A cost function for similarity-based hierarchical clustering

The development of algorithms for hierarchical clustering has been hampered by a shortage of precise objective functions. To help address this situation, we introduce a simple cost function on hierarchies over a set of points, given pairwise similarities between those points. We show that this criterion behaves sensibly in canonical instances and that it admits a top-down construction procedure with a provably good approximation ratio

Cascade diagrams for depicting complex interventions in randomised trials

Many medical interventions—particularly non-pharmacological ones—are complex, consisting of multiple interacting components targeted at different organisational levels.1 2 Published descriptions of complex interventions often do not contain enough detail to enable their replication.2-5 Reports of behaviour change interventions should include descriptions of setting, mode, intensity, and duration, and characteristics of the participants.6 Graphical methods, such as that showing the relative timing of assessments and intervention components,7 may improve clarity of reporting. However, these approaches do not reveal the connections between the different “actors” in a complex intervention.8 Different audiences may want different things from a description of an intervention, but visualising relationships between actors can clarify crucial features such as the fidelity with which the intervention is passed down a chain of actors and possible routes of contamination between treatment arms. Here we describe a new graphical approach—the cascade diagram—that highlights these potential problems

Arkansas Soybean Performance Tests 2008

Soybean cultivar performance tests are conducted each year in Arkansas by the University of Arkansas Division of Agriculture. The tests provide information to companies developing cultivars and/or marketing seed within the state, and aid the Arkansas Cooperative Extension Service in formulating cultivar recommendations for soybean producer

Core-collapse supernovae ages and metallicities from emission-line diagnostics of nearby stellar populations

Massive stars are the main objects that illuminate H II regions and they evolve quickly to end their lives in core-collapse supernovae (CCSNe). Thus it is important to investigate the association between CCSNe and H II regions. In this paper, we present emission line diagnostics of the stellar populations around nearby CCSNe, that include their host H II regions, from the PMAS/PPAK Integral-field Supernova hosts COmpilation (PISCO). We then use BPASS stellar population models to determine the age, metallicity and gas parameters for H II regions associated with CCSNe, contrasting models that consider either single star evolution alone or incorporate interacting binaries. We find binary-star models, that allow for ionizing photon loss, provide a more realistic fit to the observed CCSN hosts with metallicities that are closer to those derived from the oxygen abundance in O3N2. We also find that type II and type Ibc SNe arise from progenitor stars of similar age, mostly from 7 to 45 Myr, which corresponds to stars with masses < 20 solar mass . However these two types SNe have little preference in their host environment metallicity measured by oxygen abundance or in progenitor initial mass. We note however that at lower metallicities supernovae are more likely to be of type II.Comment: 22 pages, 19 Figures, 6 Tables. Accepted by MNRAS. Comments welcom

FRANKLIN COUNTY, IOWA'S PROGRAM IN PUBLIC AFFAIRS

Public Economics,

Arkansas Soybean Performance Tests 2007

Soybean cultivar performance tests are conducted each year in Arkansas by the University of Arkansas Division of Agriculture. The tests provide information to companies developing cultivars and/or marketing seed within the State, and aid the Arkansas Cooperative Extension Service in formulating cultivar recommendations for soybean producers

Consent processes in cluster-randomised trials in residential facilities for older adults : a systematic review of reporting practices and proposed guidelines

Objective: To assess the quality of reported consent processes of cluster-randomised trials conducted in residential facilities for older people and to explore whether the focus on improving the general conduct and reporting of cluster-randomised trials influenced the quality of conduct and reporting of ethical processes in these trials. Design: Systematic review of cluster-randomised trials reports, published up to the end of 2010. Data sources: National Library of Medicine (Medline) via PubMed, hand-searches of BMJ, Journal of the American Medical Association, BMC Health Services Research, Age and Ageing and Journal of the American Geriatrics Society, reference search in Web of Knowledge and consultation with experts. Eligibility for selecting studies: Published cluster-randomised trials where the unit of randomisation is a part or the whole of a residential facility for older people, without language or year of publication restrictions. Results: We included 73 trials. Authors reported ethical approval in 59, obtaining individual consent in 51, and using proxies for this consent in 37, but the process to assess residents’ capacity to consent was clearly reported in only eight. We rated only six trials high for the quality of consent processes. We considered that individual informed consent could have been waived legitimately in 14 of 22 trials not reporting obtaining consent. The proportions reporting ethical approval and quality of consent processes were higher in recent trials. Conclusions: Recently published international recommendations regarding ethical conduct in cluster-randomised trials are much needed. In relation to consent processes when cognitively impaired individuals are included in these trials, we provide a six-point checklist and recommend the minimum information to be reported. Those who lack capacity in trials with complex designs should be afforded the same care in relation to consent as competent adults in trials with simpler designs

Representing and analysing molecular and cellular function in the computer

Determining the biological function of a myriad of genes, and understanding how they interact to yield a living cell, is the major challenge of the post genome-sequencing era. The complexity of biological systems is such that this cannot be envisaged without the help of powerful computer systems capable of representing and analysing the intricate networks of physical and functional interactions between the different cellular components. In this review we try to provide the reader with an appreciation of where we stand in this regard. We discuss some of the inherent problems in describing the different facets of biological function, give an overview of how information on function is currently represented in the major biological databases, and describe different systems for organising and categorising the functions of gene products. In a second part, we present a new general data model, currently under development, which describes information on molecular function and cellular processes in a rigorous manner. The model is capable of representing a large variety of biochemical processes, including metabolic pathways, regulation of gene expression and signal transduction. It also incorporates taxonomies for categorising molecular entities, interactions and processes, and it offers means of viewing the information at different levels of resolution, and dealing with incomplete knowledge. The data model has been implemented in the database on protein function and cellular processes 'aMAZE' (http://www.ebi.ac.uk/research/pfbp/), which presently covers metabolic pathways and their regulation. Several tools for querying, displaying, and performing analyses on such pathways are briefly described in order to illustrate the practical applications enabled by the model