two women with signs and symptoms compatible with lower urinary tract infections were randomized to receive single-dose tetracycline (2 g), multi-dose tetracycline (500 mg four times per day for 10 days), or single-dose amoxicillin (3 g). Urine cultures were obtained upon entry into the study and on days 4, 14, and 28 after therapy. Single-dose tetracycline cured 12 of 16 (75%) of women with documented urinary tract infections, compared with 15 of 16 (94%) in the multi-dose tetracycline group and 7 of 13 (54%) receiving single-dose amoxicillin. Mild nausea in 3 of 20 patients (15%) was the only complication in the single-dose tetracycline group. Two grams of single-dose tetracycline is as effective as other reported regimens regardless of the susceptibility of the initial pathogen and has minimal toxicity.

Improved detection of bacterial antigens by latex agglutination after rapid extraction from body fluids

Nonspecific agglutination of antibody-coated latex particles, unrelated to the presence of specific bacterial antigens, is a major difficulty with commercial latex particle agglutination tests. Rheumatoid and other factors are known to interfere with latex tests. We studied the use of six chelating, reducing, and anticoagulatory reagents in a rapid extraction of antigen procedure to free heat-stable antigens of Haemophilus influenzae type b and group B streptococcus which had been added to human sera. We also screened sera for the incidence of nonspecific agglutination from the three following groups: 123 patients with positive serology tests, 112 hospitalized patients, and 87 blood donors. The rapid extraction of antigen procedure involved a 1:4 dilution of the sera with each of the six reagents, incubation at 100 degrees C for 3 min, and centrifugation at 13,000 X g for 5 min. Two commercial latex kits were tested (Bactigen and Wellcogen). Nonspecific agglutination was entirely eliminated by each of the six extraction reagents. Sera from 52% of the patients with positive serology tests, 29% of the hospitalized patients, and 28% of the blood donors showed nonspecific agglutination with Bactigen before extraction. Nonspecific agglutination was eliminated in all but one sample after the rapid extraction of antigen procedure. This simple, rapid extraction procedure eliminated nonspecific reactions in cerebrospinal fluids and amniotic fluids and reduced this problem in urines and sera with each commercial kit used on clinical specimens.

Avoidance of false-negative blood culture results by rapid detection of pneumococcal antigen

False-negative blood culture results may occur in children with pneumococcal bacteremia due to bacterial autolysis. We describe four patients with pneumococcal bacteremia whose aerobic blood cultures showed partial or complete autolysis of the pneumococci. Pneumococcal antigen, however, was rapidly detected in media from the blood culture bottles, using an agglutination assay. Processing of the media before analysis was necessary to prevent nonspecific agglutination and to allow the detection of a specific reaction. It is important that physicians and laboratory personnel be aware that pneumococci may rapidly autolyze during incubation, yielding false-negative culture results. Antigen detection methods may provide rapid and specific identification of the etiologic agent.