Showing papers by "University of Colorado Boulder published in 2007"

The human microbiome project.

Abstract: A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.

Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases

Abstract: The two primary human inflammatory bowel diseases, Crohn's disease (CD) and ulcerative colitis (UC), are idiopathic relapsing disorders characterized by chronic inflammation of the intestinal tract. Although several lines of reasoning suggest that gastrointestinal (GI) microbes influence inflammatory bowel disease (IBD) pathogenesis, the types of microbes involved have not been adequately described. Here we report the results of a culture-independent rRNA sequence analysis of GI tissue samples obtained from CD and UC patients, as well as non-IBD controls. Specimens were obtained through surgery from a variety of intestinal sites and included both pathologically normal and abnormal states. Our results provide comprehensive molecular-based analysis of the microbiota of the human small intestine. Comparison of clone libraries reveals statistically significant differences between the microbiotas of CD and UC patients and those of non-IBD controls. Significantly, our results indicate that a subset of CD and UC samples contained abnormal GI microbiotas, characterized by depletion of commensal bacteria, notably members of the phyla Firmicutes and Bacteroidetes. Patient stratification by GI microbiota provides further evidence that CD represents a spectrum of disease states and suggests that treatment of some forms of IBD may be facilitated by redress of the detected microbiological imbalances.

Toward an ecological classification of soil bacteria.

Abstract: Although researchers have begun cataloging the incredible diversity of bacteria found in soil, we are largely unable to interpret this information in an ecological context, including which groups of bacteria are most abundant in different soils and why. With this study, we examined how the abundances of major soil bacterial phyla correspond to the biotic and abiotic characteristics of the soil environment to determine if they can be divided into ecologically meaningful categories. To do this, we collected 71 unique soil samples from a wide range of ecosystems across North America and looked for relationships between soil properties and the relative abundances of six dominant bacterial phyla (Acidobacteria, Bacteroidetes, Firmicutes, Actinobacteria, alpha-Proteobacteria, and the beta-Proteobacteria). Of the soil properties measured, net carbon (C) mineralization rate (an index of C availability) was the best predictor of phylum-level abundances. There was a negative correlation between Acidobacteria abundance and C mineralization rates (r2 = 0.26, P < 0.001), while the abundances of beta-Proteobacteria and Bacteroidetes were positively correlated with C mineralization rates (r2 = 0.35, P < 0.001 and r2 = 0.34, P < 0.001, respectively). These patterns were explored further using both experimental and meta-analytical approaches. We amended soil cores from a specific site with varying levels of sucrose over a 12-month period to maintain a gradient of elevated C availabilities. This experiment confirmed our survey results: there was a negative relationship between C amendment level and the abundance of Acidobacteria (r2 = 0.42, P < 0.01) and a positive relationship for both Bacteroidetes and beta-Proteobacteria (r2 = 0.38 and 0.70, respectively; P < 0.01 for each). Further support for a relationship between the relative abundances of these bacterial phyla and C availability was garnered from an analysis of published bacterial clone libraries from bulk and rhizosphere soils. Together our survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r- and K-selected categories used to describe the ecological attributes of plants and animals. By applying the copiotroph-oligotroph concept to soil microorganisms we can make specific predictions about the ecological attributes of various bacterial taxa and better understand the structure and function of soil bacterial communities.

IPython: A System for Interactive Scientific Computing

Abstract: Python offers basic facilities for interactive work and a comprehensive library on top of which more sophisticated systems can be built. The IPython project provides on enhanced interactive environment that includes, among other features, support for data visualization and facilities for distributed and parallel computation

Ubiquity and dominance of oxygenated species in organic aerosols in anthropogenically-influenced Northern Hemisphere midlatitudes

