WormBase 2024: status and transitioning to Alliance infrastructure

WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects.

Updates to the Alliance of Genome Resources central infrastructure

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).

FAIR Header Reference genome: a TRUSTworthy standard

The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability and Technology. The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.

DATA RESOURCES AND ANALYSES FAIR Header Reference genome: A TRUSTworthy standard

The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR-bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability, and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability, and Technology (TRUST). The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility, and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.

Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, C. elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and APIs. Here we focus on developments over the last two years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse. We describe our progress towards a central persistent database to support curation, the data modeling that underpins harmonization, and progress towards a state-of-the art literature curation system with integrated Artificial Intelligence and Machine Learning (AI/ML).

JBrowse 2: a modular genome browser with views of synteny and structural variation

We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.

JBrowse Jupyter: a Python interface to JBrowse 2

MOTIVATION

JBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically they have been deployed at the end of bioinformatics pipelines, typically decoupled from the analysis itself. However, emerging technologies such as Jupyter notebooks enable a more rapid iterative cycle of development, analysis and visualization.

RESULTS

We have developed a package that provides a Python interface to JBrowse 2's suite of embeddable components, including the primary Linear Genome View. The package enables users to quickly set up, launch and customize JBrowse views from Jupyter notebooks. In addition, users can share their data via Google's Colab notebooks, providing reproducible interactive views.

AVAILABILITY AND IMPLEMENTATION

JBrowse Jupyter is released under the Apache License and is available for download on PyPI. Source code and demos are available on GitHub at https://github.com/GMOD/jbrowse-jupyter.

Concurrent Prostatic Adenocarcinoma and Lymphoma: Clinicopathologic Study of 10 Cases

Introduction/Objective

Synchronous and meta-synchronous hematolymphoid neoplasms and prostatic adenocarcinomas are known to occur, albeit rarely. The purpose of this study is to identify the clinicopathologic features of patients with coexisting prostatic adenocarcinoma and a lymphoma diagnosis.

Methods/Case Report

The institutional pathology archive was searched from 2016 to 2021. Data such as patient age, Gleason score, pathologic tumor stage, type of lymphoma and follow up data were collected.

Results (if a Case Study enter NA)

Ten patients were identified. Mean patient age was 65.4 ± 5.7 years. Nine specimens were prostatectomies and 1 was a needle core biopsy. Four patients had previous lymphoma diagnoses while 6 were diagnosed with lymphoma on lymph node dissection for prostatectomies. Seven patients had Gleason grade 3 + 4=7 disease, two had Gleason grade 4 + 3=7 and one had Gleason grade 4 + 5=9. Seven patients had small lymphocytic lymphoma/chronic lymphocytic leukemia, one had follicular lymphoma, one had mantle cell lymphoma and one had peripheral T-cell lymphoma. The patient with peripheral T-cell lymphoma died 18 months after lymphoma diagnosis and 11 months after prostate cancer diagnosis. The remaining 9 patients were alive for a mean of 27.7 ± 22.6 months after prostate cancer diagnosis.

Conclusion

There is minimal literature on patients with synchronous/meta-synchronous hematolymphoid neoplasms and prostatic adenocarcinoma. Our data provides one of the largest institutional series in this regard. Additional data and follow up is needed to evaluate if the concurrent low grade hematolymphoid malignancy, specifically small lymphocytic lymphoma/chronic lymphocytic leukemia, affects the survival outcome in these patients.

Abstract 6400: JBrowse 2: An extensible open-source platform for modern genome analysis

Introduction: Genome browsers are useful tools for research in human genetics, able to display and integrate biological information such as long and short read sequencing data, variant calls, and annotations. While traditional linear genome browsers have demonstrated broad utility for many applications, there is an increasing need for visualizing complex structural variants (SVs) beyond the linear view. To meet these challenges, we created JBrowse 2: an extensible open-source platform for visualizing and integrating genomic data.

