Showing papers by "Pennsylvania State University published in 2005"

The Amber biomolecular simulation programs

Abstract: We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

Detection of the baryon acoustic peak in the large-scale correlation function of SDSS luminous red galaxies

Abstract: We present the large-scale correlation function measured from a spectroscopic sample of 46,748 luminous red galaxies from the Sloan Digital Sky Survey. The survey region covers 0.72h −3 Gpc 3 over 3816 square degrees and 0.16 < z < 0.47, making it the best sample yet for the study of large-scale structure. We find a well-detected peak in the correlation function at 100h −1 Mpc separation that is an excellent match to the predicted shape and location of the imprint of the recombination-epoch acoustic oscillations on the low-redshift clustering of matter. This detection demonstrates the linear growth of structure by gravitational instability between z ≈ 1000 and the present and confirms a firm prediction of the standard cosmological theory. The acoustic peak provides a standard ruler by which we can measure the ratio of the distances to z = 0.35 and z = 1089 to 4% fractional accuracy and the absolute distance to z = 0.35 to 5% accuracy. From the overall shape of the correlation function, we measure the matter density mh 2 to 8% and find agreement with the value from cosmic microwave background (CMB) anisotropies. Independent of the constraints provided by the CMB acoustic scale, we find m = 0.273 ±0.025+0.123(1+ w0)+0.137K. Including the CMB acoustic scale, we find that the spatial curvature is K = −0.010 ± 0.009 if the dark energy is a cosmological constant. More generally, our results provide a measurement of cosmological distance, and hence an argument for dark energy, based on a geometric method with the same simple physics as the microwave background anisotropies. The standard cosmological model convincingly passes these new and robust tests of its fundamental properties. Subject headings: cosmology: observations — large-scale structure of the universe — distance scale — cosmological parameters — cosmic microwave background — galaxies: elliptical and lenticular, cD

Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms

Abstract: Today's surface ocean is saturated with respect to calcium carbonate, but increasing atmospheric carbon dioxide concentrations are reducing ocean pH and carbonate ion concentrations, and thus the level of calcium carbonate saturation. Experimental evidence suggests that if these trends continue, key marine organisms—such as corals and some plankton—will have difficulty maintaining their external calcium carbonate skeletons. Here we use 13 models of the ocean–carbon cycle to assess calcium carbonate saturation under the IS92a 'business-as-usual' scenario for future emissions of anthropogenic carbon dioxide. In our projections, Southern Ocean surface waters will begin to become undersaturated with respect to aragonite, a metastable form of calcium carbonate, by the year 2050. By 2100, this undersaturation could extend throughout the entire Southern Ocean and into the subarctic Pacific Ocean. When live pteropods were exposed to our predicted level of undersaturation during a two-day shipboard experiment, their aragonite shells showed notable dissolution. Our findings indicate that conditions detrimental to high-latitude ecosystems could develop within decades, not centuries as suggested previously.

Growth of the plant cell wall

Abstract: Plant cells encase themselves within a complex polysaccharide wall, which constitutes the raw material that is used to manufacture textiles, paper, lumber, films, thickeners and other products. The plant cell wall is also the primary source of cellulose, the most abundant and useful biopolymer on the Earth. The cell wall not only strengthens the plant body, but also has key roles in plant growth, cell differentiation, intercellular communication, water movement and defence. Recent discoveries have uncovered how plant cells synthesize wall polysaccharides, assemble them into a strong fibrous network and regulate wall expansion during cell growth.

The Swift X-ray telescope

Abstract: he Swift Gamma-Ray Explorer is designed to make prompt multiwavelength observations of gamma-ray bursts (GRBs) and GRB afterglows. The X-ray telescope (XRT) enables Swift to determine GRB positions with a few arcseconds accuracy within 100 s of the burst onset. The XRT utilizes a mirror set built for JET-X and an XMM-Newton/EPIC MOS CCD detector to provide a sensitive broad-band (0.2–10 keV) X-ray imager with effective area of > 120 cm2 at 1.5 keV, field of view of 23.6 × 23.6 arcminutes, and angular resolution of 18 arcseconds (HPD). The detection sensitivity is 2×10−14 erg cm−2 s−1 in 104 s. The instrument is designed to provide automated source detection and position reporting within 5 s of target acquisition. It can also measure the redshifts of GRBs with Fe line emission or other spectral features. The XRT operates in an auto-exposure mode, adjusting the CCD readout mode automatically to optimize the science return for each frame as the source intensity fades. The XRT will measure spectra and lightcurves of the GRB afterglow beginning about a minute after the burst and will follow each burst for days or weeks.

