Farms, pipes, streams and reforestation : reasoning about structured parallel processes using types and hylomorphisms

The increasing importance of parallelism has motivated the creation of better abstractions for writing parallel software, including structured parallelism using nested algorithmic skeletons. Such approaches provide high-level abstractions that avoid common problems, such as race conditions, and often allow strong cost models to be defined. However, choosing a combination of algorithmic skeletons that yields good parallel speedups for a program on some specific parallel architecture remains a difficult task. In order to achieve this, it is necessary to simultaneously reason both about the costs of different parallel structures and about the semantic equivalences between them. This paper presents a new type-based mechanism that enables strong static reasoning about these properties. We exploit well-known properties of a very general recursion pattern, hylomorphisms, and give a denotational semantics for structured parallel processes in terms of these hylomorphisms. Using our approach, it is possible to determine formally whether it is possible to introduce a desired parallel structure into a program without altering its functional behaviour, and also to choose a version of that parallel structure that minimises some given cost model.Postprin

Constructing living buildings: a review of relevant technologies for a novel application of biohybrid robotics

Biohybrid robotics takes an engineering approach to the expansion and exploitation of biological behaviours for application to automated tasks. Here, we identify the construction of living buildings and infrastructure as a high-potential application domain for biohybrid robotics, and review technological advances relevant to its future development. Construction, civil infrastructure maintenance and building occupancy in the last decades have comprised a major portion of economic production, energy consumption and carbon emissions. Integrating biological organisms into automated construction tasks and permanent building components therefore has high potential for impact. Live materials can provide several advantages over standard synthetic construction materials, including self-repair of damage, increase rather than degradation of structural performance over time, resilience to corrosive environments, support of biodiversity, and mitigation of urban heat islands. Here, we review relevant technologies, which are currently disparate. They span robotics, self-organizing systems, artificial life, construction automation, structural engineering, architecture, bioengineering, biomaterials, and molecular and cellular biology. In these disciplines, developments relevant to biohybrid construction and living buildings are in the early stages, and typically are not exchanged between disciplines. We, therefore, consider this review useful to the future development of biohybrid engineering for this highly interdisciplinary application.publishe

Whitepaper: Understanding land-atmosphere interactions through tower-based flux and continuous atmospheric boundary layer measurements

Executive summary ● Target audience: AmeriFlux community, AmeriFlux Science Steering Committee & Department of Energy (DOE) program managers [ARM/ASR (atmosphere), TES (surface), and SBR (subsurface)] ● Problem statement: The atmospheric boundary layer mediates the exchange of energy and matter between the land surface and the free troposphere integrating a range of physical, chemical, and biological processes. However, continuous atmospheric boundary layer observations at AmeriFlux sites are still scarce. How can adding measurements of the atmospheric boundary layer enhance the scientific value of the AmeriFlux network? ● Research opportunities: We highlight four key opportunities to integrate tower-based flux measurements with continuous, long-term atmospheric boundary layer measurements: (1) to interpret surface flux and atmospheric boundary layer exchange dynamics at flux tower sites, (2) to support regionalscale modeling and upscaling of surface fluxes to continental scales, (3) to validate land-atmosphere coupling in Earth system models, and (4) to support flux footprint modelling, the interpretation of surface fluxes in heterogeneous terrain, and quality control of eddy covariance flux measurements. ● Recommended actions: Adding a suite of atmospheric boundary layer measurements to eddy covariance flux tower sites would allow the Earth science community to address new emerging research questions, to better interpret ongoing flux tower measurements, and would present novel opportunities for collaboration between AmeriFlux scientists and atmospheric and remote sensing scientists. We therefore recommend that (1) a set of instrumentation for continuous atmospheric boundary layer observations be added to a subset of AmeriFlux sites spanning a range of ecosystem types and climate zones, that (2) funding agencies (e.g., Department of Energy, NASA) solicit research on land-atmosphere processes where the benefits of fully integrated atmospheric boundary layer observations can add value to key scientific questions, and that (3) the AmeriFlux Management Project acquires loaner instrumentation for atmospheric boundary layer observations for use in experiments and short-term duration campaigns

The Palomar Testbed Interferometer Calibrator Catalog

The Palomar Testbed Interferometer (PTI) archive of observations between 1998 and 2005 is examined for objects appropriate for calibration of optical long-baseline interferometer observations - stars that are predictably point-like and single. Approximately 1,400 nights of data on 1,800 objects were examined for this investigation. We compare those observations to an intensively studied object that is a suitable calibrator, HD217014, and statistically compare each candidate calibrator to that object by computing both a Mahalanobis distance and a Principal Component Analysis. Our hypothesis is that the frequency distribution of visibility data associated with calibrator stars differs from non-calibrator stars such as binary stars. Spectroscopic binaries resolved by PTI, objects known to be unsuitable for calibrator use, are similarly tested to establish detection limits of this approach. From this investigation, we find more than 350 observed stars suitable for use as calibrators (with an additional $\approx 140$ being rejected), corresponding to $\gtrsim 95$ sky coverage for PTI. This approach is noteworthy in that it rigorously establishes calibration sources through a traceable, empirical methodology, leveraging the predictions of spectral energy distribution modeling but also verifying it with the rich body of PTI's on-sky observations.Comment: 100 pages, 7 figures, 7 tables; to appear in the May 2008ApJS, v176n