Results: JBrowse 2 is a flexible platform that provides the foundation for the development of applications and web dashboards that combine novel views and representations extending beyond linear displays in genomic reference coordinates. For example, a flagship JBrowse 2 application is the SV Inspector, which lets users open a list of structural variants in a data table and see the results in a whole-genome circular view. Clicking on a given variant in the table or circular view opens up a linear view that displays the read evidence supporting the SV, even across complex breakpoints like translocations. Dotplot and synteny views are built-in, enabling “long read vs reference” dotplot visualizations, or alignments of de-novo assembled contigs to the genome. These views are integrated with each other, so that (for example) a long read is just a few clicks away from the corresponding dotplot.

In addition to including these new views, the JBrowse 2 platform is designed from the ground up to enable third-party plugins to add new views, data adapters, and track types, which has facilitated the creation of new plugins that address some very specific use cases. These include our MSA view plugin for viewing multiple sequence alignments, data adapters that download data from UCSC and CIVIC APIs, and the Quantseq plugin for viewing quantitative motif scores as a genome browser track.

JBrowse 2 is available as both a web app or a local desktop app. We also offer re-usable components on NPM, and users of R can programmatically create an instance of JBrowse 2 with the JBrowseR package on CRAN. JBrowse 2 can also generate high quality SVG snapshots from inside the app, and we also created a CLI tool called jb2export to perform automated or bulk exports of JBrowse 2 visualizations. We anticipate that JBrowse 2 will better serve genome scientists with its structural variant visualization capabilities, and will provide the flexibility to adapt to new visualization and analysis challenges as they emerge in the coming years.

Citation Format: Scott Cain, Robin Haw, Caroline Bridge, Junjun Zhang, Robert Buels, Colin Diesh, Garrett Stevens, Teresa Martinez, Peter K. Xie, Elliot Hershberg, Shihab Dider, Lincoln Stein, Ian Holmes. JBrowse 2: An extensible open-source platform for modern genome analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6400.

Abstract LB503: Using JBrowse 2 plugins to visualize cancer genomic data

Genome browsers are essential tools for integrating, exploring, and visualizing data from large cancer genomics datasets. JBrowse 2 is a JavaScript genome browser with novel features for visualizing structural variants, syntenic alignments, and multiple types of genomic data. Although JBrowse 2 is available as a web-based or desktop application, the capabilities and features are not fixed and can be expanded through a comprehensive plugin system. To help address users' needs, we launched the new JBrowse 2 Plugin Store (https://jbrowse.org/jb2/plugin_store/). The overarching goals of the Plugin Store are to showcase the crucial features plugins add to JBrowse 2, to enable researchers to search for plugins they need, and for developers to highlight their plugins. The plugin system spans all aspects of the JBrowse 2 application and enables new track types (e.g. Manhattan plots, Hi-C data, ideograms), data adapters (e.g. API endpoint adapters for NCI Genomic Data Commons and the International Cancer Genome Consortium), and views (e.g. dot plots and multiple sequence alignments). Here, we present the capabilities of JBrowse 2 plugins and describe usage scenarios for cancer biologists and bioinformaticians, and software developers.

Citation Format: Robin Andrew Haw, Colin Diesh, Caroline Bridge, Rob Buels, Garrett Stevens, Peter Xie, Teresa Martinez, Elliot Hershberg, Junjun Zhang, Shihab Dider, Scott Cain, Lincoln Stein, Ian Holmes. Using JBrowse 2 plugins to visualize cancer genomic data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB503.

Harmonizing model organism data in the Alliance of Genome Resources

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans

WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.

WormBase: a modern Model Organism Information Resource

WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.