Galaxy: A platform for interactive large-scale genome analysis

Abstract: Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results. The heart of Galaxy is a flexible history system that stores the queries from each user; performs operations such as intersections, unions, and subtractions; and links to other computational tools. Galaxy can be accessed at http://g2.bx.psu.edu.

X-inactivation profile reveals extensive variability in X-linked gene expression in females

Abstract: In female mammals, most genes on one X chromosome are silenced as a result of X-chromosome inactivation. However, some genes escape X-inactivation and are expressed from both the active and inactive X chromosome. Such genes are potential contributors to sexually dimorphic traits, to phenotypic variability among females heterozygous for X-linked conditions, and to clinical abnormalities in patients with abnormal X chromosomes. Here, we present a comprehensive X-inactivation profile of the human X chromosome, representing an estimated 95% of assayable genes in fibroblast-based test systems. In total, about 15% of X-linked genes escape inactivation to some degree, and the proportion of genes escaping inactivation differs dramatically between different regions of the X chromosome, reflecting the evolutionary history of the sex chromosomes. An additional 10% of X-linked genes show variable patterns of inactivation and are expressed to different extents from some inactive X chromosomes. This suggests a remarkable and previously unsuspected degree of expression heterogeneity among females.

The Swift Ultra-Violet/Optical Telescope

Abstract: The Ultra-Violet/Optical Telescope (UVOT) is one of three instruments flying aboard the Swift Gamma-ray Observatory. It is designed to capture the early (∼1 min) UV and optical photons from the afterglow of gamma-ray bursts in the 170–600 nm band as well as long term observations of these afterglows. This is accomplished through the use of UV and optical broadband filters and grisms. The UVOT has a modified Ritchey–Chretien design with micro-channel plate intensified charged-coupled device detectors that record the arrival time of individual photons and provide sub-arcsecond positioning of sources. We discuss some of the science to be pursued by the UVOT and the overall design of the instrument.

Principal Manifolds and Nonlinear Dimensionality Reduction via Tangent Space Alignment

Abstract: We present a new algorithm for manifold learning and nonlinear dimensionality reduction. Based on a set of unorganized data points sampled with noise from a parameterized manifold, the local geometry of the manifold is learned by constructing an approximation for the tangent space at each data point, and those tangent spaces are then aligned to give the global coordinates of the data points with respect to the underlying manifold. We also present an error analysis of our algorithm showing that reconstruction errors can be quite small in some cases. We illustrate our algorithm using curves and surfaces both in two-dimensional/three-dimensional (2D/3D) Euclidean spaces and in higher-dimensional Euclidean spaces. We also address several theoretical and algorithmic issues for further research and improvements.

New york university value-added galaxy catalog: a galaxy catalog based on new public surveys

Abstract: Here we present the New York University Value-Added Galaxy Catalog (NYU-VAGC), a catalog of local galaxies (mostly below z ≈ 0.3) based on a set of publicly released surveys matched to the Sloan Digital Sky Survey (SDSS) Data Release 2. The photometric catalog consists of 693,319 galaxies, QSOs, and stars; 343,568 of these have redshift determinations, mostly from the SDSS. Excluding areas masked by bright stars, the photometric sample covers 3514 deg2, and the spectroscopic sample covers 2627 deg2 (with about 85% completeness). Earlier, proprietary versions of this catalog have formed the basis of many SDSS investigations of the power spectrum, correlation function, and luminosity function of galaxies. Future releases will follow future public releases of the SDSS. The catalog includes matches to the Two Micron All Sky Survey Point Source Catalog and Extended Source Catalog, the IRAS Point Source Catalog Redshift Survey, the Two-Degree Field Galaxy Redshift Survey, the Third Reference Catalogue of Bright Galaxies, and the Faint Images of the Radio Sky at Twenty cm survey. We calculate and compile derived quantities from the images and spectra of the galaxies in the catalogs (for example, K-corrections and structural parameters for the galaxies). The SDSS catalog presented here is photometrically calibrated in a more consistent way than that distributed by the SDSS Data Release 2 Archive Servers and is thus more appropriate for large-scale structure statistics, reducing systematic calibration errors across the sky from ~2% to ~1%. We include an explicit description of the geometry of the catalog, including all imaging and targeting information as a function of sky position. Finally, we have performed eyeball quality checks on a large number of objects in the catalog in order to flag errors (such as errors in deblending). This catalog is complementary to the SDSS Archive Servers in that NYU-VAGC's calibration, geometric description, and conveniently small size are specifically designed for studying galaxy properties and large-scale structure statistics using the SDSS spectroscopic catalog.

Online selection of discriminative tracking features

Abstract: This paper presents an online feature selection mechanism for evaluating multiple features while tracking and adjusting the set of features used to improve tracking performance. Our hypothesis is that the features that best discriminate between object and background are also best for tracking the object. Given a set of seed features, we compute log likelihood ratios of class conditional sample densities from object and background to form a new set of candidate features tailored to the local object/background discrimination task. The two-class variance ratio is used to rank these new features according to how well they separate sample distributions of object and background pixels. This feature evaluation mechanism is embedded in a mean-shift tracking system that adaptively selects the top-ranked discriminative features for tracking. Examples are presented that demonstrate how this method adapts to changing appearances of both tracked object and scene background. We note susceptibility of the variance ratio feature selection method to distraction by spatially correlated background clutter and develop an additional approach that seeks to minimize the likelihood of distraction.

Scale-free networks in cell biology

Abstract: A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes, allowing them to respond to and adapt to an ever-changing environment. The large number of components, the degree of interconnectivity and the complex control of cellular networks are becoming evident in the integrated genomic and proteomic analyses that are emerging. It is increasingly recognized that the understanding of properties that arise from whole-cell function require integrated, theoretical descriptions of the relationships between different cellular components. Recent theoretical advances allow us to describe cellular network structure with graph concepts and have revealed organizational features shared with numerous non-biological networks. We now have the opportunity to describe quantitatively a network of hundreds or thousands of interacting components. Moreover, the observed topologies of cellular networks give us clues about their evolution and how their organization influences their function and dynamic responses.

Concerted and birth-and-death evolution of multigene families.

Abstract: Until around 1990, most multigene families were thought to be subject to concerted evolution, in which all member genes of a family evolve as a unit in concert. However, phylogenetic analysis of MHC and other immune system genes showed a quite different evolutionary pattern, and a new model called birth-and-death evolution was proposed. In this model, new genes are created by gene duplication and some duplicate genes stay in the genome for a long time, whereas others are inactivated or deleted from the genome. Later investigations have shown that most non-rRNA genes including highly conserved histone or ubiquitin genes are subject to this type of evolution. However, the controversy over the two models is still continuing because the distinction between the two models becomes difficult when sequence differences are small. Unlike concerted evolution, the model of birth-and-death evolution can give some insights into the origins of new genetic systems or new phenotypic characters.

A particle swarm optimization for economic dispatch with nonsmooth cost functions

Abstract: This work presents a new approach to economic dispatch (ED) problems with nonsmooth cost functions using a particle swarm optimization (PSO) technique. The practical ED problems have nonsmooth cost functions with equality and inequality constraints that make the problem of finding the global optimum difficult using any mathematical approaches. A modified PSO (MPSO) mechanism is suggested to deal with the equality and inequality constraints in the ED problems. A constraint treatment mechanism is devised in such a way that the dynamic process inherent in the conventional PSO is preserved. Moreover, a dynamic search-space reduction strategy is devised to accelerate the optimization process. To show its efficiency and effectiveness, the proposed MPSO is applied to test ED problems, one with smooth cost functions and others with nonsmooth cost functions considering valve-point effects and multi-fuel problems. The results of the MPSO are compared with the results of conventional numerical methods, Tabu search method, evolutionary programming approaches, genetic algorithm, and modified Hopfield neural network approaches.

A signature of persistent natural thermohaline circulation cycles in observed climate

Abstract: [1] Analyses of global climate from measurements dating back to the nineteenth century show an ‘Atlantic Multidecadal Oscillation’ (AMO) as a leading large-scale pattern of multidecadal variability in surface temperature. Yet it is not possible to determine whether these fluctuations are genuinely oscillatory from the relatively short observational record alone. Using a 1400 year climate model calculation, we are able to simulate the observed pattern and amplitude of the AMO. The results imply the AMO is a genuine quasi-periodic cycle of internal climate variability persisting for many centuries, and is related to variability in the oceanic thermohaline circulation (THC). This relationship suggests we can attempt to reconstruct past THC changes, and we infer an increase in THC strength over the last 25 years. Potential predictability associated with the mode implies natural THC and AMO decreases over the next few decades independent of anthropogenic climate change.

