Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease

Background: Clostridium difficile infections (CDI) are a significant health problem to humans and food animals. Clostridial toxins ToxA and ToxB encoded by genes tcdA and tcdB are located on a pathogenicity locus known as the PaLoc and are the major virulence factors of C. difficile. While toxin-negative strains of C. difficile are often isolated from faeces of animals and patients suffering from CDI, they are not considered to play a role in disease. Toxin-negative strains of C. difficile have been used successfully to treat recurring CDI but their propensity to acquire the PaLoc via lateral gene transfer and express clinically relevant levels of toxins has reinforced the need to characterise them genetically. In addition, further studies that examine the pathogenic potential of toxin-negative strains of C. difficile and the frequency by which toxin-negative strains may acquire the PaLoc are needed. Results: We undertook a comparative genomic analysis of five Australian toxin-negative isolates of C. difficile that lack tcdA, tcdB and both binary toxin genes cdtA and cdtB that were recovered from humans and farm animals with symptoms of gastrointestinal disease. Our analyses show that the five C. difficile isolates cluster closely with virulent toxigenic strains of C. difficile belonging to the same sequence type (ST) and have virulence gene profiles akin to those in toxigenic strains. Furthermore, phage acquisition appears to have played a key role in the evolution of C. difficile. Conclusions: Our results are consistent with the C. difficile global population structure comprising six clades each containing both toxin-positive and toxin-negative strains. Our data also suggests that toxin-negative strains of C. difficile encode a repertoire of putative virulence factors that are similar to those found in toxigenic strains of C. difficile, raising the possibility that acquisition of PaLoc by toxin-negative strains poses a threat to human health. Studies in appropriate animal models are needed to examine the pathogenic potential of toxin-negative strains of C. difficile and to determine the frequency by which toxin-negative strains may acquire the PaLoc

Mental Imagery and Visual Working Memory

Visual working memory provides an essential link between past and future events. Despite recent efforts, capacity limits, their genesis and the underlying neural structures of visual working memory remain unclear. Here we show that performance in visual working memory - but not iconic visual memory - can be predicted by the strength of mental imagery as assessed with binocular rivalry in a given individual. In addition, for individuals with strong imagery, modulating the background luminance diminished performance on visual working memory and imagery tasks, but not working memory for number strings. This suggests that luminance signals were disrupting sensory-based imagery mechanisms and not a general working memory system. Individuals with poor imagery still performed above chance in the visual working memory task, but their performance was not affected by the background luminance, suggesting a dichotomy in strategies for visual working memory: individuals with strong mental imagery rely on sensory-based imagery to support mnemonic performance, while those with poor imagery rely on different strategies. These findings could help reconcile current controversy regarding the mechanism and location of visual mnemonic storage

Worldwide Esophageal Cancer Collaboration : clinical staging data

Peer reviewe

School Smoking Policy Characteristics and Individual Perceptions of the School Tobacco Context: Are They Linked to Students’ Smoking Status?

The purpose of this study was to explore individual- and school-level policy characteristics on student smoking behavior using an ecological perspective. Participants were 24,213 (51% female) Grade 10–11 students from 81 schools in five Canadian provinces. Data were collected using student self-report surveys, written policies collected from schools, interviews with school administrators, and school property observations to assess multiple dimensions of the school tobacco policy. The multi-level modeling results revealed that the school a student attended was associated with his/her smoking behavior. Individual-level variables that were associated with student smoking included lower school connectedness, a greater number of family and friends who smoked, higher perceptions of student smoking prevalence, lower perceptions of student smoking frequency, and stronger perceptions of the school tobacco context. School-level variables associated with student smoking included weaker policy intention indicating prohibition and assistance to overcome tobacco addiction, weaker policy implementation involving strategies for enforcement, and a higher number of students smoking on school property. These findings suggest that the school environment is important to tobacco control strategies, and that various policy dimensions have unique relationships to student smoking. School tobacco policies should be part of a comprehensive approach to adolescent tobacco use

Shared Agency with Parents for Educational Goals: Ethnic Differences and Implications for College Adjustment