WormBase 2017: molting into a new stage

WormBase (http://www.wormbase.org) is an important knowledge resource for biomedical researchers worldwide. To accommodate the ever increasing amount and complexity of research data, WormBase continues to advance its practices on data acquisition, curation and retrieval to most effectively deliver comprehensive knowledge about Caenorhabditis elegans, and genomic information about other nematodes and parasitic flatworms. Recent notable enhancements include user-directed submission of data, such as micropublication; genomic data curation and presentation, including additional genomes and JBrowse, respectively; new query tools, such as SimpleMine, Gene Enrichment Analysis; new data displays, such as the Person Lineage browser and the Summary of Ontology-based Annotations. Anticipating more rapid data growth ahead, WormBase continues the process of migrating to a cutting-edge database technology to achieve better stability, scalability, reproducibility and a faster response time. To better serve the broader research community, WormBase, with five other Model Organism Databases and The Gene Ontology project, have begun to collaborate formally as the Alliance of Genome Resources.

Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes

WormBase ( www.wormbase.org ) provides the nematode research community with a centralized database for information pertaining to nematode genes and genomes. As more nematode genome sequences are becoming available and as richer data sets are published, WormBase strives to maintain updated information, displays, and services to facilitate efficient access to and understanding of the knowledge generated by the published nematode genetics literature. This chapter aims to provide an explanation of how to use basic features of WormBase, new features, and some commonly used tools and data queries. Explanations of the curated data and step-by-step instructions of how to access the data via the WormBase website and available data mining tools are provided.

WormBase 2016: expanding to enable helminth genomic research

WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.

The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data

Linking phenotypic with genotypic diversity has become a major requirement for basic and applied genome-centric biological research. To meet this need, a comprehensive database backend for efficiently storing, querying and analyzing large experimental data sets is necessary. Chado, a generic, modular, community-based database schema is widely used in the biological community to store information associated with genome sequence data. To meet the need to also accommodate large-scale phenotyping and genotyping projects, a new Chado module called Natural Diversity has been developed. The module strictly adheres to the Chado remit of being generic and ontology driven. The flexibility of the new module is demonstrated in its capacity to store any type of experiment that either uses or generates specimens or stock organisms. Experiments may be grouped or structured hierarchically, whereas any kind of biological entity can be stored as the observed unit, from a specimen to be used in genotyping or phenotyping experiments, to a group of species collected in the field that will undergo further lab analysis. We describe details of the Natural Diversity module, including the design approach, the relational schema and use cases implemented in several databases.

GMODWeb: a web framework for the Generic Model Organism Database

GMODWeb is a software framework designed to speed the development of websites for model organism databases.

The Generic Model Organism Database (GMOD) initiative provides species-agnostic data models and software tools for representing curated model organism data. Here we describe GMODWeb, a GMOD project designed to speed the development of model organism database (MOD) websites. Sites created with GMODWeb provide integration with other GMOD tools and allow users to browse and search through a variety of data types. GMODWeb was built using the open source Turnkey web framework and is available from .

ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data

ParameciumDB (http://paramecium.cgm.cnrs-gif.fr) is a new model organism database associated with the genome sequencing project of the unicellular eukaryote Paramecium tetraurelia. Built with the core components of the Generic Model Organism Database (GMOD) project, ParameciumDB currently contains the genome sequence and annotations, linked to available genetic data including the Gif Paramecium stock collection. It is thus possible to navigate between sequences and stocks via the genes and alleles. Phenotypes, of mutant strains and of knockdowns obtained by RNA interference, are captured using controlled vocabularies according to the Entity-Attribute-Value model. ParameciumDB currently supports browsing of phenotypes, alleles and stocks as well as querying of sequence features (genes, UniProt matches, InterPro domains, Gene Ontology terms) and of genetic data (phenotypes, stocks, RNA interference experiments). Forms allow submission of RNA interference data and some bioinformatics services are available. Future ParameciumDB development plans include coordination of human curation of the near 40 000 gene models by members of the research community.

