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ObjectiveIn randomized trials a higher proportion of women prescribed continuous combined hormone replacement therapy complete the full course of treatment compared with those prescribed sequential therapy. We sought to determine adherence to hormone therapy in a less-selected population.Study designWomen enrolled in a prepaid health plan participated in a telephone interview 12 to 15 months after newly initiating use of hormone replacement therapy. The interview elicited information on whether the women were still taking the hormones as first prescribed and reasons for switching or discontinuation. A computerized pharmacy database was used to determine initial doses, prescription renewal, and dates of switching or discontinuation.ResultsThe proportion continuing the originally prescribed hormone regimen at 1 year was higher among continuous combined therapy users (68.9%, 62/90) than among sequential therapy users (54.4%, 62/114). Women who initiated continuous combined therapy were less likely to have switched regimens (10.0%) than were sequential users (20.2%; relative risk, 0.5; 95% confidence interval, 0.2-1.0) but only somewhat less likely to have discontinued use (21.2% vs 25.4%; relative risk, 0.7; 95% confidence interval, 0.4-1.3). Examined as a whole, women prescribed continuous combined therapy were less likely than those prescribed sequential therapy to quit or switch during the first year (relative risk, 0.6; 95% confidence interval, 0.4-1.0).ConclusionAlthough adherence was higher among women prescribed continuous combined hormone replacement therapy than sequential therapy, the high level of nonadherence in both groups suggests room for improvement of menopausal therapies so that women find them acceptable for sustained use.

In our previous studies, we demonstrated the usefulness of TanDEM-X interferometric bistatic mode with single polarization to obtain forest heights for the purposes of large area mapping. A key feature of our approach has been the use of a simplified Random Volume Over Ground (RVOG) model that locally estimates forest height. The model takes TanDEM-X interferometric coherence amplitude as an input and uses an external Digital Surface Model (DSM) to account for local slope variations due to terrain topography in order to achieve accurate forest height estimation. The selection of DSM for use as a local slope reference is essential, as an inaccurate DSM will result in less accurate terrain-correction and forest height estimation. In this paper, we assessed TanDEM-X height estimates associated with scale variations in different DSMs used in the model over a remote sensing supersite in Petawawa, Canada. The DSMs used for assessments and comparisons included ASTER GDEM, ALOS GDSM, airborne DRAPE DSM, Canadian DSM and TanDEM-X DSM. Airborne Laser Scanning (ALS) data were used as reference for terrain slope and forest height comparisons. The results showed that, with the exception of the ASTER GDEM, all DSMs were sufficiently accurate for the simplified RVOG model to provide a satisfactory estimate of stand-level forest height. When compared to the ALS 95th height percentile, the modeled forest heights had R2 values greater than 80% and Root-Mean-Square Errors (RMSE) less than 2 m. For a close similarity in slope estimation with the ALS reference, coverage across Canada and open data access, the 0.75 arc-second (20 m) resolution Canadian DSM was selected as a preferred choice for the simplified RVOG model to provide TanDEM-X height estimation in Canada.

Objective: To evaluate the 2010 "Anatomy by whole body dissection" course, a 7-week elective course offered to senior medical students at the University of Sydney at the end of their third year.Design, Setting and Participants: In the 2010 course, 29 students divided into eight groups carried out whole-body dissections on eight cadavers over a 34-day period. Surgical trainees acted as demonstrators, and surgeons and anatomists as supervisors. The students were assessed by practical tests involving the identification of 20 tagged structures in four wet specimens before, during, at the end of, and 1 month after the course. In addition, students were asked to complete an anonymous feedback questionnaire about the course.Main Outcome Measure: Acquisition of topographical anatomical knowledge, and student feedback on the usefulness of the course.Results: A significant increase in topographical clinical anatomical knowledge was demonstrated among the participants and was maintained in the short term. The median pre-course assessment score was 8/20 (interquartile range [IQR], 4) and the median post-course assessment score was 19/20 (IQR, 1). This difference was statistically significant (P<0.001). All students rated the course as "very good", and unanimously recommended that the course be available to all students as part of the medical curriculum.Conclusion: Students' knowledge of anatomy improved significantly between the pre-course and post-course assessments, and all students rated the course very favourably. This supports our view that dissection anatomy should be an integral component of medical education. [ABSTRACT FROM AUTHOR]

