Identifying individuals using proteomics: are we there yet?

Multi-omics approaches including proteomics analyses are becoming an integral component of precision medicine. As clinical proteomics studies gain momentum and their sensitivity increases, research on identifying individuals based on their proteomics data is here examined for risks and ethics-related issues. A great deal of work has already been done on this topic for DNA/RNA sequencing data, but it has yet to be widely studied in other omics fields. The current state-of-the-art for the identification of individuals based solely on proteomics data is explained. Protein sequence variation analysis approaches are covered in more detail, including the available analysis workflows and their limitations. We also outline some previous forensic and omics proteomics studies that are relevant for the identification of individuals. Following that, we discuss the risks of patient reidentification using other proteomics data types such as protein expression abundance and post-translational modification (PTM) profiles. In light of the potential identification of individuals through proteomics data, possible legal and ethical implications are becoming increasingly important in the field.

Ion Heating and Flow Driven by an Instability Found in Plasma Couette Flow

We present the first observation of instability in weakly magnetized, pressure dominated plasma Couette flow firmly in the Hall regime. Strong Hall currents couple to a low frequency electromagnetic mode that is driven by high-β (>1) pressure profiles. Spectroscopic measurements show heating (factor of 3) of the cold, unmagnetized ions via a resonant Landau damping process. A linear theory of this instability is derived that predicts positive growth rates at finite β and shows the stabilizing effect of very large β, in line with observations.

GENCODE 2021

The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.

Using Deep Learning to Extrapolate Protein Expression Measurements

Mass spectrometry (MS)-based quantitative proteomics experiments typically assay a subset of up to 60% of the ≈20 000 human protein coding genes. Computational methods for imputing the missing values using RNA expression data usually allow only for imputations of proteins measured in at least some of the samples. In silico methods for comprehensively estimating abundances across all proteins are still missing. Here, a novel method is proposed using deep learning to extrapolate the observed protein expression values in label-free MS experiments to all proteins, leveraging gene functional annotations and RNA measurements as key predictive attributes. This method is tested on four datasets, including human cell lines and human and mouse tissues. This method predicts the protein expression values with average R 2 scores between 0.46 and 0.54, which is significantly better than predictions based on correlations using the RNA expression data alone. Moreover, it is demonstrated that the derived models can be "transferred" across experiments and species. For instance, the model derived from human tissues gave a R 2 = 0.51 when applied to mouse tissue data. It is concluded that protein abundances generated in label-free MS experiments can be computationally predicted using functional annotated attributes and can be used to highlight aberrant protein abundance values.

A Survey of Clinical Usage of Non-steroidal Intra-Articular Therapeutics by Equine Practitioners

There are several non-steroidal intra-articular therapeutics (NSIATs) available for use by equine practitioners for the treatment of performance-limiting joint-related pathology. Information is limited on perceived clinical efficacy, recommended treatment protocols, and associated complications. Our objective with this cross-sectional survey was to investigate the current clinical usage of NSIATs by equine practitioners. An electronic cross-sectional convenience survey inquiring about the use of steroidal and NSIATS (platelet-rich plasma, autologous conditioned serum, autologous protein solution, cellular therapies, and polyacrylamide hydrogel) was distributed internationally to equine practitioners. A total of 353 surveys were completed. NSIATs were used by 87.5% of the participants. Corticosteroids and hyaluronic acid remain the intra-articular therapeutic of choice among practitioners, followed by autologous conditioned serum, platelet-rich plasma and autologous conditioned protein. Polyacrylamide hydrogel was the least used. Practitioners were more likely to use NSIATs if their caseload was > 50% equine (P < 0.001), they treated more than 10 horses intra-articularly per month (P < 0.001), and horses treated were considered English sport horses (P = 0.02). Years in practice and practice location did not influence the use of NSIATs. One of the most common reasons why NSIATs were chosen was to treat acute articular pathologies. As survey limitations, answers to questions regarding clinical response and complication rates were based on subjective estimation and practitioners recall, not clinical records. In conclusion, corticosteroids remain the most widely used intra-articular therapeutic. Among the NSIATs, blood-based products are more commonly used by practitioners, followed by cellular and synthetic products. Equine practitioners frequently use NSIATs, choosing to treat acute joint pathology more than previously reported.

Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon

BACKGROUND

POLG, located on nuclear chromosome 15, encodes the DNA polymerase γ(Pol γ). Pol γ is responsible for the replication and repair of mitochondrial DNA (mtDNA). Pol γ is the only DNA polymerase found in mitochondria for most animal cells. Mutations in POLG are the most common single-gene cause of diseases of mitochondria and have been mapped over the coding region of the POLG ORF.

RESULTS

Using PhyloCSF to survey alternative reading frames, we found a conserved coding signature in an alternative frame in exons 2 and 3 of POLG, herein referred to as ORF-Y that arose de novo in placental mammals. Using the synplot2 program, synonymous site conservation was found among mammals in the region of the POLG ORF that is overlapped by ORF-Y. Ribosome profiling data revealed that ORF-Y is translated and that initiation likely occurs at a CUG codon. Inspection of an alignment of mammalian sequences containing ORF-Y revealed that the CUG codon has a strong initiation context and that a well-conserved predicted RNA stem-loop begins 14 nucleotides downstream. Such features are associated with enhanced initiation at near-cognate non-AUG codons. Reanalysis of the Kim et al. (2014) draft human proteome dataset yielded two unique peptides that map unambiguously to ORF-Y. An additional conserved uORF, herein referred to as ORF-Z, was also found in exon 2 of POLG. Lastly, we surveyed Clinvar variants that are synonymous with respect to the POLG ORF and found that most of these variants cause amino acid changes in ORF-Y or ORF-Z.

CONCLUSIONS

We provide evidence for a novel coding sequence, ORF-Y, that overlaps the POLG ORF. Ribosome profiling and mass spectrometry data show that ORF-Y is expressed. PhyloCSF and synplot2 analysis show that ORF-Y is subject to strong purifying selection. An abundance of disease-correlated mutations that map to exons 2 and 3 of POLG but also affect ORF-Y provides potential clinical significance to this finding.

Phage constructs targeting gonadotropin-releasing hormone for fertility control: evaluation in cats

OBJECTIVES

Phage-gonadotropin-releasing hormone (GnRH) constructs with potential contraceptive properties were generated in our previous study via selection from a phage display library using neutralizing GnRH antibodies as selection targets. In mice, these constructs invoked the production of antibodies against GnRH and suppressed serum testosterone. The goal of this study was to evaluate this vaccine against GnRH for its potential to suppress reproductive characteristics in cats.