A resorbable porous ceramic composite bone graft substitute in a rabbit metaphyseal defect model

The success of converted corals as a bone graft substitute relies on a complex sequence of events of vascular ingrowth, differentiation of osteoprogenitor cells, bone remodeling and graft resorption occurring together with host bone ingrowth into and onto the porous coralline microstructure or voids left behind during resorption. This study examined the resorption rates and bone infiltration into a family of resorbable porous ceramic placed bilaterally in critical sized defects in the tibial metaphyseal-diaphyseal of rabbits. The ceramics are made resorbable by partially converting the calcium carbonate of corals to form a hydroxyapatite (HA) layer on all surfaces. Attempts have been made to control the resorption rate of the implant by varying the HA thickness. New bone was observed at the periosteal and endosteal cortices, which flowed into the centre of the defect supporting the osteoconductive nature of partially converted corals. The combination of an HA layer and calcium carbonate core provides a composite bone graft substitute for new tissue integration. The HA-calcium carbonate composite demonstrated an initial resorption of the inner calcium carbonate phase but the overall implant resorption and bone ingrowth behaviour did not differ with HA thickness.

Surface roughness of the proximal and distal bearing surface of mobile bearing total knee prostheses

Proximal and distal articulations surface roughness measurements were done on 8 mobile bearing knee designs immediately after removal from sterile packaging. Roughness parameters Ra and Rp based on ISO 97, representing mean deviation from the smooth surface line and mean peak to smooth surface line, were recorded using a contact surface profilometer at 10 random sites in the anteroposterior and mediolateral direction on the femoral and tibial metal components and the proximal and distal surface of the ultra-high molecular weight polyethylene (PE) inserts. No differences were found for surface roughness values for the metal components. Surface roughness values were greater for the distal PE bearing surfaces compared with the proximal PE bearing surfaces for each design tested. The roughness values for the PE inserts showed a directional dependence. Complex kinematics of mobile bearing knees coupled with this rougher distal interface could influence the rate of generation of wear particles and total volume of particles produced especially in the early postoperative period.

The function of the posterior cruciate ligament in an anteroposterior-gliding rotating platform total knee arthroplasty

Knee kinematics after total knee arthroplasty is dictated primarily by implant geometry and native soft tissue constraints. This study highlights the importance of a functioning posterior cruciate ligament in limiting excessive anteroposterior translation in a mobile bearing knee design that relies on native posterior cruciate ligament integrity and postarthroplasty tensioning for stability rather than any inherent mechanical design stability, such as anterior rails or stops.

Creation of genome-wide protein expression libraries using random activation of gene expression

Here we report the use of random activation of gene expression (RAGE) to create genome-wide protein expression libraries. RAGE libraries containing only 5 x 10(6) individual clones were found to express every gene tested, including genes that are normally silent in the parent cell line. Furthermore, endogenous genes were activated at similar frequencies and expressed at similar levels within RAGE libraries created from multiple human cell lines, demonstrating that RAGE libraries are inherently normalized. Pools of RAGE clones were used to isolate 19,547 human gene clusters, approximately 53% of which were novel when tested against public databases of expressed sequence tag (EST) and complementary DNA (cDNA). Isolation of individual clones confirmed that the activated endogenous genes can be expressed at high levels to produce biologically active proteins. The properties of RAGE libraries and RAGE expression clones are well suited for a number of biotechnological applications including gene discovery, protein characterization, drug development, and protein manufacturing.

Back-casting sociality in extinct species: new perspectives using mass death assemblages and sex ratios

Despite 150 years of interest in the ecology of dinosaurs, mammoths, proto-hominids and other extinct vertebrates, a general framework to recreate patterns of sociality has been elusive. Based on our recent discovery of a contemporary heterospecific mass death assemblage in the Gobi Desert (Mongolia), we fit predictions about gender-specific associations and group living in extant ungulates to extinct ones. We relied on comparative data on sex-ratio variation and body-size dimorphism, basing analyses on 38 additional mass mortality sites from Asia, Africa, Europe and North America that span 50 million years. Both extant and extinct species died in aggregations with biased adult sex ratios, but the skew (from 1:1) was greater for extinct dimorphic taxa, suggesting that sociality in these extinct species can be predicted from spatial and demographic traits of extant ones. However, extinct rhinos, horses and zebras were inconsistent with predictions about adult sex ratios, which underscores the inherent difficulty in backcasting historic patterns to some monomorphic taxa. These findings shed light not only on the sociality of extinct species but provide a sound, although limited, footing for interpretation of modern death assemblages within the context of the emerging science of taphonomy and palaeobehaviour.

