Ecosystem Services in Decision Making: Time to Deliver

Over the past decade, efforts to value and protect ecosystem services have been promoted by many as the last, best hope for making conservation mainstream – attractive and commonplace worldwide. In theory, if we can help individuals and institutions to recognize the value of nature, then this should greatly increase investments in conservation, while at the same time fostering human well-being. In practice, however, we have not yet developed the scientific basis, nor the policy and finance mechanisms, for incorporating natural capital into resource- and land-use decisions on a large scale. Here, we propose a conceptual framework and sketch out a strategic plan for delivering on the promise of ecosystem services, drawing on emerging examples from Hawai‘i. We describe key advances in the science and practice of accounting for natural capital in the decisions of individuals, communities, corporations, and governments

Ecosystem Services in Decision Making: Time to Deliver

Over the past decade, efforts to value and protect ecosystem services have been promoted by many as the last, best hope for making conservation mainstream – attractive and commonplace worldwide. In theory, if we can help individuals and institutions to recognize the value of nature, then this should greatly increase investments in conservation, while at the same time fostering human well-being. In practice, however, we have not yet developed the scientific basis, nor the policy and finance mechanisms, for incorporating natural capital into resource- and land-use decisions on a large scale. Here, we propose a conceptual framework and sketch out a strategic plan for delivering on the promise of ecosystem services, drawing on emerging examples from Hawai‘i. We describe key advances in the science and practice of accounting for natural capital in the decisions of individuals, communities, corporations, and governments

Yes, The Government Should Tax Soft Drinks: Findings from a Citizens’ Jury in Australia

Taxation has been suggested as a possible preventive strategy to address the serious public health concern of childhood obesity. Understanding the public’s viewpoint on the potential role of taxation is vital to inform policy decisions if they are to be acceptable to the wider community. A Citizens’ Jury is a deliberative method for engaging the public in decision making and can assist in setting policy agendas. A Citizens’ Jury was conducted in Brisbane, Australia in May 2013 to answer the question: Is taxation on food and drinks an acceptable strategy to the public in order to reduce rates of childhood obesity? Citizens were randomly selected from the electoral roll and invited to participate. Thirteen members were purposively sampled from those expressing interest to broadly reflect the diversity of the Australian public. Over two days, participants were presented with evidence on the topic by experts, were able to question witnesses and deliberate on the evidence. The jurors unanimously supported taxation on sugar-sweetened drinks but generally did not support taxation on processed meats, snack foods and foods eaten/ purchased outside the home. They also supported taxation on snack foods on the condition that traffic light labelling was also introduced. Though they were not specifically asked to deliberate strategies outside of taxation, the jurors strongly recommended more nutritional information on all food packaging using the traffic light and teaspoon labelling systems for sugar, salt and fat content. The Citizens’ Jury suggests that the general public may support taxation on sugar-sweetened drinks to reduce rates of obesity in children. Regulatory reforms of taxation on sugar-sweetened drinks and improved labelling of nutritional information on product packaging were strongly supported by all members of the jury. These reforms should be considered by governments to prevent childhood obesity and the future burden on society from the consequences of obesity

CIViCpy: A Python software evelopment and analysis toolkit for the CIViC knowledgebase

PURPOSE: Precision oncology depends on the matching of tumor variants to relevant knowledge describing the clinical significance of those variants. We recently developed the Clinical Interpretations for Variants in Cancer (CIViC; civicdb.org) crowd-sourced, expert-moderated, and open-access knowledgebase. CIViC provides a structured framework for evaluating genomic variants of various types (eg, fusions, single-nucleotide variants) for their therapeutic, prognostic, predisposing, diagnostic, or functional utility. CIViC has a documented application programming interface for accessing CIViC records: assertions, evidence, variants, and genes. Third-party tools that analyze or access the contents of this knowledgebase programmatically must leverage this application programming interface, often reimplementing redundant functionality in the pursuit of common analysis tasks that are beyond the scope of the CIViC Web application. METHODS: To address this limitation, we developed CIViCpy (civicpy.org), a software development kit for extracting and analyzing the contents of the CIViC knowledgebase. CIViCpy enables users to query CIViC content as dynamic objects in Python. We assess the viability of CIViCpy as a tool for advancing individualized patient care by using it to systematically match CIViC evidence to observed variants in patient cancer samples. RESULTS: We used CIViCpy to evaluate variants from 59,437 sequenced tumors of the American Association for Cancer Research Project GENIE data set. We demonstrate that CIViCpy enables annotation of \u3e 1,200 variants per second, resulting in precise variant matches to CIViC level A (professional guideline) or B (clinical trial) evidence for 38.6% of tumors. CONCLUSION: The clinical interpretation of genomic variants in cancers requires high-throughput tools for interoperability and analysis of variant interpretation knowledge. These needs are met by CIViCpy, a software development kit for downstream applications and rapid analysis. CIViCpy is fully documented, open-source, and available free online

'Pre-endoscopy point of care test (Simtomax- IgA/IgG-Deamidated Gliadin Peptide) for coeliac disease in iron deficiency anaemia: diagnostic accuracy and a cost saving economic model'.

BACKGROUND: International guidelines recommend coeliac serology in iron deficiency anaemia, and duodenal biopsy for those tested positive to detect coeliac disease. However, pre-endoscopy serology is often unavailable, thus committing endoscopists to take routine duodenal biopsies. Some endoscopists consider duodenal biopsy mandatory in anaemia to exclude other pathologies. We hypothesise that using a point of care test at endoscopy could fill this gap, by providing rapid results to target anaemic patients who require biopsies, and save costs by biopsy avoidance. We therefore assessed three key aspects to this hypothesis: 1) the availability of pre-endoscopy serology in anaemia; 2) the sensitivities and cost effectiveness of pre-endoscopy coeliac screening with Simtomax in anaemia; 3) whether other anaemia-related pathologies could be missed by this targeted-biopsy approach. METHODS: Group 1: pre-endoscopy serology availability was retrospectively analysed in a multicentre cohort of 934 anaemic patients at 4 UK hospitals. Group 2: the sensitivities of Simtomax, endomysial and tissue-transglutaminase antibodies were compared in 133 prospectively recruited patients with iron deficiency anaemia attending for a gastroscopy. The sensitivities were measured against duodenal histology as the reference standard in all patients. The cost effectiveness of Simtomax was calculated based on the number of biopsies that could have been avoided compared to an all-biopsy approach. Group 3: the duodenal histology of 153 patients presenting to a separate iron deficiency anaemia clinic were retrospectively reviewed. RESULTS: In group 1, serology was available in 361 (33.8 %) patients. In group 2, the sensitivity and negative predictive value (NPV) were 100 % and 100 % for Simtomax, 96.2 % and 98.9 % for IgA-TTG, and 84.6 % and 96.4 % for EMA respectively. In group 3, the duodenal histology found no causes for anaemia other than coeliac disease. CONCLUSION: Simtomax had excellent diagnostic accuracy in iron deficiency anaemia and was comparable to conventional serology. Duodenal biopsy did not identify any causes other than coeliac disease for iron deficiency anaemia, suggesting that biopsy avoidance in Simtomax negative anaemic patients is unlikely to miss other anaemia-related pathologies. Due to its 100 % NPV, Simtomax could reduce unnecessary biopsies by 66 % if only those with a positive Simtomax were biopsied, potentially saving £3690/100 gastroscopies. TRIAL REGISTRATION: The group 2 study was retrospectively registered with clinicaltrials.gov. Trial registration date: 13(th) July 2016; TRIAL REGISTRATION NUMBER: NCT02834429

The BLAST View of the Star Forming Region in Aquila (ell=45deg,b=0deg)

We have carried out the first general submillimeter analysis of the field towards GRSMC 45.46+0.05, a massive star forming region in Aquila. The deconvolved 6 deg^2 (3\degree X 2\degree) maps provided by BLAST in 2005 at 250, 350, and 500 micron were used to perform a preliminary characterization of the clump population previously investigated in the infrared, radio, and molecular maps. Interferometric CORNISH data at 4.8 GHz have also been used to characterize the Ultracompact HII regions (UCHIIRs) within the main clumps. By means of the BLAST maps we have produced an initial census of the submillimeter structures that will be observed by Herschel, several of which are known Infrared Dark Clouds (IRDCs). Our spectral energy distributions of the main clumps in the field, located at ~7 kpc, reveal an active population with temperatures of T~35-40 K and masses of ~10^3 Msun for a dust emissivity index beta=1.5. The clump evolutionary stages range from evolved sources, with extended HII regions and prominent IR stellar population, to massive young stellar objects, prior to the formation of an UCHIIR.The CORNISH data have revealed the details of the stellar content and structure of the UCHIIRs. In most cases, the ionizing stars corresponding to the brightest radio detections are capable of accounting for the clump bolometric luminosity, in most cases powered by embedded OB stellar clusters

The Lantern, 2010-2011

• The Graterford Department of Corrections • Visiting Room: Lewis Considers the Space & Time Continuum • String • The Tale of Lad Wadley • The Devout • One Moment in the Garden • Water, Focused and Tumbling • Bomber • Another • I Walked Home • Perhe • I Describe the Last Time My Parents Had Sex • Butterflies • Ship Without Fools • The Interview • Cyane • An Imaginary Portrait of Stella as a Young Girl • At the Farm Market in Early Autumn • Victor Jorgenson\u27s Photograph of the V-J Day Kiss • Lightning • The Citadel • Whenever You Come Home From School • It Came in a Dream • What I Know About Fission • Please Don\u27t Fire Me for Saying Such Things • Femina Irata • Thank You For Shopping • Sunday, November 27th • An Introduction to The Lifestyle • Laid-Off Perception • Good-Night, Sweet Prince • Requiem for a Marriage • Gertrude\u27s Book • Passing • Elk Run II • Shady Tides • A Quiet House • Tell Him. A Manual • Silence • Google This • The Dinner Table Dance • The Inevitable Extinction of Filing Cabinets • Chateau d\u27If • Man Smoking in Charcoal • Inside Auschwitz • Bark Glow • Anticipation • Look Up • Major News Networks • Others Wage War • Insert Bible Verse Here • The Empress • Candy Castle • Venice, Italy • Quebec • Bhutanese Child • Jumper • Pomegranates • Cover Image: Octopus Hathttps://digitalcommons.ursinus.edu/lantern/1176/thumbnail.jp

Evaluation of integrin αvβ6 cystine knot PET tracers to detect cancer and idiopathic pulmonary fibrosis.

Advances in precision molecular imaging promise to transform our ability to detect, diagnose and treat disease. Here, we describe the engineering and validation of a new cystine knot peptide (knottin) that selectively recognizes human integrin αvβ6 with single-digit nanomolar affinity. We solve its 3D structure by NMR and x-ray crystallography and validate leads with 3 different radiolabels in pre-clinical models of cancer. We evaluate the lead tracer's safety, biodistribution and pharmacokinetics in healthy human volunteers, and show its ability to detect multiple cancers (pancreatic, cervical and lung) in patients at two study locations. Additionally, we demonstrate that the knottin PET tracers can also detect fibrotic lung disease in idiopathic pulmonary fibrosis patients. Our results indicate that these cystine knot PET tracers may have potential utility in multiple disease states that are associated with upregulation of integrin αvβ6

Genome modeling system: A knowledge management platform for genomics

In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms