Stepwise basis set selection

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146410/1/jcc25363.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146410/2/jcc25363_am.pd

High potential for weathering and climate effects of non-vascular vegetation in the Late Ordovician

It has been hypothesized that predecessors of today’s bryophytes significantly increased global chemical weathering in the Late Ordovician, thus reducing atmospheric CO2 concentration and contributing to climate cooling and an interval of glaciations. Studies that try to quantify the enhancement of weathering by non-vascular vegetation, however, are usually limited to small areas and low numbers of species, which hampers extrapolating to the global scale and to past climatic conditions. Here we present a spatially explicit modelling approach to simulate global weathering by non-vascular vegetation in the Late Ordovician. We estimate a potential global weathering flux of 2.8 (km3 rock) yr−1, defined here as volume of primary minerals affected by chemical transformation. This is around three times larger than today’s global chemical weathering flux. Moreover, we find that simulated weathering is highly sensitive to atmospheric CO2 concentration. This implies a strong negative feedback between weathering by non-vascular vegetation and Ordovician climate

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Methane exchange in a boreal forest estimated by gradient method

Forests are generally considered to be net sinks of atmospheric methane (CH4) because of oxidation by methanotrophic bacteria in well-aerated forests soils. However, emissions from wet forest soils, and sometimes canopy fluxes, are often neglected when quantifying the CH4 budget of a forest. We used a modified Bowen ratio method and combined eddy covariance and gradient methods to estimate net CH4 exchange at a boreal forest site in central Sweden. Results indicate that the site is a net source of CH4. This is in contrast to soil, branch and leaf chamber measurements of uptake of CH4. Wetter soils within the footprint of the canopy are thought to be responsible for the discrepancy. We found no evidence for canopy emissions per se. However, the diel pattern of the CH4 exchange with minimum emissions at daytime correlated well with gross primary production, which supports an uptake in the canopy. More distant source areas could also contribute to the diel pattern; their contribution might be greater at night during stable boundary layer conditions

Quality control of CarboEurope flux data – Part I: Footprint analyses to evaluate sites in forest ecosystems

International audienceWe applied a site evaluation approach combining Lagrangian Stochastic footprint modelling with a quality assessment approach for eddy-covariance data to 25 forested sites of the CarboEurope-IP network. The analysis addresses the spatial representativeness of the flux measurements, instrumental effects on data quality, spatial patterns in the data quality, and the performance of the coordinate rotation method. Our findings demonstrate that application of a footprint filter could strengthen the CarboEurope-IP flux database, since only one third of the sites is situated in truly homogeneous terrain. Almost half of the sites experience a significant reduction in eddy-covariance data quality under certain conditions, though these effects are mostly constricted to a small portion of the dataset. Reductions in data quality of the sensible heat flux are mostly induced by characteristics of the surrounding terrain, while the latent heat flux is subject to instrumentation-related problems. The Planar-Fit coordinate rotation proved to be a reliable tool for the majority of the sites using only a single set of rotation angles. Overall, we found a high average data quality for the CarboEurope-IP network, with good representativeness of the measurement data for the specified target land cover types

Biological and geophysical feedbacks with fire in the Earth system

Roughly 3% of the Earth’s land surface burns annually, representing a critical exchange of energy and matter between the land and atmosphere via combustion. Fires range from slow smouldering peat fires, to low-intensity surface fires, to intense crown fires, depending on vegetation structure, fuel moisture, prevailing climate, and weather conditions. While the links between biogeochemistry, climate and fire are widely studied within Earth system science, these relationships are also mediated by fuels—namely plants and their litter—that are the product of evolutionary and ecological processes. Fire is a powerful selective force and, over their evolutionary history, plants have evolved traits that both tolerate and promote fire numerous times and across diverse clades. Here we outline a conceptual framework of how plant traits determine the flammability of ecosystems and interact with climate and weather to influence fire regimes. We explore how these evolutionary and ecological processes scale to impact biogeochemical and Earth system processes. Finally, we outline several research challenges that, when resolved, will improve our understanding of the role of plant evolution in mediating the fire feedbacks driving Earth system processes. Understanding current patterns of fire and vegetation, as well as patterns of fire over geological time, requires research that incorporates evolutionary biology, ecology, biogeography, and the biogeosciences