Venoarterial CO(2) difference during regional ischemic or hypoxic hypoxia

To test the role of blood flow in tissue hypoxia-related increased veno-arterial PCO(2) difference (DeltaPCO(2)), we decreased O(2) delivery (&Ddot;O(2)) by either decreasing flow [ischemic hypoxia (IH)] or arterial PO(2) [hypoxic hypoxia (HH)] in an in situ, vascularly isolated, innervated dog hindlimb perfused with a pump-membrane oxygenator system. Twelve anesthetized and ventilated dogs were studied, with systemic hemodynamics maintained within normal range. In the IH group (n = 6), hindlimb DO(2) was progressively lowered every 15 min by decreasing pump-controlled flow from 60 to 10 ml. kg(-1). min(-1), with arterial PO(2) constant at 100 Torr. In the HH group (n = 6), hindlimb DO(2) was progressively lowered every 15 min by decreasing PO(2) from 100 to 15 Torr, when flow was constant at 60 ml. kg(-1). min(-1). Limb DO(2), O(2) uptake (VO(2)), and DeltaPCO(2) were obtained every 15 min. Below the critical DO(2), VO(2) decreased, indicating dysoxia, and O(2) extraction ratio (VO(2)/DO(2)) rose continuously and similarly in both groups, reaching a maximal value of approximately 90%. DeltaPCO(2) significantly increased in IH but never differed from baseline in HH. We conclude that absence of increased DeltaPCO(2) does not preclude the presence of tissue dysoxia and that decreased flow is a major determinant in increased DeltaPCO(2).

Comparison of analytical methods for quantitation of isolated porcine hepatocyte yields

As cell-based therapies receive approval for clinical evaluation and use, the development of reliable methods to quantify cell number and control the dose of therapy delivered is becoming increasingly important. An example is the determination of the number and volume of primary porcine hepatocytes used in an extracorporeal treatment for patients with liver disease. Conventional cell counting using optical microscopy was compared against two alternate methods to quantify isolated porcine hepatocytes: (1) automated cell counting using a commercially available particle characterization instrument, and (2) quantitation by cell mass. Methods were compared based on accuracy, precision, specificity, linear range, and ruggedness. The automated method delivered substantially improved accuracy, precision, and ruggedness when compared to the conventional optical method. It also provided valuable information about the size distribution of cell preparations, which often contained clumps of cells, and showed that processing steps such as cryopreservation can alter the size characteristics of a cell population. The automated method was also faster, and was well suited to use in a commercial manufacturing process. The mass-based method was simple and inexpensive, but suffered from nonlinearity at low cell concentrations. Automated cell quantitation using a commercially available particle characterization instrument proved to be the preferred method for obtaining accurate and consistent porcine hepatocyte counts in a timely manner.

Ovariectomy of adult rats leads to increased expression of astrocytic basic fibroblast growth factor in the ventral tegmental area and in dopaminergic projection regions of the entorhinal and prefrontal cortex