Preterm premature rupture of membranes is the rupture of membranes during pregnancy before 37 weeks' gestation. It occurs in 3 percent of pregnancies and is the cause of approximately one third of preterm deliveries. It can lead to significant perinatal morbidity, including respiratory distress syndrome, neonatal sepsis, umbilical cord prolapse, placental abruption, and fetal death. Appropriate evaluation and management are important for improving neonatal outcomes. Speculum examination to determine cervical dilation is preferred because digital examination is associated with a decreased latent period and with the potential for adverse sequelae. Treatment varies depending on gestational age and includes consideration of delivery when rupture of membranes occurs at or after 34 weeks' gestation. Corticosteroids can reduce many neonatal complications, particularly intraventricular hemorrhage and respiratory distress syndrome, and antibiotics are effective for increasing the latency period. [ABSTRACT FROM AUTHOR]

The authors examined the association between pesticide use and breast cancer incidence among farmers' wives in a large prospective cohort study in Iowa and North Carolina. Participants were 30,454 women with no history of breast cancer prior to cohort enrollment in 1993-1997. Information on pesticide use and other information was obtained by self-administered questionnaire at enrollment from the women and their husbands. Through 2000, 309 incident breast cancer cases were identified via population-based cancer registries. Rate ratios were calculated for individual pesticides using Poisson regression, controlling for confounding factors. Breast cancer standardized incidence ratios were 0.87 (95% confidence interval: 0.74, 1.02) for women who reported ever applying pesticides and 1.05 (95% confidence interval: 0.89, 1.24) for women who reported never applying pesticides. There was some evidence of increased risk associated with use of 2,4,5-trichloro-phenoxypropionic acid (2,4,5-TP) and possibly use of dieldrin, captan, and 2,4,5-trichlorophenoxyacetic acid (2,4,5-TP), but small numbers of cases among those who had personally used the pesticides precluded firm conclusions. The authors found no clear association of breast cancer risk with farm size or washing of clothes worn during pesticide application, but risk was modestly elevated among women whose homes were closest to areas of pesticide application. Further follow-up of this cohort should help clarify the relation between pesticide exposure and breast cancer risk. [ABSTRACT FROM AUTHOR]

CONTEXT: The perinatal mortality rate (PMR) in Macedonia is among the highest in Europe. The World Bank supported a consultant (HEJ) to collaborate with a Macedonian team to develop a national perinatal strategy with the goal of reducing the PMR. Education was given priority in the form of a hospital-based initiative to develop the capacity of health professionals to introduce evidence-based perinatal practice into 16 participating hospitals. A 'train the teachers' approach was used, with trainees introduced to modern education and clinical practice in Sydney and subsequently supported to train their colleagues in Skopje. OBJECTIVES: To describe the development, implementation and evaluation of the educational intervention. METHODS: A curriculum, based on specific Macedonian needs, was developed in order to integrate teaching in the knowledge, skills and attitudinal domains of learning, using small group, interactive techniques. Twenty-five Macedonian doctors and nurses participated in 4-month (phase 1a) and 6-month (phase 1b) teaching programmes at a tertiary perinatal unit in Sydney. Australian staff conducted 4 2-week modules for 36 trainees in Macedonia (phase 2). The phase 1 trainees conducted 8 modules for 57 colleagues in Skopje (phase 3). The intervention was evaluated by trainee questionnaires, assessments of competence, changes in hospital practice and pre- (1997-99) and post-intervention (2000-01) comparisons of PMR. RESULTS: A total of 115 doctors and nurses graduated from the programme. Positive responses to the education programme exceeded 80%. Evidence-based practice in 16 participating hospitals (covering 91% of all Macedonian births) was verified in 6 key areas of neonatology. The PMR fell significantly from 27.4 to 21.5 per 1000 births (RR 0.79, 95% CI 0.73, 0.85). The early neonatal death rate in babies weighing over 1000 g fell by 36%. CONCLUSIONS: The intervention has increased the capacity of Macedonians to practise best-evidence perinatal medicine and improve outcomes. Sustainability is predicted by the 'train the teachers' approach, with concurrent strengthening of the infrastructure and organisational framework. [ABSTRACT FROM AUTHOR]