METHODS

Sexually mature male cats were injected with a phage-GnRH vaccine using the following treatment groups: (1) single phage-GnRH vaccine with adjuvant; (2) phage-GnRH vaccine without adjuvant and half-dose booster 1 month later; or (3) phage-GnRH vaccine with adjuvant and two half-dose boosters with adjuvant 3 and 6 months later. Anti-GnRH antibodies and serum testosterone, testicular volume and sperm characteristics were evaluated monthly for 7-9 months.

RESULTS

All cats developed anti-GnRH antibodies following immunization. Serum antibody titers increased significantly after booster immunizations. In group 3, serum testosterone was suppressed 8 months after primary immunization. Total testicular volume decreased in group 1 by 24-42% and in group 3 by 15-36% at 7 months after immunization, indicating potential gonadal atrophy. Vacuolation of epididymides was observed histologically. Although all cats produced sperm at the conclusion of the study, normal morphology was decreased as much as 38%. Phage alone produced no local or systemic reactions. Immunization of phage with AdjuVac produced unacceptable injection site reactions.

CONCLUSIONS AND RELEVANCE

Our phage-based vaccine against GnRH demonstrated a potential for fertility impairment in cats. Future research is required to optimize vaccine regimens and identify animal age groups most responsive to the vaccine. If permanent contraception (highly desirable in feral and shelter cats) cannot be achieved, the vaccine has a potential use in zoo animals or pets where multiple administrations are more practical and/or reversible infertility is desirable.

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

The most widely appreciated role of DNA is to encode protein, yet the exact portion of the human genome that is translated remains to be ascertained. We previously developed PhyloCSF, a widely used tool to identify evolutionary signatures of protein-coding regions using multispecies genome alignments. Here, we present the first whole-genome PhyloCSF prediction tracks for human, mouse, chicken, fly, worm, and mosquito. We develop a workflow that uses machine learning to predict novel conserved protein-coding regions and efficiently guide their manual curation. We analyze more than 1000 high-scoring human PhyloCSF regions and confidently add 144 conserved protein-coding genes to the GENCODE gene set, as well as additional coding regions within 236 previously annotated protein-coding genes, and 169 pseudogenes, most of them disabled after primates diverged. The majority of these represent new discoveries, including 70 previously undetected protein-coding genes. The novel coding genes are additionally supported by single-nucleotide variant evidence indicative of continued purifying selection in the human lineage, coding-exon splicing evidence from new GENCODE transcripts using next-generation transcriptomic data sets, and mass spectrometry evidence of translation for several new genes. Our discoveries required simultaneous comparative annotation of other vertebrate genomes, which we show is essential to remove spurious ORFs and to distinguish coding from pseudogene regions. Our new coding regions help elucidate disease-associated regions by revealing that 118 GWAS variants previously thought to be noncoding are in fact protein altering. Altogether, our PhyloCSF data sets and algorithms will help researchers seeking to interpret these genomes, while our new annotations present exciting loci for further experimental characterization.

The Citrobacter rodentium type III secretion system effector EspO affects mucosal damage repair and antimicrobial responses

Infection with Citrobacter rodentium triggers robust tissue damage repair responses, manifested by secretion of IL-22, in the absence of which mice succumbed to the infection. Of the main hallmarks of C. rodentium infection are colonic crypt hyperplasia (CCH) and dysbiosis. In order to colonize the host and compete with the gut microbiota, C. rodentium employs a type III secretion system (T3SS) that injects effectors into colonic intestinal epithelial cells (IECs). Once injected, the effectors subvert processes involved in innate immune responses, cellular metabolism and oxygenation of the mucosa. Importantly, the identity of the effector/s triggering the tissue repair response is/are unknown. Here we report that the effector EspO ,an orthologue of OspE found in Shigella spp, affects proliferation of IECs 8 and 14 days post C. rodentium infection as well as secretion of IL-22 from colonic explants. While we observed no differences in the recruitment of group 3 innate lymphoid cells (ILC3s) and T cells, which are the main sources of IL-22 at the early and late stages of C. rodentium infection respectively, infection with ΔespO was characterized by diminished recruitment of sub-mucosal neutrophils, which coincided with lower abundance of Mmp9 and chemokines (e.g. S100a8/9) in IECs. Moreover, mice infected with ΔespO triggered significantly lesser nutritional immunity (e.g. calprotectin, Lcn2) and expression of antimicrobial peptides (Reg3β, Reg3γ) compared to mice infected with WT C. rodentium. This overlapped with a decrease in STAT3 phosphorylation in IECs. Importantly, while the reduced CCH and abundance of antimicrobial proteins during ΔespO infection did not affect C. rodentium colonization or the composition of commensal Proteobacteria, they had a subtle consequence on Firmicutes subpopulations. EspO is the first bacterial virulence factor that affects neutrophil recruitment and secretion of IL-22, as well as expression of antimicrobial and nutritional immunity proteins in IECs.

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells

Assessing the impact of genomic alterations on protein networks is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used isobaric labeling to characterize the proteomic landscapes of 50 colorectal cancer cell lines and to decipher the functional consequences of somatic genomic variants. The robust quantification of over 9,000 proteins and 11,000 phosphopeptides on average enabled the de novo construction of a functional protein correlation network, which ultimately exposed the collateral effects of mutations on protein complexes. CRISPR-cas9 deletion of key chromatin modifiers confirmed that the consequences of genomic alterations can propagate through protein interactions in a transcript-independent manner. Lastly, we leveraged the quantified proteome to perform unsupervised classification of the cell lines and to build predictive models of drug response in colorectal cancer. Overall, we provide a deep integrative view of the functional network and the molecular structure underlying the heterogeneity of colorectal cancer cells.

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics

Proteogenomics leverages information derived from proteomic data to improve genome annotations. Of particular interest are “novel” peptides that provide direct evidence of protein expression for genomic regions not previously annotated as protein-coding. We present a modular, automated data analysis pipeline aimed at detecting such “novel” peptides in proteomic data sets. This pipeline implements criteria developed by proteomics and genome annotation experts for high-stringency peptide identification and filtering. Our pipeline is based on the OpenMS computational framework; it incorporates multiple database search engines for peptide identification and applies a machine-learning approach (Percolator) to post-process search results. We describe several new and improved software tools that we developed to facilitate proteogenomic analyses that enhance the wealth of tools provided by OpenMS. We demonstrate the application of our pipeline to a human testis tissue data set previously acquired for the Chromosome-Centric Human Proteome Project, which led to the addition of five new gene annotations on the human reference genome.

Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever

Enteric fever, caused by Salmonella enterica serovar Typhi, is an important public health problem in resource-limited settings and, despite decades of research, human responses to the infection are poorly understood. In 41 healthy adults experimentally infected with wild-type S. Typhi, we detected significant cytokine responses within 12 h of bacterial ingestion. These early responses did not correlate with subsequent clinical disease outcomes and likely indicate initial host-pathogen interactions in the gut mucosa. In participants developing enteric fever after oral infection, marked transcriptional and cytokine responses during acute disease reflected dominant type I/II interferon signatures, which were significantly associated with bacteremia. Using a murine and macrophage infection model, we validated the pivotal role of this response in the expression of proteins of the host tryptophan metabolism during Salmonella infection. Corresponding alterations in tryptophan catabolites with immunomodulatory properties in serum of participants with typhoid fever confirmed the activity of this pathway, and implicate a central role of host tryptophan metabolism in the pathogenesis of typhoid fever.

DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics

Accurate statistical evaluation of sequence database peptide identifications from tandem mass spectra is essential in mass spectrometry based proteomics experiments. These statistics are dependent on accurately modelling random identifications. The target-decoy approach has risen to become the de facto approach to calculating FDR in proteomic datasets. The main principle of this approach is to search a set of decoy protein sequences that emulate the size and composition of the target protein sequences searched whilst not matching real proteins in the sample. To do this, it is commonplace to reverse or shuffle the proteins and peptides in the target database. However, these approaches have their drawbacks and limitations. A key confounding issue is the peptide redundancy between target and decoy databases leading to inaccurate FDR estimation. This inaccuracy is further amplified at the protein level and when searching large sequence databases such as those used for proteogenomics. Here, we present a unifying hybrid method to quickly and efficiently generate decoy sequences with minimal overlap between target and decoy peptides. We show that applying a reversed decoy approach can produce up to 5% peptide redundancy and many more additional peptides will have the exact same precursor mass as a target peptide. Our hybrid method addresses both these issues by first switching proteolytic cleavage sites with preceding amino acid, reversing the database and then shuffling any redundant sequences. This flexible hybrid method reduces the peptide overlap between target and decoy peptides to about 1% of peptides, making a more robust decoy model suitable for large search spaces. We also demonstrate the anti-conservative effect of redundant peptides on the calculation of q-values in mouse brain tissue data.

Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation

We present a workflow using an ETD-optimised version of Mascot Percolator and a modified version of SLoMo (turbo-SLoMo) for analysis of phosphoproteomic data. We have benchmarked this against several database searching algorithms and phosphorylation site localisation tools and show that it offers highly sensitive and confident phosphopeptide identification and site assignment with PSM-level statistics, enabling rigorous comparison of data acquisition methods. We analysed the Plasmodium falciparum schizont phosphoproteome using for the first time, a data-dependent neutral loss-triggered-ETD (DDNL) strategy and a conventional decision-tree method. At a posterior error probability threshold of 0.01, similar numbers of PSMs were identified using both methods with a 73% overlap in phosphopeptide identifications. The false discovery rate associated with spectral pairs where DDNL CID/ETD identified the same phosphopeptide was < 1%. 72% of phosphorylation site assignments using turbo-SLoMo without any score filtering, were identical and 99.8% of these cases are associated with a false localisation rate of < 5%. We show that DDNL acquisition is a useful approach for phosphoproteomics and results in an increased confidence in phosphopeptide identification without compromising sensitivity or duty cycle. Furthermore, the combination of Mascot Percolator and turbo-SLoMo represents a robust workflow for phosphoproteomic data analysis using CID and ETD fragmentation.

Biological significance

Protein phosphorylation is a ubiquitous post-translational modification that regulates protein function. Mass spectrometry-based approaches have revolutionised its analysis on a large-scale but phosphorylation sites are often identified by single phosphopeptides and therefore require more rigorous data analysis to unsure that sites are identified with high confidence for follow-up experiments to investigate their biological significance. The coverage and confidence of phosphoproteomic experiments can be enhanced by the use of multiple complementary fragmentation methods. Here we have benchmarked a data analysis pipeline for analysis of phosphoproteomic data generated using CID and ETD fragmentation and used it to demonstrate the utility of a data-dependent neutral loss triggered ETD fragmentation strategy for high confidence phosphopeptide identification and phosphorylation site localisation.

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We report and benchmark a data analysis pipeline for phosphoproteomic data analysis.

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Combined use of Mascot Percolator and turbo-SLoMo to compare fragmentation methods

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CID and ETD fragmentation for phosphorylation site identification

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Demonstrate the utility of data-dependent neutral loss triggered ETD fragmentation

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High confidence of phosphoproteomic analysis using ETD/CID spectral pairs

The OMSSAPercolator: an automated tool to validate OMSSA results

Protein identification by MS/MS is an important technique in proteome studies. The Open Mass Spectrometry Search Algorithm (OMSSA) is an open-source search engine that can be used to identify MS/MS spectra acquired in these experiments. Here, we present a software tool, termed OMSSAPercolator, which interfaces OMSSA with Percolator, a post-search machine learning method for rescoring database search results. We demonstrate that it outperforms the standard OMSSA scoring scheme, and provides reliable significant measurements. OMSSAPercolator is programmed using JAVA and can be readily used as a standalone tool or integrated into existing data analysis pipelines. OMSSAPercolator is freely available and can be downloaded at http://sourceforge.net/projects/omssapercolator/.

Effect of enteric biopsy closure orientation on enteric circumference and volume of saline needed for leak testing

This study describes the effect of enteric biopsy closure orientation on circumference and volume of saline needed for leak testing. There were significant differences in circumference measurements at baseline, central circumference of longitudinally closed sites, and volume of saline for leak testing.

Reported rabies pre-exposure immunization of students at US Colleges of Veterinary Medicine

In 2008, the US experienced a disruption in human rabies vaccine supplies, leading public health authorities to prioritize vaccine release for post-exposure prophylaxis (PEP) and limit vaccine supplies for pre-exposure prophylaxis (PreEP) in high-risk groups. In 2008, the Association of American Veterinary Medical Colleges (AAVMC) surveyed its member institutions on rabies vaccination policies and practices. Senior administrators at Colleges of Veterinary Medicine (CVMs) and departments of veterinary science and comparative medicine were asked to identify the person most knowledgeable about their institution's student rabies vaccination program. Respondents were asked to describe their policies and procedures for administering PreEP to veterinary medical students and staff and to estimate the annual demand for student and staff PreEP vaccine. Twenty-one CVMs responded. Twenty (95%) reported requiring PreEP of veterinary medical students and 16 (80%) of those 20 required vaccination upon matriculation. An estimated 7,309 doses of vaccine were required for PreEP of an estimated 2,436 first-year US veterinary medical students. Seventy-two percent of respondents administered PreEP in August, September, and October, coinciding with the highest public demand for PEP. CVMs should consider altering the timing of rabies vaccine administration to veterinary medical students and staff to other months, thereby helping to ensure that PEP rabies vaccine will be available to people with validated rabies exposures and to ensure that supplies will be available for PreEP of students and staff. AAVMC may wish to identify and support a point of coordination to facilitate the purchase and distribution of human rabies vaccine among its US member CVMs.

