Biological diversity of prokaryotic type IV secretion systems.

Type IV secretion systems (T4SS) translocate DNA and protein substrates across prokaryotic cell envelopes generally by a mechanism requiring direct contact with a target cell. Three types of T4SS have been described: (i) conjugation systems, operationally defined as machines that translocate DNA substrates intercellularly by a contact-dependent process; (ii) effector translocator systems, functioning to deliver proteins or other macromolecules to eukaryotic target cells; and (iii) DNA release/uptake systems, which translocate DNA to or from the extracellular milieu. Studies of a few paradigmatic systems, notably the conjugation systems of plasmids F, R388, RP4, and pKM101 and the Agrobacterium tumefaciens VirB/VirD4 system, have supplied important insights into the structure, function, and mechanism of action of type IV secretion machines. Information on these systems is updated, with emphasis on recent exciting structural advances. An underappreciated feature of T4SS, most notably of the conjugation subfamily, is that they are widely distributed among many species of gram-negative and -positive bacteria, wall-less bacteria, and the Archaea. Conjugation-mediated lateral gene transfer has shaped the genomes of most if not all prokaryotes over evolutionary time and also contributed in the short term to the dissemination of antibiotic resistance and other virulence traits among medically important pathogens. How have these machines adapted to function across envelopes of distantly related microorganisms? A survey of T4SS functioning in phylogenetically diverse species highlights the biological complexity of these translocation systems and identifies common mechanistic themes as well as novel adaptations for specialized purposes relating to the modulation of the donor-target cell interaction.

Biological diversity of prokaryotic type IV secretion systems.

Type IV secretion systems (T4SS) translocate DNA and protein substrates across prokaryotic cell envelopes generally by a mechanism requiring direct contact with a target cell. Three types of T4SS have been described: (i) conjugation systems, operationally defined as machines that translocate DNA substrates intercellularly by a contact-dependent process; (ii) effector translocator systems, functioning to deliver proteins or other macromolecules to eukaryotic target cells; and (iii) DNA release/uptake systems, which translocate DNA to or from the extracellular milieu. Studies of a few paradigmatic systems, notably the conjugation systems of plasmids F, R388, RP4, and pKM101 and the Agrobacterium tumefaciens VirB/VirD4 system, have supplied important insights into the structure, function, and mechanism of action of type IV secretion machines. Information on these systems is updated, with emphasis on recent exciting structural advances. An underappreciated feature of T4SS, most notably of the conjugation subfamily, is that they are widely distributed among many species of gram-negative and -positive bacteria, wall-less bacteria, and the Archaea. Conjugation-mediated lateral gene transfer has shaped the genomes of most if not all prokaryotes over evolutionary time and also contributed in the short term to the dissemination of antibiotic resistance and other virulence traits among medically important pathogens. How have these machines adapted to function across envelopes of distantly related microorganisms? A survey of T4SS functioning in phylogenetically diverse species highlights the biological complexity of these translocation systems and identifies common mechanistic themes as well as novel adaptations for specialized purposes relating to the modulation of the donor-target cell interaction.

Hybrid stochastic simulations of intracellular reaction-diffusion systems.

With the observation that stochasticity is important in biological systems, chemical kinetics have begun to receive wider interest. While the use of Monte Carlo discrete event simulations most accurately capture the variability of molecular species, they become computationally costly for complex reaction-diffusion systems with large populations of molecules. On the other hand, continuous time models are computationally efficient but they fail to capture any variability in the molecular species. In this study a hybrid stochastic approach is introduced for simulating reaction-diffusion systems. We developed an adaptive partitioning strategy in which processes with high frequency are simulated with deterministic rate-based equations, and those with low frequency using the exact stochastic algorithm of Gillespie. Therefore the stochastic behavior of cellular pathways is preserved while being able to apply it to large populations of molecules. We describe our method and demonstrate its accuracy and efficiency compared with the Gillespie algorithm for two different systems. First, a model of intracellular viral kinetics with two steady states and second, a compartmental model of the postsynaptic spine head for studying the dynamics of Ca+2 and NMDA receptors.

Optimizing Triage and Hospitalization in Adult General Medical Emergency Patients. The Triage Project

Background: Patients presenting to the emergency department (ED) currently face inacceptable delays in initial treatment, and long, costly hospital stays due to suboptimal initial triage and site-of-care decisions. Accurate ED triage should focus not only on initial treatment priority, but also on prediction of medical risk and nursing needs to improve site-of-care decisions and to simplify early discharge management. Different triage scores have been proposed, such as the Manchester triage system (MTS). Yet, these scores focus only on treatment priority, have suboptimal performance and lack validation in the Swiss health care system. Because the MTS will be introduced into clinical routine at the Kantonsspital Aarau, we propose a large prospective cohort study to optimize initial patient triage. Specifically, the aim of this trial is to derive a three-part triage algorithm to better predict (a) treatment priority; (b) medical risk and thus need for in-hospital treatment; (c) post-acute care needs of patients at the most proximal time point of ED admission. Methods/design: Prospective, observational, multicenter, multi-national cohort study. We will include all consecutive medical patients seeking ED care into this observational registry. There will be no exclusions except for non-adult and non-medical patients. Vital signs will be recorded and left over blood samples will be stored for later batch analysis of blood markers. Upon ED admission, the post-acute care discharge score (PACD) will be recorded. Attending ED physicians will adjudicate triage priority based on all available results at the time of ED discharge to the medical ward. Patients will be reassessed daily during the hospital course for medical stability and readiness for discharge from the nurses and if involved social workers perspective. To assess outcomes, data from electronic medical records will be used and all patients will be contacted 30 days after hospital admission to assess vital and functional status, re-hospitalization, satisfaction with care and quality of life measures. We aim to include between 5000 and 7000 patients over one year of recruitment to derive the three-part triage algorithm. The respective main endpoints were defined as (a) initial triage priority (high vs. low priority) adjudicated by the attending ED physician at ED discharge, (b) adverse 30 day outcome (death or intensive care unit admission) within 30 days following ED admission to assess patients risk and thus need for in-hospital treatment and (c) post acute care needs after hospital discharge, defined as transfer of patients to a post-acute care institution, for early recognition and planning of post-acute care needs. Other outcomes are time to first physician contact, time to initiation of adequate medical therapy, time to social worker involvement, length of hospital stay, reasons fordischarge delays, patient’s satisfaction with care, overall hospital costs and patients care needs after returning home. Discussion: Using a reliable initial triage system for estimating initial treatment priority, need for in-hospital treatment and post-acute care needs is an innovative and persuasive approach for a more targeted and efficient management of medical patients in the ED. The proposed interdisciplinary , multi-national project has unprecedented potential to improve initial triage decisions and optimize resource allocation to the sickest patients from admission to discharge. The algorithms derived in this study will be compared in a later randomized controlled trial against a usual care control group in terms of resource use, length of hospital stay, overall costs and patient’s outcomes in terms of mortality, re-hospitalization, quality of life and satisfaction with care.

An investigation into the factors that encourage learner participation in a large group medical classroom