Abstract: Organic aerosol (OA) data acquired by the Aerosol Mass Spectrometer (AMS) in 37 field campaigns were deconvolved into hydrocarbon-like OA (HOA) and several types of oxygenated OA (OOA) components. HOA has been linked to primary combustion emissions (mainly from fossil fuel) and other primary sources such as meat cooking. OOA is ubiquitous in various atmospheric environments, on average accounting for 64%, 83% and 95% of the total OA in urban, urban downwind, and rural/remote sites, respectively. A case study analysis of a rural site shows that the OOA concentration is much greater than the advected HOA, indicating that HOA oxidation is not an important source of OOA, and that OOA increases are mainly due to SOA. Most global models lack an explicit representation of SOA which may lead to significant biases in the magnitude, spatial and temporal distributions of OA, and in aerosol hygroscopic properties.

Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities

Abstract: The assessment of microbial diversity and distribution is a major concern in environmental microbiology. There are two general approaches for measuring community diversity: quantitative measures, which use the abundance of each taxon, and qualitative measures, which use only the presence/absence of data. Quantitative measures are ideally suited to revealing community differences that are due to changes in relative taxon abundance (e.g., when a particular set of taxa flourish because a limiting nutrient source becomes abundant). Qualitative measures are most informative when communities differ primarily by what can live in them (e.g., at high temperatures), in part because abundance information can obscure significant patterns of variation in which taxa are present. We illustrate these principles using two 16S rRNA-based surveys of microbial populations and two phylogenetic measures of community β diversity: unweighted UniFrac, a qualitative measure, and weighted UniFrac, a new quantitative measure, which we have added to the UniFrac website (http://bmf.colorado.edu/unifrac). These studies considered the relative influences of mineral chemistry, temperature, and geography on microbial community composition in acidic thermal springs in Yellowstone National Park and the influences of obesity and kinship on microbial community composition in the mouse gut. We show that applying qualitative and quantitative measures to the same data set can lead to dramatically different conclusions about the main factors that structure microbial diversity and can provide insight into the nature of community differences. We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny.

Processing seismic ambient noise data to obtain reliable broad-band surface wave dispersion measurements

Abstract: SUMMARY Ambient noise tomography is a rapidly emerging field of seismological research. This paper presents the current status of ambient noise data processing as it has developed over the past several years and is intended to explain and justify this development through salient examples. The ambient noise data processing procedure divides into four principal phases: (1) single station data preparation, (2) cross-correlation and temporal stacking, (3) measurement of dispersion curves (performed with frequency‐time analysis for both group and phase speeds) and (4) quality control, including error analysis and selection of the acceptable measurements. The procedures that are described herein have been designed not only to deliver reliable measurements, but to be flexible, applicable to a wide variety of observational settings, as well as being fully automated. For an automated data processing procedure, data quality control measures are particularly important to identify and reject bad measurements and compute quality assurance statistics for the accepted measurements. The principal metric on which to base a judgment of quality is stability, the robustness of the measurement to perturbations in the conditions under which it is obtained. Temporal repeatability, in particular, is a significant indicator of reliability and is elevated to a high position in our assessment, as we equate seasonal repeatability with measurement uncertainty. Proxy curves relating observed signal-to-noise ratios to average measurement uncertainties show promise to provide useful expected measurement error estimates in the absence of the long time-series needed for temporal subsetting.

Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database

Abstract: The past decade has witnessed hundreds of reports declaring or refuting genetic association with putative Alzheimer disease susceptibility genes. This wealth of information has become increasingly difficult to follow, much less interpret. We have created a publicly available, continuously updated database that comprehensively catalogs all genetic association studies in the field of Alzheimer disease (http://www.alzgene.org). We performed systematic meta-analyses for each polymorphism with available genotype data in at least three case-control samples. In addition to identifying the epsilon4 allele of APOE and related effects, we pinpointed over a dozen potential Alzheimer disease susceptibility genes (ACE, CHRNB2, CST3, ESR1, GAPDHS, IDE, MTHFR, NCSTN, PRNP, PSEN1, TF, TFAM and TNF) with statistically significant allelic summary odds ratios (ranging from 1.11-1.38 for risk alleles and 0.92-0.67 for protective alleles). Our database provides a powerful tool for deciphering the genetics of Alzheimer disease, and it serves as a potential model for tracking the most viable gene candidates in other genetically complex diseases.

C:N:P stoichiometry in soil: is there a “Redfield ratio” for the microbial biomass?

Abstract: Well-constrained carbon:nitrogen:phosphorus (C:N:P) ratios in planktonic biomass, and their importance in advancing our understanding of biological processes and nutrient cycling in marine ecosystems, has motivated ecologists to search for similar patterns in terrestrial ecosystems. Recent analyses indicate the existence of “Redfield-like” ratios in plants, and such data may provide insight into the nature of nutrient limitation in terrestrial ecosystems. We searched for analogous patterns in the soil and the soil microbial biomass by conducting a review of the literature. Although soil is characterized by high biological diversity, structural complexity and spatial heterogeneity, we found remarkably consistent C:N:P ratios in both total soil pools and the soil microbial biomass. Our analysis indicates that, similar to marine phytoplankton, element concentrations of individual phylogenetic groups within the soil microbial community may vary, but on average, atomic C:N:P ratios in both the soil (186:13:1) and the soil microbial biomass (60:7:1) are well-constrained at the global scale. We did see significant variation in soil and microbial element ratios between vegetation types (i.e., forest versus grassland), but in most cases, the similarities in soil and microbial element ratios among sites and across large scales were more apparent than the differences. Consistent microbial biomass element ratios, combined with data linking specific patterns of microbial element stoichiometry with direct evidence of microbial nutrient limitation, suggest that measuring the proportions of C, N and P in the microbial biomass may represent another useful tool for assessing nutrient limitation of ecosystem processes in terrestrial ecosystems.

The Honest Broker: Making Sense of Science in Policy and Politics

Abstract: Scientists have a choice concerning what role they should play in political debates and policy formation, particularly in terms of how they present their research. This book is about understanding this choice, what considerations are important to think about when deciding, and the consequences of such choices for the individual scientist and the broader scientific enterprise. Rather than prescribing what course of action each scientist ought to take, the book aims to identify a range of options for individual scientists to consider in making their own judgments about how they would like to position themselves in relation to policy and politics. Using examples from a range of scientific controversies and thought-provoking analogies from other walks of life, The Honest Broker challenges us all - scientists, politicians and citizens - to think carefully about how best science can contribute to policy-making and a healthy democracy.

Chemical and microphysical characterization of ambient aerosols with the aerodyne aerosol mass spectrometer

Abstract: The application of mass spectrometric techniques to the realtime measurement and characterization of aerosols represents a significant advance in the field of atmospheric science. This review focuses on the aerosol mass spectrometer (AMS), an instrument designed and developed at Aerodyne Research, Inc. (ARI) that is the most widely used thermal vaporization AMS. The AMS uses aerodynamic lens inlet technology together with thermal vaporization and electron-impact mass spectrometry to measure the real-time non-refractory (NR) chemical speciation and mass loading as a function of particle size of fine aerosol particles with aerodynamic diameters between similar to 50 and 1,000 nm. The original AMS utilizes a quadrupole mass spectrometer (Q) with electron impact (EI) ionization and produces ensemble average data of particle properties. Later versions employ time-of-flight (ToF) mass spectrometers and can produce full mass spectral data for single particles. This manuscript presents a detailed discussion of the strengths and limitations of the AMS measurement approach and reviews how the measurements are used to characterize particle properties. Results from selected laboratory experiments and field measurement campaigns are also presented to highlight the different applications of this instrument. Recent instrumental developments, such as the incorporation of softer ionization techniques (vacuum ultraviolet (VUV) photo-ionization, Li(+) ion, and electron attachment) and high-resolution ToF mass spectrometers, that yield more detailed information about the organic aerosol component are also described. (c) 2007 Wiley Periodicals, Inc.

