Characterizations of how species mediate ecosystem properties require more comprehensive functional effect descriptors

The importance of individual species in mediating ecosystem process and functioning is generally accepted, but categorical descriptors that summarize species-specific contributions to ecosystems tend to reference a limited number of biological traits and underestimate the importance of how organisms interact with their environment. Here, we show how three functionally contrasting sediment-dwelling marine invertebrates affect fluid and particle transport - important processes in mediating nutrient cycling - and use high-resolution reconstructions of burrow geometry to determine the extent and nature of biogenic modification. We find that individual functional effect descriptors fall short of being able to adequately characterize how species mediate the stocks and flows of important ecosystem properties and that, in contrary to common practice and understanding, they are not substitutable with one another because they emphasize different aspects of species activity and behavior. When information derived from these metrics is combined with knowledge of how species behave and modify their environment, however, detailed mechanistic information emerges that increases the likelihood that a species functional standing will be appropriately summarized. Our study provides evidence that more comprehensive functional effect descriptors are required if they are to be of value to those tasked with projecting how altered biodiversity will influence future ecosystems

The development of common data elements for a multi-institute prostate cancer tissue bank: The Cooperative Prostate Cancer Tissue Resource (CPCTR) experience

BACKGROUND: The Cooperative Prostate Cancer Tissue Resource (CPCTR) is a consortium of four geographically dispersed institutions that are funded by the U.S. National Cancer Institute (NCI) to provide clinically annotated prostate cancer tissue samples to researchers. To facilitate this effort, it was critical to arrive at agreed upon common data elements (CDEs) that could be used to collect demographic, pathologic, treatment and clinical outcome data. METHODS: The CPCTR investigators convened a CDE curation subcommittee to develop and implement CDEs for the annotation of collected prostate tissues. The draft CDEs were refined and progressively annotated to make them ISO 11179 compliant. The CDEs were implemented in the CPCTR database and tested using software query tools developed by the investigators. RESULTS: By collaborative consensus the CPCTR CDE subcommittee developed 145 data elements to annotate the tissue samples collected. These included for each case: 1) demographic data, 2) clinical history, 3) pathology specimen level elements to describe the staging, grading and other characteristics of individual surgical pathology cases, 4) tissue block level annotation critical to managing a virtual inventory of cases and facilitating case selection, and 5) clinical outcome data including treatment, recurrence and vital status. These elements have been used successfully to respond to over 60 requests by end-users for tissue, including paraffin blocks from cases with 5 to 10 years of follow up, tissue microarrays (TMAs), as well as frozen tissue collected prospectively for genomic profiling and genetic studies. The CPCTR CDEs have been fully implemented in two major tissue banks and have been shared with dozens of other tissue banking efforts. CONCLUSION: The freely available CDEs developed by the CPCTR are robust, based on "best practices" for tissue resources, and are ISO 11179 compliant. The process for CDE development described in this manuscript provides a framework model for other organ sites and has been used as a model for breast and melanoma tissue banking efforts

An audit of the dietary intake of Australian children with type 1 diabetes

To understand what children with type 1 diabetes in a representative tertiary hospital clinic are eating compared to their peers and explore dietary intake impact on HbA1c outcome. An open cross-sectional dietary audit of children and adolescents with diabetes aged 2-17 years attending the Royal Children's Hospital, Melbourne was conducted using an age-appropriate validated Food Frequency Questionnaire. Total energy, macronutrient intake and diet quality were calculated and compared to dietary advice provided and national intake data. Body weight, and dietary intake influences on glycaemic control were investigated. Overall, 785 patients were recruited, from which 429 dietary surveys were completed. Dietary intakes were overall nutritionally adequate with macronutrient distribution (% total energy intake) being lower carbohydrate (48.6%), higher total sugars (22.4%), fat (32.9%), saturated fat (14.9%) and protein intake (19.1%) than recommendations, but similar to their peers. Energy intakes were excessive compared to their peers in the 4-13 year olds. Rates of overweight (30%) were significantly higher than national data (18%). Overall, 43% achieved optimal glycaemic control (HbA1c < 7.5%; <58 mmol/mol). HbA1c prediction via linear regression indicated that the following factors were associated with lower HbA1c values: being male, on pump regimen, lower rates of insulin per kg, shorter duration of disease. This audit has identified areas requiring targeted education/support to improve health outcomes including dietary adherence, rates of overweight/obesity, appropriate energy intakes and optimal glycaemic targets. Furthermore, it provides baseline data to evaluate efficacy of future interventions

Deciding not to decide : computational and neural evidence for hidden behavior in sequential choice

Understanding the cognitive and neural processes that underlie human decision making requires the successful prediction of how, but also of when, people choose. Sequential sampling models (SSMs) have greatly advanced the decision sciences by assuming decisions to emerge from a bounded evidence accumulation process so that response times (RTs) become predictable. Here, we demonstrate a difficulty of SSMs that occurs when people are not forced to respond at once but are allowed to sample information sequentially: The decision maker might decide to delay the choice and terminate the accumulation process temporarily, a scenario not accounted for by the standard SSM approach. We developed several SSMs for predicting RTs from two independent samples of an electroencephalography (EEG) and a functional magnetic resonance imaging (fMRI) study. In these studies, participants bought or rejected fictitious stocks based on sequentially presented cues and were free to respond at any time. Standard SSM implementations did not describe RT distributions adequately. However, by adding a mechanism for postponing decisions to the model we obtained an accurate fit to the data. Time-frequency analysis of EEG data revealed alternating states of de- and increasing oscillatory power in beta-band frequencies (14-30 Hz), indicating that responses were repeatedly prepared and inhibited and thus lending further support for the existence of a decision not to decide. Finally, the extended model accounted for the results of an adapted version of our paradigm in which participants had to press a button for sampling more information. Our results show how computational modeling of decisions and RTs support a deeper understanding of the hidden dynamics in cognition

Adjuvant gemcitabine after surgical removal of aggressive malignant mammary tumours in dogs

Canine mammary tumours are generally treated with surgery alone, despite the fact that 50% of them are malignant and many will eventually lead to recurrence or metastases. A prospective clinical trial in which dogs with aggressive mammary carcinoma of clinical stages IV and V were treated with surgical excision (n = 9) or with surgery and adjuvant weekly gemcitabine (n = 10) for at least four cycles was conducted. Gemcitabine was given as an intravenous infusion at the dose of 800 mg m−2. Aim of the study was to explore potential beneficial effects of gemcitabine on time to local recurrence (TTR), time to distant metastases (TTM) and overall survival (OS) in canine patients with operated mammary tumours bearing high risk for locoregional failure and distant metastases. Also, factors associated with OS, including neutering status, body weight, age, clinical stage at presentation, tumour size, histological grade and, in dogs receiving chemotherapy, the number of gemcitabine treatments, were investigated. Finally, acute toxicities related to chemotherapy and quality of life were assessed in dogs receiving gemcitabine. Dogs treated with surgery alone or surgery followed by gemcitabine had no difference in TTR, TTM or OS (P > 0.05). In the group of dogs receiving adjuvant chemotherapy, the number of gemcitabine treatments was positively correlated with OS (P = 0.017). Gemcitabine treatment was well tolerated, with no dogs experiencing clinically relevant haematological or gastrointestinal toxicity. Despite being safe at the present dose, gemcitabine chemotherapy as an adjunct treatment to surgical excision may not be recommended in dogs with aggressive mammary carcinom