Seasonal variation in results of diagnostic tests for pituitary pars intermedia dysfunction in older, clinically normal geldings

OBJECTIVE

To determine whether seasonal variations exist in endogenous plasma ACTH, plasma α-melanocyte-stimulating hormone (α-MSH), serum cortisol, and serum insulin concentrations and in the results of a dexamethasone suppression test for older, clinically normal geldings in Alabama.

DESIGN

Cohort study.

ANIMALS

15 healthy mixed-breed geldings (median age, 14 years).

PROCEDURES

Sample collection was repeated monthly for 12 months. Dexamethasone (0.04 mg/kg [0.02 mg/lb], IM) was administered and cortisol concentrations were determined at 15 and 19 hours. Radioimmunoassays were used to measure ACTH, α-MSH, cortisol, and insulin concentrations at each testing time. Hormone concentrations were compared between months via repeated-measures ANOVA and correlated with age within each month.

RESULTS

A significant time effect was found between months for α-MSH and insulin concentrations. Endogenous cortisol and ACTH concentrations remained within existing reference ranges. Significant correlations were detected between age and ACTH concentration for several fall and winter months and between age and insulin concentration for September.

CONCLUSIONS AND CLINICAL RELEVANCE

Older horses have higher ACTH concentrations in several fall and winter months and higher insulin concentrations in September than do younger horses. Seasonally specific reference ranges are required for α-MSH and insulin concentrations, with significantly higher concentrations detected in the fall. Practitioners should be advised to submit samples only to local laboratories that can provide such reference ranges for their local geographic region.

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium

The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that the tool had some limitations and could not handle several user requirements that were now becoming commonplace. This prompted us to design and implement a whole new suite of tools that would build on the successes of the original PRIDE Converter and allow users to generate submission-ready, well-annotated PRIDE XML files. The PRIDE Converter 2 tool suite allows users to convert search result files into PRIDE XML (the format needed for performing submissions to the PRIDE database), generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra, or by merging several PRIDE XML files together. All the tools have both a graphical user interface that provides a dialog-based, user-friendly way to convert and prepare files for submission, as well as a command-line interface that can be used to integrate the tools into existing or novel pipelines, for batch processing and power users. The PRIDE Converter 2 tool suite will thus become a cornerstone in the submission process to PRIDE and, by extension, to the ProteomeXchange consortium of MS-proteomics data repositories.

Evaluation of the onset of protection induced by a modified-live virus vaccine in calves challenge inoculated with type 1b bovine viral diarrhea virus

OBJECTIVE

To evaluate onset of protection induced by modified-live virus (MLV) bovine viral diarrhea virus (BVDV) vaccine administered 7, 5, or 3 days before inoculation with type 1b BVDV (strain NY-1). Animals-40 calves.

PROCEDURES

Calves were assigned to 4 groups: an unvaccinated control group or groups vaccinated with MLV vaccine containing BVDV types 1a and 2 at 7, 5, or 3 days, before inoculation with NY-1 BVDV. Blood samples were collected for leukocyte counts, serum virus neutralization, and virus isolation (VI); nasal swab specimens (NSSs) were obtained for VI, and rectal temperatures were monitored for 14 days after inoculation.

RESULTS

No significant differences in leukocyte counts or rectal temperatures were detected after BVDV inoculation in vaccinated calves. Vaccinated calves had reduced viremia and viral shedding after inoculation, compared with results for unvaccinated calves. On day 5 after inoculation, a higher proportion of calves vaccinated 3 days before inoculation had positive VI from NSSs, compared with NSS VI results for calves vaccinated 5 and 7 days before inoculation. Unvaccinated calves had leukopenia on days 3, 5, and 6 and had higher rectal temperatures on days 7 and 8 after inoculation, compared with temperatures before inoculation. All unvaccinated calves had ≥ 1 positive VI result from NSSs 3 to 11 days after inoculation, and 4 became viremic.

CONCLUSIONS AND CLINICAL RELEVANCE

MLV BVDV vaccine prevented fever, viremia, and leukopenia in calves challenge inoculated with NY-1 BVDV. A high proportion of calves vaccinated 3 days before inoculation shed BVDV after inoculation.

Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator

Peptide identification using tandem mass spectrometry is a core technology in proteomics. Latest generations of mass spectrometry instruments enable the use of electron transfer dissociation (ETD) to complement collision induced dissociation (CID) for peptide fragmentation. However, a critical limitation to the use of ETD has been optimal database search software. Percolator is a post-search algorithm, which uses semi-supervised machine learning to improve the rate of peptide spectrum identifications (PSMs) together with providing reliable significance measures. We have previously interfaced the Mascot search engine with Percolator and demonstrated sensitivity and specificity benefits with CID data. Here, we report recent developments in the Mascot Percolator V2.0 software including an improved feature calculator and support for a wider range of ion series. The updated software is applied to the analysis of several CID and ETD fragmented peptide data sets. This version of Mascot Percolator increases the number of CID PSMs by up to 80% and ETD PSMs by up to 60% at a 0.01 q-value (1% false discovery rate) threshold over a standard Mascot search, notably recovering PSMs from high charge state precursor ions. The greatly increased number of PSMs and peptide coverage afforded by Mascot Percolator has enabled a fuller assessment of CID/ETD complementarity to be performed. Using a data set of CID and ETcaD spectral pairs, we find that at a 1% false discovery rate, the overlap in peptide identifications by CID and ETD is 83%, which is significantly higher than that obtained using either stand-alone Mascot (69%) or OMSSA (39%). We conclude that Mascot Percolator is a highly sensitive and accurate post-search algorithm for peptide identification and allows direct comparison of peptide identifications using multiple alternative fragmentation techniques.

Validation of a low-dose ACTH stimulation test in healthy adult horses

OBJECTIVE

To determine the lowest ACTH dose that would induce a maximum increase in serum cortisol concentration in healthy adult horses and identify the time to peak cortisol concentration.

DESIGN

Evaluation study.