Attempting to stop antipsychotic medication: success, supports, and efforts to cope

Purpose To explore supports and coping strategies used during attempts to discontinue antipsychotic medication and test for associations with success. Method 144 people who were taking or had taken antipsychotics completed The Experiences of Antipsychotic Medication Survey. Among them, 105 people had made at least one discontinuation attempt and answered a series of questions about their most recent attempt to stop. Content analysis and Chi-square tests of independence were used to categorise the data and explore associations. Success was defined as stopping all AM use irrespective of the duration of the medication-free period or whether relapse occurred, which were explored separately. Results Among the 105 people who had attempted discontinuation, 61.9% described unwanted withdrawal effects and 27.6% of the group described psychotic or manic relapse during the withdrawal period. Within this group 55% described successfully stopping all AM for varying lengths of time, half reported no current use, and half described having some form of professional, family, friend, and/or service user or peer support for their attempt. Having support was positively associated with success and negatively associated with both current use, and relapse during withdrawal. A range of coping efforts were described, but having coping strategies failed to show significant associations with any of the dependent variables explored. Among those who described successfully stopping, some described returning to AM for short periods when needed, while others reported managing well with alternative methods alone. Conclusions Findings cannot be readily generalised due to sampling constraints, but results suggest a wide range of supports and coping strategies may be used when attempting to discontinue antipsychotics. Many people may attempt to discontinue antipsychotics without any support. Those who have support for their attempts may be significantly less likely to relapse during withdrawal and more likely to succeed in their attempt. There is a pressing need for further research in this area

Seasonal variation of carbon fluxes in a sparse savanna in semi arid Sudan

<p>Abstract</p> <p>Background</p> <p>Large spatial, seasonal and annual variability of major drivers of the carbon cycle (precipitation, temperature, fire regime and nutrient availability) are common in the Sahel region. This causes large variability in net ecosystem exchange and in vegetation productivity, the subsistence basis for a major part of the rural population in Sahel. This study compares the 2005 dry and wet season fluxes of CO₂for a grass land/sparse savanna site in semi arid Sudan and relates these fluxes to water availability and incoming photosynthetic photon flux density (PPFD). Data from this site could complement the current sparse observation network in Africa, a continent where climatic change could significantly impact the future and which constitute a weak link in our understanding of the global carbon cycle.</p> <p>Results</p> <p>The dry season (represented by Julian day 35–46, February 2005) was characterized by low soil moisture availability, low evapotranspiration and a high vapor pressure deficit. The mean daily NEE (net ecosystem exchange, Eq. 1) was -14.7 mmol d^-1for the 12 day period (negative numbers denote sinks, i.e. flux from the atmosphere to the biosphere). The water use efficiency (WUE) was 1.6 mmol CO₂mol H₂O^-1and the light use efficiency (LUE) was 0.95 mmol CO₂mol PPFD^-1. Photosynthesis is a weak, but linear function of PPFD. The wet season (represented by Julian day 266–273, September 2005) was, compared to the dry season, characterized by slightly higher soil moisture availability, higher evapotranspiration and a slightly lower vapor pressure deficit. The mean daily NEE was -152 mmol d^-1for the 8 day period. The WUE was lower, 0.97 mmol CO₂mol H₂O^-1and the LUE was higher, 7.2 <it>μ</it>mol CO₂mmol PPFD^-1during the wet season compared to the dry season. During the wet season photosynthesis increases with PPFD to about 1600 <it>μ</it>mol m^-2s^-1and then levels off.</p> <p>Conclusion</p> <p>Based on data collected during two short periods, the studied ecosystem was a sink of carbon both during the dry and wet season 2005. The small sink during the dry season is surprising and similar dry season sinks have not to our knowledge been reported from other similar savanna ecosystems and could have potential management implications for agroforestry. A strong response of NEE versus small changes in plant available soil water content was found. Collection and analysis of flux data for several consecutive years including variations in precipitation, available soil moisture and labile soil carbon are needed for understanding the year to year variation of the carbon budget of this grass land/sparse savanna site in semi arid Sudan.</p

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts