Results of precipitation monitoring at Yucca Mountain

This is the final report presenting precipitation data collected under task ORD-FYO4-007 “Precipitation Monitoring at Yucca Mountain”. This task acquired data using tipping bucket rain gauges to measure, with known accuracy, the accumulation and timing of precipitation in the vicinity of Yucca Mountain. Operation of the tipping bucket precipitation monitoring network was assumed by the Harry Reid Center for Environmental Studies (HRC) at the University of Nevada, Las Vegas (UNLV) in March of 2001. Precipitation monitoring data collection concluded June of 2008. All data presented in this report were collected during that time

Seasonal rates of benthic primary production in a Greenland fjord measured by aquatic eddy correlation

We present the first year-round estimates of benthic primary production at four contrasting shallow (3–22 m depth) benthic habitats in a southwest Greenland fjord. In situ measurements were performed using the noninvasive aquatic eddy-correlation (EC) oxygen (O2) flux method. A series of high-quality multiple-day EC data sets document the presence of a year-round productive benthic phototrophic community. The shallow-water sites were on average autotrophic during the spring and summer months, up to 43.6 mmol O2 m22 d21, and heterotrophic or close to metabolic balance during the autumn and winter. Substantial benthic gross primary production (GPP) was measured year-round. The highest GPP rates were measured during the spring, up to 5.7 mmol O2 m22 h21 (136.8 mmol O2 m22 d21), and even at low light levels (, 80 mmol quanta m22 s21) during late autumn and winter we measured rates of up to 1.8 mmol O2 m22 h21 (43.2 mmol O2 m22 d21) during peak irradiance. The benthic phototrophic communities responded seasonally to ambient light levels and exhibited year-round high photosynthetic efficiency. In situ downwelling irradiances as low as , 2 mmol quanta m22 s21 induced an autotrophic response and light saturation indices (Ik) were as low as 11 mmol quanta m22 s21 in the winter. On an annual timescale, the average areal rate of benthic GPP was 11.5 mol O2 m22 yr21, which is , 1.4 times higher than the integrated gross pelagic primary production of the , 30–50 m deep photic zone of the fjord. These results document the importance of benthic photosynthesis on an ecosystem level and indicate that the benthic phototrophic compartment should be accounted for when assessing carbon and nutrient budgets as well as responses of coastal Arctic ecosystems to climate change

Assessment of total organic carbon concentrations in two streams of Northwest Arkansas: Town Branch and Brush Creek

Within a stream, changes in flow rate and local environment can affect the total organic content (TOC) concentrations in the stream water and TOC delivery downstream to water supply reservoirs. Disinfection by-products (DBPs) result from various chemical reactions between chlorine, bromine, and organic carbon in raw water during the drinking water treatment process; DBPs are potential carcinogens and are regulated by the U.S. Environmental Protection Agency. In this project, we measured the TOC concentrations in two streams in the Beaver Lake Watershed: Town Branch and Brush Creek. We then compared TOC concentrations between the two streams and to that observed in streams draining in forested areas to determine if differences in mean concentrations might be related to the streams’ catchment. Finally, using instantaneous discharge at the time of sampling, we determined if TOC concentrations were significantly correlated to the volumetric flow of a stream. The data suggest that there is a positive linear relationship between the TOC concentration and the flow rate of a stream. While TOC concentrations did not vary between sites, TOC flux and yield were significantly different between the two streams

Pressure ulcer related pain in community populations: a prevalence survey.

BACKGROUND: Pressure ulcers are costly to the healthcare provider and can have a major impact on patient's quality of life. One of the most distressing symptoms reported is pain. There is very little published data on the prevalence and details of pain experienced by patients with pressure ulcers, particularly in community populations. The study was conducted in two community NHS sites in the North of England. METHODS: The aim was to estimate the prevalence of pressure area related pain within a community population. We also explored the type and severity of the pain and its association with pressure ulcer classification. A cross-sectional survey was performed of community nurses caseloads to identify adult patients with pressure ulcers and associated pain. Consenting patients then had a full pain assessment and verification of pressure ulcer grade. RESULTS: A total of 287 patients were identified with pressure ulcers (0.51 per 1000 adult population). Of the 176 patients who were asked, 133 (75.6%) reported pain. 37 patients consented to a detailed pain assessment. Painful pressure ulcers of all grades and on nearly all body sites were identified. Pain intensity was not related to number or severity of pressure ulcer. Both inflammatory and neuropathic pain were reported at all body sites however the proportion of neuropathic pain was greater in pressure ulcers on lower limbs. CONCLUSIONS: This study has identified the extent and type of pain suffered by community patients with pressure ulcers and indicates the need for systematic and regular pain assessment and treatment