ANIMALS

8 healthy adult horses.

PROCEDURES

Saline (0.9% NaCl) solution or 1 of 4 doses (0.02, 0.1, 0.25, and 0.5 μg/kg [0.009, 0.045, 0.114, and 0.227 μg/lb]) of cosyntropin (synthetic ACTH) were administered IV (5 treatments/horse). Serum cortisol concentrations were measured before and 30, 60, 90, 120, 180, and 240 minutes after injection of cosyntropin or saline solution; CBCs were performed before and 30, 60, 120, and 240 minutes after injection.

RESULTS

For all 4 doses, serum cortisol concentration was significantly increased, compared with the baseline value, by 30 minutes after administration of cosyntropin; no significant differences were detected among maximum serum cortisol concentrations obtained in response to administration of doses of 0.1, 0.25, and 0.5 μg/kg. Serum cortisol concentration peaked 30 minutes after administration of cosyntropin at a dose of 0.02 or 0.1 μg/kg, with peak concentrations 1.5 and 1.9 times, respectively, the baseline concentration. Serum cortisol concentration peaked 90 minutes after administration of cosyntropin at a dose of 0.25 or 0.5 μg/kg, with peak concentrations 2.0 and 2.3 times, respectively, the baseline concentration. Cosyntropin administration significantly affected WBC, neutrophil, and eosinophil counts and the neutrophil-to-lymphocyte ratio.

CONCLUSIONS AND CLINICAL RELEVANCE

Results suggested that in healthy horses, administration of cosyntropin at a dose of 0.1 μg/kg resulted in maximum adrenal stimulation, with peak cortisol concentration 30 minutes after cosyntropin administration.

General public health considerations for responding to animal hoarding cases

Animal hoarding is an under-recognized problem that exists in most communities and adversely impacts the health, welfare, and safety of humans, animals, and the environment. These guidelines address public health and worker safety concerns in handling situations where animal hoarding or other dense concentrations of animals have caused unhealthy and unsafe conditions. Because animal hoarding situations are often complex, a full response is likely to be prolonged and require a cross-jurisdictional multiagency effort. Each animal hoarding case has unique circumstances related to the types and numbers of animals involved, the physical structure(s) where they are being kept, and the health status of the animals, among other factors that must be taken into account in planning a response. Some general public health considerations and associated recommendations for personal protective equipment use are presented that apply to all cases, however.

Cross species proteomics

Proteomics has advanced in leaps and bounds over the past couple of decades. However, the continuing dependency of mass spectrometry-based protein identification on the searching of spectra against protein sequence databases limits many proteomics experiments. If there is no sequenced genome for a given species, then cross species proteomics is required, attempting to identify proteins across the species boundary, typically using the sequenced genome of a closely related species. Unlike sequence searching for homologues, the proteomics equivalent is confounded by small differences in amino acid sequences, leading to large differences in peptide masses; this renders mass matching of peptides and their product ions difficult. Therefore, the phylogenetic distance between the two species and the attendant level of conservation between the homologous proteins play a huge part in determining the extent of protein identification that is possible across the species boundary. In this chapter, we review the cross species challenge itself, as well as various approaches taken to deal with it and the success met with in past studies. This is followed by recommendations of best practice and suggestions to researchers facing this challenge as well as a final section predicting developments, which may help improve cross species proteomics in the future.

Recent developments in proteome informatics for mass spectrometry analysis

Mass spectrometry has become the pre-eminent analytical method for the study of proteins and proteomes in post-genome science. The high volumes of complex spectra and data generated from such experiments represent new challenges for the field of bioinformatics. The past decade has seen an explosion of informatics tools targeted towards the processing, analysis, storage, and integration of mass spectrometry based proteomic data. In this review, some of the more recent developments in proteome informatics will be discussed. This includes new tools for predicting the properties of proteins and peptides which can be exploited in experimental proteomic design, and tools for the identification of peptides and proteins from their mass spectra. Similarly, informatics approaches are required for the move towards quantitative proteomics which are also briefly discussed. Finally, the growing number of proteomic data repositories and emerging data standards developed for the field are highlighted. These tools and technologies point the way towards the next phase of experimental proteomics and informatics challenges that the proteomics community will face.

Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

BACKGROUND

Proteomic data is a potentially rich, but arguably unexploited, data source for genome annotation. Peptide identifications from tandem mass spectrometry provide prima facie evidence for gene predictions and can discriminate over a set of candidate gene models. Here we apply this to the recently sequenced Aspergillus niger fungal genome from the Joint Genome Institutes (JGI) and another predicted protein set from another A.niger sequence. Tandem mass spectra (MS/MS) were acquired from 1d gel electrophoresis bands and searched against all available gene models using Average Peptide Scoring (APS) and reverse database searching to produce confident identifications at an acceptable false discovery rate (FDR).

RESULTS

405 identified peptide sequences were mapped to 214 different A.niger genomic loci to which 4093 predicted gene models clustered, 2872 of which contained the mapped peptides. Interestingly, 13 (6%) of these loci either had no preferred predicted gene model or the genome annotators' chosen "best" model for that genomic locus was not found to be the most parsimonious match to the identified peptides. The peptides identified also boosted confidence in predicted gene structures spanning 54 introns from different gene models.

CONCLUSION

This work highlights the potential of integrating experimental proteomics data into genomic annotation pipelines much as expressed sequence tag (EST) data has been. A comparison of the published genome from another strain of A.niger sequenced by DSM showed that a number of the gene models or proteins with proteomics evidence did not occur in both genomes, further highlighting the utility of the method.

Respiratory alkalosis and primary hypocapnia in Labrador Retrievers participating in field trials in high-ambient-temperature conditions

OBJECTIVE

To determine whether Labrador Retrievers participating in field trials develop respiratory alkalosis and hypocapnia primarily in conditions of high ambient temperatures.

ANIMALS

16 Labrador Retrievers.

PROCEDURES

At each of 5 field trials, 5 to 10 dogs were monitored during a test (retrieval of birds over a variable distance on land [1,076 to 2,200 m]; 36 assessments); ambient temperatures ranged from 2.2 degrees to 29.4 degrees C. For each dog, rectal temperature was measured and a venous blood sample was collected in a heparinized syringe within 5 minutes of test completion. Blood samples were analyzed on site for Hct; pH; sodium, potassium, ionized calcium, glucose, lactate, bicarbonate, and total CO2 concentrations; and values of PvO2 and PvCO2. Scatterplots of each variable versus ambient temperature were reviewed. Regression analysis was used to evaluate the effect of ambient temperature (< or = 21 degrees C and > 21 degrees C) on each variable.