Changes in astrocytic function may underlie the neurochemical and morphological alterations in limbic and cortical areas after estrogen loss in adult females. We assessed whether increased expression of basic fibroblast growth factor (bFGF), an astrocytic response involved in injury-induced neuronal plasticity, occurs after ovariectomy. We examined bFGF immunoreactivity (IR) in ovariectomized rats with oil or estradiol benzoate (5 microgram every 4 d; Experiment 1) and in ovariectomized and intact animals (Experiment 2). In the ventral tegmental area (VTA), bFGF-IR and glial fibrillary acidic protein (GFAP)-IR were greater in ovariectomized animals than in animals with estrogen replacement. bFGF-IR in the VTA was greater in ovariectomized than in intact females. In the dorsal raphe, no differences between groups were found in GFAP-IR or bFGF-IR. In mesolimbic dopaminergic target areas within entorhinal cortex (Ent), prefrontal cortex, and nucleus accumbens, bFGF-IR was higher in Ent of ovariectomized animals 4 weeks after surgery in both experiments, but no differences were seen in nucleus accumbens or in an occipital cortical, control, area in either study. In Experiment 2, small increases in bFGF-IR were seen in the prefrontal cortex after ovariectomy. In the VTA and Ent, changes in bFGF-IR developed gradually, peaking at 4 weeks and waning at 40 weeks. Furthermore, increased dendritic arbor of Ent layer II/III pyramidal cells was found in ovariectomized females with the use of a modified Golgi-Cox staining procedure. These findings suggest that, within specific regions, ovariectomy induces astrocytic responses similar to those observed after injury that may affect neuronal chemistry and morphology.

In rats, odor-induced Fos in the olfactory pathways depends on the phase of the circadian clock

We used immunostaining for Fos to study the effect of circadian clock phase on odor-induced neuronal activation in the olfactory system in rats. Brief presentation of cedar odor to rats housed in constant darkness stimulated Fos expression in the main olfactory bulb, anterior olfactory nucleus, piriform cortex, and several other odor-responsive structures, both in the subjective day and subjective night phases of the cycle. Fos expression in response to odor, but not basal expression, was greatly enhanced in the subjective night in all structures examined. These findings are consistent with the idea that odor-induced neuronal activation in the olfactory pathways is modulated by the phase of the circadian clock.

Olfactory stimulation enhances light-induced phase shifts in free-running activity rhythms and Fos expression in the suprachiasmatic nucleus

There is evidence to suggest that the olfactory and circadian systems are linked, functionally, and that olfactory stimuli can modulate circadian rhythms in mammals. Furthermore, olfactory bulb removal can alter free-running rhythms in animals housed in constant darkness and can attenuate the effect of social stimuli on photic entrainment of circadian rhythms. The mechanisms through which olfactory stimuli influence circadian rhythms are not known. One possibility is that olfactory stimuli influence circadian rhythms by modulating the activity of the circadian clock located in the hypothalamic suprachiasmatic nucleus. To study this, we assessed the effect of olfactory stimulation on free-running rhythms and on photic resetting of the circadian clock in rats using phase shifts in wheel-running rhythms and expression of the transcription factor Fos in the suprachiasmatic nucleus. We found that brief exposure to an olfactory stimulus, cedar wood essence, in the subjective day or subjective night had no effect on either free-running rhythms or Fos expression in the suprachiasmatic nucleus, but that when presented in combination with light, the odor dramatically enhanced light-induced phase shifts and Fos expression in the suprachiasmatic nucleus. Olfactory stimulation alone induced Fos expression in several structures that innervate the suprachiasmatic nucleus, pointing to ways by which stimulus information transmitted in the olfactory pathways could gain access to the suprachiasmatic nucleus to modulate photic resetting. These findings, showing that clock resetting by light can be facilitated by olfactory stimulation, point to a mechanism by which olfactory cues can modulate entrainment of circadian rhythms.

Fast registration and reconstruction of aliased low-resolution frames by use of a modified maximum-likelihood approach

During the process of microscanning a controlled vibrating mirror typically is used to produce subpixel shifts in a sequence of forward-looking infrared (FLIR) images. If the FLIR is mounted on a moving platform, such as an aircraft, uncontrolled random vibrations associated with the platform can be used to generate the shifts. Iterative techniques such as the expectation-maximization (EM) approach by means of the maximum-likelihood algorithm can be used to generate high-resolution images from multiple randomly shifted aliased frames. In the maximum-likelihood approach the data are considered to be Poisson random variables and an EM algorithm is developed that iteratively estimates an unaliased image that is compensated for known imager-system blur while it simultaneously estimates the translational shifts. Although this algorithm yields high-resolution images from a sequence of randomly shifted frames, it requires significant computation time and cannot be implemented for real-time applications that use the currently available high-performance processors. The new image shifts are iteratively calculated by evaluation of a cost function that compares the shifted and interlaced data frames with the corresponding values in the algorithm's latest estimate of the high-resolution image. We present a registration algorithm that estimates the shifts in one step. The shift parameters provided by the new algorithm are accurate enough to eliminate the need for iterative recalculation of translational shifts. Using this shift information, we apply a simplified version of the EM algorithm to estimate a high-resolution image from a given sequence of video frames. The proposed modified EM algorithm has been found to reduce significantly the computational burden when compared with the original EM algorithm, thus making it more attractive for practical implementation. Both simulation and experimental results are presented to verify the effectiveness of the proposed technique.

