The characterization and role of aeolian deposition on water quality, McMurdo Dry Valleys, Antarctica

The connection of ecosystems by wind-driven transport of material has become a topic of increasing interest and importance. Less than 1% of dust transported worldwide is exported to the Southern Ocean and Antarctic cryosphere; however, aeolian transport on the Antarctic continent is predominantly locally derived from the abrasion of bedrock. The deposition of the aeolian material is integral to nutrient and solute dispersal in the Antarctic ecosystem. This is particularly true in the ice-free areas of Antarctica, such as the McMurdo Dry Valleys (MDV), where aeolian material deposited in the aquatic system is solubilized during the melt season. The material is predominantly locally-derived from the abrasion of bedrock. In this study, a two-step leaching experiment simulates the melt season and we quantify the flux of solutes and nutrients to the aquatic ecosystem. Soluble salts were removed from the aeolian material first during cold water leaching followed by an increase in carbonate and silicate dissolution during freeze–thaw. Major ion fluxes on glaciers and lakes are at least two orders of magnitude greater than nutrient fluxes. However, the fluxes derived from these experiments are less than the estimated flux from streams to lakes and probably represent minima. Aeolian redistribution of local soils is important because they are the only source of new solutes and nutrients to the aquatic ecosystem of the MDV

Emerging aspects of oesophageal and gastro-oesophageal junction cancer histopathology – an update for the surgical oncologist

Adenocarcinoma of the oesophagus and gastro-oesophageal junction are rapidly increasing in incidence and have a well described sequence of carcinogenesis: the Barrett's metaplasia-dysplasia-adenocarcinoma sequence. During recent years there have been changes in the knowledge surrounding disease progression, cancer management and histopathology specimen reporting. Tumours around the gastro-oesophageal junction (GOJ) pose several specific challenges. Numerous difficulties arise when the existing TNM staging systems for gastric and oesophageal cancers are applied to GOJ tumours. The issues facing the current TNM staging and GOJ tumour classification systems are reviewed in this article. Recent evidence regarding the importance of several histopathologically derived prognostic factors, such as circumferential resection margin status and lymph node metastases, have implications for specimen reporting. With the rising use of multimodal treatments for oesophageal cancer it is important that the response of the tumour to this therapy is carefully documented pathologically. In addition, several controversial and novel areas such as endoscopic mucosal resection, lymph node micrometastases and the sentinel node concept are being studied. We aim to review these aspects, with special relevance to oesophageal and gastro-oesophageal cancer specimen reporting, to update the surgical oncologist with an interest in upper gastrointestinal cancer

Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing

© 2008 Huse et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Genetics 4 (2008): e1000255, doi:10.1371/journal.pgen.1000255.Massively parallel pyrosequencing of hypervariable regions from small subunit ribosomal RNA (SSU rRNA) genes can sample a microbial community two or three orders of magnitude more deeply per dollar and per hour than capillary sequencing of full-length SSU rRNA. As with full-length rRNA surveys, each sequence read is a tag surrogate for a single microbe. However, rather than assigning taxonomy by creating gene trees de novo that include all experimental sequences and certain reference taxa, we compare the hypervariable region tags to an extensive database of rRNA sequences and assign taxonomy based on the best match in a Global Alignment for Sequence Taxonomy (GAST) process. The resulting taxonomic census provides information on both composition and diversity of the microbial community. To determine the effectiveness of using only hypervariable region tags for assessing microbial community membership, we compared the taxonomy assigned to the V3 and V6 hypervariable regions with the taxonomy assigned to full-length SSU rRNA sequences isolated from both the human gut and a deep-sea hydrothermal vent. The hypervariable region tags and full-length rRNA sequences provided equivalent taxonomy and measures of relative abundance of microbial communities, even for tags up to 15% divergent from their nearest reference match. The greater sampling depth per dollar afforded by massively parallel pyrosequencing reveals many more members of the “rare biosphere” than does capillary sequencing of the full-length gene. In addition, tag sequencing eliminates cloning bias and the sequences are short enough to be completely sequenced in a single read, maximizing the number of organisms sampled in a run while minimizing chimera formation. This technique allows the cost-effective exploration of changes in microbial community structure, including the rare biosphere, over space and time and can be applied immediately to initiatives, such as the Human Microbiome Project.Woods Hole Center for Oceans and Human Health from the National Institutes of Health and National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724-J Stegeman PI to MLS). NIH Director's Pioneer Award and Doris Duke Distinguished Clinical Scientist Award to DAR

African-Americans and the Administration of Justice

The status of African Americans in relationship to the administration of justice has improved since the 1940s. Significantly, however, researchers continue to find racial discrimination and racial disadvantage operating in various aspects of the criminal justice process in numerous jurisdictions. Such findings are unacceptable in a society that claims to honor equal justice under law. This article is reprinted from Summary, Volume 1 of the Assessment of the Status of African-Americans series, published in 1990 by the William Monroe Trotter Institute, University of Massachusetts at Boston, and edited by Wornie L. Reed. Materials included in the article were adapted from papers submitted by members of the Assessment of the Status of African-Americans Study Group on Political Participation and the Administration of Justice

VAMPS : a website for visualization and analysis of microbial population structures

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 15 (2014): 41, doi:10.1186/1471-2105-15-41.The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 105–108 reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing. We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu webcite) to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators’ private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships. VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next-generation sequence data. Any web-capable device can be used to upload, process, explore, and extract data and results from VAMPS. VAMPS encourages researchers to share sequence and metadata, and fosters collaboration between researchers of disparate biomes who recognize common patterns in shared data.Funding provided by the National Science Foundation [grant NSF/BDI 0960626 to SMH] and the Sloan Foundation through a collaborative project with the Microbiology of the Built Environment program

Impact of anthropogenic disturbance on the chemistry of a small urban pond

Mirror Lake, one of the scenic locations on The Ohio State University\u27s campus, experiences an intense bioturbation event as part of an annual tradition revolving around the rivalry football game against the University of Michigan. This tradition involves thousands of students jumping into the lake over one night in the week leading up to the football game. Water samples were collected from several locations in the lake before, during, and after the Mirror Lake Jump to determine the impact of this event on lake water chemistry. There were significant and systematic increases in the concentrations of Na+, K+, Cl−, total nitrogen, ammonia, and dissolved organic carbon (DOC) associated with the jump, especially in the eastern side of the lake where most of the students entered. Over the 3-h period from 10 p.m. to 1 a.m. on the eastern side of the lake, Na+, K+, and Cl− concentrations increased by about 2–4 ppm, 1.5–3 ppm, and 4–6 ppm, respectively. The total nitrogen concentration increased about five to six fold, from 450–500 ppb to 2300–2800 ppb over the height of the event on the eastern side of the lake. Similar increases were observed for DOC, increasing from 3.6 to 18 ppm. This DOC increase was coincident with a 5‰ shift in δ13C, from a mean of around −28‰ in the early hours of the evening to a maximum of −23‰, implying a large influx of isotopically heavy carbon into the lake. Ammonia concentrations varied substantially from year to year, but always showed a systematic increase in concentration during the event. Smaller changes in major ion and nutrient concentrations were observed in the middle and western side of the lake, where fewer students entered the lake. The changes in concentration and the timing and spatial distribution of these changes are primarily attributed to anthropogenic input from jumpers in the form of bodily fluids (e.g., evaporated sweat, sebum and urine). Over a single night, these anthropogenic event inputs represent roughly 10% of the annual nitrogen budget of the lake, emphasizing the direct impact humans can have on urban water bodies on short time scales

DBT-enhanced cognitive-behavioral treatment for trichotillomania: A randomized controlled trial

