Development of the Digital Arthritis Index, a Novel Metric to Measure Disease Parameters in a Rat Model of Rheumatoid Arthritis

Despite a broad spectrum of anti-arthritic drugs currently on the market, there is a constant demand to develop improved therapeutic agents. Efficient compound screening and rapid evaluation of treatment efficacy in animal models of rheumatoid arthritis (RA) can accelerate the development of clinical candidates. Compound screening by evaluation of disease phenotypes in animal models facilitates preclinical research by enhancing understanding of human pathophysiology; however, there is still a continuous need to improve methods for evaluating disease. Current clinical assessment methods are challenged by the subjective nature of scoring-based methods, time-consuming longitudinal experiments, and the requirement for better functional readouts with relevance to human disease. To address these needs, we developed a low-touch, digital platform for phenotyping preclinical rodent models of disease. As a proof-of-concept, we utilized the rat collagen-induced arthritis (CIA) model of RA and developed the Digital Arthritis Index (DAI), an objective and automated behavioral metric that does not require human-animal interaction during the measurement and calculation of disease parameters. The DAI detected the development of arthritis similar to standard in vivo methods, including ankle joint measurements and arthritis scores, as well as demonstrated a positive correlation to ankle joint histopathology. The DAI also determined responses to multiple standard-of-care (SOC) treatments and nine repurposed compounds predicted by the SMarTR^TM Engine to have varying degrees of impact on RA. The disease profiles generated by the DAI complemented those generated by standard methods. The DAI is a highly reproducible and automated approach that can be used in-conjunction with standard methods for detecting RA disease progression and conducting phenotypic drug screens.

Abstract P6-07-31: Assessing germline Homologous Recombination pathway deficiency in BRCA1 mutation carriers using Single Cell Network Profiling

Background: Inherited alterations in BRCA1/2 genes increase genomic instability and cancer susceptibility. DNA sequencing detects BRCA1/2 mutations, but has the following limitations; 1) mutations may have unknown functional significance, 2) epigenetic alterations and mutations in other Homologous Recombination (HR) pathway components are not detected, and 3) the combined effects of pathway mutations are not understood. Thus a functional assessment of HR competence at the single cell level remains an unmet need as BRCA1/2 sequencing does not holistically inform on functionality of the HR pathway. Single Cell Network Profiling (SCNP) is a multiparametric flow cytometry-based assay that simultaneously measures, at the single cell level, extracellular surface markers and functional changes in intracellular signaling in response to extracellular modulators (Kornblau et al. Clin Cancer Res 2010). In this study, we tested the ability of SCNP to detect and quantify functional changes in HR signaling using peripheral blood mononuclear cell (PBMC) samples from BRCA1 mutation carriers (MUT) and wild type (WT) subjects.

Methods: HR pathway activity was examined in PBMCs from BRCA1 MUT (n = 21) or WT (n = 20) subjects. Cell lines carrying BRCA1 MUTor WT genes were used as controls. PBMCs were stimulated with anti-CD3 and anti-CD28 for 24 hours to induce T cell proliferation then treated with PARP inhibitor (PARPi) AZD2281 +/− Temozolomide (TMZ) for 48h or 72h to induce DNA damage. DNA damage response (DDR) readouts were measured in both CyclinA2- and CyclinA2+ T cell subsets. Measurements included induced levels of p21, p53 and phosphorylation (p−) of p-H2AX, p-DNA-PKcs, p-RPA2/32, and p-BRCA1.

Results: As expected based on the mechanism of action of PARPi, higher levels of induced p-H2AX and p53 were observed in CyclinA2+ cells of BRCA1 MUT versus WT cell line controls. In PBMCs, T cell proliferation (%CyclinA2+) was positively associated with PARPi induced DDR readouts. After controlling for proliferation, statistically significant differences in PARPi induced DDR signaling were observed between BRCA1 MUT and WT samples in many simultaneously assessed readouts including p-H2AX, p53 and p21 (increased in MUT), particularly in CyclinA2+ cells. Additionally, BRCA1 MUT samples displayed lower basal p-BRCA1 but higher induced p-BRCA1 levels compared to BRCA1 WT samples.

Conclusions: SCNP was able to detect and quantify functional differences between PBMC samples from BRCA1 MUT (haploinsufficient) and WT donors by quantitatively assessing DDR signaling in CyclinA2+ T cells. Once verified on a larger data set, the assay could form the basis for the development of screening tests to identify subjects at higher risk of developing cancer or stratification tests to inform on cancer patient selection for treatment with PARP inhibitors.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P6-07-31.

The necessity of adjusting tests of protein category enrichment in discovery proteomics

MOTIVATION

Enrichment tests are used in high-throughput experimentation to measure the association between gene or protein expression and membership in groups or pathways. The Fisher's exact test is commonly used. We specifically examined the associations produced by the Fisher test between protein identification by mass spectrometry discovery proteomics, and their Gene Ontology (GO) term assignments in a large yeast dataset. We found that direct application of the Fisher test is misleading in proteomics due to the bias in mass spectrometry to preferentially identify proteins based on their biochemical properties. False inference about associations can be made if this bias is not corrected. Our method adjusts Fisher tests for these biases and produces associations more directly attributable to protein expression rather than experimental bias.

RESULTS

Using logistic regression, we modeled the association between protein identification and GO term assignments while adjusting for identification bias in mass spectrometry. The model accounts for five biochemical properties of peptides: (i) hydrophobicity, (ii) molecular weight, (iii) transfer energy, (iv) beta turn frequency and (v) isoelectric point. The model was fit on 181 060 peptides from 2678 proteins identified in 24 yeast proteomics datasets with a 1% false discovery rate. In analyzing the association between protein identification and their GO term assignments, we found that 25% (134 out of 544) of Fisher tests that showed significant association (q-value ≤0.05) were non-significant after adjustment using our model. Simulations generating yeast protein sets enriched for identification propensity show that unadjusted enrichment tests were biased while our approach worked well.

Quantifying protein function specificity in the gene ontology

Quantitative or numerical metrics of protein function specificity made possible by the Gene Ontology are useful in that they enable development of distance or similarity measures between protein functions. Here we describe how to calculate four measures of function specificity for GO terms: 1) number of ancestor terms; 2) number of offspring terms; 3) proportion of terms; and 4) Information Content (IC). We discuss the relationship between the metrics and the strengths and weaknesses of each.

Modeling sequence and function similarity between proteins for protein functional annotation

A common task in biological research is to predict function for proteins by comparing sequences between proteins of known and unknown function. This is often done using pair-wise sequence alignment algorithms (e.g. BLAST). A problem with this approach is the assumption of a simple equivalence between a minimum sequence similarity threshold and the function similarity between proteins. This assumption is based on the binary concept of homology in that proteins are or not homologous. The relationship between sequence and function however is more complex as well as pertinent for predicting protein function, e.g. evaluating BLAST alignments or developing training sets for profile models based on functional rather than homologous groupings. Our motivation for this study was to model sequence and function similarity between proteins to gain insights into the "sequence-function similarity relationship between proteins for predicting function. Using our model we found that function similarity generally increases with sequence similarity but with a high degree of variability. This result has implications for pair-wise approaches in that it appears sequence similarity must be very high to ensure high function similarity. Profile models which enable higher sensitivity are a potential solution. However, multiple sequences alignments (a necessary prerequisite) are a problem in that current algorithms have difficulty aligning sequences with very low sequence similarity, which is common in our data set, or are intractable for high numbers of sequences. Given the importance of predicting protein function and the need for multiple sequence alignments, algorithms for accomplishing this task should be further refined and developed.

A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions

Background

Predicting protein function from primary sequence is an important open problem in modern biology. Not only are there many thousands of proteins of unknown function, current approaches for predicting function must be improved upon. One problem in particular is overly-specific function predictions which we address here with a new statistical model of the relationship between protein sequence similarity and protein function similarity.

Methodology

Our statistical model is based on sets of proteins with experimentally validated functions and numeric measures of function specificity and function similarity derived from the Gene Ontology. The model predicts the similarity of function between two proteins given their amino acid sequence similarity measured by statistics from the BLAST sequence alignment algorithm. A novel aspect of our model is that it predicts the degree of function similarity shared between two proteins over a continuous range of sequence similarity, facilitating prediction of function with an appropriate level of specificity.

Significance

Our model shows nearly exact function similarity for proteins with high sequence similarity (bit score >244.7, e-value >1e⁻⁶², non-redundant NCBI protein database (NRDB)) and only small likelihood of specific function match for proteins with low sequence similarity (bit score <54.6, e-value <1e⁻⁰⁵, NRDB). For sequence similarity ranges in between our annotation model shows an increasing relationship between function similarity and sequence similarity, but with considerable variability. We applied the model to a large set of proteins of unknown function, and predicted functions for thousands of these proteins ranging from general to very specific. We also applied the model to a data set of proteins with previously assigned, specific functions that were electronically based. We show that, on average, these prior function predictions are more specific (quite possibly overly-specific) compared to predictions from our model that is based on proteins with experimentally determined function.

HIV is hyperendemic among men who have sex with men in San Francisco: 10-year trends in HIV incidence, HIV prevalence, sexually transmitted infections and sexual risk behaviour

OBJECTIVES

To evaluate trends in the HIV epidemic among men who have sex with men (MSM) in San Francisco and the implications for HIV prevention.

METHODS

An ecological approach assessed temporal trends in sexual risk behaviour, sexually transmitted infections (STI), HIV incidence and prevalence from multiple data sources between 1998 and 2007.

RESULTS

By 2007, there were over 13 000 HIV-infected MSM living in San Francisco. No consistent upward or downward temporal trends were found in HIV incidence, newly reported HIV cases, AIDS deaths, proportion of AIDS cases using antiretroviral therapy, rectal gonorrhoea or primary and secondary syphilis cases among MSM during the study period. Trends in indicators of sexual risk behaviour among MSM were mixed. Overall, unprotected anal intercourse (UAI) increased in community-based surveys. Among HIV-positive MSM, no significant trends were noted for UAI. Among HIV-negative MSM, UAI with unknown serostatus partners decreased but increased with potentially discordant serostatus partners. Among MSM seeking HIV testing, increases were noted in insertive UAI at anonymous testing sites and at the STI clinic, in receptive UAI at anonymous test sites and in receptive UAI with a known HIV-positive partner at the STI clinic.

CONCLUSIONS

Temporal trends in multiple biological and behavioural indicators over the past decade describe a hyperendemic state of HIV infection among MSM in San Francisco, whereby prevalence has stabilised at a very high level. In the absence of new, effective prevention strategies this state will persist.

Validating annotations for uncharacterized proteins in Shewanella oneidensis

Proteins of unknown function are a barrier to our understanding of molecular biology. Assigning function to these "uncharacterized" proteins is imperative, but challenging. The usual approach is similarity searches using annotation databases, which are useful for predicting function. However, since the performance of these databases on uncharacterized proteins is basically unknown, the accuracy of their predictions is suspect, making annotation difficult. To address this challenge, we developed a benchmark annotation dataset of 30 proteins in Shewanella oneidensis. The proteins in the dataset were originally uncharacterized after the initial annotation of the S. oneidensis proteome in 2002. In the intervening 5 years, the accumulation of new experimental evidence has enabled specific functions to be predicted. We utilized this benchmark dataset to evaluate several commonly utilized annotation databases. According to our criteria, six annotation databases accurately predicted functions for at least 60% of proteins in our dataset. Two of these six even had a "conditional accuracy" of 90%. Conditional accuracy is another evaluation metric we developed which excludes results from databases where no function was predicted. Also, 27 of the 30 proteins' functions were correctly predicted by at least one database. These represent one of the first performance evaluations of annotation databases on uncharacterized proteins. Our evaluation indicates that these databases readily incorporate new information and are accurate in predicting functions for uncharacterized proteins, provided that experimental function evidence exists.

Increases in sexually transmitted infections and sexual risk behaviour without a concurrent increase in HIV incidence among men who have sex with men in San Francisco: a suggestion of HIV serosorting?

BACKGROUND

Sexually transmitted infections (STI) and unprotected anal intercourse (UAI) have been increasing among men who have sex with men (MSM) in San Francisco. However, HIV incidence has stabilised.

OBJECTIVES

To describe recent trends in sexual risk behaviour, STI, and HIV incidence among MSM in San Francisco and to assess whether increases in HIV serosorting (that is, selective unprotected sex with partners of the same HIV status) may contribute to preventing further expansion of the epidemic.