RESULTS

Compared with findings at ambient temperatures < or = 21 degrees C, venous blood pH was increased (mean, 7.521 vs 7.349) and PvCO2 was decreased (mean, 17.8 vs 29.3 mm Hg) at temperatures > 21 degrees C; rectal temperature did not differ. Two dogs developed signs of heat stress in 1 test at an ambient temperature of 29 degrees C; their rectal temperatures were higher and PvCO2 values were lower than findings in other dogs.

CONCLUSIONS AND CLINICAL RELEVANCE

When running distances frequently encountered at field trials, healthy Labrador Retrievers developed hyperthermia regardless of ambient temperature. Dogs developed respiratory alkalosis and hypocapnia at ambient temperatures > 21 degrees C.

Public-health instruction necessary to supplement the veterinary professional curriculum: the DVM/MPH coordinated-degree program at Auburn University

To meet long-term needs, many veterinary colleges and schools are participating in dual-degree DVM/MPH programs. Auburn University's College of Veterinary Medicine and the School of Public Health at the University of Alabama at Birmingham have developed a coordinated-degree curriculum in which the DVM and the MPH are not necessarily awarded simultaneously. Other opportunities at Auburn include Public Health Careers Day, trips to the Centers for Disease Control and Prevention, several elective courses related to veterinary epidemiology, and online access to the Emerging and Exotic Diseases of Animals course available from the Veterinary Information Network. We have been able to increase our students' exposure to the role of the veterinarian in public health and to develop a program to augment their training in public practice.

Veterinary accreditation and some new imperatives for national preparedness

IN the first of a 5-part series of articles examining the role of the veterinary profession in national preparedness, the authors examine the skills, knowledge, and aptitudes expected of accredited veterinarians and discuss additional skills and knowledge likely to be expected in the future.

Comparison of Multistix PRO dipsticks with other biochemical assays for determining urine protein (UP), urine creatinine (UC) and UP:UC ratio in dogs and cats

BACKGROUND

Urine protein: urine creatinine (UP:UC) ratio determined from the quantitative measurement of protein and creatinine in a single urine sample is the best feasible assessment of clinically significant proteinuria in dogs and cats. A dipstick that measures urine protein, urine creatinine, and UP:UC ratio has been used in human medicine and could have application for veterinary practice.

OBJECTIVE

The objective of this study was to compare the Multistix PRO dipstick (Bayer Corporation, Elkhart, IN, USA) to other biochemical methods for determination of urine protein and creatinine, and UP:UC ratio in canine and feline urine.

METHODS

A complete urinalysis, including sulfosalicylic acid (SSA) precipitation, was performed on urine samples submitted to our laboratory between February and April 2003 from 100 dogs and 49 cats. Urine protein and creatinine concentrations were determined by the Multistix PRO dipstick using a Clinitek 50 analyzer (Bayer) and compared with the results of SSA precipitation and quantitative biochemical analysis. The UP:UC ratios from the dipstick results (calculated by the Clinitek 50 and also manually) were compared with those calculated from quantitative values. Pearson product-moment correlation analysis and diagnostic sensitivity and specificity (using quantitative results as the gold standard) were determined.

RESULTS

For both canine and feline urine, protein and creatinine concentrations determined by the Multistix PRO correlated closely with quantitative concentrations for protein (dogs r = .78, P = .0001; cats r = .87, P = .0001) and creatinine (dogs r = .78, P = .0001; cats r = .76, P = .0001). The Multistix PRO was more sensitive and less specific than SSA precipitation for diagnosing clinically significant proteinuria. UP:UC ratios obtained by manual calculation of dipstick results correlated best with quantitative UP:UC ratios in dogs, and had higher specificity but lower sensitivity for the diagnosis of proteinuria. In cats, UP:UC ratios determined by the dipstick method did not correlate (r = -.24, P = .0974) with quantitative values.

CONCLUSIONS

The Multistix PRO, with manual calculation of UP:UC, may be a good alternative for the diagnosis of clinically significant proteinuria in dogs, but not cats. Dipstick creatinine concentration should be considered as an estimate.

Changes in mitotic rate and GFAP expression in the primary olfactory axis of streptozotocin-induced diabetic rats

Many diabetic individuals develop anosmia but the mechanism(s) causing the dysfunction in the olfactory system is (are) unknown. Glial fibrillary acidic protein expression is reduced in diabetic retinopathy and is also reduced, with unknown consequences, in other brain regions of diabetic rats. We used immunohistochemistry and immunoblotting from untreated control and streptozotocin-induced type 1 (insulin dependent) diabetic rats to investigate main olfactory epithelial mitotic rate and glial fibrillary acidic protein expression in the lamina propria of the sensory epithelium and in the olfactory bulb. Numbers of bromodeoxyuridine-positive cells were significantly lower in the diabetic sensory epithelium compared to non-diabetic controls. Immunohistochemical observations suggested a qualitative difference in glial fibrillary acidic protein expression in both regions examined especially in the olfactory bulb external plexiform layer and the lamina propria. Immunoblot analysis confirmed that the diabetic olfactory bulb and lamina propria expressed less glial fibrillary acidic protein compared to the non-diabetic control group. The lower expression levels in the olfactory bulb external plexiform layer suggested by immunohistochemistry do not reflect a change in the number of astrocytes since the numbers of S100B(+) cells were not different between the two groups.

Comparison of the Role of the Subcutaneous Tissues in Cutaneous Wound Healing in the Dog and Cat

OBJECTIVE

To describe and compare the contribution of the subcutaneous tissues to 1st and 2nd intention cutaneous wound healing in the dog and cat.

STUDY DESIGN

Experimental study.

ANIMALS

Domestic shorthaired cats (n=6) and 6 beagle dogs.

METHODS

Paired wounds were created on either side of the dorsal midline; the subcutaneous tissue was removed on 1 side and left intact on the other. Square, open wounds of the dorsal aspect of the thorax were observed for 21 days to monitor granulation tissue formation, wound contraction, epithelialization, and total healing (contraction+epithelialization). Breaking strength of sutured linear wounds was measured 7 days after wounding. Laser-Doppler perfusion imaging (LDPI) was used to measure cutaneous perfusion.

RESULTS

First intention healing: subcutaneous tissue removal had no consistent effect on sutured wound strength at 7 days in dogs or cats. Second intention healing: removal of subcutaneous tissue reduced wound perfusion, granulation, contraction, epithelialization, and total healing. Granulation tissue formation and wound contraction were delayed to a significantly greater degree in cats than in dogs (P<.05). Two dogs (33%) had minor wound infections.

