Conversion of boreal forests to agricultural systems: soil microbial responses along a land-conversion chronosequence.

Background: Boreal regions are warming at more than double the global average, creating opportunities for the northward expansion of agriculture. Expanding agricultural production in these regions will involve the conversion of boreal forests to agricultural fields, with cumulative impacts on soil microbial communities and associated biogeochemical cycling processes. Understanding the magnitude or rate of change that will occur with these biological processes will provide information that will enable these regions to be developed in a more sustainable manner, including managing carbon and nitrogen losses.

The founding charter of the Omic Biodiversity Observation Network (Omic BON).

Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge.

Using metatranscriptomics to better understand the role of microbial nitrogen cycling in coastal sediment benthic flux denitrification efficiency.

Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus.

Temporal profiling resolves the drivers of microbial nitrogen cycling variability in coastal sediments.

Here we describe the potential for sediment microbial nitrogen-cycling gene (DNA) and activity (RNA) abundances to spatially resolve coastal areas impacted by seasonal variability in external nutrient inputs. Three sites were chosen within a nitrogen-limited embayment, Port Phillip Bay (PPB), Australia that reflect variability in both proximity to external nutrient inputs and the dominant form of available nitrogen. At three sediment depths (0-1; 1-5; 5-10 cm) across a 2 year study key genes involved in nitrification (archaeal amoA and bacterial β-amoA), nitrite reduction (clade I nirS and cluster I nirK, archaeal nirK-a), anaerobic oxidation of ammonium (anammox 16S rRNA phylogenetic marker) and nitrogen fixation (nifH) were quantified.

Oral health in primary care: Integration of enhanced oral health education in a nurse practitioner residency program.

Access to oral health care is challenging, especially for vulnerable populations and those in rural and underserved areas. The purpose of this brief report is to discuss the implementation strategies of enhanced content in oral health educational materials and share results of acquisition of knowledge and confidence in oral health content by residents in a nurse practitioner residency program. The method included the use of 3 surveys of 34 questions administered at different time points measuring confidence levels and sustainability.

The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada.

Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.

Web services for data warehouses: OMOP and PCORnet on i2b2.

Objective: Healthcare organizations use research data models supported by projects and tools that interest them, which often means organizations must support the same data in multiple models. The healthcare research ecosystem would benefit if tools and projects could be adopted independently from the underlying data model. Here, we introduce the concept of a reusable application programming interface (API) for healthcare and show that the i2b2 API can be adapted to support diverse patient-centric data models.

Primer selection influences abundance estimates of ammonia oxidizing archaea in coastal marine sediments.

Quantification of the α-subunit of ammonia monooxygenase (amoA) through PCR is an established technique for estimating the abundance of ammonia oxidizing archaea (AOA) in environmental samples. This study quantified AOA with two established primer sets in 1 cm increments from the sediment surface (0-1 cm) to a depth of 10 cm at two locations within Port Phillip Bay (PPB), Australia. Primer choice had a significant effect on within sample estimates of AOA with copy numbers ranging from 10 to 10 copies per ng DNA.

Combining clinical and genomics queries using i2b2 - Three methods.

We are fortunate to be living in an era of twin biomedical data surges: a burgeoning representation of human phenotypes in the medical records of our healthcare systems, and high-throughput sequencing making rapid technological advances. The difficulty representing genomic data and its annotations has almost by itself led to the recognition of a biomedical "Big Data" challenge, and the complexity of healthcare data only compounds the problem to the point that coherent representation of both systems on the same platform seems insuperably difficult. We investigated the capability for complex, integrative genomic and clinical queries to be supported in the Informatics for Integrating Biology and the Bedside (i2b2) translational software package.

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database.

Background: Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The 'Biomes of Australian Soil Environments' (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function.

A numerical similarity approach for using retired Current Procedural Terminology (CPT) codes for electronic phenotyping in the Scalable Collaborative Infrastructure for a Learning Health System (SCILHS).

Background: Interoperable phenotyping algorithms, needed to identify patient cohorts meeting eligibility criteria for observational studies or clinical trials, require medical data in a consistent structured, coded format. Data heterogeneity limits such algorithms' applicability. Existing approaches are often: not widely interoperable; or, have low sensitivity due to reliance on the lowest common denominator (ICD-9 diagnoses).

Taking advantage of continuity of care documents to populate a research repository.

Objective: Clinical data warehouses have accelerated clinical research, but even with available open source tools, there is a high barrier to entry due to the complexity of normalizing and importing data. The Office of the National Coordinator for Health Information Technology's Meaningful Use Incentive Program now requires that electronic health record systems produce standardized consolidated clinical document architecture (C-CDA) documents. Here, we leverage this data source to create a low volume standards based import pipeline for the Informatics for Integrating Biology and the Bedside (i2b2) clinical research platform.

Whole genome sequencing reveals potential targets for therapy in patients with refractory KRAS mutated metastatic colorectal cancer.

Background: The outcome of patients with metastatic colorectal carcinoma (mCRC) following first line therapy is poor, with median survival of less than one year. The purpose of this study was to identify candidate therapeutically targetable somatic events in mCRC patient samples by whole genome sequencing (WGS), so as to obtain targeted treatment strategies for individual patients.

Methods: Four patients were recruited, all of whom had received > 2 prior therapy regimens.

Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma.

Advanced cholangiocarcinoma continues to harbor a difficult prognosis and therapeutic options have been limited. During the course of a clinical trial of whole genomic sequencing seeking druggable targets, we examined six patients with advanced cholangiocarcinoma. Integrated genome-wide and whole transcriptome sequence analyses were performed on tumors from six patients with advanced, sporadic intrahepatic cholangiocarcinoma (SIC) to identify potential therapeutically actionable events.

Simultaneous characterization of somatic events and HPV-18 integration in a metastatic cervical carcinoma patient using DNA and RNA sequencing.

Objective: Integration of carcinogenic human papillomaviruses (HPVs) into the host genome is a significant tumorigenic factor in specific cancers including cervical carcinoma. Although major strides have been made with respect to HPV diagnosis and prevention, identification and development of efficacious treatments for cervical cancer patients remains a goal and thus requires additional detailed characterization of both somatic events and HPV integration. Given this need, the goal of this study was to use the next generation sequencing to simultaneously evaluate somatic alterations and expression changes in a patient's cervical squamous carcinoma lesion metastatic to the lung and to detect and analyze HPV infection in the same sample.

A pilot study using next-generation sequencing in advanced cancers: feasibility and challenges.

Purpose: New anticancer agents that target a single cell surface receptor, up-regulated or amplified gene product, or mutated gene, have met with some success in treating advanced cancers. However, patients' tumors still eventually progress on these therapies. If it were possible to identify a larger number of targetable vulnerabilities in an individual's tumor, multiple targets could be exploited with the use of specific therapeutic agents, thus possibly giving the patient viable therapeutic alternatives.

Ectomycorrhizal fungi contribute to soil organic matter cycling in sub-boreal forests.

Soils of northern temperate and boreal forests represent a large terrestrial carbon (C) sink. The fate of this C under elevated atmospheric CO2 and climate change is still uncertain. A fundamental knowledge gap is the extent to which ectomycorrhizal fungi (EMF) and saprotrophic fungi contribute to C cycling in the systems by soil organic matter (SOM) decomposition.

Long insert whole genome sequencing for copy number variant and translocation detection.

As next-generation sequencing continues to have an expanding presence in the clinic, the identification of the most cost-effective and robust strategy for identifying copy number changes and translocations in tumor genomes is needed. We hypothesized that performing shallow whole genome sequencing (WGS) of 900-1000-bp inserts (long insert WGS, LI-WGS) improves our ability to detect these events, compared with shallow WGS of 300-400-bp inserts. A priori analyses show that LI-WGS requires less sequencing compared with short insert WGS to achieve a target physical coverage, and that LI-WGS requires less sequence coverage to detect a heterozygous event with a power of 0.

Natural killer cell-activating receptor NKG2D mediates innate immune targeting of allogeneic neural progenitor cell grafts.

Cell replacement therapy holds promise for a number of untreatable neurological or psychiatric diseases but the immunogenicity of cellular grafts remains controversial. Emerging stem cell and reprogramming technologies can be used to generate autologous grafts that minimize immunological concerns but autologous grafts may carry an underlying genetic vulnerability that reduces graft efficacy or survival. Healthy allogeneic grafts are an attractive and commercially scalable alternative if immunological variables can be controlled.

Apps to display patient data, making SMART available in the i2b2 platform.

The Substitutable Medical Apps, Reusable Technologies (SMART) project provides a framework of core services to facilitate the use of substitutable health-related web applications. The platform offers a common interface used to "SMART-ready" health IT systems allowing any SMART application to be able to interact with those systems. At Partners Healthcare, we have SMART-enabled the Informatics for Integrating Biology and the Bedside (i2b2) open source analytical platform, enabling the use of SMART applications directly within the i2b2 web client.

Fungal endophytes of the obligate parasitic dwarf mistletoe Arceuthobium americanum (Santalaceae) act antagonistically in vitro against the native fungal pathogen Cladosporium (Davidiellaceae) of their host.

Premise Of The Study: Endophytic fungi likely occur in all plants, yet little is known about those of parasitic plants, despite their potential to influence parasite success. Arceuthobium americanum is a parasitic angiosperm that greatly compromises the North American timber industry. We hypothesized that (1) A.