METHODS

The study applies an ecological approach and follows the principles of second generation HIV surveillance. Temporal trends in biological and behavioural measures among MSM were assessed using multiple pre-existing

DATA SOURCES

STI case reporting, prevention outreach programmatic data, and voluntary HIV counselling and testing data.

RESULTS

Reported STI cases among MSM rose from 1998 through 2004, although the rate of increase slowed between 2002 and 2004. Rectal gonorrhoea cases increased from 157 to 389 while early syphilis increased from nine to 492. UAI increased overall from 1998 to 2004 (p<0.001) in community based surveys; however, UAI with partners of unknown HIV serostatus decreased overall (p<0.001) among HIV negative MSM, and among HIV positive MSM it declined from 30.7% in 2001 to a low of 21.0% in 2004 (p<0.001). Any UAI, receptive UAI, and insertive UAI with a known HIV positive partner decreased overall from 1998 to 2004 (p<0.001) among MSM seeking anonymous HIV testing and at the STI clinic testing programme. HIV incidence using the serological testing algorithm for recent HIV seroconversion (STARHS) peaked in 1999 at 4.1% at the anonymous testing sites and 4.8% at the STI clinic voluntary testing programme, with rates levelling off through 2004.

CONCLUSIONS

HIV incidence among MSM appears to have stabilised at a plateau following several years of resurgence. Increases in the selection of sexual partners of concordant HIV serostatus may be contributing to the stabilisation of the epidemic. However, current incidence rates of STI and HIV remain high. Moreover, a strategy of risk reduction by HIV serosorting can be severely limited by imperfect knowledge of one's own and one's partners' serostatus.

Integration of data for gene annotation using the BioMediator system

Gene annotation requires integration of data from multiple sources in order to functionally classify genes. We are using BioMediator, a general purpose data-integration solution, to develop a gene annotation system to automate the process of collecting data from disparate genomic databases. Integration of annotation data from multiple sources into a single format will facilitate use of analytic tools for the proper functional classification of genes.

Differences in the temporal trends of HIV seroincidence and seroprevalence among sexually transmitted disease clinic patients, 1989-1998: application of the serologic testing algorithm for recent HIV seroconversion

The authors compared temporal trends in the prevalence and incidence of human immunodeficiency virus (HIV) infection based upon 34,866 specimens from patients who attended the San Francisco, California, municipal sexually transmitted disease clinic between 1989 and 1998. HIV infection data were collected during annual blinded HIV serologic surveys. Incidence was determined by applying a serologic testing algorithm for recent HIV seroconversion that uses both a sensitive and a less sensitive enzyme immunoassay to stored HIV positive sera. The HIV seroprevalence declined from 15.2% in 1989 to 7.2% in 1998 (odds ratio per year = 0.92, 95% confidence interval (CI): 0.91, 0.94). Among homosexual men, the HIV prevalence declined from 50.9% in 1989 to 19.9% in 1998 (odds ratio per year = 0.86, 95% CI: 0.85, 0.88). The pooled seroincidence was 1.6% and did not change significantly over time (odds ratio per year = 1.0, 95% CI: 0.98, 1.1). The pooled seroincidence among homosexual men was 6.6% per year and remained steady between 1989 and 1998 (odds ratio per year = 0.99, 95% CI: 0.92, 1.1). During a dramatic, 10-year decline in seroprevalence of HIV infection, the incidence of HIV infection remained remarkably stable.

A high-resolution radiation hybrid map of the human genome draft sequence

We have constructed a physical map of the human genome by using a panel of 90 whole-genome radiation hybrids (the TNG panel) in conjunction with 40,322 sequence-tagged sites (STSs) derived from random genomic sequences as well as expressed sequences. Of 36,678 STSs on the TNG radiation hybrid map, only 3604 (9.8%) were absent from the unassembled draft sequence of the human genome. Of 20,030 STSs ordered on the TNG map as well as the assembled human genome draft sequence and the Celera assembled human genome sequence, 36% of the STSs had a discrepant order between the working draft sequence and the Celera sequence. The TNG map order was identical to one of the two sequence orders in 60% of these discrepant cases.

