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The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated byDNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2333 genera (17%). A “first pass” angiospermtree of lifewas inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactivepresentation in the KewTree of Life Explorer. This species treewas generated using methods thatwere rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of theworld’s natural history collections.

Background Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics. SoyKB is designed to handle the management and integration of soybean genomics, transcriptomics, proteomics and metabolomics data along with annotation of gene function and biological pathway. It contains information on four entities, namely genes, microRNAs, metabolites and single nucleotide polymorphisms (SNPs). Methods SoyKB has many useful tools such as Affymetrix probe ID search, gene family search, multiple gene/metabolite search supporting co-expression analysis, and protein 3D structure viewer as well as download and upload capacity for experimental data and annotations. It has four tiers of registration, which control different levels of access to public and private data. It allows users of certain levels to share their expertise by adding comments to the data. It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, producers and consumers. Conclusions SoyKB addresses the increasing need of the soybean research community to have a one-stop-shop functional and translational omics web resource for information retrieval and analysis in a user-friendly way. SoyKB can be publicly accessed at http://soykb.org/ .

Significant controversy surrounds the use of hydraulic fracturing (fracking) in oil and gas extraction in the United States. To address some of these concerns, states are leading the charge by regulating the process. Yet, variations exist in state regulatory approaches, and it is still unclear what drives these differences. Thus, this research applies policy subsystem theory to examine original interview data to determine what may cause these variations in regulations through an examination of Colorado, Wyoming, and Louisiana. This research finds that policy subsystem theory is useful in explaining this variation. In particular, the position of agency staff and privileged stakeholder groups, often industry related, help to explain why Colorado has a much stronger regulatory program than Louisiana. In comparison, Wyoming’s stringent regulations represent the anomaly in this case, but the results of this research suggest that this dominant energy subsystem will likely not be setting any pro-environment trends going forward. Environmental Practice 16: 102–112 (2014)

Extant literature demonstrates that interest groups impact regulatory outcomes at each stage in the rulemaking process. It is unclear whether earlier involvement during the pre-proposal stage affects a group’s ability to influence outcomes during the notice and comment stage as well. This research addresses this gap, through an analysis of three case studies of rulemakings completed at the Environmental Protection Agency. The original interviews and public comment analysis illustrate a relationship between earlier involvement and influence during the notice and comment stage. Those interviewees that participated during the pre-proposal stage were more successful in receiving rule changes than those that did not. This suggests that scholars should analyze interest group involvement and impact across the rulemaking process to more effectively explain rulemaking outcomes and clarify group influence.

The United States Environmental Protection Agency (EPA) has been considered one of the most innovative federal agencies in the nation, and the agency recently has employed a new stakeholder engagement practice in rule makings termed shuttle diplomacy. Though the agency has long been experimenting with new stakeholder practices, it is unclear what factors explain the agency’s decision to settle on shuttle diplomacy. This study conducts original interviews with senior career civil servants at the EPA to unpack this decision-making process. These data are then structured by applying Toddi Steelman’s (2010) implementing innovation framework so as to assess what factors are most impactful in the adoption of this new innovative procedure at the EPA. This research suggests that Steelman’s structure and individual variable are of value in explaining the EPA’s rationale for adopting this new practice. Finally, this research discusses the implications of this approach and the practical and political constraints that impact its use. Environmental Practice 16: 171–181 (2014)

We sought to identify factors increasing the odds of ED utilization among intellectually disabled (ID) adults and differentiate their discharge diagnoses from the general adult ED population. This was a retrospective, observational open cohort study of all ID adults residing at an intermediate care facility and their ED visits to a tertiary center (January 1, 2007–July 30, 2008). We abstracted from the intermediate care facility database subjects' demographic, ID, health and adaptive status variables, and their requirement of ED care/hospitalization. We obtained from the hospital database the primary International Classification of Diseases 9 ED/hospital discharge diagnoses for the study and general adult population. Using multivariate logistic regression, we computed odds ratios (OR) for ED utilization/hospitalization in the cohort. Using the conditional large-sample binomial test, we differentiated the study and general populations' discharge diagnoses. A total of 433 subjects met the inclusion criteria. Gastrostomy/jejunostomy increased the odds of ED utilization (OR, 4.16; confidence interval [CI], 1.64-10.58). Partial help to feed (OR, 2.59; CI, 1.14-5.88), gastrostomy/jejunostomy (OR, 3.26; CI, 1.30-8.18), and increasing number of prescribed medications (OR, 1.08; CI, 1.03-1.14) increased the odds of hospitalization. Auditory impairment (OR, 0.45; CI, 0.23-0.88) decreased the odds of hospitalization. For ED discharge diagnoses, ID adults were more likely ( P < .05) than the general population to have diagnoses among digestive disorders and ill-defined symptoms/signs. For hospital discharge diagnoses, ID adults were more likely ( P < .05) to have diagnoses among infectious/parasitic, nervous system, and respiratory disorders. Among ID adults, feeding status increased the odds of ED utilization, feeding status, and increasing number of prescribed medications of that hospitalization. Intellectually disabled adults' discharge diagnoses differed significantly from the general adult ED population.

This study provides descriptive information and 2-year outcome data on the first intensive, outpatient, coping skills training program for forward-deployed troops in the Western Pacific Ocean region. Established in February 2003 by the Mental Health Department of the U.S. Naval Hospital in Okinawa, Japan, the Outpatient Crisis Prevention Program was designed as a multidisciplinary training program to reduce anxiety and depression and to enhance the coping skills of active duty personnel. This study describes the rationale for creating the program, the patient population, and treatment outcome data collected during the first 2 years. The Beck Depression Inventory II and the Beck Anxiety Inventory were administered as pretraining and posttraining measures to patients who completed the program between February 2003 and February 2005 (N = 326). Results revealed that the Outpatient Crisis Prevention Program was effective in reducing depression and anxiety symptoms and promoting healthy coping behaviors among participants. Follow-up data indicated that gains were maintained 1 month after treatment.

Extant literature demonstrates that interest groups impact regulatory outcomes at each stage in the rulemaking process. It is unclear whether earlier involvement during the pre-proposal stage affects a group's ability to influence outcomes during the notice and comment stage as well. This research addresses this gap, through an analysis of three case studies of rulemakings completed at the Environmental Protection Agency. The original interviews and public comment analysis illustrate a relationship between earlier involvement and influence during the notice and comment stage. Those interviewees that participated during the pre-proposal stage were more successful in receiving rule changes than those that did not. This suggests that scholars should analyze interest group involvement and impact across the rulemaking process to more effectively explain rulemaking outcomes and clarify group influence.