Mars Reconnaissance Orbiter's High Resolution Imaging Science Experiment (HiRISE)

Abstract: [1] The HiRISE camera features a 0.5 m diameter primary mirror, 12 m effective focal length, and a focal plane system that can acquire images containing up to 28 Gb (gigabits) of data in as little as 6 seconds. HiRISE will provide detailed images (0.25 to 1.3 m/pixel) covering ∼1% of the Martian surface during the 2-year Primary Science Phase (PSP) beginning November 2006. Most images will include color data covering 20% of the potential field of view. A top priority is to acquire ∼1000 stereo pairs and apply precision geometric corrections to enable topographic measurements to better than 25 cm vertical precision. We expect to return more than 12 Tb of HiRISE data during the 2-year PSP, and use pixel binning, conversion from 14 to 8 bit values, and a lossless compression system to increase coverage. HiRISE images are acquired via 14 CCD detectors, each with 2 output channels, and with multiple choices for pixel binning and number of Time Delay and Integration lines. HiRISE will support Mars exploration by locating and characterizing past, present, and future landing sites, unsuccessful landing sites, and past and potentially future rover traverses. We will investigate cratering, volcanism, tectonism, hydrology, sedimentary processes, stratigraphy, aeolian processes, mass wasting, landscape evolution, seasonal processes, climate change, spectrophotometry, glacial and periglacial processes, polar geology, and regolith properties. An Internet Web site (HiWeb) will enable anyone in the world to suggest HiRISE targets on Mars and to easily locate, view, and download HiRISE data products.

Global patterns in bacterial diversity

Abstract: Microbes are difficult to culture. Consequently, the primary source of information about a fundamental evolutionary topic, life's diversity, is the environmental distribution of gene sequences. We report the most comprehensive analysis of the environmental distribution of bacteria to date, based on 21,752 16S rRNA sequences compiled from 111 studies of diverse physical environments. We clustered the samples based on similarities in the phylogenetic lineages that they contain and found that, surprisingly, the major environmental determinant of microbial community composition is salinity rather than extremes of temperature, pH, or other physical and chemical factors represented in our samples. We find that sediments are more phylogenetically diverse than any other environment type. Surprisingly, soil, which has high species-level diversity, has below-average phylogenetic diversity. This work provides a framework for understanding the impact of environmental factors on bacterial evolution and for the direction of future sequencing efforts to discover new lineages.

Becoming a scientist: The role of undergraduate research in students' cognitive, personal, and professional development

Abstract: In this ethnographic study of summer undergraduate research (UR) experiences at four liberal arts colleges, where faculty and students work collaboratively on a project of mutual interest in an apprenticeship of authentic science research work, analysis of the accounts of faculty and student participants yields comparative insights into the structural elements of this form of UR program and its benefits for students. Comparison of the perspectives of faculty and their students revealed considerable agreement on the nature, range, and extent of students' UR gains. Specific student gains relating to the process of “becoming a scientist” were described and illustrated by both groups. Faculty framed these gains as part of professional socialization into the sciences. In contrast, students emphasized their personal and intellectual development, with little awareness of their socialization into professional practice. Viewing study findings through the lens of social constructivist learning theories demonstrates that the characteristics of these UR programs, how faculty practice UR in these colleges, and students' outcomes—including cognitive and personal growth and the development of a professional identity—strongly exemplify many facets of these theories, particularly, student-centered and situated learning as part of cognitive apprenticeship in a community of practice. © 2006 Wiley Periodicals, Inc. Sci Ed91:36–74, 2007