BACKGROUND: Effective lectures often incorporate activities that encourage learner participation. A challenge for educators is how to facilitate this in the large group lecture setting. This study investigates the individual student characteristics involved in encouraging (or dissuading) learners to interact, ask questions, and make comments in class. METHODS: Students enrolled in a Doctor of Veterinary Medicine program at Ross University School of Veterinary Medicine, St Kitts, were invited to complete a questionnaire canvassing their participation in the large group classroom. Data from the questionnaire were analyzed using Excel (Microsoft, Redmond, WA, USA) and the R software environment (http://www.r-project.org/). RESULTS: One hundred and ninety-two students completed the questionnaire (response rate, 85.7%). The results showed statistically significant differences between male and female students when asked to self-report their level of participation (P=0.011) and their confidence to participate (P<0.001) in class. No statistically significant difference was identified between different age groups of students (P=0.594). Student responses reflected that an "aversion to public speaking" acted as the main deterrent to participating during a lecture. Female participants were 3.56 times more likely to report a fear of public speaking than male participants (odds ratio 3.56, 95% confidence interval 1.28-12.33, P=0.01). Students also reported "smaller sizes of class and small group activities" and "other students participating" as factors that made it easier for them to participate during a lecture. CONCLUSION: In this study, sex likely played a role in learner participation in the large group veterinary classroom. Male students were more likely to participate in class and reported feeling more confident to participate than female students. Female students in this study commonly identified aversion to public speaking as a factor which held them back from participating in the large group lecture setting. These are important findings for veterinary and medical educators aiming to improve learner participation in the classroom. Potential ways of addressing this challenge include addition of small group activities and audience response systems during lectures, and inclusion of training interventions in public speaking at an early stage of veterinary and medical curricula.

Risk factors for patient-reported medical errors in eleven countries

OBJECTIVES The aim of this study was to identify common risk factors for patient-reported medical errors across countries. In country-level analyses, differences in risks associated with error between health care systems were investigated. The joint effects of risks on error-reporting probability were modelled for hypothetical patients with different health care utilization patterns. DESIGN Data from the Commonwealth Fund's 2010 lnternational Survey of the General Public's Views of their Health Care System's Performance in 11 Countries. SETTING Representative population samples of 11 countries were surveyed (total sample = 19,738 adults). Utilization of health care, coordination of care problems and reported errors were assessed. Regression analyses were conducted to identify risk factors for patients' reports of medical, medication and laboratory errors across countries and in country-specific models. RESULTS Error was reported by 11.2% of patients but with marked differences between countries (range: 5.4-17.0%). Poor coordination of care was reported by 27.3%. The risk of patient-reported error was determined mainly by health care utilization: Emergency care (OR = 1.7, P < 0.001), hospitalization (OR = 1.6, P < 0.001) and the number of providers involved (OR three doctors = 2.0, P < 0.001) are important predictors. Poor care coordination is the single most important risk factor for reporting error (OR = 3.9, P < 0.001). Country-specific models yielded common and country-specific predictors for self-reported error. For high utilizers of care, the probability that errors are reported rises up to P = 0.68. CONCLUSIONS Safety remains a global challenge affecting many patients throughout the world. Large variability exists in the frequency of patient-reported error across countries. To learn from others' errors is not only essential within countries but may also prove a promising strategy internationally.

Physician adoption of a practice guideline: Effect on the cost of medical care for adult patients with diabetes

In the demanding environment of healthcare reform, reduction of unwanted physician practice variation is promoted, often through evidence-based guidelines. Guidelines represent innovations that direct change(s) in physician practice; however, compliance has been disappointing. Numerous studies have analyzed guideline development and dissemination, while few have evaluated the consequences of guideline adoption. The primary purpose of this study was to explore and analyze the relationship between physician adoption of the glycated hemoglobin test guideline for management of adult patients with diabetes, and the cost of medical care. The study also examined six personal and organizational characteristics of physicians and their association with innovativeness, or adoption of the guideline. ^ Cost was represented by approved charges from a managed care claims database. Total cost, and diabetes and related complications cost, first were compared for all patients of adopter physicians with those of non-adopter physicians. Then, data were analyzed controlling for disease severity based on insulin dependency, and for high cost cases. There was no statistically significant difference in any of eight cost categories analyzed. This study represented a twelve-month period, and did not reflect cost associated with future complications known to result from inadequate management of glycemia. Guideline compliance did not increase annual cost, which, combined with the future benefit of glycemic control, lends support to the cost effectiveness of the guideline in the long term. Physician adoption of the guideline was recommended to reduce the future personal and economic burden of this chronic disease. ^ Only half of physicians studied had adopted the glycated hemoglobin test guideline for at least 75% of their diabetic patients. No statistically significant relationship was found between any physician characteristic and guideline adoption. Instead, it was likely that the innovation-decision process and guideline dissemination methods were most influential. ^ A multidisciplinary, multi-faceted approach, including interventions for each stage of the innovation-decision process, was proposed to diffuse practice guidelines more effectively. Further, it was recommended that Organized Delivery Systems expand existing administrative databases to include clinical information, decision support systems, and reminder mechanisms, to promote and support physician compliance with this and other evidence-based guidelines. ^