Neonatal handling selectively alters the phosphorylation of a 47,000 mol. wt. protein in male rat hippocampus

Beginning on postnatal day 1, rat pups were handled for 7 min daily for 23-30 days. This treatment diminished the in vitro phosphorylation of phosphoprotein F-1 [mol. wt. approximately 47 K daltons, protein B-50] in the hippocampus of male rats. Other major phosphoproteins (D-1-2. mol. wt. 80-86 K daltons: E-2-3. mol. wt. 50-55 K daltons) were not influenced by handling. These findings confirm and extend the results of Holmes et al. who observed a decrease in ECS-induced protein kinase activity subsequent to handling.

The psychodynamics of the presidential assassin and an examination of the theme/graphic variables of his threatening correspondence

Many document examiners recognize the importance of an individuals 'state of mind' and its effect on handwriting but historically have steered clear of working closely with psychiatrists, linguists, or psychologists in understanding the interaction of nervous impulses and motor responses on the final handwritten product. In an attempt to better understand and evaluate those fears and motivational influences which should exist within the writings of the mentally disturbed in his threatening correspondence, research was conducted to ascertain whether there are consistently reappearing delusional value systems/hostilities which characterize the writings of the paranoid schizophrenic assassin subject. The results of this preliminary investigation revealed substantial evidence to suggest that most U.S. assassins have been psychotic at the time they attempted to kill their victims and that the most frequently rendered diagnosis was 'paranoid schizophrenia'. It was also reported that many of the assassin subjects had either sent threatening correspondence to their victims prior to the assassination attempt or had recanted the justifiable nature of their 'heroic deed' in letters or personal diaries which were recovered shortly after the assault. It is also apparent that over the years, the Secret Service has investigated a number of threatening letter writers who were later diagnosed as suffering from some sort of schizophrenic reaction and characterized as 'potentially dangerous' to the President. Most of the insight to be gained from an examination of what researchers have discovered regarding those unique graphic traits found in 'schizophrenic writing' can be gleaned from those published papers contributed by graphologists/document examiners and that offered by the behavioral science/medical community in the form of psychiatrists, neurologists, psychologists and psycholinguists. The results of bonafide scientific and forensic literature research strongly suggest that the threatening writings of the paranoid schizophrenic and/or potential assassin will probably reveal distinctive graphic 'abnormalities' which are found to act in combination with certain combinations of reoccurring delusional value systems, frustrations, and hostilities.

The importance of monitoring intramyocardial temperature during hypothermic myocardial protection

In 50 patients undergoing cardiac operation, hypothermic cardioplegic solution was infused into the root of the aorta immediately after aortic cross-clamping. Cardiac standstill was achieved within 1 to 3 minutes. However, monitoring of intramyocardial temperature with a needle thermistor revealed that such core cooling is unpredictable (the intramyocardial temperature achieved ranged from 7 degrees to 33 degrees C), unstable (this temperature can rise at more than 0.5 degrees C per minute), and uneven (a difference of up to 17 degrees C was observed between the intramyocardial temperature of the anterior and posterior left ventricular sites). The area supplied by the stenotic coronary artery was least protected. Monitoring of intramyocardial temperature enables one to know when supplementary cooling is indicated. We conclude that widespread differences in this temperature during cardiac operation make monitoring advisable for optimal myocardial protection.