CMS physics technical design report, volume II: Physics performance

Abstract: CMS is a general purpose experiment, designed to study the physics of pp collisions at 14 TeV at the Large Hadron Collider (LHC). It currently involves more than 2000 physicists from more than 150 institutes and 37 countries. The LHC will provide extraordinary opportunities for particle physics based on its unprecedented collision energy and luminosity when it begins operation in 2007. The principal aim of this report is to present the strategy of CMS to explore the rich physics programme offered by the LHC. This volume demonstrates the physics capability of the CMS experiment. The prime goals of CMS are to explore physics at the TeV scale and to study the mechanism of electroweak symmetry breaking--through the discovery of the Higgs particle or otherwise. To carry out this task, CMS must be prepared to search for new particles, such as the Higgs boson or supersymmetric partners of the Standard Model particles, from the start-up of the LHC since new physics at the TeV scale may manifest itself with modest data samples of the order of a few fb−1 or less. The analysis tools that have been developed are applied to study in great detail and with all the methodology of performing an analysis on CMS data specific benchmark processes upon which to gauge the performance of CMS. These processes cover several Higgs boson decay channels, the production and decay of new particles such as Z' and supersymmetric particles, Bs production and processes in heavy ion collisions. The simulation of these benchmark processes includes subtle effects such as possible detector miscalibration and misalignment. Besides these benchmark processes, the physics reach of CMS is studied for a large number of signatures arising in the Standard Model and also in theories beyond the Standard Model for integrated luminosities ranging from 1 fb−1 to 30 fb−1. The Standard Model processes include QCD, B-physics, diffraction, detailed studies of the top quark properties, and electroweak physics topics such as the W and Z0 boson properties. The production and decay of the Higgs particle is studied for many observable decays, and the precision with which the Higgs boson properties can be derived is determined. About ten different supersymmetry benchmark points are analysed using full simulation. The CMS discovery reach is evaluated in the SUSY parameter space covering a large variety of decay signatures. Furthermore, the discovery reach for a plethora of alternative models for new physics is explored, notably extra dimensions, new vector boson high mass states, little Higgs models, technicolour and others. Methods to discriminate between models have been investigated. This report is organized as follows. Chapter 1, the Introduction, describes the context of this document. Chapters 2-6 describe examples of full analyses, with photons, electrons, muons, jets, missing ET, B-mesons and τ's, and for quarkonia in heavy ion collisions. Chapters 7-15 describe the physics reach for Standard Model processes, Higgs discovery and searches for new physics beyond the Standard Model

Simulation of networks of spiking neurons: A review of tools and strategies

Abstract: We review different aspects of the simulation of spiking neural networks. We start by reviewing the different types of simulation strategies and algorithms that are currently implemented. We next review the precision of those simulation strategies, in particular in cases where plasticity depends on the exact timing of the spikes. We overview different simulators and simulation environments presently available (restricted to those freely available, open source and documented). For each simulation tool, its advantages and pitfalls are reviewed, with an aim to allow the reader to identify which simulator is appropriate for a given task. Finally, we provide a series of benchmark simulations of different types of networks of spiking neurons, including Hodgkin-Huxley type, integrate-and-fire models, interacting with current-based or conductance-based synapses, using clock-driven or event-driven integration strategies. The same set of models are implemented on the different simulators, and the codes are made available. The ultimate goal of this review is to provide a resource to facilitate identifying the appropriate integration strategy and simulation tool to use for a given modeling problem related to spiking neural networks.

Effectiveness of Adjunctive Antidepressant Treatment for Bipolar Depression

Abstract: �Background Episodes of depression are the most frequent cause of disability among patients with bipolar disorder. The effectiveness and safety of standard antidepressant agents for depressive episodes associated with bipolar disorder (bipolar depression) have not been well studied. Our study was designed to determine whether adjunctive antidepressant therapy reduces symptoms of bipolar depression without increasing the risk of mania. Methods In this double-blind, placebo-controlled study, we randomly assigned subjects with bipolar depression to receive up to 26 weeks of treatment with a mood stabilizer plus adjunctive antidepressant therapy or a mood stabilizer plus a matching placebo, under conditions generalizable to routine clinical care. A standardized clinical monitoring form adapted from the mood-disorder modules of the Structured Clinical Interview for the Diagnostic and Statistical Manual of Mental Disorders, fourth edition, was used at all follow-up visits. The primary outcome was the percentage of subjects in each treatment group meeting the criterion for a durable recovery (8 consecutive weeks of euthymia). Secondary effectiveness outcomes and rates of treatment-emergent affective switch (a switch to mania or hypomania early in the course of treatment) were also examined. Results Forty-two of the 179 subjects (23.5%) receiving a mood stabilizer plus adjunctive antidepressant therapy had a durable recovery, as did 51 of the 187 subjects (27.3%) receiving a mood stabilizer plus a matching placebo (P = 0.40). Modest nonsignificant trends favoring the group receiving a mood stabilizer plus placebo were observed across the secondary outcomes. Rates of treatment-emergent affective switch were similar in the two groups. Conclusions The use of adjunctive, standard antidepressant medication, as compared with the use of mood stabilizers, was not associated with increased efficacy or with increased risk of treatment-emergent affective switch. Longer-term outcome studies are needed to fully assess the benefits and risks of antidepressant therapy for bipolar disorder. (ClinicalTrials.gov number, NCT00012558.)

Correlation of the highest-energy cosmic rays with nearby extragalactic objects.

Abstract: Using data collected at the Pierre Auger Observatory during the past 3.7 years, we demonstrate that there is a correlation between the arrival directions of cosmic rays with energy above {approx} 6 x 10{sup 19} eV and the positions of active galactic nuclei (AGN) lying within {approx} 75 Mpc. We reject the hypothesis of an isotropic distribution of these cosmic rays at over 99% confidence level from a prescribed a priori test. The correlation we observe is compatible with the hypothesis that the highest energy particles originate from nearby extragalactic sources whose flux has not been significantly reduced by interaction with the cosmic background radiation. AGN or objects having a similar spatial distribution are possible sources.

Microbial nitrogen limitation increases decomposition

Abstract: With anthropogenic nutrient inputs to ecosystems increasing globally, there are long-standing, fundamental questions about the role of nutrients in the decomposition of organic matter. We tested the effects of exogenous nitrogen and phosphorus inputs on litter decomposition across a broad suite of litter and soil types. In one experiment, C mineralization was compared across a wide array of plants individually added to a single soil, while in the second, C mineralization from a single substrate was compared across 50 soils. Counter to basic stoichiometric decomposition theory, low N availability can increase litter decomposition as microbes use labile substrates to acquire N from recalcitrant organic matter. This "microbial nitrogen mining" is consistently suppressed by high soil N supply or substrate N concentrations. There is no evidence for phosphorus mining as P fertilization increases short- and long-term mineralization. These results suggest that basic stoichiometric decomposition theory needs to be revised and ecosystem models restructured accordingly in order to predict ecosystem carbon storage responses to anthropogenic changes in nutrient availability.

Guidelines on nicotine dose selection for in vivo research

Abstract: Rationale This review provides insight for the judicious selection of nicotine dose ranges and routes of administration for in vivo studies. The literature is replete with reports in which a dosaging regimen chosen for a specific nicotine-mediated response was suboptimal for the species used. In many cases, such discrepancies could be attributed to the complex variables comprising species-specific in vivo responses to acute or chronic nicotine exposure.

Education for strategic environmental behavior

Abstract: This article reviews four bodies of research that shed light on how to promote active care for the environment in children and youth: research on sources of proenvironmental behavior, socialization for democratic skills and values, the development of a personal sense of competence, and the development of collective competence. The article begins with an overview of studies of formative childhood experiences reported by environmental activists and educators, followed by correlational and experimental studies with young people regarding factors associated with their taking action for the environment. Because behaviors with the largest potential benefits for the environment require political engagement, the article also reviews experiences associated with young people’s interest and engagement in public issues. Action for the environment in the home or in public arena like schools and communities requires a personal sense of competence and a sense of collective competence, or confidence in one’s ability to a...