CONCLUSIONS

The subcutaneous tissues make an important contribution to 2nd intention cutaneous healing. Dog and cat wounds had delayed 2nd intention healing when subcutaneous tissues were removed; wounds in dogs, but not cats, had largely recovered from this delay by 21 days.

CLINICAL RELEVANCE

Extensive debridement of subcutaneous tissue may delay wound healing particularly in feline patients. A higher risk for wound infections may accompany extensive removal of subcutaneous tissues in dogs.

Candidacy of LPS-based glycoconjugates to prevent invasive meningococcal disease: Developmental chemistry and investigation of immunological responses following immunization of mice and rabbits

Glycoconjugates were prepared by covalently linking the immunogenic protein carrier CRM(197) to O-deacylated lipopolysaccharide (LPS) derived from Neisseria meningitidis (strain H44/76), immunotype L3 galE LPS. This mutant strain elaborates a truncated LPS structure that displays immunological epitopes characteristic of 76% of Group B meningococcal (NmB) strains. CRM(197) was covalently linked either to the reducing glucosamine residue of the lipid A region of the O-deacylated LPS or to a 2-keto-3-deoxy-octulosonic acid (Kdo) residue in the inner core region of the O-deacylated LPS. In both rabbits and mice a much stronger IgG response to the immunising antigen was generated in those animals that received conjugates linked via the lipid A region. Sera from mice that were immunized with these conjugates were assayed for their reactivity with LPS, both mutant and wild-type, of several homologous and heterologous NmB strains. Sera obtained from mice immunized with conjugates in which the carrier protein was linked via the Kdo moiety were only able to react with O-deacylated, but not fully acylated (native), LPS from the homologous strain. However, sera obtained from mice that were immunized with conjugates, in which the carrier protein was coupled to the lipid A region, reacted predominately with inner core epitopes that contained phosphoethanolamine at the same 3-position of the distal heptose residue (HepII) of the inner core LPS as was present on the immunising antigen. Additionally it was observed that sera from rabbits immunised with lipid A linked conjugates, unlike the mice responses, were generally not as specific for LPS antigens that contained phosphoethanolamine at the same 3-position as was present on the immunising antigen, but showed a broader inner core recognition, whereas those rabbits that received the Kdo-linked conjugates gave only a very weak non-specific response to all immunotypes. Finally, the sera from two out of six mice that had received lipid A linked conjugates had bactericidal activity against L3 wild-type NmB strain 8047 and one of these was able to passively protect against meningococcal infection in an infant rat model. This study demonstrates evidence towards the proof-in-principle that by using Nm inner core LPS conjugates coupled via the lipid A region with an intact phosphoethanolamine at the O-3 position of the HepII of the inner core LPS, it is possible to elicit functional and protective antibodies against meningococcal infection.

An investigation of the ability of the glutaraldehyde test to distinguish between acute and chronic inflammatory disease in horses

The Glutaraldehyde test (GT), a rapid and inexpensive test, has been utilized empirically for many years in bovine practice for diagnosing inflammatory diseases. GT is used primarily to demonstrate increased serum concentrations of fibrinogen and globulin. Glutaraldehyde binds with free amino groups in fibrinogen and immunoglobulin to create a clot in a first degree chemical reaction. The clotting time of the GT estimates the content of proteins produced in response to inflammation. The applicability of GT for diagnosing inflammation in the horse has never been investigated. The objective of this study was to determine the ability of GT to distinguish between acute and chronic inflammatory disease in horses. Thirty-seven horses with suspected inflammatory diseases were evaluated using the GT, history, complete clinical examination and routine blood analysis. GT-times, laboratory results and clinical outcome were compared statistically. Horses that were determined to be acutely affected (based on history, clinical examination and routine blood analysis) tended to have a negative GT (75%). Results of the GT did not correlate with blood fibrinogen concentration. Positive GT also predicted a fatal outcome in 69% of the clinical cases. The results of this trial indicate that GT can be a useful screening test to distinguish between acute and chronic inflammatory disease in horses.

Cutaneous Wound Healing in the Cat: A Macroscopic Description and Comparison with Cutaneous Wound Healing in the Dog

OBJECTIVE

To describe the macroscopic features of first and second intention cutaneous wound healing in the cat and compare with the dog.

STUDY DESIGN

Experimental study.

ANIMALS

Domestic shorthaired cats (6) and beagle dogs (6).

METHODS

Square, open cutaneous wounds created on the dorsal aspect of the thorax were evaluated for 21 days for temporal and spatial development of granulation tissue, wound contraction, epithelialization, and total healing. To evaluate first intention healing, breaking strength of sutured linear cutaneous wounds was measured at 7 days post-wounding. Laser-Doppler perfusion imaging was used to measure cutaneous perfusion.

RESULTS

First intention healing: sutured wounds in cats were only half as strong as those in dogs at day 7 (0.406 versus 0.818 kg breaking strength). Second intention healing: cats produced significantly less granulation tissue than dogs, with a peripheral, rather than central distribution. Wound epithelialization and total wound healing (total reduction in open wound area from contraction and epithelialization) were greater for dogs than for cats over 21 days. Wound contraction on day 7 was greater for dogs, but not on day 14 or 21. Cutaneous perfusion was initially greater for dogs than for cats, but no differences were detected after day 7.

CONCLUSIONS

Significant, previously unreported differences in cutaneous wound healing exist between cats and dogs. In general, cutaneous wounds in cats are slower to heal. Cats and dogs also appear to use different mechanisms of second intention healing. In cats wounds close mainly by contraction of the wound edges, whereas in dogs wounds close more from central pull, and epithelialization.

CLINICAL RELEVANCE

Surgeons should view the cat as a unique species, which presents its own special challenges in wound healing, and should take this into account when planning treatment of feline wounds, either by primary closure, or by second intention healing.

Acid resistance systems required for survival of Escherichia coli O157:H7 in the bovine gastrointestinal tract and in apple cider are different

Escherichia coli O157:H7 is a highly acid-resistant food-borne pathogen that survives in the bovine and human gastrointestinal tracts and in acidic foods such as apple cider. This property is thought to contribute to the low infectious dose of the organism. Three acid resistance (AR) systems are expressed in stationary-phase cells. AR system 1 is sigma(S) dependent, while AR systems 2 and 3 are glutamate and arginine dependent, respectively. In this study, we sought to determine which AR systems are important for survival in acidic foods and which are required for survival in the bovine intestinal tract. Wild-type and mutant E. coli O157:H7 strains deficient in AR system 1, 2, or 3 were challenged with apple cider and inoculated into calves. Wild-type cells, adapted at pH 5.5 in the absence of glucose (AR system 1 induced), survived well in apple cider. Conversely, the mutant deficient in AR system 1, shown previously to survive poorly in calves, was susceptible to apple cider (pH 3.5), and this sensitivity was shown to be caused by low pH. Interestingly, the AR system 2-deficient mutant survived in apple cider at high levels, but its shedding from calves was significantly decreased compared to that of wild-type cells. AR system 3-deficient cells survived well in both apple cider and calves. Taken together, these results indicate that E. coli O157:H7 utilizes different acid resistance systems based on the type of acidic environment encountered.

Electron heat transport measured in a stochastic magnetic field

New profile measurements have allowed the electron thermal diffusivity profile to be estimated from power balance in the Madison Symmetric Torus where magnetic islands overlap and field lines are stochastic. The measurements show that (1) the electron energy transport is conductive not convective, (2) the measured thermal diffusivities are in good agreement with numerical simulations of stochastic transport, and (3) transport is greatly reduced near the reversal surface where magnetic diffusion is small.

Absence of Humoral Response in Flamingos and Red-Tailed Hawks to Experimental Vaccination with a Killed West Nile Virus Vaccine

Sixteen Chilean flamingos, Phoenicopterus chiles, and 10 red-tailed hawks, Buteo jamacensis, were vaccinated in the pectoral muscle with 0.2 ml of a commercially produced killed West Nile virus vaccine intended for use in horses. Half the birds of each species received a booster vaccination 3 weeks after the first injection. Three weeks after the booster vaccination, none of 13 birds surveyed had detectable antibody to West Nile virus.

Long-term survival following intensive care: subgroup analysis and comparison with the general population

This study aimed to compare the very long-term survival of critically ill patients with that of the general population, and examine the association among age, sex, admission diagnosis, APACHE II score and mortality. In a retrospective observational cohort study of prospectively gathered data, 2104 adult patients admitted to the intensive care unit (ICU) of a teaching hospital in Glasgow from 1985 to 1992, were followed until 1997. Vital status at five years was compared with that of an age- and sex-matched Scottish population. Five-year mortality for the ICU patients was 47.1%, 3.4 times higher than that of the general population. For those surviving intensive care the five-year mortality was 33.4%. Mortality was greater than that of the general population for four years following intensive care unit admission (95% confidence interval included 1.0 at four years). Multivariate analysis showed that risk factors for mortality in those admitted to ICU were age, APACHE II score on admission and diagnostic category. Mortality was higher for those admitted with haematological (87.5%) and neurological diseases (61.7%) and septic shock (62.9%). A risk score was produced: Risk Score = 10 (age hazard ratio + APACHE II hazard ratio + diagnosis hazard ratio). None of the patients with a risk score > 100 survived more than five years and for those who survived to five years the mean risk score was 57. Long-term survival following intensive care is not only related to age and severity of illness but also diagnostic category. The risk of mortality in survivors of critical illness matches that of the normal population after four years. Age, severity of illness and diagnosis can be combined to provide an estimate of five-year survival.

Sheared poloidal flow driven by mode conversion in tokamak plasmas

A two-dimensional integral full-wave model is used to calculate poloidal forces driven by mode conversion in tokamak plasmas. In the presence of a poloidal magnetic field, mode conversion near the ion-ion hybrid resonance is dominated by a transition from the fast magnetosonic wave to the slow ion cyclotron wave. The poloidal field generates strong variations in the parallel wave spectrum that cause wave damping in a narrow layer near the mode conversion surface. The resulting poloidal forces in this layer drive sheared poloidal flows comparable to those in direct launch ion Bernstein wave experiments.

Evaluation of sensitivity and specificity of cytologic examination: 269 cases (1999-2000)

OBJECTIVE

To determine sensitivity and specificity of cytologic examination used in a clinical setting.

DESIGN

Retrospective study.

ANIMALS

216 dogs, 44 cats, 4 horses, 2 ferrets, 1 llama, 1 rat, and 1 mouse.

PROCEDURE

Records were reviewed of cases in which a cytologic diagnosis was followed by a surgical biopsy or postmortem examination within 3 days with subsequent histopathologic diagnosis. Diagnoses were compared for agreement at various levels, including complete agreement, partial agreement, no agreement, or no comparison possible because of insufficient or incorrect cytologic specimen. Levels of agreement were compared for different categories of lesions, including neoplastic, inflammatory, dysplastic-hyperplastic-other, and normal tissue. Additionally, levels of agreement for neoplastic lesions were categorized with regard to cell type, degree of malignancy, and location. Sensitivity and specificity of cytologic examination were calculated.

RESULTS

At the level of general agreement (complete and partial agreement), the sensitivity of cytologic examination ranged from 33.3 to 66.1%, depending on the location of the lesion. Cytologic examination was most accurate when used to diagnose cutaneous and subcutaneous lesions and least accurate for diagnosis of liver lesions. Cytologic examination was most effective in diagnosis of neoplastic disease and least effective in diagnosis of dysplastic or hyperplastic conditions.

CONCLUSIONS AND CLINICAL RELEVANCE

Cytologic examination is a valuable diagnostic tool, although our results indicated lower accuracy than previously reported. False-negative results (missing a diagnosis) were far more common than false-positive results (categorizing a healthy animal as diseased): therefore, if the clinical index of suspicion is high, cytologic examination should be repeated or another technique should be selected to rule out the suspected condition.

Portosystemic shunts: diagnosis, prognosis, and treatment of 64 cases (1993-2001)

Cases diagnosed with portosystemic shunting between the years 1993 and 2001 were reviewed. Sensitivities of screening tests and abdominal ultrasonographic evaluation for the detection of portosystemic shunting were evaluated. Prognosis for surgically treated shunts was also evaluated. Results indicated that both paired serum bile acids and blood ammonia levels were useful screening tests for portosystemic shunting. However, paired bile acid tests were significantly more sensitive than blood ammonia levels. Overall postoperative mortality rates for extrahepatic shunts and intrahepatic shunts were 8.7% and 20%, respectively. Postoperative mortality rates were slightly higher for animals treated with partial ligation when compared to those treated with ameroid ring placement, although this did not reach statistical significance. Long-term complication rates for animals with single extrahepatic portosystemic shunts treated with complete ligation, ameroid ring placement, and partial ligation alone were 9%, 15.4%, and 42%, respectively. Animals >2 years of age with extrahepatic shunts had almost identical postoperative mortality and long-term complication rates as animals < or = 2 years of age. No animal in this study had paired bile acid samples within the reference range postoperatively, indicating continued abnormal liver function after surgery.