BioPartsDB: a synthetic biology workflow web-application for education and research

Synthetic biology has become a widely used technology, and expanding applications in research, education and industry require progress tracking for team-based DNA synthesis projects. Although some vendors are beginning to supply multi-kilobase sequence-verified constructs, synthesis workflows starting with short oligos remain important for cost savings and pedagogical benefit. We developed BioPartsDB as an open source, extendable workflow management system for synthetic biology projects with entry points for oligos and larger DNA constructs and ending with sequence-verified clones

Longitudinal comparison of factors influencing choice of dental treatment by private general practitioners

The document attached has been archived with permission from the Australian Dental Association. An external link to the publisher’s copy is included.Background: Service rate variations and appropriateness of care issues have focused attention on factors that influence treatment decisions. The aims of this study were to examine what factors dentists consider in choosing alternative treatments, the stability of these factors over time and whether stability of treatment choice was related to age of dentist. Methods: Baseline data were collected by mailed self-complete questionnaires from a random sample of Australian dentists (response rate=60.3 per cent, n=345 private general practitioners provided service data from a typical day) in 1997–1998 and followup data were collected in 2004 (response rate=76.8 per cent, n=177 matched longitudinal cases). Results: The most frequent factors considered important across six alternative treatment pair choice scenarios were caries rate for ‘exam v. x-ray’, age of patient for ‘preventive v. restorative intervention’, cost of treatment for ‘crown v. buildup’, ‘root canal v. extraction’ and ‘bridge v. denture’, and calculus for ‘prophylaxis v. scaling’. The only differences over time were (t-test, P<0.05): higher proportions of responses in the mouth status group at follow-up for ‘exam v. x-ray’; higher proportions of responses in the visit history group at follow-up for ‘preventive v. restorative intervention’; a lower proportion of responses in the caries group at follow-up for ‘crown v. build-up’; and a higher proportion of responses in the treatment constraints group at follow-up for ‘prophylaxis v. scaling’. Conclusions: While a wide range of responses were offered as factors influencing the choice of alternative treatments, cost of treatment was a major consideration in situations where significantly cheaper alternatives existed, while patient preference was commonly included as a secondary consideration across a wide range of treatment choice scenarios. The treatment choice responses showed a high degree of stability over time across all age groups of dentists, suggesting that if routines are developed these are established before or soon after graduation as a dentist.DS Brennan, AJ Spence

Practice belief scales among private general dental practitioners

The document attached has been archived with permission from the Australian Dental Association (8th Jan 2008). An external link to the publisher’s copy is included.Background: Practice beliefs have been related to service rate variation. The aims of this study were to replicate practice belief scales in Australia and investigate associations with dentist and practice characteristics and services. Method: A random sample of Australian dentists completed mailed questionnaires (response rate 60.3 per cent). Results: Private general practitioners (n=345) provided service data from a typical day. Eight practice belief items were recorded on a five-point Likert scale, yielding four factor-based scales. Approximately 85 per cent of responses were on the agreement side of the midpoint for the scales of Information giving and Patient influence, 45 per cent for Preventive orientation and approximately 10 per cent for Controlling active disease rather than developing better preventive advice. Capital city dentists had higher agreement with the Preventive orientation scale, while males and older dentists showed less disagreement with the Controlling active disease item (Mann-Whitney, Kruskal-Wallis P<0.05). Those agreeing with the scales (that is scores ≤ the median) showed (Poisson regression P<0.05): a higher rate of crown and bridge, a rate ratio (RR) of 1.31, but lower rates of extraction (RR=0.76) and prosthodontic services (RR=0.64) for the Information giving scale; a higher rate of restorative (RR=1.22) and total services per visit (RR=1.06) for the Preventive orientation scale; a higher rate of preventive services (RR=1.14), but a lower rate of crown and bridge services (0.78) for the Patient influence scale; and higher rates of crown and bridge (RR=1.40) and prosthodontic (RR=1.59) but lower rates of periodontic (RR=0.60) and extraction services (RR=0.62) for the Controlling active disease item. Conclusions: These findings confirm the factor structure of practice beliefs and demonstrate small to moderate associations with variation in service rates.DS Brennan and AJ Spence

Knowledge, attitude and practices of pediatricians regarding the prevention of oral diseases in Italy

BACKGROUND: Pediatricians are in an ideal position to advise families about the prevention and management of oral diseases in children. The objective of the study was to determine knowledge, attitude, and practices regarding the prevention of oral diseases among pediatricians in Italy. METHODS: A systematic random sample of 1000 pediatricians received a questionnaire on socio-demographic and practice characteristics; knowledge on risk factors; attitude and practices towards the prevention of oral diseases. RESULTS: A total of 507 pediatricians participated. More than half knew the main risk factors for oral diseases and this knowledge was higher in primary care pediatricians (p = 0.007), in those with a higher number of hours worked per week (p = 0.012), and who believed that oral diseases may be prevented (p = 0.017). Pediatricians with higher knowledge about the main risk factors (p = 0.006) believe that they have an important role in preventing oral diseases and that they can perform an oral examination. Almost all (89%) prescribed fluoride supplements and those younger (p = 0.016), with a higher number of patients seen in workday (p = 0.001), with longer practice activity (p = 0.004), those who believe that fluoride is effective in preventing caries (p < 0.0001), and who learned about prevention from scientific sources (p = 0.002) were more likely to prescribe fluoride. One-fourth and 40.6% provides and recommends a dental visit once a year and primary care pediatricians (p = 0.014) and those who believed that routine visit is important in preventing oral diseases (p < 0.0001) were more likely to recommend a dental visit once a year. CONCLUSION: The results showed a lack of knowledge among pediatricians although almost all believed that they had an important responsibility in preventing oral diseases and provided an oral examination

Recruitment of pre-dementia participants: main enrollment barriers in a longitudinal amyloid-PET study

Background: The mismatch between the limited availability versus the high demand of participants who are in the pre-dementia phase of Alzheimer’s disease (AD) is a bottleneck for clinical studies in AD. Nevertheless, potential enrollment barriers in the pre-dementia population are relatively under-reported. In a large European longitudinal biomarker study (the AMYPAD-PNHS), we investigated main enrollment barriers in individuals with no or mild symptoms recruited from research and clinical parent cohorts (PCs) of ongoing observational studies. Methods: Logistic regression was used to predict study refusal based on sex, age, education, global cognition (MMSE), family history of dementia, and number of prior study visits. Study refusal rates and categorized enrollment barriers were compared between PCs using chi-squared tests. Results: 535/1856 (28.8%) of the participants recruited from ongoing studies declined participation in the AMYPAD-PNHS. Only for participants recruited from clinical PCs (n = 243), a higher MMSE-score (β = − 0.22, OR = 0.80, p <.05), more prior study visits (β = − 0.93, OR = 0.40, p <.001), and positive family history of dementia (β = 2.08, OR = 8.02, p <.01) resulted in lower odds on study refusal. General study burden was the main enrollment barrier (36.1%), followed by amyloid-PET related burden (PCresearch = 27.4%, PCclinical = 9.0%, X 2 = 10.56, p =.001), and loss of research interest (PCclinical = 46.3%, PCresearch = 16.5%, X 2 = 32.34, p <.001). Conclusions: The enrollment rate for the AMYPAD-PNHS was relatively high, suggesting an advantage of recruitment via ongoing studies. In this observational cohort, study burden reduction and tailored strategies may potentially improve participant enrollment into trial readiness cohorts such as for phase-3 early anti-amyloid intervention trials. The AMYPAD-PNHS (EudraCT: 2018–002277-22) was approved by the ethical review board of the VU Medical Center (VUmc) as the Sponsor site and in every affiliated site

Design of the Prevention of Adult Caries Study (PACS): A randomized clinical trial assessing the effect of a chlorhexidine dental coating for the prevention of adult caries

<p>Abstract</p> <p>Background</p> <p>Dental caries is one of the primary causes of tooth loss among adults. It is estimated to affect a majority of Americans aged 55 and older, with a disproportionately higher burden in disadvantaged populations. Although a number of treatments are currently in use for caries prevention in adults, evidence for their efficacy and effectiveness is limited.</p> <p>Methods/Design</p> <p>The Prevention of Adult Caries Study (PACS) is a multicenter, placebo-controlled, double-blind, randomized clinical trial of the efficacy of a chlorhexidine (10% w/v) dental coating in preventing adult caries. Participants (n = 983) were recruited from four different dental delivery systems serving four diverse communities, including one American Indian population, and were randomized to receive either chlorhexidine or a placebo treatment. The primary outcome is the net caries increment (including non-cavitated lesions) from baseline to 13 months of follow-up. A cost-effectiveness analysis also will be considered.</p> <p>Discussion</p> <p>This new dental treatment, if efficacious and approved for use by the Food and Drug Administration (FDA), would become a new in-office, anti-microbial agent for the prevention of adult caries in the United States.</p> <p>Trial Registration Number</p> <p>NCT00357877</p

A cluster randomised controlled trial in primary dental care based intervention to improve professional performance on routine oral examinations and the management of asymptomatic impacted third molars: study protocol

BACKGROUND: Routine oral examination (ROE) refers to periodic monitoring of the general and oral health status of patients. In most developed Western countries a decreasing prevalence of oral diseases underpins the need for a more individualised approach in assigning individualised recall intervals for regular attendees instead of systematic fixed intervals. From a quality-of-care perspective, the effectiveness of the widespread prophylactic removal of mandibular impacted asymptomatic third molars (MIM) in adolescents and adults is also questionable. Data on the effectiveness of appropriate interventions to tackle such problems, and for promoting continuing professional development in oral health care are rare. METHODS/DESIGN: This study is a cluster randomised controlled trial with groups of GDPs as the unit of randomisation. The aim is to determine the effectiveness and efficiency of small group quality improvement on professional decision-making of general dental practitioners (GDPs) in daily practice. Six peer groups ('IQual-groups') shall be randomised either to the intervention arm I or arm II. Groups of GDPs allocated to either of these arms act as each other's control group. An IQual peer group consists of eight to ten GDPs who meet in monthly structured sessions scheduled for discussion on practice-related topics. GDPs in both trial arms receive recently developed evidence-based clinical practice guidelines (CPG) on ROE or MIM. The implementation strategy consists of one interactive IQual group meeting of two to three hours. In addition, both groups of GDPs receive feedback on personal and group characteristics, and are invited to make use of web-based patient risk vignettes for further individual training on risk assessment policy. Reminders (flow charts) will be sent by mail several weeks after the meeting. The main outcome measure for the ROE intervention arm is the use and appropriateness of individualised risk assessment in assigning recall intervals, and for the MIM-intervention group the use and appropriateness of individualised mandibular impacted third molar risk management. Both groups act as each other's control. Pre-intervention data will be collected in study months one through three. Post-intervention data collection will be performed after nine months

MINE: Module Identification in Networks

<p>Abstract</p> <p>Background</p> <p>Graphical models of network associations are useful for both visualizing and integrating multiple types of association data. Identifying modules, or groups of functionally related gene products, is an important challenge in analyzing biological networks. However, existing tools to identify modules are insufficient when applied to dense networks of experimentally derived interaction data. To address this problem, we have developed an agglomerative clustering method that is able to identify highly modular sets of gene products within highly interconnected molecular interaction networks.</p> <p>Results</p> <p>MINE outperforms MCODE, CFinder, NEMO, SPICi, and MCL in identifying non-exclusive, high modularity clusters when applied to the <it>C. elegans </it>protein-protein interaction network. The algorithm generally achieves superior geometric accuracy and modularity for annotated functional categories. In comparison with the most closely related algorithm, MCODE, the top clusters identified by MINE are consistently of higher density and MINE is less likely to designate overlapping modules as a single unit. MINE offers a high level of granularity with a small number of adjustable parameters, enabling users to fine-tune cluster results for input networks with differing topological properties.</p> <p>Conclusions</p> <p>MINE was created in response to the challenge of discovering high quality modules of gene products within highly interconnected biological networks. The algorithm allows a high degree of flexibility and user-customisation of results with few adjustable parameters. MINE outperforms several popular clustering algorithms in identifying modules with high modularity and obtains good overall recall and precision of functional annotations in protein-protein interaction networks from both <it>S. cerevisiae </it>and <it>C. elegans</it>.</p

MCL-CAw: A refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure

Abstract Background The reconstruction of protein complexes from the physical interactome of organisms serves as a building block towards understanding the higher level organization of the cell. Over the past few years, several independent high-throughput experiments have helped to catalogue enormous amount of physical protein interaction data from organisms such as yeast. However, these individual datasets show lack of correlation with each other and also contain substantial number of false positives (noise). Over these years, several affinity scoring schemes have also been devised to improve the qualities of these datasets. Therefore, the challenge now is to detect meaningful as well as novel complexes from protein interaction (PPI) networks derived by combining datasets from multiple sources and by making use of these affinity scoring schemes. In the attempt towards tackling this challenge, the Markov Clustering algorithm (MCL) has proved to be a popular and reasonably successful method, mainly due to its scalability, robustness, and ability to work on scored (weighted) networks. However, MCL produces many noisy clusters, which either do not match known complexes or have additional proteins that reduce the accuracies of correctly predicted complexes. Results Inspired by recent experimental observations by Gavin and colleagues on the modularity structure in yeast complexes and the distinctive properties of "core" and "attachment" proteins, we develop a core-attachment based refinement method coupled to MCL for reconstruction of yeast complexes from scored (weighted) PPI networks. We combine physical interactions from two recent "pull-down" experiments to generate an unscored PPI network. We then score this network using available affinity scoring schemes to generate multiple scored PPI networks. The evaluation of our method (called MCL-CAw) on these networks shows that: (i) MCL-CAw derives larger number of yeast complexes and with better accuracies than MCL, particularly in the presence of natural noise; (ii) Affinity scoring can effectively reduce the impact of noise on MCL-CAw and thereby improve the quality (precision and recall) of its predicted complexes; (iii) MCL-CAw responds well to most available scoring schemes. We discuss several instances where MCL-CAw was successful in deriving meaningful complexes, and where it missed a few proteins or whole complexes due to affinity scoring of the networks. We compare MCL-CAw with several recent complex detection algorithms on unscored and scored networks, and assess the relative performance of the algorithms on these networks. Further, we study the impact of augmenting physical datasets with computationally inferred interactions for complex detection. Finally, we analyse the essentiality of proteins within predicted complexes to understand a possible correlation between protein essentiality and their ability to form complexes. Conclusions We demonstrate that core-attachment based refinement in MCL-CAw improves the predictions of MCL on yeast PPI networks. We show that affinity scoring improves the performance of MCL-CAw.http://deepblue.lib.umich.edu/bitstream/2027.42/78256/1/1471-2105-11-504.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/2/1471-2105-11-504-S1.PDFhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/3/1471-2105-11-504-S2.ZIPhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/4/1471-2105-11-504.pdfPeer Reviewe