Enhanced Photocleavage of Water Using Titania Nanotube Arrays

Abstract: In this study highly ordered titania nanotube arrays of variable wall thickness are used to photocleave water under ultraviolet irradiation. We demonstrate that the wall thickness and length of the nanotubes can be controlled via anodization bath temperature. We find that the nanotube wall thickness is a key parameter influencing the magnitude of the photoanodic response and the overall efficiency of the water-splitting reaction. For 22 nm inner pore diameter nanotube arrays, those fabricated in a 5 °C anodization bath, 224 nm length and 34 nm wall thickness produced a photoanodic response that was thrice that of a nanotube array fabricated in a 50 °C anodization bath, 120 nm length and 9 nm wall-thickness. At high anodic polarization, above 1 V, the quantum efficiency under 337 nm illumination was greater than 90%. For the 5 °C anodization bath samples (22 nm pore-diameter, 34 nm wall thickness), upon 320−400 nm illumination at an intensity of 100 mW/cm2, hydrogen gas was generated at the power−time norm...

Cosmological parameter analysis including SDSS Lyα forest and galaxy bias: Constraints on the primordial spectrum of fluctuations, neutrino mass, and dark energy

Abstract: We combine the constraints from the recent Ly$\ensuremath{\alpha}$ forest analysis of the Sloan Digital Sky Survey (SDSS) and the SDSS galaxy bias analysis with previous constraints from SDSS galaxy clustering, the latest supernovae, and 1st year WMAP cosmic microwave background anisotropies. We find significant improvements on all of the cosmological parameters compared to previous constraints, which highlights the importance of combining Ly$\ensuremath{\alpha}$ forest constraints with other probes. Combining WMAP and the Ly$\ensuremath{\alpha}$ forest we find for the primordial slope ${n}_{s}=0.98\ifmmode\pm\else\textpm\fi{}0.02$. We see no evidence of running, $dn/d\mathrm{ln} k=\ensuremath{-}0.003\ifmmode\pm\else\textpm\fi{}0.010$, a factor of $3$ improvement over previous constraints. We also find no evidence of tensors, $rl0.36$ ($95%$ c.l.). Inflationary models predict the absence of running and many among them satisfy these constraints, particularly negative curvature models such as those based on spontaneous symmetry breaking. A positive correlation between tensors and primordial slope disfavors chaotic inflation-type models with steep slopes: while the $V\ensuremath{\propto}{\ensuremath{\phi}}^{2}$ model is within the 2-sigma contour, $V\ensuremath{\propto}{\ensuremath{\phi}}^{4}$ is outside the 3-sigma contour. For the amplitude we find ${\ensuremath{\sigma}}_{8}=0.90\ifmmode\pm\else\textpm\fi{}0.03$ from the Ly$\ensuremath{\alpha}$ forest and WMAP alone. We find no evidence of neutrino mass: for the case of $3$ massive neutrino families with an inflationary prior, $\ensuremath{\sum}_{}^{}{m}_{\ensuremath{ u}}l0.42$ eV and the mass of lightest neutrino is ${m}_{1}l0.13$ eV at $95%$ c.l. For the 3 massless $+1$ massive neutrino case we find ${m}_{\ensuremath{ u}}l0.79$ eV for the massive neutrino, excluding at $95%$ c.l. all neutrino mass solutions compatible with the LSND results. We explore dark energy constraints in models with a fairly general time dependence of dark energy equation of state, finding ${\ensuremath{\Omega}}_{\ensuremath{\lambda}}=0.72\ifmmode\pm\else\textpm\fi{}0.02$, $\mathrm{w}(z=0.3)=\ensuremath{-}{0.98}_{\ensuremath{-}0.12}^{+0.10}$, the latter changing to $\mathrm{w}(z=0.3)=\ensuremath{-}{0.92}_{\ensuremath{-}0.10}^{+0.09}$ if tensors are allowed. We find no evidence for variation of the equation of state with redshift, $\mathrm{w}(z=1)=\ensuremath{-}{1.03}_{\ensuremath{-}0.28}^{+0.21}$. These results rely on the current understanding of the Ly$\ensuremath{\alpha}$ forest and other probes, which need to be explored further both observationally and theoretically, but extensive tests reveal no evidence of inconsistency among different data sets used here.

Antarctic climate change during the last 50 years

Abstract: The Reference Antarctic Data for Environmental Research (READER) project data set of monthly mean Antarctic nearsurface temperature, mean sea-level pressure (MSLP) and wind speed has been used to investigate trends in these quantities over the last 50 years for 19 stations with long records. Eleven of these had warming trends and seven had cooling trends in their annual data (one station had too little data to allow an annual trend to be computed), indicating the spatial complexity of change that has occurred across the Antarctic in recent decades. The Antarctic Peninsula has experienced a major warming over the last 50 years, with temperatures at Faraday/Vernadsky station having increased at a rate of 0.56 °C decade −1 over the year and 1.09 °C decade −1 during the winter; both figures are statistically significant at less than the 5% level. Overlapping 30 year trends of annual mean temperatures indicate that, at all but two of the 10 coastal stations for which trends could be computed back to 1961, the warming trend was greater (or the cooling trend less) during the 1961–90 period compared with 1971–2000. All the continental stations for which MSLP data were available show negative trends in the annual mean pressures over the full length of their records, which we attribute to the trend in recent decades towards the Southern Hemisphere annular mode (SAM) being in its high-index state. Except for Halley, where the trends are constant, the MSLP trends for all stations on the Antarctic continent for 1971–2000 were more negative than for 1961–90. All but two of the coastal stations have recorded increasing mean wind speeds over recent decades, which is also consistent with the change in the nature of the SAM. Copyright  2005 Royal Meteorological Society.

On the Nature of Reactance and its Role in Persuasive Health Communication

Abstract: Reactance theory might be profitably applied to understanding failures in persuasive health communication but for one drawback: The developer of the theory contends that reactance cannot be measured. Rejecting this position, this paper develops four alternative conceptual perspectives on the nature of reactance (i.e., combinations of cognition and affect), then provides an empirical test of each. Two parallel studies were conducted, one advocating flossing (N = 196), the other urging students to limit their alcohol intake (N = 200). In both cases, a composite index of anger and negative cognitions fully mediated the effects of threat-to-freedom and trait reactance on attitude and intention. The data showed that, in fact, reactance can be operationalized as a composite of self-report indices of anger and negative cognitions. The implications for persuasive communication, in general, are considered as well the specific findings for flossing and drinking.

Input-based and time-based models of international adjustment: Meta-analytic evidence and theoretical extensions

Abstract: Integrating work on international assignments and domestic stress, we conducted meta-analyses of over 50 determinants and consequences of expatriate adjustment using data from 8,474 expatriates in ...

The great Sumatra-Andaman earthquake of 26 December 2004

Abstract: The two largest earthquakes of the past 40 years ruptured a 1600-kilometer-long portion of the fault boundary between the Indo-Australian and southeastern Eurasian plates on 26 December 2004 [seismic moment magnitude (Mw) = 9.1 to 9.3] and 28 March 2005 (Mw = 8.6). The first event generated a tsunami that caused more than 283,000 deaths. Fault slip of up to 15 meters occurred near Banda Aceh, Sumatra, but to the north, along the Nicobar and Andaman Islands, rapid slip was much smaller. Tsunami and geodetic observations indicate that additional slow slip occurred in the north over a time scale of 50 minutes or longer.

SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans

Abstract: Lighter variations of pigmentation in humans are associated with diminished number, size, and density of melanosomes, the pigmented organelles of melanocytes. Here we show that zebrafish golden mutants share these melanosomal changes and that golden encodes a putative cation exchanger slc24a5 (nckx5) that localizes to an intracellular membrane, likely the melanosome or its precursor. The human ortholog is highly similar in sequence and functional in zebrafish. The evolutionarily conserved ancestral allele of a human coding polymorphism predominates in African and East Asian populations. In contrast, the variant allele is nearly fixed in European populations, is associated with a substantial reduction in regional heterozygosity, and correlates with lighter skin pigmentation in admixed populations, suggesting a key role for the SLC24A5 gene in human pigmentation.

Production of Electricity from Acetate or Butyrate Using a Single-Chamber Microbial Fuel Cell

Abstract: Hydrogen can be recovered by fermentation of organic material rich in carbohydrates, but much of the organic matter remains in the form of acetate and butyrate. An alternative to methane production from this organic matter is the direct generation of electricity in a microbial fuel cell (MFC). Electricity generation using a single-chambered MFC was examined using acetate or butyrate. Power generated with acetate (800 mg/L) (506 mW/m2 or 12.7 mW/L) was up to 66% higher than that fed with butyrate (1000 mg/L) (305 mW/m2 or 7.6 mW/L), demonstrating that acetate is a preferred aqueous substrate for electricity generation in MFCs. Power output as a function of substrate concentration was well described by saturation kinetics, although maximum power densities varied with the circuit load. Maximum power densities and half-saturation constants were Pmax = 661 mW/m2 and Ks = 141 mg/L for acetate (218 Ω) and Pmax = 349 mW/m2 and Ks = 93 mg/L for butyrate (1000 Ω). Similar open circuit potentials were obtained in us...

Electrochemically Assisted Microbial Production of Hydrogen from Acetate

Abstract: Hydrogen production via bacterial fermentation is currently limited to a maximum of 4 moles of hydrogen per mole of glucose, and under these conditions results in a fermentation end product (acetate; 2 mol/mol glucose) that bacteria are unable to further convert to hydrogen. It is shown here that this biochemical barrier can be circumvented by generating hydrogen gas from acetate using a completely anaerobic microbial fuel cell (MFC). By augmenting the electrochemical potential achieved by bacteria in this MFC with an additional voltage of 250 mV or more, it was possible to produce hydrogen at the cathode directly from the oxidized organic matter. More than 90% of the protons and electrons produced by the bacteria from the oxidation of acetate were recovered as hydrogen gas, with an overall Coulombic efficiency (total recovery of electrons from acetate) of 60−78%. This is equivalent to an overall yield of 2.9 mol H2/mol acetate (assuming 78% Coulombic efficiency and 92% recovery of electrons as hydrogen)....

Intrinsic and Extrinsic Size Effects in Fine-Grained Morphotropic-Phase-Boundary Lead Zirconate Titanate Ceramics

Abstract: The processing, electromechanical properties, and microstructure of lead zirconate titanate (PZT) ceramics over the grain-size range of 0.1-10 μm were studied. Using measurements over a large temperature range (15-600 K), the relative role of extrinsic contribution (i.e., domain-wall motion) was deduced to be influenced strongly by the grain size, particularly for donor-doped PZT. Analytical transmission electron microscopy studies were conducted to investigate the trend in domain configurations with the reduction of grain size. The correlations between domain density, domain variants, domain configurations (before and after poling), spontaneous deformation, and the elastodielectric properties were qualitatively discussed, leading to new insights into the intrinsic and extrinsic effects and relevant size effects in ferroelectric polycrystalline materials.

Power generation in fed-batch microbial fuel cells as a function of ionic strength, temperature, and reactor configuration

Abstract: Power density, electrode potential, coulombic efficiency, and energy recovery in single-chamber microbial fuel cells (MFCs) were examined as a function of solution ionic strength, electrode spacing and composition, and temperature. Increasing the solution ionic strength from 100 to 400 mM by adding NaCl increased power output from 720 to 1330 mW/m2. Power generation was also increased from 720 to 1210 mW/m2 by decreasing the distance between the anode and cathode from 4to 2 cm. The power increases due to ionic strength and electrode spacing resulted from a decrease in the internal resistance. Power output was also increased by 68% by replacing the cathode (purchased from a manufacturer) with our own carbon cloth cathode containing the same Pt loading. The performance of conventional anaerobic treatment processes, such as anaerobic digestion, are adversely affected by temperatures below 30 degrees C. However, decreasing the temperature from 32 to 20 degrees C reduced power output by only 9%, primarily as a result of the reduction of the cathode potential. Coulombic efficiencies and overall energy recovery varied as a function of operating conditions, but were a maximum of 61.4 and 15.1% (operating conditions of 32 degrees C, carbon paper cathode, and the solution amended with 300 mM NaCl). These results, which demonstrate that power densities can be increased to over 1 W/m2 by changing the operating conditions or electrode spacing, should lead to further improvements in power generation and energy recovery in single-chamber, air-cathode MFCs.