Estimating causal networks in biosphere–atmosphere interaction with the PCMCI approach

Local meteorological conditions and biospheric activity are tightly coupled. Understanding these links is an essential prerequisite for predicting the Earth system under climate change conditions. However, many empirical studies on the interaction between the biosphere and the atmosphere are based on correlative approaches that are not able to deduce causal paths, and only very few studies apply causal discovery methods. Here, we use a recently proposed causal graph discovery algorithm, which aims to reconstruct the causal dependency structure underlying a set of time series. We explore the potential of this method to infer temporal dependencies in biosphere-atmosphere interactions. Specifically we address the following questions: How do periodicity and heteroscedasticity influence causal detection rates, i.e. the detection of existing and non-existing links? How consistent are results for noise-contaminated data? Do results exhibit an increased information content that justifies the use of this causal-inference method? We explore the first question using artificial time series with well known dependencies that mimic real-world biosphere-atmosphere interactions. The two remaining questions are addressed jointly in two case studies utilizing observational data. Firstly, we analyse three replicated eddy covariance datasets from a Mediterranean ecosystem at half hourly time resolution allowing us to understand the impact of measurement uncertainties. Secondly, we analyse global NDVI time series (GIMMS 3g) along with gridded climate data to study large-scale climatic drivers of vegetation greenness. Overall, the results confirm the capacity of the causal discovery method to extract time-lagged linear dependencies under realistic settings. The violation of the method's assumptions increases the likelihood to detect false links. Nevertheless, we consistently identify interaction patterns in observational data. Our findings suggest that estimating a directed biosphere-atmosphere network at the ecosystem level can offer novel possibilities to unravel complex multi-directional interactions. Other than classical correlative approaches, our findings are constrained to a few meaningful set of relations which can be powerful insights for the evaluation of terrestrial ecosystem models

Dynamic Nuclear Polarization in Double Quantum Dots

We theoretically investigate the controlled dynamic polarization of lattice nuclear spins in GaAs double quantum dots containing two electrons. Three regimes of long-term dynamics are identified, including the build up of a large difference in the Overhauser fields across the dots, the saturation of the nuclear polarization process associated with formation of so-called "dark states," and the elimination of the difference field. We show that in the case of unequal dots, build up of difference fields generally accompanies the nuclear polarization process, whereas for nearly identical dots, build up of difference fields competes with polarization saturation in dark states. The elimination of the difference field does not, in general, correspond to a stable steady state of the polarization process.Comment: 4 pages, 2 figure

Methodology for vetting heavily doped semiconductors for intermediate band photovoltaics: A case study in sulfur-hyperdoped silicon

We present a methodology for estimating the efficiency potential for candidate impurity-band photovoltaic materials from empirical measurements. This methodology employs both Fourier transform infrared spectroscopy and low-temperature photoconductivity to calculate a “performance figure of merit” and to determine both the position and bandwidth of the impurity band. We evaluate a candidate impurity-band material, silicon hyperdoped with sulfur; we find that the figure of merit is more than one order of magnitude too low for photovoltaic devices that exceed the thermodynamic efficiency limit for single band gap materials.National Science Foundation (U.S.) (Energy, Power, and Adaptive Systems Grant Contract ECCS-1102050)National Science Foundation (U.S.) (United States. Dept. of Energy NSF CA EEC-1041895)Center for Clean Water and Clean Energy at MIT and KFUP

Deactivation of metastable single-crystal silicon hyperdoped with sulfur

Silicon supersaturated with sulfur by ion implantation and pulsed laser melting exhibits broadband optical absorption of photons with energies less than silicon's band gap. However, this metastable, hyperdoped material loses its ability to absorb sub-band gap light after subsequent thermal treatment. We explore this deactivation process through optical absorption and electronic transport measurements of sulfur-hyperdoped silicon subject to anneals at a range of durations and temperatures. The deactivation process is well described by the Johnson-Mehl-Avrami-Kolmogorov framework for the diffusion-mediated transformation of a metastable supersaturated solid solution, and we find that this transformation is characterized by an apparent activation energy of E[subscript A] = 1.7 ± 0.1  eV. Using this activation energy, the evolution of the optical and electronic properties for all anneal duration-temperature combinations collapse onto distinct curves as a function of the extent of reaction. We provide a mechanistic interpretation of this deactivation based on short-range thermally activated atomic movements of the dopants to form sulfur complexes.Center for Clean Water and Clean Energy at MIT and KFUPMNational Science Foundation (U.S.) (Energy, Power, and Adaptive Systems Grant Contract ECCS-1102050)National Science Foundation (U.S.) (United States. Dept. of Energy Contract EEC-1041895

Increased shedding of HU177 correlates with worse prognosis in primary melanoma

<p>Abstract</p> <p>Background</p> <p>Increased levels of cryptic collagen epitope HU177 in the sera of melanoma patients have been shown to be associated with thicker primary melanomas and with the nodular histologic subtype. In this study, we investigate the association between HU177 shedding in the sera and clinical outcome in terms of disease-free survival (DFS) and overall survival (OS).</p> <p>Methods</p> <p>Serum samples from 209 patients with primary melanoma prospectively enrolled in the Interdisciplinary Melanoma Cooperative Group at the New York University Langone Medical Center (mean age = 58, mean thickness = 2.09 mm, stage I = 136, stage II = 41, stage III = 32, median follow-up = 54.9 months) were analyzed for HU177 concentration using a validated ELISA assay. HU177 serum levels at the time of diagnosis were used to divide the study cohort into two groups: low and high HU177. DFS and OS were estimated by Kaplan-Meier survival analysis, and the log-rank test was used to compare DFS and OS between the two HU177 groups. Multivariate Cox proportional hazards regression models were employed to examine the independent effect of HU177 category on DFS and OS.</p> <p>Results</p> <p>HU177 sera concentrations ranged from 0-139.8 ng/ml (mean and median of 6.2 ng/ml and 3.7 ng/ml, respectively). Thirty-eight of the 209 (18%) patients developed recurrences, and 34 of the 209 (16%) patients died during follow-up. Higher HU177 serum level was associated with an increased rate of melanoma recurrence (p = 0.04) and with increasing mortality (p = 0.01). The association with overall survival remained statistically significant after controlling for thickness and histologic subtype in a multivariate model (p = 0.035).</p> <p>Conclusions</p> <p>Increased shedding of HU177 in the serum of primary melanoma patients is associated with poor prognosis. Further studies are warranted to determine the clinical utility of HU177 in risk stratification compared to the current standard of care.</p

The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine

AbstractA SAGE library was prepared from hand-dissected intestines from adult Caenorhabditis elegans, allowing the identification of >4000 intestinally-expressed genes; this gene inventory provides fundamental information for understanding intestine function, structure and development. Intestinally-expressed genes fall into two broad classes: widely-expressed “housekeeping” genes and genes that are either intestine-specific or significantly intestine-enriched. Within this latter class of genes, we identified a subset of highly-expressed highly-validated genes that are expressed either exclusively or primarily in the intestine. Over half of the encoded proteins are candidates for secretion into the intestinal lumen to hydrolyze the bacterial food (e.g. lysozymes, amoebapores, lipases and especially proteases). The promoters of this subset of intestine-specific/intestine-enriched genes were analyzed computationally, using both a word-counting method (RSAT oligo-analysis) and a method based on Gibbs sampling (MotifSampler). Both methods returned the same over-represented site, namely an extended GATA-related sequence of the general form AHTGATAARR, which agrees with experimentally determined cis-acting control sequences found in intestine genes over the past 20 years. All promoters in the subset contain such a site, compared to <5% for control promoters; moreover, our analysis suggests that the majority (perhaps all) of genes expressed exclusively or primarily in the worm intestine are likely to contain such a site in their promoters. There are three zinc-finger GATA-type factors that are candidates to bind this extended GATA site in the differentiating C. elegans intestine: ELT-2, ELT-4 and ELT-7. All evidence points to ELT-2 being the most important of the three. We show that worms in which both the elt-4 and the elt-7 genes have been deleted from the genome are essentially wildtype, demonstrating that ELT-2 provides all essential GATA-factor functions in the intestine. The SAGE analysis also identifies more than a hundred other transcription factors in the adult intestine but few show an RNAi-induced loss-of-function phenotype and none (other than ELT-2) show a phenotype primarily in the intestine. We thus propose a simple model in which the ELT-2 GATA factor directly participates in the transcription of all intestine-specific/intestine-enriched genes, from the early embryo through to the dying adult. Other intestinal transcription factors would thus modulate the action of ELT-2, depending on the worm's nutritional and physiological needs

Efficient spin filter using multi-terminal quantum dot with spin-orbit interaction

We propose a multi-terminal spin filter using a quantum dot with spin-orbit interaction. First, we formulate the spin Hall effect (SHE) in a quantum dot connected to three leads. We show that the SHE is significantly enhanced by the resonant tunneling if the level spacing in the quantum dot is smaller than the level broadening. We stress that the SHE is tunable by changing the tunnel coupling to the third lead. Next, we perform a numerical simulation for a multi-terminal spin filter using a quantum dot fabricated on semiconductor heterostructures. The spin filter shows an efficiency of more than 50% when the conditions for the enhanced SHE are satisfied