An assessment of juvenile lake sturgeon movement and habitat use in the Namakan River of Northwestern Ontario

The Namakan River of Northwestern Ontario is home to a recovering population of lake sturgeon (Acipenser fulvescens). Although the adult portion of this population has been well studied in recent years, very little information has been available for the juvenile (< 61 cm) portion. This study was designed to gather baseline information focused primarily at locating "nursery areas" used by juvenile lake sturgeon. Netting at 5 locations returned catches ranging from 0.9 juveniles per net at the mouth of the Namakan River and Little Eva Lake to 4.1 juveniles per net in Bill Lake, about 14 km upstream from the river mouth. Movements of ten juvenile lake sturgeon caught in Bill Lake and later aged at 4-6 years were tracked and matched to local water depth and flow

A novel PCFT gene mutation (p.Cys66LeufsX99) causing hereditary folate malabsorption

Hereditary folate malabsorption (HFM) is a rare autosomal recessive disorder which is characterized by impaired intestinal folate malabsorption and impaired folate transport into the central nervous system. Mutations in the intestinal folate transporter PCFT have been reported previously in only 10 individuals with this disorder. The purpose of the current study was to describe the clinical phenotype and determine the molecular basis for this disorder in a family with four affected individuals. A consanguineous family of Pakistani origin with autosomal recessive HFM was ascertained and clinically phenotyped. After genetic linkage studies all coding exons of the PCFT gene were screened for mutations by direct sequencing. The clinical phenotype of four affected patients is described. Direct sequencing of PCFT revealed a novel homozygous frameshift mutation (c.194dupG) at a mononucleotide repeat in exon 1 predicted to result in a truncated protein (p.Cys66LeufsX99). This report extends current knowledge on the phenotypic manifestations of HFM and the PCFT mutation spectrum

Meeting the challenge of environmental data publication: an operational infrastructure and workflow for publishing data

Here we describe the defined workflow and its supporting infrastructure, which are used by the Natural Environment Research Council’s (NERC) Environmental Information Data Centre (EIDC) (http://​eidc.​ceh.​ac.​uk/​) to enable publication of environmental data in the fields of ecology and hydrology. The methods employed and issues discussed are also relevant to publication in other domains. By utilising a clearly defined workflow for data publication, we operate a fully auditable, quality controlled series of steps permitting publication of environmental data. The described methodology meets the needs of both data producers and data users, whose requirements are not always aligned. A stable, logically created infrastructure supporting data publication allows the process to occur in a well-managed and secure fashion, while remaining flexible enough to deal with a range of data types and user requirements. We discuss the primary issues arising from data publication, and describe how many of them have been resolved by the methods we have employed, with demonstrable results. In conclusion, we expand on future directions we wish to develop to aid data publication by both solving problems for data generators and improving the end-user experience

Implementation of a workflow for publishing citeable environmental data: successes, challenges and opportunities from a data centre perspective

In recent years, the development and implementation of a robust way to cite data have encouraged many previously sceptical environmental researchers to publish the data they create, thus ensuring that more data than ever are now open and available for re-use within and between research communities. Here, we describe a workflow for publishing citeable data in the context of the environmental sciences—an area spanning many domains and generating a vast array of heterogeneous data products. The processes and tools we have developed have enabled rapid publication of quality data products including datasets, models and model outputs which can be accessed, re-used and subsequently cited. However, there are still many challenges that need to be addressed before researchers in the environmental sciences fully accept the notion that datasets are valued outputs and time should be spent in properly describing, storing and citing them. Here, we identify current challenges such as citation of dynamic datasets and issues of recording and presenting citation metrics. In conclusion, whilst data centres may have the infrastructure, tools, resources and processes available to publish citeable datasets, further work is required before large-scale uptake of the services offered is achieved. We believe that once current challenges are met, data resources will be viewed similarly to journal publications as valued outputs in a researcher’s portfolio, and therefore both the quality and quantity of data published will increase

Investigation of second genetic hits at the BMPR2 locus as a modulator of disease progression in familial pulmonary arterial hypertension

BACKGROUND: Primary pulmonary arterial hypertension (PAH) is a potentially devastating condition resulting from occlusion of the pulmonary arterioles by the formation of vascular lesions. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type II (BMPR2) have been identified in both familial (FPAH) and idiopathic PAH. Mutant alleles are typically of low penetrance, indicating that other factors are required for the onset of PAH. Previous reports have suggested that the characteristic plexiform lesions in affected lungs are akin to neoplasia, showing monoclonal expansion and microsatellite instability. We hypothesized that in patients with germline mutations, BMPR2 might behave as a classic tumor suppressor gene, with somatic loss of the wild-type allele contributing to disease progression. METHODS AND RESULTS: To test this hypothesis, plexiform and concentric vascular lesions were serially microdissected from lung explant tissue derived from 7 FPAH cases. DNA was analyzed for loss of heterozygosity at BMPR2 and for microsatellite instability (MSI) at 5 loci. MSI was detected in 1 of 37 lesions at a single locus, BAT-26, whereas heterozygosity at BMPR2 was retained at all informative loci. We also describe a FPAH patient carrying biallelic constitutional missense mutations of BMPR2 who manifested disease at a stage and manner similar to heterozygous patients. CONCLUSIONS: Taken together, these data demonstrate that MSI is uncommon in FPAH and suggest that somatic loss of the remaining wild-type BMPR2 allele in heterozygous mutation carriers likely does not play a significant role in modulating the onset or progression of FPAH

Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses

To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteobacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5′-phosphosulfate reductase α-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no ^(15)NH^+_4 assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active ‘free-living’ population, and are not dependent on methane or ANME activity. We investigated the possibility of N_2 fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic Deltaproteobacteria. However, nifH expression was methane-dependent. ^(15)N_2 incorporation was not observed in single DSS cells, but was detected in single DSB cells. Interestingly, ^(15)N_2 incorporation in single DSB cells was methane-dependent, raising the possibility that DSB cells acquired reduced ^(15)N products from diazotrophic ANME while spatially coupled, and then subsequently dissociated. With this combined data set we address several outstanding questions in methane seep microbial ecosystems and highlight the benefit of measuring microbial activity in the context of spatial associations

Overcoming data scarcity of Twitter: using tweets as bootstrap with application to autism-related topic content analysis

Notwithstanding recent work which has demonstrated the potential of using Twitter messages for content-specific data mining and analysis, the depth of such analysis is inherently limited by the scarcity of data imposed by the 140 character tweet limit. In this paper we describe a novel approach for targeted knowledge exploration which uses tweet content analysis as a preliminary step. This step is used to bootstrap more sophisticated data collection from directly related but much richer content sources. In particular we demonstrate that valuable information can be collected by following URLs included in tweets. We automatically extract content from the corresponding web pages and treating each web page as a document linked to the original tweet show how a temporal topic model based on a hierarchical Dirichlet process can be used to track the evolution of a complex topic structure of a Twitter community. Using autism-related tweets we demonstrate that our method is capable of capturing a much more meaningful picture of information exchange than user-chosen hashtags.Comment: IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, 201

Profiling aerosol optical, microphysical and hygroscopic properties in ambient conditions by combining in situ and remote sensing

We present the In situ/Remote sensing aerosol Retrieval Algorithm (IRRA) that combines airborne in situ and lidar remote sensing data to retrieve vertical profiles of ambient aerosol optical, microphysical and hygroscopic properties, employing the ISORROPIA II model for acquiring the particle hygroscopic growth. Here we apply the algorithm on data collected from the Facility for Airborne Atmospheric Measurements (FAAM) BAe-146 research aircraft during the ACEMED campaign in the Eastern Mediterranean. Vertical profiles of aerosol microphysical properties have been derived successfully for an aged smoke plume near the city of Thessaloniki with aerosol optical depth of ∼0.4 at 532 nm, single scattering albedos of ∼0.9-0.95 at 550 nm and typical lidar ratios for smoke of ∼60-80 sr at 532 nm. IRRA retrieves highly hydrated particles above land, with 55 and 80% water volume content for ambient relative humidity of 80 and 90%, respectively. The proposed methodology is highly advantageous for aerosol characterization in humid conditions and can find valuable applications in aerosol-cloud interaction schemes. Moreover, it can be used for the validation of active space-borne sensors, as is demonstrated here for the case of CALIPSO

Ice formation and development in aged, wintertime cumulus over the UK: observations and modelling

In situ high resolution aircraft measurements of cloud microphysical properties were made in coordination with ground based remote sensing observations of a line of small cumulus clouds, using Radar and Lidar, as part of the Aerosol Properties, PRocesses And InfluenceS on the Earth's climate (APPRAISE) project. A narrow but extensive line (~100 km long) of shallow convective clouds over the southern UK was studied. Cloud top temperatures were observed to be higher than −8 °C, but the clouds were seen to consist of supercooled droplets and varying concentrations of ice particles. No ice particles were observed to be falling into the cloud tops from above. Current parameterisations of ice nuclei (IN) numbers predict too few particles will be active as ice nuclei to account for ice particle concentrations at the observed, near cloud top, temperatures (−7.5 °C). The role of mineral dust particles, consistent with concentrations observed near the surface, acting as high temperature IN is considered important in this case. It was found that very high concentrations of ice particles (up to 100 L−1) could be produced by secondary ice particle production providing the observed small amount of primary ice (about 0.01 L−1) was present to initiate it. This emphasises the need to understand primary ice formation in slightly supercooled clouds. It is shown using simple calculations that the Hallett-Mossop process (HM) is the likely source of the secondary ice. Model simulations of the case study were performed with the Aerosol Cloud and Precipitation Interactions Model (ACPIM). These parcel model investigations confirmed the HM process to be a very important mechanism for producing the observed high ice concentrations. A key step in generating the high concentrations was the process of collision and coalescence of rain drops, which once formed fell rapidly through the cloud, collecting ice particles which caused them to freeze and form instant large riming particles. The broadening of the droplet size-distribution by collision-coalescence was, therefore, a vital step in this process as this was required to generate the large number of ice crystals observed in the time available. Simulations were also performed with the WRF (Weather, Research and Forecasting) model. The results showed that while HM does act to increase the mass and number concentration of ice particles in these model simulations it was not found to be critical for the formation of precipitation. However, the WRF simulations produced a cloud top that was too cold and this, combined with the assumption of continual replenishing of ice nuclei removed by ice crystal formation, resulted in too many ice crystals forming by primary nucleation compared to the observations and parcel modelling