Do Clouds Save the Great Barrier Reef? Satellite Imagery Elucidates the Cloud-SST Relationship at the Local Scale

Evidence of global climate change and rising sea surface temperatures (SSTs) is now well documented in the scientific literature. With corals already living close to their thermal maxima, increases in SSTs are of great concern for the survival of coral reefs. Cloud feedback processes may have the potential to constrain SSTs, serving to enforce an “ocean thermostat” and promoting the survival of coral reefs. In this study, it was hypothesized that cloud cover can affect summer SSTs in the tropics. Detailed direct and lagged relationships between cloud cover and SST across the central Great Barrier Reef (GBR) shelf were investigated using data from satellite imagery and in situ temperature and light loggers during two relatively hot summers (2005 and 2006) and two relatively cool summers (2007 and 2008). Across all study summers and shelf positions, SSTs exhibited distinct drops during periods of high cloud cover, and conversely, SST increases during periods of low cloud cover, with a three-day temporal lag between a change in cloud cover and a subsequent change in SST. Cloud cover alone was responsible for up to 32.1% of the variation in SSTs three days later. The relationship was strongest in both El Niño (2005) and La Niña (2008) study summers and at the inner-shelf position in those summers. SST effects on subsequent cloud cover were weaker and more variable among study summers, with rising SSTs explaining up to 21.6% of the increase in cloud cover three days later. This work quantifies the often observed cloud cooling effect on coral reefs. It highlights the importance of incorporating local-scale processes into bleaching forecasting models, and encourages the use of remote sensing imagery to value-add to coral bleaching field studies and to more accurately predict risks to coral reefs

Pharmacy Handbook 2009

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Adaptive carbon export response to warming in the Sargasso Sea

Ocean ecosystem models predict that warming and increased surface ocean stratification will trigger a series of ecosystem events, reducing the biological export of particulate carbon to the ocean interior. We present a nearly three-decade time series from the open ocean that documents a biological response to ocean warming and nutrient reductions wherein particulate carbon export is maintained, counter to expectations. Carbon export is maintained through a combination of phytoplankton community change to favor cyanobacteria with highcellular carbon-to-phosphorus ratios and enhanced shallow phosphorus recycling leading to increased nutrient use efficiency. These results suggest that surface ocean ecosystems may be more responsive and adapt more rapidly to changes in the hydrographic system than is currently envisioned in earth ecosystem models, with positive consequences for ocean carbon uptake

Cognitive flexibility training for chronic pain: A randomized clinical study

INTRODUCTION: Previous studies suggest an association between cognitive flexibility and development of chronic pain after surgery. It is not known whether cognitive flexibility can be improved in patients with chronic pain. OBJECTIVES: This study tested whether a neurocognitive training program results in improved cognitive flexibility and pain in patients with chronic pain. METHODS: We conducted a single-center, prospective, randomized study investigating 5-week daily neurocognitive training in patients with chronic pain. Participants (n = 145) were randomized into neurocognitive training or care as usual, and they completed assessments at baseline, posttreatment, and 3 months. The treatment group was asked to spend 35 minutes daily completing a program with tasks on cognitive flexibility, memory, attention, and speed. The primary outcome was performance on the neurocognitive performance test (NCPT). Secondary outcomes included levels of pain interference and severity. RESULTS: At 5 weeks, the treatment group showed greater improvements on NCPT compared with the control group ( CONCLUSIONS: Outcomes suggest that using neurocognitive training to modify cognitive flexibility in patients with chronic pain may improve pain severity. This study provided effect size estimates to inform sample size calculations for randomized controlled trials to test the effectiveness of neurocognitive interventions for the prevention and treatment of chronic pain

The Price of Anarchy in Transportation Networks: Efficiency and Optimality Control

Uncoordinated individuals in human society pursuing their personally optimal strategies do not always achieve the social optimum, the most beneficial state to the society as a whole. Instead, strategies form Nash equilibria which are often socially suboptimal. Society, therefore, has to pay a price of anarchy for the lack of coordination among its members. Here we assess this price of anarchy by analyzing the travel times in road networks of several major cities. Our simulation shows that uncoordinated drivers possibly waste a considerable amount of their travel time. Counterintuitively,simply blocking certain streets can partially improve the traffic conditions. We analyze various complex networks and discuss the possibility of similar paradoxes in physics.Comment: major revisions with multicommodity; Phys. Rev. Lett., accepte