Simple, robust eddy correlation amplifier for aquatic dissolved oxygen and hydrogen sulfide flux measurements

The aquatic application of the eddy correlation (EC) technique is growing more popular and is gradually becoming a standard method for resolving benthic O2 fluxes. By including the effects of the local hydrodynamics, the EC technique provides greater insight into the nature of benthic O2 exchange than traditional methods (i.e., benthic chambers and lander microprofilers). The growing popularity of the EC technique has led to a greater demand for easily accessible and robust EC instrumentation. Currently, the EC instrumentation is limited to two commercially available systems that are still in the development stage. Here, we present a robust, open source EC picoamplifier that is simple in design and can be easily adapted to both new and existing acoustic Doppler velocimeters (ADV). The picoamplifier has a response time of < 0.1 ms and features galvanic isolation that ensures very low noise contamination of the signal. It can be adjusted to accommodate varying ranges of microelectrode sensitivity as well as other types of amperometric microelectrodes. We show that the extracted flux values are not sensitive to reduced microelectrode operational ranges (i.e., lower resolution) and that no signal loss results from using either a 16- or 14-bit analog-to-digital converter. Finally, we demonstrate the capabilities of the picoamplifier with field studies measuring both dissolved O2 and H2S EC fluxes. The picoamplifier presented here consistently acquires high-quality EC data and provides a simple solution for those who wish to obtain EC instrumentation. The schematic of the amplifier’s circuitry is given in the Web Appendix

Sequence alignment, mutual information, and dissimilarity measures for constructing phylogenies

Existing sequence alignment algorithms use heuristic scoring schemes which cannot be used as objective distance metrics. Therefore one relies on measures like the p- or log-det distances, or makes explicit, and often simplistic, assumptions about sequence evolution. Information theory provides an alternative, in the form of mutual information (MI) which is, in principle, an objective and model independent similarity measure. MI can be estimated by concatenating and zipping sequences, yielding thereby the "normalized compression distance". So far this has produced promising results, but with uncontrolled errors. We describe a simple approach to get robust estimates of MI from global pairwise alignments. Using standard alignment algorithms, this gives for animal mitochondrial DNA estimates that are strikingly close to estimates obtained from the alignment free methods mentioned above. Our main result uses algorithmic (Kolmogorov) information theory, but we show that similar results can also be obtained from Shannon theory. Due to the fact that it is not additive, normalized compression distance is not an optimal metric for phylogenetics, but we propose a simple modification that overcomes the issue of additivity. We test several versions of our MI based distance measures on a large number of randomly chosen quartets and demonstrate that they all perform better than traditional measures like the Kimura or log-det (resp. paralinear) distances. Even a simplified version based on single letter Shannon entropies, which can be easily incorporated in existing software packages, gave superior results throughout the entire animal kingdom. But we see the main virtue of our approach in a more general way. For example, it can also help to judge the relative merits of different alignment algorithms, by estimating the significance of specific alignments.Comment: 19 pages + 16 pages of supplementary materia

Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells.

Steering the differentiation of induced pluripotent stem cells (iPSCs) toward specific cell types is crucial for patient-specific disease modeling and drug testing. This effort requires the capacity to predict and control when and how multipotent progenitor cells commit to the desired cell fate. Cell fate commitment represents a critical state transition or tipping point at which complex systems undergo a sudden qualitative shift. To characterize such transitions during iPSC to cardiomyocyte differentiation, we analyzed the gene expression patterns of 96 developmental genes at single-cell resolution. We identified a bifurcation event early in the trajectory when a primitive streak-like cell population segregated into the mesodermal and endodermal lineages. Before this branching point, we could detect the signature of an imminent critical transition: increase in cell heterogeneity and coordination of gene expression. Correlation analysis of gene expression profiles at the tipping point indicates transcription factors that drive the state transition toward each alternative cell fate and their relationships with specific phenotypic readouts. The latter helps us to facilitate small molecule screening for differentiation efficiency. To this end, we set up an analysis of cell population structure at the tipping point after systematic variation of the protocol to bias the differentiation toward mesodermal or endodermal cell lineage. We were able to predict the proportion of cardiomyocytes many days before cells manifest the differentiated phenotype. The analysis of cell populations undergoing a critical state transition thus affords a tool to forecast cell fate outcomes and can be used to optimize differentiation protocols to obtain desired cell populations

Quantifying tidally-driven benthic oxygen exchange across permeable sediments: An aquatic eddy correlation study

Continental shelves are predominately (~70%) covered with permeable, sandy sediments. While identified as critical sites for intense oxygen, carbon, and nutrient turnover, constituent exchange across permeable sediments remains poorly quantified. The central North Sea largely consists of permeable sediments and has been identified as increasingly at risk for developing hypoxia. Therefore, we investigate the benthic O2 exchange across the permeable North Sea sediments using a combination of in situ microprofiles, a benthic chamber, and aquatic eddy correlation. Tidal bottom currents drive the variable sediment O2 penetration depth (from ~3 to 8 mm) and the concurrent turbulence-driven 25-fold variation in the benthic sediment O2 uptake. The O2 flux and variability were reproduced using a simple 1-D model linking the benthic turbulence to the sediment pore water exchange. The high O2 flux variability results from deeper sediment O2 penetration depths and increased O2 storage during high velocities, which is then utilized during low-flow periods. The study reveals that the benthic hydrodynamics, sediment permeability, and pore water redox oscillations are all intimately linked and crucial parameters determining the oxygen availability. These parameters must all be considered when evaluating mineralization pathways of organic matter and nutrients in permeable sediments

Pilot feasibility randomized clinical trial of negative-pressure wound therapy versus usual care in patients with surgical wounds healing by secondary intention

Background Surgical wounds healing by secondary intention (SWHSI) are increasingly being treated with negative‐pressure wound therapy (NPWT) despite a lack of high‐quality research evidence regarding its clinical and cost‐effectiveness. This pilot feasibility RCT aimed to assess the methods for and feasibility of conducting a future definitive RCT of NPWT for the treatment of SWHSI. Methods Eligible consenting adult patients receiving care at the study sites (2 acute and 1 community) and with a SWHSI appropriate for NPWT or wound dressing treatment were randomized 1 : 1 centrally to receive NPWT or usual care (no NPWT). Participants were followed up every 1–2 weeks for 3 months. Feasibility (recruitment rate, time to intervention delivery) and clinical (time to wound healing) outcomes were assessed. Results A total of 248 participants were screened for eligibility; 40 (16·1 per cent) were randomized, 19 to NPWT and 21 to usual care. Twenty‐four of the 40 wounds were located on the foot. Participants received NPWT for a median of 18 (range 0–72) days. Two participants in the NPWT group never received the intervention and 14 received NPWT within 48 h of randomization. Five participants in the usual care group received NPWT during the study. Ten of the 40 wounds were deemed to have healed during the study. Conclusion A full‐scale RCT to investigate the clinical and cost‐effectiveness of NPWT for SWHSI is feasible. This study identified crucial information on recruitment rates and data collection methods to consider during the design of a definitive RCT. Registration number: ISRCTN12761776 (www.iscrtn.com

Oxygen fluxes beneath Arctic land-fast ice and pack ice: towards estimates of ice productivity

Sea-ice ecosystems are among the most extensive of Earth's habitats; yet its autotrophic and heterotrophic activities remain poorly constrained. We employed the in situ aquatic eddy-covariance (AEC) O-2 flux method and laboratory incubation techniques ((HCO3-)-C-14, [H-3] thymidine and [H-3] leucine) to assess productivity in Arctic sea-ice using different methods, in conditions ranging from land-fast ice during winter, to pack ice within the central Arctic Ocean during summer. Laboratory tracer measurements resolved rates of bacterial C demand of 0.003-0.166mmolCm(-2)day(-1) and primary productivity rates of 0.008-0.125mmolCm(-2)day(-1) for the different ice floes. Pack ice in the central Arctic Ocean was overall net autotrophic (0.002-0.063mmolCm(-2)day(-1)), whereas winter land-fast ice was net heterotrophic (-0.155mmol C m(-2) day(-1)). AEC measurements resolved an uptake of O-2 by the bottom-ice environment, from similar to-2mmolO(2)m(-2) day(-1) under winter land-fast ice to similar to-6mmolO(2)m(-2)day(-1) under summer pack ice. Flux of O-2-deplete meltwater and changes in water flow velocity masked potential biological-mediated activity. AEC estimates of primary productivity were only possible at one study location. Here, productivity rates of 1.3 +/- 0.9mmolO(2)m(-2)day(-1), much larger than concurrent laboratory tracer estimates (0.03mmolCm(-2)day(-1)), indicate that ice algal production and its importance within the marine Arctic could be underestimated using traditional approaches. Given careful flux interpretation and with further development, the AEC technique represents a promising new tool for assessing oxygen dynamics and sea-ice productivity in ice-covered regions.Peer reviewe