A survey of the implementation status of environmental management systems in U.S. colleges and universities, and, An environmental management system implementation model for U.S. colleges and universities

A census of 925 U.S. colleges and universities offering masters and doctorate degrees was conducted in order to study the number of elements of an environmental management system as defined by ISO 14001 possessed by small, medium and large institutions. A 30% response rate was received with 273 responses included in the final data analysis. Overall, the number of ISO 14001 elements implemented among the 273 institutions ranged from 0 to 16, with a median of 12. There was no significant association between the number of elements implemented among institutions and the size of the institution (p = 0.18; Kruskal-Wallis test) or among USEPA regions (p = 0.12; Kruskal-Wallis test). The proportion of U.S. colleges and universities that reported having implemented a structured, comprehensive environmental management system, defined by answering yes to all 16 elements, was 10% (95% C.I. 6.6%–14.1%); however 38% (95% C.I. 32.0%–43.8%) reported that they had implemented a structured, comprehensive environmental management system, while 30.0% (95% C.I. 24.7%–35.9%) are planning to implement a comprehensive environmental management system within the next five years. Stratified analyses were performed by institution size, Carnegie Classification and job title. ^ The Osnabruck model, and another under development by the South Carolina Sustainable Universities Initiative, are the only two environmental management system models that have been proposed specifically for colleges and universities, although several guides are now available. The Environmental Management System Implementation Model for U.S. Colleges and Universities developed is an adaptation of the ISO 14001 standard and USEPA recommendations and has been tailored to U.S. colleges and universities for use in streamlining the implementation process. In using this implementation model created for the U.S. research and academic setting, it is hoped that these highly specialized institutions will be provided with a clearer and more cost-effective path towards the implementation of an EMS and greater compliance with local, state and federal environmental legislation. ^

High-resolution microarray analysis of chromosome 20q in human colon cancer metastasis model systems

Amplification of human chromosome 20q DNA is the most frequently occurring chromosomal abnormality detected in sporadic colorectal carcinomas and shows significant correlation with liver metastases. Through comprehensive high-resolution microarray comparative genomic hybridization and microarray gene expression profiling, we have characterized chromosome 20q amplicon genes associated with human colorectal cancer metastasis in two in vitro metastasis model systems. The results revealed increasing complexity of the 20q genomic profile from the primary tumor-derived cell lines to the lymph node and liver metastasis derived cell lines. Expression analysis of chromosome 20q revealed a subset of over expressed genes residing within the regions of genomic copy number gain in all the tumor cell lines, suggesting these are Chromosome 20q copy number responsive genes. Bases on their preferential expression levels in the model system cell lines and known biological function, four of the over expressed genes mapping to the common intervals of genomic copy gain were considered the most promising candidate colorectal metastasis-associated genes. Validation of genomic copy number and expression array data was carried out on these genes, with one gene, DNMT3B, standing out as expressed at a relatively higher levels in the metastasis-derived cell lines compared with their primary-derived counterparts in both the models systems analyzed. The data provide evidence for the role of chromosome 20q genes with low copy gain and elevated expression in the clonal evolution of metastatic cells and suggests that such genes may serve as early biomarkers of metastatic potential. The data also support the utility of the combined microarray comparative genomic hybridization and expression array analysis for identifying copy number responsive genes in areas of low DNA copy gain in cancer cells. ^