Nausea and vomiting of pregnancy, commonly known as 'morning sickness,' affects approximately 80 percent of pregnant women. Although several theories have been proposed, the exact cause remains unclear. Recent research has implicated Helicobacter pylori as one possible cause. Nausea and vomiting of pregnancy is generally a mild, self-limited condition that may be controlled with conservative measures. A small percentage of pregnant women have a more profound course, with the most severe form being hyperemesis gravidarum. Unlike morning sickness, hyperemesis gravidarum may have negative implications for maternal and fetal health. Physicians should carefully evaluate patients with nonresolving or worsening symptoms to rule out the most common pregnancy-related and nonpregnancy-related causes of severe vomiting. Once pathologic causes have been ruled out, treatment is individualized. Initial treatment should be conservative and should involve dietary changes, emotional support, and perhaps alternative therapy such as ginger or acupressure. Women with more complicated nausea and vomiting of pregnancy also may need pharmacologic therapy. Several medications, including pyridoxine and doxylamine, have been shown to be safe and effective treatments. Pregnant women who have severe vomiting may require hospitalization, orally or intravenously administered corticosteroid therapy, and total parenteral nutrition. [ABSTRACT FROM AUTHOR]

Pregnant women commonly use over-the-counter medications. Although most over-the-counter drugs have an excellent safety profile, some have unproven safety or are known to adversely affect the fetus. The safety profile of some medications may change according to the gestational age of the fetus. Because an estimated 10 percent or more of birth defects result from maternal drug exposure, the U.S. Food and Drug Administration has assigned a risk category to each drug. Many drugs have not been evaluated in controlled trials and probably will not be because of ethical considerations. Of the commonly used over-the-counter medications, acetaminophen, chlorpheniramine, kaolin and pectin preparations, and most antacids have a good safety record. Other drugs, such as histamine H2-receptor blockers, pseudoephedrine, and atropine/diphenoxylate should be used with caution. If use of smoking cessation products is desired, the intermediate-release preparations minimize the amount of nicotine while maintaining efficacy. With all over-the-counter medications used during pregnancy, the benefit of the drug should outweigh the risk to the fetus. [ABSTRACT FROM AUTHOR]

Maternal illness during pregnancy is not uncommon and sometimes requires radiographic imaging for proper diagnosis and treatment. The patient and her physician may be concerned about potential harm to the fetus from radiation exposure. In reality, however, the risks to the developing fetus are quite small. The accepted cumulative dose of ionizing radiation during pregnancy is 5 rad, and no single diagnostic study exceeds this maximum. For example, the amount of exposure to the fetus from a two-view chest x-ray of the mother is only 0.00007 rad. The most sensitive time period for central nervous system teratogenesis is between 10 and 17 weeks of gestation. Nonurgent radiologic testing should be avoided during this time. Rare consequences of prenatal radiation exposure include a slight increase in the incidence of childhood leukemia and, possibly, a very small change in the frequency of genetic mutations. Such exposure is not an indication for pregnancy termination. Appropriate counseling of patients before radiologic studies are performed is critical. [ABSTRACT FROM AUTHOR]

Bartholin gland cysts and abscesses are common problems in women of reproductive age. Although the cysts are usually asymptomatic, they may become enlarged or infected and cause significant pain. Often the clinician is tempted simply to lance the cyst or abscess, since this technique can be effective for other common abscesses. However, simple lancing of a Bartholin gland cyst or abscess may result in recurrence. More effective treatment methods include use of a Word catheter and marsupialization, both of which can be performed in the office. [ABSTRACT FROM AUTHOR]

Abstract To address the challenges of information integration and retrieval, the computational genomics community increasingly has come to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). Here we address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations, in the hope that this will lead both to better representations of biological reality through annotation and ontology development and to more informed use of GO resources by experimental scientists.