Adaptively inferring human transcriptional subnetworks

Although the human genome has been sequenced, progress in understanding gene regulation in humans has been particularly slow. Many computational approaches developed for lower eukaryotes to identify cis-regulatory elements and their associated target genes often do not generalize to mammals, largely due to the degenerate and interactive nature of such elements. Motivated by the switch-like behavior of transcriptional responses, we present a systematic approach that allows adaptive determination of active transcriptional subnetworks (cis-motif combinations, the direct target genes and physiological processes regulated by the corresponding transcription factors) from microarray data in mammals, with accuracy similar to that achieved in lower eukaryotes. Our analysis uncovered several new subnetworks active in human liver and in cell-cycle regulation, with similar functional characteristics as the known ones. We present biochemical evidence for our predictions, and show that the recently discovered G2/M-specific E2F pathway is wider than previously thought; in particular, E2F directly activates certain mitotic genes involved in hepatocellular carcinomas. Additionally, we demonstrate that this method can predict subnetworks in a condition-specific manner, as well as regulatory crosstalk across multiple tissues. Our approach allows systematic understanding of how phenotypic complexity is regulated at the transcription level in mammals and offers marked advantage in systems where little or no prior knowledge of transcriptional regulation is available

Addressing student models of energy loss in quantum tunnelling

We report on a multi-year, multi-institution study to investigate student reasoning about energy in the context of quantum tunnelling. We use ungraded surveys, graded examination questions, individual clinical interviews, and multiple-choice exams to build a picture of the types of responses that students typically give. We find that two descriptions of tunnelling through a square barrier are particularly common. Students often state that tunnelling particles lose energy while tunnelling. When sketching wave functions, students also show a shift in the axis of oscillation, as if the height of the axis of oscillation indicated the energy of the particle. We find inconsistencies between students' conceptual, mathematical, and graphical models of quantum tunnelling. As part of a curriculum in quantum physics, we have developed instructional materials to help students develop a more robust and less inconsistent picture of tunnelling, and present data suggesting that we have succeeded in doing so.Comment: Originally submitted to the European Journal of Physics on 2005 Feb 10. Pages: 14. References: 11. Figures: 9. Tables: 1. Resubmitted May 18 with revisions that include an appendix with the curriculum materials discussed in the paper (4 page small group UW-style tutorial

Towards a transformative understanding of the ocean’s biological pump: Priorities for future research - Report on the NSF Biology of the Biological Pump Workshop

NSF Biology of the Biological Pump Workshop, February 19–20, 2016 (Hyatt Place New Orleans, New Orleans, LA)The net transfer of organic matter from the surface to the deep ocean is a key function of ocean food webs. The combination of biological, physical, and chemical processes that contribute to and control this export is collectively known as the “biological pump”, and current estimates of the global magnitude of this export range from 5 – 12 Pg C yr-1. This material can be exported in dissolved or particulate form, and many of the biological processes that regulate the composition, quantity, timing, and distribution of this export are poorly understood or constrained. Export of organic material is of fundamental importance to the biological and chemical functioning of the ocean, supporting deep ocean food webs and controlling the vertical and horizontal segregation of elements throughout the ocean. Remineralization of exported organic matter in the upper mesopelagic zone provides nutrients for surface production, while material exported to depths of 1000 m or more is generally considered to be sequestered — i.e. out of contact with the atmosphere for centuries or longer. The ability to accurately model a system is a reflection of the degree to which the system is understood. In the case of export, semi-empirical and simple mechanistic models show a wide range of predictive skill. This is, in part, due to the sparseness of available data, which impedes our inability to accurately represent, or even include, all relevant processes (sometimes for legitimate computational reasons). Predictions will remain uncertain without improved understanding and parameterization of key biological processes affecting export.Funding for this workshop was provided by the National Science Foundation (NSF). Coordination and logistical support for this workshop was provided by the Ocean Carbon and Biogeochemistry (OCB) Program (www.us-ocb.org

SeqAnt: A web service to rapidly identify and annotate DNA sequence variations

<p>Abstract</p> <p>Background</p> <p>The enormous throughput and low cost of second-generation sequencing platforms now allow research and clinical geneticists to routinely perform single experiments that identify tens of thousands to millions of variant sites. Existing methods to annotate variant sites using information from publicly available databases via web browsers are too slow to be useful for the large sequencing datasets being routinely generated by geneticists. Because sequence annotation of variant sites is required before functional characterization can proceed, the lack of a high-throughput pipeline to efficiently annotate variant sites can act as a significant bottleneck in genetics research.</p> <p>Results</p> <p>SeqAnt (<it>Seq</it>uence <it>An</it>notator) is an open source web service and software package that rapidly annotates DNA sequence variants and identifies recessive or compound heterozygous loci in human, mouse, fly, and worm genome sequencing experiments. Variants are characterized with respect to their functional type, frequency, and evolutionary conservation. Annotated variants can be viewed on a web browser, downloaded in a tab-delimited text file, or directly uploaded in a BED format to the UCSC genome browser. To demonstrate the speed of SeqAnt, we annotated a series of publicly available datasets that ranged in size from 37 to 3,439,107 variant sites. The total time to completely annotate these data completely ranged from 0.17 seconds to 28 minutes 49.8 seconds.</p> <p>Conclusion</p> <p>SeqAnt is an open source web service and software package that overcomes a critical bottleneck facing research and clinical geneticists using second-generation sequencing platforms. SeqAnt will prove especially useful for those investigators who lack dedicated bioinformatics personnel or infrastructure in their laboratories.</p