Background and aims: Limited treatment options are available for trichotillomania (TTM) and most have modest outcomes. Suboptimal treatment results may be due to the failure of existing approaches to address all TTM styles. Methods: Thirty-eight DSM-IV TTM participants were randomly assigned across two study sites to Dialectical Behavior Therapy (DBT) -enhanced cognitive-behavioral treatment (consisting of an 11-week acute treatment and 3-month maintenance treatment) or a minimal attention control (MAC) condition. MAC participants had active treatment after the 11-week control condition. Follow-up study assessments were conducted three and six months after the maintenance period. Results: Open trial treatment resulted in significant improvement in TTM severity, emotion regulation (ER) capacity, experiential avoidance, anxiety and depression with changes generally maintained over time. In the randomized controlled trial, those with active treatment had greater improvement than those in the MAC condition for both TTM severity and ER capacity. Correlations between changes in TTM severity and ER capacity were not reported at post-treatment but did occur in maintenance and follow-up indicating reduced TTM severity with improved ER capacity. Conclusions: DBT-enhanced cognitive-behavioral treatment is a promising treatment for TTM. Future studies should compare this approach to other credible treatment interventions and investigate the efficacy of this approach in more naturalistic samples with greater comorbidity

Family nurture intervention (FNI): methods and treatment protocol of a randomized controlled trial in the NICU

The stress that results from preterm birth, requisite acute care and prolonged physical separation in the Neonatal Intensive Care Unit (NICU) can have adverse physiological/psychological effects on both the infant and the mother. In particular, the experience compromises the establishment and maintenance of optimal mother-infant relationship, the subsequent development of the infant, and the mother's emotional well-being. These findings highlight the importance of investigating early interventions that are designed to overcome or reduce the effects of these environmental insults and challenges. This study is a randomized controlled trial (RCT) with blinded assessment comparing Standard Care (SC) with a novel Family Nurture Intervention (FNI). FNI targets preterm infants born 26-34 weeks postmenstrual age (PMA) and their mothers in the NICU. The intervention incorporates elements of mother-infant interventions with known efficacy and organizes them under a new theoretical context referred to collectively as calming activities. This intervention is facilitated by specially trained Nurture Specialists in three ways: 1) In the isolette through calming interactions between mother and infant via odor exchange, firm sustained touch and vocal soothing, and eye contact; 2) Outside the isolette during holding and feeding via the Calming Cycle; and 3) through family sessions designed to engage help and support the mother. In concert with infant neurobehavioral and physiological assessments from birth through 24 months corrected age (CA), maternal assessments are made using standard tools including anxiety, depression, attachment, support systems, temperament as well as physiological stress parameters. Quality of mother-infant interaction is also assessed. Our projected enrolment is 260 families (130 per group). The FNI is designed to increase biologically important activities and behaviors that enhance maternally-mediated sensory experiences of preterm infants, as well as infant-mediated sensory experiences of the mother. Consequently, we are enlarging the testing of preterm infant neurodevelopment beyond that of previous research to include outcomes related to mother-infant interactions and mother-infant co-regulation. Our primary objective is to determine whether repeated engagement of the mother and her infant in the intervention's calming activities will improve the infant's developmental trajectory with respect to multiple outcomes. Our secondary objective is to assess the effectiveness of FNI in the physiological and psychological co-regulation of the mother and infant. We include aspects of neurodevelopment that have not been comprehensively measured in previous NICU interventions. Trial Registration: ClinicalTrials.gov: NCT0143926

Atomic Resonance and Scattering

Contains reports on eight research projects.National Science Foundation (Grant PHY79-09743)National Bureau of Standards (Grant NB-8-NAHA-3017)Joint Services Electronics Program (Contract DAAG29-80-C-0104)National Science Foundation (Grant PHY82-10486)U.S. Navy - Office of Naval Research (Contract N00014-79-C-0183)National Science Foundation (Grant CHE79-02967-A04)U.S. Air Force - Office of Scientific Research (Contract AFOSR-81-0067)Joint Services Electronics Program (Contract DAAG29-83-K-0003