Toxics Release Inventory facilities and childhood cancer: Geographic information systems based approach

Purpose. To examine the association between living in proximity to Toxics Release Inventory (TRI) facilities and the incidence of childhood cancer in the State of Texas. ^ Design. This is a secondary data analysis utilizing the publicly available Toxics release inventory (TRI), maintained by the U.S. Environmental protection agency that lists the facilities that release any of the 650 TRI chemicals. Total childhood cancer cases and childhood cancer rate (age 0-14 years) by county, for the years 1995-2003 were used from the Texas cancer registry, available at the Texas department of State Health Services website. Setting: This study was limited to the children population of the State of Texas. ^ Method. Analysis was done using Stata version 9 and SPSS version 15.0. Satscan was used for geographical spatial clustering of childhood cancer cases based on county centroids using the Poisson clustering algorithm which adjusts for population density. Pictorial maps were created using MapInfo professional version 8.0. ^ Results. One hundred and twenty five counties had no TRI facilities in their region, while 129 facilities had at least one TRI facility. An increasing trend for number of facilities and total disposal was observed except for the highest category based on cancer rate quartiles. Linear regression analysis using log transformation for number of facilities and total disposal in predicting cancer rates was computed, however both these variables were not found to be significant predictors. Seven significant geographical spatial clusters of counties for high childhood cancer rates (p<0.05) were indicated. Binomial logistic regression by categorizing the cancer rate in to two groups (<=150 and >150) indicated an odds ratio of 1.58 (CI 1.127, 2.222) for the natural log of number of facilities. ^ Conclusion. We have used a unique methodology by combining GIS and spatial clustering techniques with existing statistical approaches in examining the association between living in proximity to TRI facilities and the incidence of childhood cancer in the State of Texas. Although a concrete association was not indicated, further studies are required examining specific TRI chemicals. Use of this information can enable the researchers and public to identify potential concerns, gain a better understanding of potential risks, and work with industry and government to reduce toxic chemical use, disposal or other releases and the risks associated with them. TRI data, in conjunction with other information, can be used as a starting point in evaluating exposures and risks. ^

A review of the published literature on interventions to increase compliance with follow-up outpatient medical appointments in primary care practice

Effective strategies for patient follow-up compliance in family practice are essential for the prevention and early detection of disease with the consequences of decreasing morbidity and mortality. With effective appointment reminder systems in place, physicians can better manage the overall health of their patients by providing preventive care as well. This literature review examines intervention strategies used by the authors, the compliance rate of appointment adherence using these techniques, as well as theories relating to study outcomes. The findings of this study may be used as an educational tool by practices to suggest which intervention strategies might be the most effective for their clinic.^

Assessing maintenance of evaporative cooling systems in Legionellosis outbreaks

Evaporative cooling systems continue to be associated with outbreaks of Legionnaires’ disease despite widely available maintenance guidelines intended to reduce these outbreaks. Yet, the guidelines vary widely regarding the recommendations that are made to maintain evaporative cooling systems and it is unclear whether guidelines were in place or, if they were, whether they were being followed when the outbreaks of Legionnaires’ disease occurred. Thus, this study was designed to conduct two systematic reviews of (1) evaporative cooling system maintenance guidelines; and (2) published Legionnaires’ disease outbreaks. For each maintenance guideline identified in the systematic review, recommended maintenance practices were abstracted and similarities and/or differences in the reported recommendations were assessed. Following the systematic review of outbreak investigations that meet the inclusion criteria established for the study, information about the state of the evaporative cooling system during the outbreak investigation was abstracted to summarize, when reported, which maintenance practices were implemented. As expected, the recommended maintenance procedures varied greatly across the guidelines and were not always specific. Overall, the outbreak investigations tended to report similar maintenance issues that were unclear in the maintenance guidelines. Generally, these maintenance issues were biocide use, microbiological testing, frequency of general inspections, and protocols and frequency of total system cleanings. The role in which non-standardized and generalized maintenance guidelines plays in the continued association between Legionnaires’ disease and evaporative cooling systems is still not fully understood. However, this study suggests that more specific and standardized maintenance guidelines, that have been scientifically established to be effective in controlling Legionella bacteria, are needed and then these guidelines must be properly implemented in order to help reduce further Legionnaires’ disease outbreaks associated with evaporative cooling systems.^

Using small area estimation and geographic information systems technology to target health services for the uninsured

The three articles that comprise this dissertation describe how small area estimation and geographic information systems (GIS) technologies can be integrated to provide useful information about the number of uninsured and where they are located. Comprehensive data about the numbers and characteristics of the uninsured are typically only available from surveys. Utilization and administrative data are poor proxies from which to develop this information. Those who cannot access services are unlikely to be fully captured, either by health care provider utilization data or by state and local administrative data. In the absence of direct measures, a well-developed estimation of the local uninsured count or rate can prove valuable when assessing the unmet health service needs of this population. However, the fact that these are “estimates” increases the chances that results will be rejected or, at best, treated with suspicion. The visual impact and spatial analysis capabilities afforded by geographic information systems (GIS) technology can strengthen the likelihood of acceptance of area estimates by those most likely to benefit from the information, including health planners and policy makers. ^ The first article describes how uninsured estimates are currently being performed in the Houston metropolitan region. It details the synthetic model used to calculate numbers and percentages of uninsured, and how the resulting estimates are integrated into a GIS. The second article compares the estimation method of the first article with one currently used by the Texas State Data Center to estimate numbers of uninsured for all Texas counties. Estimates are developed for census tracts in Harris County, using both models with the same data sets. The results are statistically compared. The third article describes a new, revised synthetic method that is being tested to provide uninsured estimates at sub-county levels for eight counties in the Houston metropolitan area. It is being designed to replicate the same categorical results provided by a current U.S. Census Bureau estimation method. The estimates calculated by this revised model are compared to the most recent U.S. Census Bureau estimates, using the same areas and population categories. ^

Use of short term test systems for the prediction of the hazard represented by potential chemical carcinogens

It has been hypothesized that results from the short term bioassays will ultimately provide information that will be useful for human health hazard assessment. Although toxicologic test systems have become increasingly refined, to date, no investigator has been able to provide qualitative or quantitative methods which would support the use of short term tests in this capacity.^ Historically, the validity of the short term tests have been assessed using the framework of the epidemiologic/medical screens. In this context, the results of the carcinogen (long term) bioassay is generally used as the standard. However, this approach is widely recognized as being biased and, because it employs qualitative data, cannot be used in the setting of priorities. In contrast, the goal of this research was to address the problem of evaluating the utility of the short term tests for hazard assessment using an alternative method of investigation.^ Chemical carcinogens were selected from the list of carcinogens published by the International Agency for Research on Carcinogens (IARC). Tumorigenicity and mutagenicity data on fifty-two chemicals were obtained from the Registry of Toxic Effects of Chemical Substances (RTECS) and were analyzed using a relative potency approach. The relative potency framework allows for the standardization of data "relative" to a reference compound. To avoid any bias associated with the choice of the reference compound, fourteen different compounds were used.^ The data were evaluated in a format which allowed for a comparison of the ranking of the mutagenic relative potencies of the compounds (as estimated using short term data) vs. the ranking of the tumorigenic relative potencies (as estimated from the chronic bioassays). The results were statistically significant (p $<$.05) for data standardized to thirteen of the fourteen reference compounds. Although this was a preliminary investigation, it offers evidence that the short term test systems may be of utility in ranking the hazards represented by chemicals which may be human carcinogens. ^