Mapping protein post-translational modifications with mass spectrometry

Abstract: Post-translational modifications of proteins control many biological processes, and examining their diversity is critical for understanding mechanisms of cell regulation. Mass spectrometry is a fundamental tool for detecting and mapping covalent modifications and quantifying their changes. Modern approaches have made large-scale experiments possible, screening complex mixtures of proteins for alterations in chemical modifications. By profiling protein chemistries, biologists can gain deeper insight into biological control. The aim of this review is introduce biologists to current strategies in mass spectrometry–based proteomics that are used to characterize protein post-translational modifications, noting strengths and shortcomings of various approaches.

Short pyrosequencing reads suffice for accurate microbial community analysis

Abstract: Pyrosequencing technology allows us to characterize microbial communities using 16S ribosomal RNA (rRNA) sequences orders of magnitude faster and more cheaply than has previously been possible. However, results from different studies using pyrosequencing and traditional sequencing are often difficult to compare, because amplicons covering different regions of the rRNA might yield different conclusions. We used sequences from over 200 globally dispersed environments to test whether studies that used similar primers clustered together mistakenly, without regard to environment. We then tested whether primer choice affects sequence-based community analyses using UniFrac, our recently-developed method for comparing microbial communities. We performed three tests of primer effects. We tested whether different simulated amplicons generated the same UniFrac clustering results as near-full-length sequences for three recent large-scale studies of microbial communities in the mouse and human gut, and the Guerrero Negro microbial mat. We then repeated this analysis for short sequences (100-, 150-, 200- and 250-base reads) resembling those produced by pyrosequencing. The results show that sequencing effort is best focused on gathering more short sequences rather than fewer longer ones, provided that the primers are chosen wisely, and that community comparison methods such as UniFrac are surprisingly robust to variation in the region sequenced.

Scatter Search and Local NLP Solvers: A Multistart Framework for Global Optimization

Abstract: The algorithm described here, called OptQuest/NLP or OQNLP, is a heuristic designed to find global optima for pure and mixed integer nonlinear problems with many constraints and variables, where all problem functions are differentiable with respect to the continuous variables. It uses OptQuest, a commercial implementation of scatter search developed by OptTek Systems, Inc., to provide starting points for any gradient-based local solver for nonlinear programming (NLP) problems. This solver seeks a local solution from a subset of these points, holding discrete variables fixed. The procedure is motivated by our desire to combine the superior accuracy and feasibility-seeking behavior of gradient-based local NLP solvers with the global optimization abilities of OptQuest. Computational results include 155 smooth NLP and mixed integer nonlinear program (MINLP) problems due to Floudas et al. (1999), most with both linear and nonlinear constraints, coded in the GAMS modeling language. Some are quite large for global optimization, with over 100 variables and 100 constraints. Global solutions to almost all problems are found in a small number of local solver calls, often one or two.

Evaluation of Various Turbulence Models in Predicting Airflow and Turbulence in Enclosed Environments by CFD: Part 2—Comparison with Experimental Data from Literature

Abstract: Numerous turbulence models have been developed in the past two decades, and many of them can be used in predicting airflows and turbulence in enclosed environments. It is important to evaluate the generality and robustness of the turbulence models for various indoor airflow scenarios. This study evaluated the performance of eight turbulence models, potentially suitable for indoor airflow, in terms of accuracy and computing cost. These models cover a wide range of computational fluid dynamics (CFD) approaches, including Reynolds averaged Navier-Stokes (RANS) modeling, hybrid RANS and large-eddy simulation (or detached-eddy simulation [DES]), and large-eddy simulation (LES). The RANS turbulence models tested include the indoor zero-equation model, three two-equation models (the RNG k-∊, low Reynolds number k-∊, and SST k-ω models), a three-equation model ( model), and a Reynolds-stress model (RSM). The investigation tested these models for representative airflows in enclosed environments, such as forced con...