Abstract Background The aim of this study was to determine the proportions and predictors of first-degree relatives (FDRs) of colorectal cancer (CRC) patients (i) ever receiving any CRC testing and (ii) receiving CRC screening in accordance with CRC screening guidelines. Methods Colorectal cancer patients and their FDRs were recruited through the population-based Victorian Cancer Registry, Victoria, Australia. Seven hundred and seven FDRs completed telephone interviews. Of these, 405 FDRs were deemed asymptomatic and eligible for analysis. Results Sixty-nine percent of FDRs had ever received any CRC testing. First-degree relatives of older age, those with private health insurance, siblings and FDRs who had ever been asked about family history of CRC by a doctor were significantly more likely than their counterparts to have ever received CRC testing. Twenty-five percent of FDRs “at or slightly above average risk” were adherent to CRC screening guidelines. For this group, adherence to guideline-recommended screening was significantly more likely to occur for male FDRs and those with a higher level of education. For persons at “moderately increased risk” and “potentially high risk”, 47% and 49% respectively adhered to CRC screening guidelines. For this group, guideline-recommended screening was significantly more likely to occur for FDRs who were living in metropolitan areas, siblings, those married or partnered and those ever asked about family history of CRC. Conclusions A significant level of non-compliance with screening guidelines was evident among FDRs. Improved CRC screening in accordance with guidelines and effective systematic interventions to increase screening rates among population groups experiencing inequality are needed. Trial Registration Australian and New Zealand Clinical Trial Registry: ACTRN12609000628246

Abstract Background Although systematic use of the Perinatal Society of Australia and New Zealand internationally endorsed Clinical Practice Guideline for Perinatal Mortality (PSANZ-CPG) improves health outcomes, implementation is inadequate. Its complexity is a feature known to be associated with non-compliance. Interactive education is effective as a guideline implementation strategy, but lacks an agreed definition. SCORPIO is an educational framework containing interactive and didactic teaching, but has not previously been used to implement guidelines. Our aim was to transform the PSANZ-CPG into an education workshop to develop quality standardised interactive education acceptable to participants for learning skills in collaborative interprofessional care. Methods The workshop was developed using the construct of an educational framework (SCORPIO), the PSANZ-CPG, a transformation process and tutor training. After a pilot workshop with key target and stakeholder groups, modifications were made to this and subsequent workshops based on multisource written observations from interprofessional participants, tutors and an independent educator. This participatory action research process was used to monitor acceptability and educational standards. Standardised interactive education was defined as the attainment of content and teaching standards. Quantitative analysis of positive expressed as a percentage of total feedback was used to derive a total quality score. Results Eight workshops were held with 181 participants and 15 different tutors. Five versions resulted from the action research methodology. Thematic analysis of multisource observations identified eight recurring education themes or quality domains used for standardisation. The two content domains were curriculum and alignment with the guideline and the six teaching domains; overload, timing, didacticism, relevance, reproducibility and participant engagement. Engagement was the most challenging theme to resolve. Tutors identified all themes for revision whilst participants identified a number of teaching but no content themes. From version 1 to 5, a significant increasing trend in total quality score was obtained; participants: 55%, p=0.0001; educator: 42%, p=0.0004; tutor peers: 57%, p=0.0001. Conclusions Complex clinical guidelines can be developed into a workshop acceptable to interprofessional participants. Eight quality domains provide a framework to standardise interactive teaching for complex clinical guidelines. Tutor peer review is important for content validity. This methodology may be useful for other guideline implementation.

Abstract Background Therapeutic intervention in the pathophysiology of airway mucus hypersecretion is clinically important. Several types of drugs are available with different possible modes of action. We examined the effects of guaifenesin (GGE), N-acetylcysteine (NAC) and ambroxol (Amb) on differentiated human airway epithelial cells stimulated with IL-13 to produce additional MUC5AC. Methods After IL-13 pre-treatment (3 days), the cultures were treated with GGE, NAC or Amb (10–300 μM) in the continued presence of IL-13. Cellular and secreted MUC5AC, mucociliary transport rates (MTR), mucus rheology at several time points, and the antioxidant capacity of the drugs were assessed. Results IL-13 increased MUC5AC content (~25%) and secretion (~2-fold) and decreased MTR, but only slightly affected the G’ (elastic) or G” (viscous) moduli of the secretions. GGE significantly inhibited MUC5AC secretion and content in the IL-13-treated cells in a concentration-dependent manner (IC50s at 24 hr ~100 and 150 μM, respectively). NAC or Amb were less effective. All drugs increased MTR and decreased G’ and G” relative to IL-13 alone. Cell viability was not affected and only NAC exhibited antioxidant capacity. Conclusions Thus, GGE effectively reduces cellular content and secretion of MUC5AC, increases MTR, and alters mucus rheology, and may therefore be useful in treating airway mucus hypersecretion and mucostasis in airway diseases.

Abstract Background Human T-cell leukemia virus type 1 (HTLV-1) and type 2 both target T lymphocytes, yet induce radically different phenotypic outcomes. HTLV-1 is a causative agent of Adult T-cell leukemia (ATL), whereas HTLV-2, highly similar to HTLV-1, causes no known overt disease. HTLV gene products are engaged in a dynamic struggle of activating and antagonistic interactions with host cells. Investigations focused on one or a few genes have identified several human factors interacting with HTLV viral proteins. Most of the available interaction data concern the highly investigated HTLV-1 Tax protein. Identifying shared and distinct host-pathogen protein interaction profiles for these two viruses would enlighten how they exploit distinctive or common strategies to subvert cellular pathways toward disease progression. Results We employ a scalable methodology for the systematic mapping and comparison of pathogen-host protein interactions that includes stringent yeast two-hybrid screening and systematic retest, as well as two independent validations through an additional protein interaction detection method and a functional transactivation assay. The final data set contained 166 interactions between 10 viral proteins and 122 human proteins. Among the 166 interactions identified, 87 and 79 involved HTLV-1 and HTLV-2 -encoded proteins, respectively. Targets for HTLV-1 and HTLV-2 proteins implicate a diverse set of cellular processes including the ubiquitin-proteasome system, the apoptosis, different cancer pathways and the Notch signaling pathway. Conclusions This study constitutes a first pass, with homogeneous data, at comparative analysis of host targets for HTLV-1 and -2 retroviruses, complements currently existing data for formulation of systems biology models of retroviral induced diseases and presents new insights on biological pathways involved in retroviral infection.

Abstract Background Colorectal cancer (CRC) is among the leading causes of cancer-related morbidity and mortality worldwide. Despite clinical practice guidelines to guide surveillance care for those who have completed treatment for this disease as well as screening for first degree relatives of people with CRC, the level of uptake of these recommendations remains uncertain. If outcomes for both patients and their families are to be improved, it is important to establish systematic and cost-effective interventions to improve adherence to guideline recommendations for CRC surveillance and screening. Methods/Design A randomized controlled trial will be used to test the effectiveness of a print-based intervention to improve adherence to colonoscopy surveillance among people with CRC and adherence to CRC screening recommendations among their first degree relatives (FDRs). People diagnosed with CRC in the past 10 months will be recruited through a population-based cancer registry. Consenting participants will be asked if their first degree relatives might also be willing to participate in the trial. Information on family history of CRC will be obtained from patients at baseline. Patients and their families will be randomized to either minimal ethical care or the print-based intervention. The print-based intervention for FDRs will be tailored to the participant's level of risk of CRC as determined by the self-reported family history assessment. Follow up data on surveillance and screening participation will be collected from patients and their FDRs respectively at 12, 24 and 36 months' post recruitment. The primary analyses will relate to comparing levels of guideline adherence in usual care group versus print-based group in the patient sample and the FDR sample respectively. Discussion Results of this study will provide contribute to the evidence base about effective strategies to a) improve adherence to surveillance recommendation for people with CRC; and b) improve adherence to screening recommendation for FDRs of people with CRC. The use of a population-based cancer registry to access the target population may have significant advantages in increasing the reach of the intervention. Trial registration This trial is registered with the Australian and New Zealand Clinical Trials Registry Registration Number (ACTRN): ACTRN12609000628246.

Abstract Background Duchenne muscular dystrophy (DMD) is a severe neuromuscular disease that affects 1 in 3500 boys. The disease is characterized by progressive muscle degeneration that results from mutations in or loss of the cytoskeletal protein, dystrophin, from the glycoprotein membrane complex, thus increasing the susceptibility of contractile muscle to injury. To date, disease progression is typically assessed using invasive techniques such as muscle biopsies, and while there are recent reports of the use of magnetic resonance, ultrasound and optical imaging technologies to address the issue of disease progression and monitoring therapeutic intervention in dystrophic mice, our study aims to validate the use of imaging biomarkers (muscle perfusion and metabolism) in a longitudinal assessment of skeletal muscle degeneration/regeneration in two murine models of muscular dystrophy. Methods Wild-type (w.t.) and dystrophic mice (weakly-affected mdx mice that are characterized by a point mutation in dystrophin; severely-affected mdx:utrn-/- (udx) mice that lack functional dystrophin and are null for utrophin) were exercised three times a week for 30 minutes. To follow the progression of DMD, accumulation of 18 F-FDG, a measure of glucose metabolism, in both wild-type and affected mice was measured with a small animal PET scanner (GE eXplore Vista). To assess changes in blood flow and blood volume in the hind limb skeletal muscle, mice were injected intravenously with a CT contrast agent, and imaged with a small animal CT scanner (GE eXplore Ultra). Results In hind limb skeletal muscle of both weakly-affected mdx mice and in severely-affected udx mice, we demonstrate an early, transient increase in both 18F-FDG uptake, and in blood flow and blood volume. Histological analysis of H&E-stained tissue collected from parallel littermates demonstrates the presence of both inflammatory infiltrate and centrally-located nuclei, a classic hallmark of myofibrillar regeneration. In both groups of affected mice, the early transient response was succeeded by a progressive decline in muscle perfusion and metabolism; this was also evidenced histologically. Conclusions The present study demonstrates the utility of non-invasive imaging biomarkers in characterizing muscle degeneration/regeneration in murine models of DMD. These techniques may now provide a promising alternative for assessing both disease progression and the efficacy of new therapeutic treatments in patients.

Abstract Background In 2006, Australia introduced graphic cigarette packet warnings. The new warnings include one of 14 pictures, many depicting tobacco-related pathology. The warnings were introduced in two sets; Set A in March and Set B from November. This study explores their impact on smokers' beliefs about smoking related illnesses. This study also examines the varying impact of different warnings, to see whether warnings with visceral images have greater impact on smokers' beliefs than other images. Methods Representative samples of South Australian smokers were interviewed in four independent cross-sectional omnibus surveys; in 2005 (n = 504), 2006 (n = 525), 2007 (n = 414) and 2008 (n = 464). Results Unprompted recall of new graphic cigarette warnings was high in the months following their introduction, demonstrating that smokers' had been exposed to them. Smokers also demonstrated an increase in awareness about smoking-related diseases specific to the warning messages. Warnings that conveyed new information and had emotive images demonstrated greater impact on recall and smokers' beliefs than more familiar information and less emotive images. Conclusions Overall graphic pack warnings have had the intended impact on smokers. Some have greater impact than others. The implications for policy makers in countries introducing similar warnings are that fresh messaging and visceral images have the greatest impact.

Abstract Cylindroma of the breast is a very rare lesion which is morphological and immunophenotypically identical to benign dermal cylindroma. We report a breast cylindroma in a previously healthy 62 year old female detected through a national breast screening program. The patient had no significant family or past medical history, and specifically no history of breast or skin diseases. The tumor consisted of well circumscribed islands of epithelial cells surrounded by a dense membrane material, and focally containing hyaline globules. At low power the islands of tumour cells formed a "jig-saw" pattern, which is typical of cylindroma, but was present within normal breast parenchyma and no had direct connection with the overlying skin. Two distinct cell populations, smaller peripheral basaloid cells and larger central cells with vesicular chromatin, were highlighted by immunohistochemistry for p63 and cytokeratin-7 respectively. Immunohistochemistry for ER, PR, and Her2/neu was negative in tumour cells. We discuss the nine previously reported cases and the distinction of breast cylindroma from adenoid cystic carcinoma, the main differential diagnosis.

Abstract Background The Gene Ontology Project provides structured controlled vocabularies for molecular biology that can be used for the functional annotation of genes and gene products. In a collaboration between the Gene Ontology (GO) Consortium and the muscle biology community, we have made large-scale additions to the GO biological process and cellular component ontologies. The main focus of this ontology development work concerns skeletal muscle, with specific consideration given to the processes of muscle contraction, plasticity, development, and regeneration, and to the sarcomere and membrane-delimited compartments. Our aims were to update the existing structure to reflect current knowledge, and to resolve, in an accommodating manner, the ambiguity in the language used by the community. Results The updated muscle terminologies have been incorporated into the GO. There are now 159 new terms covering critical research areas, and 57 existing terms have been improved and reorganized to follow their usage in muscle literature. Conclusion The revised GO structure should improve the interpretation of data from high-throughput (e.g. microarray and proteomic) experiments in the area of muscle science and muscle disease. We actively encourage community feedback on, and gene product annotation with these new terms. Please visit the Muscle Community Annotation Wiki http://wiki.geneontology.org/index.php/Muscle_Biology.

Abstract Background Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. Description To facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource http://www.agbase.msstate.edu for structural and functional annotation of agricultural genomes. The AgBase database includes a suite of computational tools to use GO annotations. We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO). The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes), return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. Our journal database helps prevent redundant manual GO curation. We encourage and publicly acknowledge GO annotations from researchers and provide a service for researchers interested in GO and analysis of functional genomics data. Conclusion The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. We use experimental data to improve structural annotation of genomes and to functionally characterize gene products. AgBase is also directly relevant for researchers in fields as diverse as agricultural production, cancer biology, biopharmaceuticals, human health and evolutionary biology. Moreover, the experimental methods and bioinformatics tools we provide are widely applicable to many other species including model organisms.

Abstract Background Cellular processes require the interaction of many proteins across several cellular compartments. Determining the collective network of such interactions is an important aspect of understanding the role and regulation of individual proteins. The Gene Ontology (GO) is used by model organism databases and other bioinformatics resources to provide functional annotation of proteins. The annotation process provides a mechanism to document the binding of one protein with another. We have constructed protein interaction networks for mouse proteins utilizing the information encoded in the GO annotations. The work reported here presents a methodology for integrating and visualizing information on protein-protein interactions. Results GO annotation at Mouse Genome Informatics (MGI) captures 1318 curated, documented interactions. These include 129 binary interactions and 125 interaction involving three or more gene products. Three networks involve over 30 partners, the largest involving 109 proteins. Several tools are available at MGI to visualize and analyze these data. Conclusions Curators at the MGI database annotate protein-protein interaction data from experimental reports from the literature. Integration of these data with the other types of data curated at MGI places protein binding data into the larger context of mouse biology and facilitates the generation of new biological hypotheses based on physical interactions among gene products.