Whole lifespan microscopic observation of budding yeast aging through a microfluidic dissection platform

Important insights into aging have been generated with the genetically tractable and short-lived budding yeast. However, it is still impossible today to continuously track cells by high-resolution microscopic imaging (e.g., fluorescent imaging) throughout their entire lifespan. Instead, the field still needs to rely on a 50-y-old laborious and time-consuming method to assess the lifespan of yeast cells and to isolate differentially aged cells for microscopic snapshots via manual dissection of daughter cells from the larger mother cell. Here, we are unique in achieving continuous and high-resolution microscopic imaging of the entire replicative lifespan of single yeast cells. Our microfluidic dissection platform features an optically prealigned single focal plane and an integrated array of soft elastomer-based micropads, used together to allow for trapping of mother cells, removal of daughter cells, monitoring gradual changes in aging, and unprecedented microscopic imaging of the whole aging process. Using the platform, we found remarkable age-associated changes in phenotypes (e.g., that cells can show strikingly differential cell and vacuole morphologies at the moment of their deaths), indicating substantial heterogeneity in cell aging and death. We envision the microfluidic dissection platform to become a major tool in aging research.

Learning to Teach Argumentation: Research and development in the science classroom

The research reported in this study focuses on an investigation into the teaching of argumentation in secondary science classrooms. Over a one-year period, a group of 12 teachers from schools in the greater London area attended a series of workshops to develop materials and strategies to support the teaching of argumentation in scientific contexts. Data were collected at the beginning and end of the year by audio and video recording lessons where the teachers attempted to implement argumentation. To assess the quality of argumentation, analytical tools derived from Toulmin's argument pattern (TAP) were developed and applied to classroom transcripts. Analysis shows there was development in teachers' use of argumentation across the year. Results indicate that the pattern of use of argumentation is teacher-specific, as is the nature of change. To inform future professional development programmes, transcripts of five teachers, three showing a significant change and two no change, were analysed in more detail to identify features of teachers' oral contributions that facilitated and supported argumentation. The analysis showed that all teachers attempted to encourage a variety of processes involved in argumentation and that the teachers whose lessons included the highest quality of argumentation (TAP analysis) also encouraged higher order processes in their teaching. The analysis of teachers' facilitation of argumentation has helped to guide the development of in-service materials and to identify the barriers to learning in the professional development of less experienced teachers

Quantum dynamics as a physical resource

How useful is a quantum dynamical operation for quantum information processing? Motivated by this question we investigate several strength measures quantifying the resources intrinsic to a quantum operation. We develop a general theory of such strength measures, based on axiomatic considerations independent of state-based resources. The power of this theory is demonstrated with applications to quantum communication complexity, quantum computational complexity, and entanglement generation by unitary operations.Comment: 19 pages, shortened by 3 pages, mainly cosmetic change

Understanding the errors of SHAPE-directed RNA structure modeling

Single-nucleotide-resolution chemical mapping for structured RNA is being rapidly advanced by new chemistries, faster readouts, and coupling to computational algorithms. Recent tests have shown that selective 2'-hydroxyl acylation by primer extension (SHAPE) can give near-zero error rates (0-2%) in modeling the helices of RNA secondary structure. Here, we benchmark the method using six molecules for which crystallographic data are available: tRNA(phe) and 5S rRNA from Escherichia coli, the P4-P6 domain of the Tetrahymena group I ribozyme, and ligand-bound domains from riboswitches for adenine, cyclic di-GMP, and glycine. SHAPE-directed modeling of these highly structured RNAs gave an overall false negative rate (FNR) of 17% and a false discovery rate (FDR) of 21%, with at least one helix prediction error in five of the six cases. Extensive variations of data processing, normalization, and modeling parameters did not significantly mitigate modeling errors. Only one varation, filtering out data collected with deoxyinosine triphosphate during primer extension, gave a modest improvement (FNR = 12%, and FDR = 14%). The residual structure modeling errors are explained by the insufficient information content of these RNAs' SHAPE data, as evaluated by a nonparametric bootstrapping analysis. Beyond these benchmark cases, bootstrapping suggests a low level of confidence (<50%) in the majority of helices in a previously proposed SHAPE-directed model for the HIV-1 RNA genome. Thus, SHAPE-directed RNA modeling is not always unambiguous, and helix-by-helix confidence estimates, as described herein, may be critical for interpreting results from this powerful methodology.Comment: Biochemistry, Article ASAP (Aug. 15, 2011

Evidence-based care of older people with suspected cognitive impairment in general practice: protocol for the IRIS cluster randomised trial

Background: Dementia is a common and complex condition. Evidence-based guidelines for the management of people with dementia in general practice exist; however, detection, diagnosis and disclosure of dementia have been identified as potential evidence-practice gaps. Interventions to implement guidelines into practice have had varying success. The use of theory in designing implementation interventions has been limited, but is advocated because of its potential to yield more effective interventions and aid understanding of factors modifying the magnitude of intervention effects across trials. This protocol describes methods of a randomised trial that tests a theory-informed implementation intervention that, if effective, may provide benefits for patients with dementia and their carers. Aims: This trial aims to estimate the effectiveness of a theory-informed intervention to increase GPs’ (in Victoria, Australia) adherence to a clinical guideline for the detection, diagnosis, and management of dementia in general practice, compared with providing GPs with a printed copy of the guideline. Primary objectives include testing if the intervention is effective in increasing the percentage of patients with suspected cognitive impairment who receive care consistent with two key guideline recommendations: receipt of a i) formal cognitive assessment, and ii) depression assessment using a validated scale (primary outcomes for the trial). Methods: The design is a parallel cluster randomised trial, with clusters being general practices. We aim to recruit 60 practices per group. Practices will be randomised to the intervention and control groups using restricted randomisation. Patients meeting the inclusion criteria, and GPs’ detection and diagnosis behaviours directed toward these patients, will be identified and measured via an electronic search of the medical records nine months after the start of the intervention. Practitioners in the control group will receive a printed copy of the guideline. In addition to receipt of the printed guideline, practitioners in the intervention group will be invited to participate in an interactive, opinion leader-led, educational face-to-face workshop. The theory-informed intervention aims to address identified barriers to and enablers of implementation of recommendations. Researchers responsible for identifying the cohort of patients with suspected cognitive impairment, and their detection and diagnosis outcomes, will be blind to group allocation. Trial registration: Australian New Zealand Clinical Trials Registry: ACTRN12611001032943 (date registered 28 September, 2011)

Wool and meat genetics - the joint possibilities

Wool and meat contribute to profit in sheep enterprises and both need to be considered in breeding programs. The relative responses expected from selection for a range of traits are presented and the realised responses that have been achieved in Merinos and variation in maternal breeds are illustrated. Knowledge of genetic parameters is required for the development of complex breeding objectives and selection indexes, comprehensive genetic evaluation of animals and the design of effective breeding programs. A review of world literature has highlighted the lack of accurate estimates of genetic parameters, especially for genetic correlations between trait groups. Analyses of a combined dataset from seven Australian Merino resource flocks comprising over 2000 sires and up to 100,000 records for each of various traits have provided accurate estimates of parameters to fill these gaps in current knowledge. The results show that there are no major genetic antagonisms between wool and meat traits and that improvement of both can be achieved by using appropriate selection indexes. Sheep Genetics Australia now provides a common system for genetic evaluation of Australian sheep, including across-flock estimated breeding values for a comprehensive range of traits and several standard indexes for various wool and meat breeding objectives

Implementation of World Health Organization Integrated Management of Childhood Illnesses (IMCI) Guidelines for the Assessment of Pneumonia in the Under 5s in Rural Malawi

The Cooking and Pneumonia Study (CAPS) is a pragmatic cluster-level randomized controlled trial of the effect of an advanced cookstove intervention on pneumonia in children under the age of 5 years (under 5s) in Malawi (www.capstudy.org). The primary outcome of the trial is the incidence of pneumonia during a two-year follow-up period, as diagnosed by healthcare providers who are using the World Health Organization (WHO) integrated management of childhood illnesses (IMCI) pneumonia assessment protocol and who are blinded to the trial arms. We evaluated the quality of pneumonia assessment in under 5s in this setting via a cross-sectional study of provider-patient encounters at nine outpatient clinics located within the catchment area of 150 village-level clusters enrolled in the trial across the two study locations of Chikhwawa and Karonga, Malawi, between May and June 2015 using the IMCI guidelines as a benchmark. Data were collected using a key equipment checklist, an IMCI pneumonia knowledge test, and a clinical evaluation checklist. The median number of key equipment items available was 6 (range 4 to 7) out of a possible 7. The median score on the IMCI pneumonia knowledge test among 23 clinicians was 75% (range 60% to 89%). Among a total of 176 consultations performed by 15 clinicians, a median of 9 (range 3 to 13) out of 13 clinical evaluation tasks were performed. Overall, the clinicians were adequately equipped for the assessment of sick children, had good knowledge of the IMCI guidelines, and conducted largely thorough clinical evaluations. We recommend the simple pragmatic approach to quality assurance described herein for similar studies conducted in challenging research settings