Improving land surface models with FLUXNET data

There is a growing consensus that land surface models (LSMs) that simulate terrestrial biosphere exchanges of matter and energy must be better constrained with data to quantify and address their uncertainties. FLUXNET, an international network of sites that measure the land surface exchanges of carbon, water and energy using the eddy covariance technique, is a prime source of data for model improvement. Here we outline a multi-stage process for "fusing" (i.e. linking) LSMs with FLUXNET data to generate better models with quantifiable uncertainty. First, we describe FLUXNET data availability, and its random and systematic biases. We then introduce methods for assessing LSM model runs against FLUXNET observations in temporal and spatial domains. These assessments are a prelude to more formal model-data fusion (MDF). MDF links model to data, based on error weightings. In theory, MDF produces optimal analyses of the modelled system, but there are practical problems. We first discuss how to set model errors and initial conditions. In both cases incorrect assumptions will affect the outcome of the MDF. We then review the problem of equifinality, whereby multiple combinations of parameters can produce similar model output. Fusing multiple independent and orthogonal data provides a means to limit equifinality. We then show how parameter probability density functions (PDFs) from MDF can be used to interpret model validity, and to propagate errors into model outputs. Posterior parameter distributions are a useful way to assess the success of MDF, combined with a determination of whether model residuals are Gaussian. If the MDF scheme provides evidence for temporal variation in parameters, then that is indicative of a critical missing dynamic process. A comparison of parameter PDFs generated with the same model from multiple FLUXNET sites can provide insights into the concept and validity of plant functional types (PFT) – we would expect similar parameter estimates among sites sharing a single PFT. We conclude by identifying five major model-data fusion challenges for the FLUXNET and LSM communities: (1) to determine appropriate use of current data and to explore the information gained in using longer time series; (2) to avoid confounding effects of missing process representation on parameter estimation; (3) to assimilate more data types, including those from earth observation; (4) to fully quantify uncertainties arising from data bias, model structure, and initial conditions problems; and (5) to carefully test current model concepts (e.g. PFTs) and guide development of new concepts

Mutant INS-Gene Induced Diabetes of Youth: Proinsulin Cysteine Residues Impose Dominant-Negative Inhibition on Wild-Type Proinsulin Transport

Recently, a syndrome of Mutant INS-gene-induced Diabetes of Youth (MIDY, derived from one of 26 distinct mutations) has been identified as a cause of insulin-deficient diabetes, resulting from expression of a misfolded mutant proinsulin protein in the endoplasmic reticulum (ER) of insulin-producing pancreatic beta cells. Genetic deletion of one, two, or even three alleles encoding insulin in mice does not necessarily lead to diabetes. Yet MIDY patients are INS-gene heterozygotes; inheritance of even one MIDY allele, causes diabetes. Although a favored explanation for the onset of diabetes is that insurmountable ER stress and ER stress response from the mutant proinsulin causes a net loss of beta cells, in this report we present three surprising and interlinked discoveries. First, in the presence of MIDY mutants, an increased fraction of wild-type proinsulin becomes recruited into nonnative disulfide-linked protein complexes. Second, regardless of whether MIDY mutations result in the loss, or creation, of an extra unpaired cysteine within proinsulin, Cys residues in the mutant protein are nevertheless essential in causing intracellular entrapment of co-expressed wild-type proinsulin, blocking insulin production. Third, while each of the MIDY mutants induces ER stress and ER stress response; ER stress and ER stress response alone appear insufficient to account for blockade of wild-type proinsulin. While there is general agreement that ultimately, as diabetes progresses, a significant loss of beta cell mass occurs, the early events described herein precede cell death and loss of beta cell mass. We conclude that the molecular pathogenesis of MIDY is initiated by perturbation of the disulfide-coupled folding pathway of wild-type proinsulin

Flowering response of pearl millet to water stress during panicle development.

In pearl millet, severe water deficit during the period of panicle development delays flowering. The flowering response of both main shoot and tillers to water stress during panicle development was investigated using four hybrids. Panicle initiation of all tillers occurred in the three early genotypes despite water stress. In the late genotype, however, panicle initiation of tillers occurred only after the release of stress. The delay in flowering due to water stress was more pronounced in the tillers than in the main shoot. However, the proportion of tillers producing an inflorescence was increased by water stress. Grain yield losses on the main shoot by water stress were compensated by an increase in tiller grain yields. Delay in flowering and buffering by tillers provide an important adaptive mechanism to overcome a period of drought stress prior to flowering

Biosphere-atmosphere exchange of CO2 in relation to climate : a cross-biome analysis across multiple time scales

Peer reviewe

8--13 um spectroscopy of YSOs: Evolution of the silicate feature

In order to investigate possible connections between dust processing and disk properties, 8--13 um spectra of 34 young stars, with a range of circumstellar environments and spectral types A to M, were obtained using the Long Wavelength Spectrometer at the W. M. Keck Observatory. The broad 9.7 um amorphous silicate feature which dominates this wavelength regime evolves from absorption in young, embedded sources, to emission in optically revealed stars, and to complete absence in older debris disk systems for both low- and intermediate-mass stars. The peak wavelength and FWHM are centered about 9.7 and ~2.3 um, corresponding to amorphous olivine, with a larger spread in FWHM for embedded sources and in peak wavelength for disks. In a few of our objects that have been previously identified as class I low-mass YSOs, the observed silicate feature is complex, with absorption near 9.5 um and emission peaking around 10 um. Although most of the emission spectra show broad classical features attributed to amorphous silicates, variations in the shape/strength may be linked to dust processing, including grain growth and/or silicate crystallization. We study quantitatively the evidence for evolutionary trends in the 8--13 um spectra through a variety of spectral shape diagnostics. Based on the lack of correlation between these diagnostics and broad-band infrared luminosity characteristics for silicate emission sources, we conclude that although spectral signatures of dust processing are present, they can not be connected clearly to disk evolutionary stage (for optically thick disks) or optical depth (for optically thin disks). The diagnostics of silicate absorption features (other than the central wavelength of the feature), however, are tightly correlated with optical depth.Comment: 27 pages, 13 figures, accepted for publication by ApJ, formatted with emulateapj using revtex4 v4.