What is the role of sugar (sucrose) in dental caries today

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Strengthening impact assessment: a call for integration and focus

We suggest that the impact assessment community has lost its way based on our observation that impact assessment is under attack because of a perceived lack of efficiency. Specifically, we contend that the proliferation of different impact assessment types creates separate silos of expertise and feeds arguments for not only a lack of efficiency but also a lack of effectiveness of the process through excessive specialisation and a lack of interdisciplinary practice. We propose that the solution is a return to the basics of impact assessment with a call for increased integration around the goal of sustainable development and focus through better scoping. We rehearse and rebut counter arguments covering silo-based expertise, advocacy, democracy, sustainability understanding and communication. We call on the impact assessment community to rise to the challenge of increasing integration and focus, and to engage in the debate about the means of strengthening impact assessment

A contribution to the conceptualisation of quality in impact assessment

Quality is much sought after in, and a basic foundation for, good impact assessment (IA). However, the term is rarely defined, has an uncertain relationship with IA effectiveness, and it means different things to different stakeholders, which can lead to debates over the legitimacy associated with an IA process. Thus, IA quality needs conceptualising to position research and practice within broader understandings. This paper contributes to this conceptualisation by identifying nine dimensions of quality through a process of literature review drawing on three fields of study in which quality and quality management have already been debated and conceptualised: education; health care; and business. This approach sidesteps the plural views on quality existing within the field of IA itself which might otherwise bias the identification of quality dimensions. We therefore propose that the dimensions of IA quality are: Efficiency; Optimacy; Conformance; Legitimacy; Equity; Capacity Maintenance; Transformative Capacity; and Quality Management. A literature review of IA research and practice confirms the relevance of the identified quality dimensions to IA. We identify, to an extent, the relationship between quality and effectiveness. Quality aligns with procedural and transactive effectiveness, partly aligns with normative effectiveness and is distinct from, but helps to deliver, substantive effectiveness

EIA decision-making and administrative justice:An empirical analysis

Environmental impact assessment (EIA) is implemented in most countries as an administrative procedure. In this context, it is subject to the principles of administrative justice. However, to date, no empirical research has been conducted to determine the extent to which EIA decisions comply with the principles of administrative justice. In this paper, empirical data from 42 EIA cases in South Africa are used to establish EIA compliance with the administrative justice principles of lawfulness, procedural fairness and reasonableness. This is achieved by measuring EIA decisions against specially developed key performance indicators (KPIs). Overall, decisions were found to mostly comply with the principles of administrative justice. However, questions arise with regards to the quality and substance of the information feeding into the decision-making process and on which decisions are ultimately based

Toward adaptive water governance: the role of systemic feedbacks for learning and adaptation in the eastern transboundary rivers of South Africa

This paper contributes to scholarship on adaptive water governance (AWG), following policy reforms in South Africa, through a focus on systemic feedbacks for learning and adaptation as critical aspects of AWG. We draw insights from three innovative and evolving water governance experiments. In 1998 South Africa adopted integrated water resources management (IWRM) as a transformative approach for achieving an equitable, sustainable, and decentralized stakeholder-centered water resources governance: all hallmarks of an enabling environment for a two-decade history of AWG, although not named as such. Progress in AWG is explored by using a longitudinal, evaluative exploration of three cases in two transboundary basins in South Africa, with a focus on the unfolding enabling environment for achieving sustainability and equity. Building on previous work, we present and discuss a range of enablers that are shown to function systemically to support feedbacks and build adaptive capacity and resilience in complex and uncertain river systems. In the Crocodile Basin, meta-governance arrangements that created an enabling space for collaborative experimentation and learning proved critical as feedbacks were progressively strengthened and embedded through evolving social and institutional arrangements. The enabling environment also supported a networked, blended system of stakeholder- and state-led platforms that have co-evolved through experimentation and learning. Despite progress, long-term persistence of action-learning feedbacks appears less certain in the Olifants Basin cases. We suggest that enabling meta-governance arrangements that offer an institutional home within which to embed learning is critical. The need to explore alternative networked governance arrangements and to explicitly manage for feedbacks that enhance learning at multiple scales is emphasized. We conclude with recommendations for future work on AWG, including reconciling differences between AWG and IWRM that originally framed South African reforms

Evaluating strategic environmental assessment in the Netherlands: Content, process and procedure as indissoluble criteria for effectiveness

To assess the effectiveness of strategic environmental assessment (SEA) we distinguish between its contribution to the quality of the ultimate policy choice (usefulness, applicability), the procedural quality of the planning process (transparency, timeliness) and the quality of stakeholder participation in the planning process (openness, equity, dialogue). In the context of two case studies involving Dutch planning practice, we argue that when and how an SEA is applied is crucial to understanding its e

Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization

<p>Abstract</p> <p>Background</p> <p>Construction and interpretation of phylogenetic trees has been a major research topic for understanding the evolution of genes. Increases in sequence data and complexity are creating a need for more powerful and insightful tree visualization tools.</p> <p>Results</p> <p>We have developed 3D Phylogeny Explorer (3DPE), a novel phylogeny tree viewer that maps trees onto three spatial axes (species on the X-axis; paralogs on Z; evolutionary distance on Y), enabling one to distinguish at a glance evolutionary features such as speciation; gene duplication and paralog evolution; lateral gene transfer; and violation of the "molecular clock" assumption. Users can input any tree on the online 3DPE, then rotate, scroll, rescale, and explore it interactively as "live" 3D views. All objects in 3DPE are clickable to display subtrees, connectivity path highlighting, sequence alignments, and gene summary views, and etc. To illustrate the value of this visualization approach for microbial genomes, we also generated 3D phylogeny analyses for all clusters from the public COG database. We constructed tree views using well-established methods and graph algorithms. We used Scientific Python to generate VRML2 3D views viewable in any web browser.</p> <p>Conclusion</p> <p>3DPE provides a novel phylogenetic tree projection method into 3D space and its web-based implementation with live 3D features for reconstruction of phylogenetic trees of COG database.</p

Active site substitutions delineate distinct classes of eubacterial flap endonuclease

FENs (flap endonucleases) play essential roles in DNA replication, pivotally in the resolution of Okazaki fragments. In eubacteria, DNA PolI (polymerase I) contains a flap processing domain, the N-terminal 5′→3′ exonuclease. We present evidence of paralogous FEN-encoding genes present in many eubacteria. Two distinct classes of these independent FEN-encoding genes exist with four groups of eubacteria, being identified based on the number and type of FEN gene encoded. The respective proteins possess distinct motifs hallmarking their differentiation. Crucially, based on primary sequence and predicted secondary structural motifs, we reveal key differences at their active sites. These results are supported by biochemical characterization of two family members - ExoIX (exonuclease IX) from Escherichia coli and SaFEN (Staphylococcus aureus FEN). These proteins displayed marked differences in their ability to process a range of branched and linear DNA structures. On bifurcated substrates, SaFEN exhibited similar substrate specificity to previously characterized FENs. In quantitative exonuclease assays, SaFEN maintained a comparable activity with that reported for PolI. However, ExoIX showed no observable enzymatic activity. A threaded model is presented for SaFEN, demonstrating the probable interaction of this newly identified class of FEN with divalent metal ions and a branched DNA substrate. The results from the present study provide an intriguing model for the cellular role of these FEN sub-classes and illustrate the evolutionary importance of processing aberrant DNA, which has led to their maintenance alongside DNA PolI in many eubacteria

Evaluation of the bacterial diversity of Pressure ulcers using bTEFAP pyrosequencing

<p>Abstract</p> <p>Background</p> <p>Decubitus ulcers, also known as bedsores or pressure ulcers, affect millions of hospitalized patients each year. The microflora of chronic wounds such as ulcers most commonly exist in the biofilm phenotype and have been known to significantly impair normal healing trajectories.</p> <p>Methods</p> <p>Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP), a universal bacterial identification method, was used to identify bacterial populations in 49 decubitus ulcers. Diversity estimators were utilized and wound community compositions analyzed in relation to metadata such as Age, race, gender, and comorbidities.</p> <p>Results</p> <p>Decubitus ulcers are shown to be polymicrobial in nature with no single bacterium exclusively colonizing the wounds. The microbial community among such ulcers is highly variable. While there are between 3 and 10 primary populations in each wound there can be hundreds of different species present many of which are in trace amounts. There is no clearly significant differences in the microbial ecology of decubitus ulcer in relation to metadata except when considering diabetes. The microbial populations and composition in the decubitus ulcers of diabetics may be significantly different from the communities in non-diabetics.</p> <p>Conclusions</p> <p>Based upon the continued elucidation of chronic wound bioburdens as polymicrobial infections, it is recommended that, in addition to traditional biofilm-based wound care strategies, an antimicrobial/antibiofilm treatment program can be tailored to each patient's respective wound microflora.</p

South African medical schools: Current state of selection criteria and medical students’ demographic profile

Background. Selection of medical students at South African (SA) medical schools must promote equitable and fair access to students from all population groups, while ensuring optimal student throughput and success, and training future healthcare practitioners who will fulfil the needs of the local society. In keeping with international practices, a variety of academic and non-academic measures are used to select applicants for medical training programmes in SA medical schools. Objectives. To provide an overview of the selection procedures used by all eight medical schools in SA, and the student demographics (race and gender) at these medical schools, and to determine to what extent collective practices are achieving the goals of student diversity and inclusivity.Methods. A retrospective, quantitative, descriptive study design was used. All eight medical schools in SA provided information regarding selection criteria, selection procedures, and student demographics (race and gender). Descriptive analysis of data was done by calculating frequencies and percentages of the variables measured.Results. Medical schools in SA make use of academic and non-academic criteria in their selection processes. The latter include indices of socioeconomic disadvantage. Most undergraduate medical students in SA are black (38.7%), followed by white (33.0%), coloured (13.4%) and Indian/Asian (13.6%). The majority of students are female (62.2%). The number of black students is still proportionately lower than in the general population, while other groups are overrepresented. Conclusion. Selection policies for undergraduate medical programmes aimed at redress should be continued and further refined, along with the provision of support to ensure student success.