Donor site morbidity following vascularized fibular grafting

We examined donor site morbidity in thirty-nine patients with avascular necrosis of the femoral head treated by curettage and transplantation of a free ipsilateral fibular graft. Utilising our donor site morbidity questionnaire, scar, functional loss, wound healing, complications, and pain were analysed. Subjective complaints and objective findings were evaluated and compared. Subjective complaints were common and included a sense of instability in 42% and a sense of weakness in 37%. However, objective findings were limited. No clinical instability could be elicited and only great toe flexion (29%) and extension (43%) were found to be mildly weak. Only one patient required reoperation for a donor site problem (2%). Eighty-nine percent were pain free at time of follow-up, and 93% felt the scar was good. Range of motion of the knee and ankle of the donor site leg was not different from the nonoperated leg. Donor site morbidity for avascular necrosis of the femoral head is low.

Low estimates of HIV seroconversions among clients of a drug treatment clinic in San Francisco, 1995 to 1998

We estimated HIV incidence among injection drug users attending a drug treatment clinic in San Francisco from 1995 to 1998 using two methods. An anonymous sequential testing method identified no seroconversions among clients seen more than once during the period (one-sided upper 95% confidence limit 1.02 per 100 person-years). A sensitive/less sensitive immunoassay testing strategy detected no early infections (one-sided upper 95% confidence limit 1.90% per year). Methods were concordant and feasible in the setting. Although detection of no new HIV infections in this population of injection drug users (IDUs) is encouraging, epidemiologic studies among IDUs not in treatment are needed to monitor the HIV epidemic effectively.

From feedback to reciprocity. Developing a student-centered approach to course evaluation

Reforms to medical education have refocused curricula on the need to produce primary care physicians through a problem-based, student-centered, community-oriented, and integrated approach to instruction. Course evaluations, originally designed for traditional lecture-based, teacher-centered curricula, provide inadequate input from students to support curriculum planning and change and to determine appropriate mixes of educational methods. At the University of Toronto Faculty of Medicine, a unique community-centered course, called "Health, Illness and the Community," developed a student-centered course evaluation to provide adequate student input to support curriculum planning and change. A 35-item evaluation was developed to obtain data to identify student concerns, student learning styles, and preferred community agency utilization. The results suggest that student-centered course evaluation can play a role in managing and identifying key relationships in integrated and systematic courses as well as establishing a method for continual improvement.

Reducing surgical length of stay: quantifying the impact

Length-of-stay (LOS) reduction is a strategy encouraged at all levels of health care to manage within a resource limited environment. However, few organizations have attempted to quantitatively understand the impact of reducing LOS. This study examines the relationship between reducing LOS and cost through a retrospective, medical records analysis of three surgical procedures (appendectomy, cholecystectomy and caesarean section) at an Ontario community hospital Department of Surgery. Hypotheses are presented and a methodology is described. The results are discussed with a focus on the factors that hospitals, administrators and physicians might consider in a LOS reduction program.

Integrating technology assessment into the capital budgeting process

Technology assessment can help hospitals rank the importance of capital requests by providing crucial information both about existing equipment and about new equipment that has been requested. Integrating technology assessment into the capital budgeting process is the best way for hospitals to determine what equipment should be purchased each year.

Building a decision-support system

To make decisions in today's dynamic health care environment, hospital managers rely on accurate and timely information--much of it compiled from hospital discharge data. For hospitals, the problem is not the lack of data but the inability to convert it to information useful to hospital management. This article describes how to build a cost-effective decision-support system that can transform HMRI (Hospital Medical Records Institute) data into a powerful management tool.

The evaluation and treatment of the febrile infant

Over a period of 5 1/2 years 305 infants less than 60 days of age with temperatures greater than or equal to 100.4 degrees F (38.0 degrees C) were evaluated for sepsis. Of these 20.6% of the infants had significant diseases although only 3.6% had bacteremia. Neither the age of the child (above or below 30 days of age) nor the height of the fever helped to identify infants with bacteremia. A white blood cell count of greater than 15,000/mm3 was useful in identifying bacteremic infants over 30 days of age only. The differential white blood cell count was not helpful in distinguishing between bacteremic and nonbacteremic infants. The appearance of the infant was the most significant predictor (P less than 0.001) of bacteremia in this age group. Infants between 30 and 60 days of age who both appeared ill and had white blood cell counts greater than or equal to 15,000/mm3 had a 27.3% chance of having bacteremia.