This study proposed and confirmed three ways in which college students can perceive shared agency and two ways in which they can perceive non-shared agency with parents when pursuing educational goals in college. Differences and similarities were examined among participants from four ethnic backgrounds (N = 515; 67% female): East Asian American, Southeast Asian American, Filipino/Pacific Islander American, and European American. Results indicated that Asian American youth reported higher levels of non-shared agency with parents (i.e., parental directing and noninvolvement), lower levels of shared agency (i.e., parental accommodation, support, or collaboration), and poorer college adjustment compared to European Americans. However, ethnic similarities were found whereby perceived shared agency in education with parents was associated with college adjustment. Multiple mediation analyses also indicated that our model of shared and non-shared agency with parents explained differences in college adjustment between Asian and European Americans, though more strongly for comparisons between European and East Asian Americans. Our results suggest that parents continue to be important in the education of older youth but that continued directing of youth’s education in college can be maladaptive

Processing and analyzing multiple genomes alignments with MafFilter

As the number of available genome sequences from both closely related species and individuals withinspecies increased, theoretical and methodological convergences between the fields of phylogenomics andpopulation genomics emerged. Population genomics typically focuses on the analysis of variants, whilephylogenomics heavily relies on genome alignments. However, these are playing an increasingly importantrole in studies at the population level. Multiple genome alignments of individuals are used when structuralvariation is of primary interest and when genome architecture permits to assemblede novogenomesequences. Here I describe MafFilter, a command-line-driven program allowing to process genome align-ments in the Multiple Alignment Format (MAF). Using concrete examples based on publicly availabledatasets, I demonstrate how MafFilter can be used to develop efficient and reproducible pipelines withquality assurance for downstream analyses. I further show how MafFilter can be used to perform both basicand advanced population genomic analyses in order to infer the patterns of nucleotide diversity alonggenomes

Study protocol: Audit and Best Practice for Chronic Disease Extension (ABCDE) Project

<p>Abstract</p> <p>Background</p> <p>A growing body of international literature points to the importance of a system approach to improve the quality of care in primary health care settings. Continuous Quality Improvement (CQI) concepts and techniques provide a theoretically coherent and practical way for primary care organisations to identify, address, and overcome the barriers to improvements. The Audit and Best Practice for Chronic Disease (ABCD) study, a CQI-based quality improvement project conducted in Australia's Northern Territory, has demonstrated significant improvements in primary care service systems, in the quality of clinical service delivery and in patient outcomes related to chronic illness care. The aims of the extension phase of this study are to examine factors that influence uptake and sustainability of this type of CQI activity in a variety of Indigenous primary health care organisations in Australia, and to assess the impact of collaborative CQI approaches on prevention and management of chronic illness and health outcomes in Indigenous communities.</p> <p>Methods/design</p> <p>The study will be conducted in 40–50 Indigenous community health centres from 4 States/Territories (Northern Territory, Western Australia, New South Wales and Queensland) over a five year period. The project will adopt a participatory, quality improvement approach that features annual cycles of: 1) organisational system assessment and audits of clinical records; 2) feedback to and interpretation of results with participating health centre staff; 3) action planning and goal setting by health centre staff to achieve system changes; and 4) implementation of strategies for change. System assessment will be carried out using a System Assessment Tool and in-depth interviews of key informants. Clinical audit tools include two essential tools that focus on diabetes care audit and preventive service audit, and several optional tools focusing on audits of hypertension, heart disease, renal disease, primary mental health care and health promotion.</p> <p>The project will be carried out in a form of collaborative characterised by a sequence of annual learning cycles with action periods for CQI activities between each learning cycle.</p> <p>Key outcome measures include uptake and integration of CQI activities into routine service activity, state of system development, delivery of evidence-based services, intermediate patient outcomes (e.g. blood pressure and glucose control), and health outcomes (complications, hospitalisations and mortality).</p> <p>Conclusion</p> <p>The ABCD Extension project will contribute directly to the evidence base on effectiveness of collaborative CQI approaches on prevention and management of chronic disease in Australia's Indigenous communities, and to inform the operational and policy environments that are required to incorporate CQI activities into routine practice.</p