Showing papers by "Iowa State University published in 2008"

The CMS experiment at the CERN LHC

Abstract: The Compact Muon Solenoid (CMS) detector is described. The detector operates at the Large Hadron Collider (LHC) at CERN. It was conceived to study proton-proton (and lead-lead) collisions at a centre-of-mass energy of 14 TeV (5.5 TeV nucleon-nucleon) and at luminosities up to 10(34)cm(-2)s(-1) (10(27)cm(-2)s(-1)). At the core of the CMS detector sits a high-magnetic-field and large-bore superconducting solenoid surrounding an all-silicon pixel and strip tracker, a lead-tungstate scintillating-crystals electromagnetic calorimeter, and a brass-scintillator sampling hadron calorimeter. The iron yoke of the flux-return is instrumented with four stations of muon detectors covering most of the 4 pi solid angle. Forward sampling calorimeters extend the pseudo-rapidity coverage to high values (vertical bar eta vertical bar <= 5) assuring very good hermeticity. The overall dimensions of the CMS detector are a length of 21.6 m, a diameter of 14.6 m and a total weight of 12500 t.

Use of U.S. Croplands for Biofuels Increases Greenhouse Gases Through Emissions from Land-Use Change

Abstract: Most prior studies have found that substituting biofuels for gasoline will reduce greenhouse gases because biofuels sequester carbon through the growth of the feedstock. These analyses have failed to count the carbon emissions that occur as farmers worldwide respond to higher prices and convert forest and grassland to new cropland to replace the grain (or cropland) diverted to biofuels. By using a worldwide agricultural model to estimate emissions from land-use change, we found that corn-based ethanol, instead of producing a 20% savings, nearly doubles greenhouse emissions over 30 years and increases greenhouse gases for 167 years. Biofuels from switchgrass, if grown on U.S. corn lands, increase emissions by 50%. This result raises concerns about large biofuel mandates and highlights the value of using waste products.

Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Abstract: Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms Recent reviews have described the range of assays that have been used for this purpose(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi) Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response

An introduction to latent class growth analysis and growth mixture modeling.

Abstract: In recent years, there has been a growing interest among researchers in the use of latent class and growth mixture modeling techniques for applications in the social and psychological sciences, in part due to advances in and availability of computer software designed for this purpose (e.g., Mplus and SAS Proc Traj). Latent growth modeling approaches, such as latent class growth analysis (LCGA) and growth mixture modeling (GMM), have been increasingly recognized for their usefulness for identifying homogeneous subpopulations within the larger heterogeneous population and for the identification of meaningful groups or classes of individuals. The purpose of this paper is to provide an overview of LCGA and GMM, compare the different techniques of latent growth modeling, discuss current debates and issues, and provide readers with a practical guide for conducting LCGA and GMM using the Mplus software. Researchers in the fields of social and psychological sciences are often interested in modeling the longitudinal developmental trajectories of individuals, whether for the study of personality development or for better understanding how social behaviors unfold over time (whether it be days, months, or years). This usually requires an extensive dataset consisting of longitudinal, repeated measures of variables, sometimes including multiple cohorts, and analyzing this data using various longitudinal latent variable modeling techniques such as latent growth curve models (cf. MacCallum & Austin, 2000). The objective of these approaches is to capture information about interindividual differences in intraindividual change over time (Nesselroade, 1991). However, conventional growth modeling approaches assume that individuals come from a single population and that a single growth trajectory can adequately approximate an entire population. Also, it is assumed that covariates that affect the growth factors influence each individual in the same way. Yet, theoretical frameworks and existing studies often categorize individuals into distinct subpopulations (e.g., socioeconomic classes, age groups, at-risk populations). For example, in the field of alcohol research, theoretical literature suggests different classes

Magnetic order close to superconductivity in the iron-based layered LaO1-xFxFeAs systems

Abstract: Following the discovery of long-range antiferromagnetic order in the parent compounds of high-transition-temperature (high-T(c)) copper oxides, there have been efforts to understand the role of magnetism in the superconductivity that occurs when mobile 'electrons' or 'holes' are doped into the antiferromagnetic parent compounds. Superconductivity in the newly discovered rare-earth iron-based oxide systems ROFeAs (R, rare-earth metal) also arises from either electron or hole doping of their non-superconducting parent compounds. The parent material LaOFeAs is metallic but shows anomalies near 150 K in both resistivity and d.c. magnetic susceptibility. Although optical conductivity and theoretical calculations suggest that LaOFeAs exhibits a spin-density-wave (SDW) instability that is suppressed by doping with electrons to induce superconductivity, there has been no direct evidence of SDW order. Here we report neutron-scattering experiments that demonstrate that LaOFeAs undergoes an abrupt structural distortion below 155 K, changing the symmetry from tetragonal (space group P4/nmm) to monoclinic (space group P112/n) at low temperatures, and then, at approximately 137 K, develops long-range SDW-type antiferromagnetic order with a small moment but simple magnetic structure. Doping the system with fluorine suppresses both the magnetic order and the structural distortion in favour of superconductivity. Therefore, like high-T(c) copper oxides, the superconducting regime in these iron-based materials occurs in close proximity to a long-range-ordered antiferromagnetic ground state.

Parallel cylindrical water nanochannels in Nafion fuel-cell membranes.

Abstract: The structure of the Nafion ionomer used in proton-exchange membranes of H(2)/O(2) fuel cells has long been contentious. Using a recently introduced algorithm, we have quantitatively simulated previously published small-angle scattering data of hydrated Nafion. The characteristic 'ionomer peak' arises from long parallel but otherwise randomly packed water channels surrounded by partially hydrophilic side branches, forming inverted-micelle cylinders. At 20 vol% water, the water channels have diameters of between 1.8 and 3.5 nm, with an average of 2.4 nm. Nafion crystallites (approximately 10 vol%), which form physical crosslinks that are crucial for the mechanical properties of Nafion films, are elongated and parallel to the water channels, with cross-sections of approximately (5 nm)(2). Simulations for various other models of Nafion, including Gierke's cluster and the polymer-bundle model, do not match the scattering data. The new model can explain important features of Nafion, including fast diffusion of water and protons through Nafion and its persistence at low temperatures.

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Abstract: Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.

Soil Moisture Measurement for Ecological and Hydrological Watershed-Scale Observatories: A Review

Abstract: At the watershed scale, soil moisture is the major control for rainfall–runoff response, especially where saturation excess runoff processes dominate. From the ecological point of view, the pools of soil moisture are fundamental ecosystem resources providing the transpirable water for plants. In drylands particularly, soil moisture is one of the major controls on the structure, function, and diversity in ecosystems. In terms of the global hydrological cycle, the overall quantity of soil moisture is small, ∼0.05%; however, its importance to the global energy balance and the distribution of precipitation far outweighs its physical amount. In soils it governs microbial activity that affects important biogeochemical processes such as nitrification and CO2 production via respiration. During the past 20 years, technology has advanced considerably, with the development of different electrical sensors for determining soil moisture at a point. However, modeling of watersheds requires areal averages. As a result, point measurements and modeling grid cell data requirements are generally incommensurate. We review advances in sensor technology, particularly emerging geophysical methods and distributed sensors, aimed at bridging this gap. We consider some of the data analysis methods for upscaling from a point to give an areal average. Finally, we conclude by offering a vision for future research, listing many of the current scientific and technical challenges.

Insect resistance to Bt crops: evidence versus theory

Abstract: Evolution of insect resistance threatens the continued success of transgenic crops producing Bacillus thuringiensis (Bt) toxins that kill pests. The approach used most widely to delay insect resistance to Bt crops is the refuge strategy, which requires refuges of host plants without Bt toxins near Bt crops to promote survival of susceptible pests. However, large-scale tests of the refuge strategy have been problematic. Analysis of more than a decade of global monitoring data reveals that the frequency of resistance alleles has increased substantially in some field populations of Helicoverpa zea, but not in five other major pests in Australia, China, Spain and the United States. The resistance of H. zea to Bt toxin Cry1Ac in transgenic cotton has not caused widespread crop failures, in part because other tactics augment control of this pest. The field outcomes documented with monitoring data are consistent with the theory underlying the refuge strategy, suggesting that refuges have helped to delay resistance.

An overlapping essential gene in the Potyviridae.

Abstract: The family Potyviridae includes >30% of known plant virus species, many of which are of great agricultural significance. These viruses have a positive sense RNA genome that is ≈10 kb long and contains a single long ORF. The ORF is translated into a large polyprotein, which is cleaved into ≈10 mature proteins. We report the discovery of a short ORF embedded within the P3 cistron of the polyprotein but translated in the +2 reading-frame. The ORF, termed pipo, is conserved and has a strong bioinformatic coding signature throughout the large and diverse Potyviridae family. Mutations that knock out expression of the PIPO protein in Turnip mosaic potyvirus but leave the polyprotein amino acid sequence unaltered are lethal to the virus. Immunoblotting with antisera raised against two nonoverlapping 14-aa antigens, derived from the PIPO amino acid sequence, reveals the expression of an ≈25-kDa PIPO fusion product in planta. This is consistent with expression of PIPO as a P3-PIPO fusion product via ribosomal frameshifting or transcriptional slippage at a highly conserved G1-2A6-7 motif at the 5′ end of pipo. This discovery suggests that other short overlapping genes may remain hidden even in well studied virus genomes (as well as cellular organisms) and demonstrates the utility of the software package MLOGD as a tool for identifying such genes.

ATLAS pixel detector electronics and sensors

Abstract: The silicon pixel tracking system for the ATLAS experiment at the Large Hadron Collider is described and the performance requirements are summarized. Detailed descriptions of the pixel detector electronics and the silicon sensors are given. The design, fabrication, assembly and performance of the pixel detector modules are presented. Data obtained from test beams as well as studies using cosmic rays are also discussed.

Genome analysis of the platypus reveals unique signatures of evolution

Abstract: We present a draft genome sequence of the platypus, Ornithorhynchus anatinus This monotreme exhibits a fascinating combination of reptilian and mammalian characters For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles Analysis of the first monotreme genome aligned these features with genetic innovations We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation

Thirty years of near room temperature magnetic cooling: Where we are today and future prospects

Abstract: The seminal study by Brown in 1976 showed that it was possible to use the magnetocaloric effect to produce a substantial cooling effect near room temperature. About 15 years later Green et al. built a device which actually cooled a load other than the magnetocaloric material itself and the heat exchange fluid. The major breakthrough, however, occurred in 1997 when the Ames Laboratory/Astronautics proof-of-principle refrigerator showed that magnetic refrigeration was competitive with conventional gas compression cooling. Since then, over 25 magnetic cooling units have been built and tested throughout the world. The current status of near room temperature magnetic cooling is reviewed, including a discussion of the major problems facing commercialization and potential solutions thereof. The future outlook for this revolutionary technology is discussed.

Predicting linear B-cell epitopes using string kernels.

Abstract: The identification and characterization of B-cell epitopes play an important role in vaccine design, immunodiagnostic tests, and antibody production Therefore, computational tools for reliably predicting linear B-cell epitopes are highly desirable We evaluated Support Vector Machine (SVM) classifiers trained utilizing five different kernel methods using fivefold cross-validation on a homology-reduced data set of 701 linear B-cell epitopes, extracted from Bcipep database, and 701 non-epitopes, randomly extracted from SwissProt sequences Based on the results of our computational experiments, we propose BCPred, a novel method for predicting linear B-cell epitopes using the subsequence kernel We show that the predictive performance of BCPred (AUC = 0758) outperforms 11 SVM-based classifiers developed and evaluated in our experiments as well as our implementation of AAP (AUC = 07), a recently proposed method for predicting linear B-cell epitopes using amino acid pair antigenicity Furthermore, we compared BCPred with AAP and ABCPred, a method that uses recurrent neural networks, using two data sets of unique B-cell epitopes that had been previously used to evaluate ABCPred Analysis of the data sets used and the results of this comparison show that conclusions about the relative performance of different B-cell epitope prediction methods drawn on the basis of experiments using data sets of unique B-cell epitopes are likely to yield overly optimistic estimates of performance of evaluated methods This argues for the use of carefully homology-reduced data sets in comparing B-cell epitope prediction methods to avoid misleading conclusions about how different methods compare to each other Our homology-reduced data set and implementations of BCPred as well as the APP method are publicly available through our web-based server, BCPREDS, at: http://ailabcsiastateedu/bcpreds/

Evolutionary Genetics of Genome Merger and Doubling in Plants

Abstract: Polyploidy is a common mode of evolution in flowering plants. The profound effects of polyploidy on gene expression appear to be caused more by hybridity than by genome doubling. Epigenetic mechanisms underlying genome-wide changes in expression are as yet poorly understood; only methylation has received much study, and its importance varies among polyploids. Genetic diploidization begins with the earliest responses to genome merger and doubling; less is known about chromosomal diploidization. Polyploidy duplicates every gene in the genome, providing the raw material for divergence or partitioning of function in homoeologous copies. Preferential retention or loss of genes occurs in a wide range of taxa, suggesting that there is an underlying set of principles governing the fates of duplicated genes. Further studies are required for general patterns to be elucidated, involving different plant families, kinds of polyploidy, and polyploids of different ages.

Do bridging ties complement strong ties? An empirical examination of alliance ambidexterity

Abstract: This study examines the underexplored tensions and complementarities between bridging ties and strong ties in innovation-seeking alliances. Bridging ties span structural holes to provide innovation potential but lack integration capacity, and strong ties provide integration capacity but lack innovation potential. We theoretically develop the idea that—notwithstanding their tensions—strong ties complement bridging ties in enhancing alliance ambidexterity at the project level. While bridging ties provide access to diverse, structural hole-spanning perspectives and capabilities, strong ties help integrate them to realize an innovation. We also propose that their effects and complementarities influence alliance ambidexterity because they facilitate knowledge integration at the project level. Tests using data on 42 innovation-seeking project alliances involving a major American services conglomerate and its alliance partners support the majority of the proposed ideas. Implications for interfirm network configuration, strategic alliances, and the broader strategy literature are also discussed. Copyright © 2007 John Wiley & Sons, Ltd.

Quality control for plant metabolomics: reporting MSI‐compliant studies

Abstract: The Metabolomics Standards Initiative (MSI) has recently released documents describing minimum parameters for reporting metabolomics experiments, in order to validate metabolomic studies and to facilitate data exchange. The reporting parameters encompassed by MSI include the biological study design, sample preparation, data acquisition, data processing, data analysis and interpretation relative to the biological hypotheses being evaluated. Herein we exemplify how such metadata can be reported by using a small case study - the metabolite profiling by GC-TOF mass spectrometry of Arabidopsis thaliana leaves from a knockout allele of the gene At1g08510 in the Wassilewskija ecotype. Pitfalls in quality control are highlighted that can invalidate results even if MSI reporting standards are fulfilled, including reliable compound identification and integration of unknown metabolites. Standardized data processing methods are proposed for consistent data storage and dissemination via databases.

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Abstract: The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those exploring the range of extant checklists.

Vulnerability Assessment of Cybersecurity for SCADA Systems

Abstract: Vulnerability assessment is a requirement of NERC's cybersecurity standards for electric power systems. The purpose is to study the impact of a cyber attack on supervisory control and data acquisition (SCADA) systems. Compliance of the requirement to meet the standard has become increasingly challenging as the system becomes more dispersed in wide areas. Interdependencies between computer communication system and the physical infrastructure also become more complex as information technologies are further integrated into devices and networks. This paper proposes a vulnerability assessment framework to systematically evaluate the vulnerabilities of SCADA systems at three levels: system, scenarios, and access points. The proposed method is based on cyber systems embedded with the firewall and password models, the primary mode of protection in the power industry today. The impact of a potential electronic intrusion is evaluated by its potential loss of load in the power system. This capability is enabled by integration of a logic-based simulation method and a module for the power flow computation. The IEEE 30-bus system is used to evaluate the impact of attacks launched from outside or from within the substation networks. Countermeasures are identified for improvement of the cybersecurity.

SERS as a bioassay platform: fundamentals, design, and applications

Abstract: Bioanalytical science is experiencing a period of unprecedented growth. Drivers behind this growth include the need to detect markers central to human and veterinary diagnostics at ever-lower levels and greater speeds. A set of parallel arguments applies to pathogens with respect to bioterrorism prevention and food and water safety. This tutorial review outlines our recent explorations on the use of surface enhanced Raman scattering (SERS) for detection of proteins, viruses, and microorganisms in heterogeneous immunoassays. It will detail the design and fabrication of the assay platform, including the capture substrate and nanoparticle-based labels. The latter, which is the cornerstone of our strategy, relies on the construction of gold nanoparticles modified with both an intrinsically strong Raman scatterer and an antibody. This labelling motif, referred to as extrinsic Raman labels (ERLs), takes advantage of the well-established signal enhancement of scatterers when coated on nanometre-sized gold particles, whereas the antibody imparts antigenic specificity. We will also examine the role of plasmon coupling between the ERLs and capture substrate, and challenges related to particle stability, nonspecific adsorption, and assay speed.

Parallel Computing Experiences with CUDA

Abstract: The CUDA programming model provides a straightforward means of describing inherently parallel computations, and NVIDIA's Tesla GPU architecture delivers high computational throughput on massively parallel problems. This article surveys experiences gained in applying CUDA to a diverse set of problems and the parallel speedups over sequential codes running on traditional CPU architectures attained by executing key computations on the GPU.

Patterns of Bat Fatalities at Wind Energy Facilities in North America

Abstract: Wind has become one of the fastest growing sources of renewable energy worldwide, but widespread and often extensive fatalities of bats have increased concern regarding the impacts of wind energy development on bats and other wildlife. We synthesized available information on patterns of bat fatalities from a review of 21 postconstruction fatality studies conducted at 19 facilities in 5 United States regions and one Canadian province. Dominance of migratory, foliage- and tree-roosting lasiurine species (e.g., hoary bat [Lasiurus cinereus]) killed by turbines was consistent among studies. Bat fatalities, although highly variable and periodic, consistently peaked in late summer and fall, coinciding with migration of lasiurines and other species. A notable exception was documented fatalities of pregnant female Brazilian free-tailed bats (Tadarida brasiliensis) in May and June at a facility in Oklahoma, USA, and female silver-haired bats (Lasionycteris noctivagans) during spring in Tennessee, USA, and...

Unexpected failure rates for modular assembly of engineered zinc fingers

Abstract: Nat. Methods 5, 374–375 (2008); corrected after print 29 May 2008. In the version of this correspondence initially published, the two previously published datasets analyzed were labeled with incorrect references in Figure 1b. Reference 2 should be associated with the second column (80 sites), and reference 3 should be associated with the third column (96 sites).

Pressure induced superconductivity in CaFe2As2.

Abstract: ${\mathrm{CaFe}}_{2}{\mathrm{As}}_{2}$ has been found to be exceptionally sensitive to the application of hydrostatic pressure and can be tuned to reveal all the salient features associated with FeAs superconductivity without introducing any disorder. The ambient pressure, 170 K, structural/magnetic, first-order phase transition is suppressed to 128 K by 3.5 kbar. At 5.5 kbar a new transition is detected at 104 K, increasing to above 300 K by 19 kbar. A low temperature, superconducting dome (${T}_{c}\ensuremath{\sim}12\text{ }\text{ }\mathrm{K}$) is centered around 5 kbar, extending down to 2.3 kbar and up to 8.6 kbar. This superconducting phase appears to exist when the low pressure transition is suppressed sufficiently, but before the high pressure transition has reduced the resistivity too dramatically.

Sediment organic carbon burial in agriculturally eutrophic impoundments over the last century

Abstract: The OC buried in these lakes originates in both autochthonous and allochthonous production. These analyses suggest that OC sequestration in moderate to large impoundments may be double the rate assumed in previous analyses. Extrapolation suggests that they may bury 4 times as much carbon (C) as the world’s oceans. The world’s farm ponds alone may bury more OC than the oceans and 33% as much as the world’s rivers deliver to the sea.

Assessment of risk of insect-resistant transgenic crops to nontarget arthropods

Abstract: An international initiative is developing a scientifically rigorous approach to evaluate the potential risks to nontarget arthropods (NTAs) posed by insect-resistant, genetically modified (IRGM) crops. It adapts the tiered approach to risk assessment that is used internationally within regulatory toxicology and environmental sciences. The approach focuses on the formulation and testing of clearly stated risk hypotheses, making maximum use of available data and using formal decision guidelines to progress between testing stages (or tiers). It is intended to provide guidance to regulatory agencies that are currently developing their own NTA risk assessment guidelines for IRGM crops and to help harmonize regulatory requirements between different countries and different regions of the world.

Sustainable Biofuels Redux

Abstract: Science-based policy is essential for guiding an environmentally sustainable approach to cellulosic biofuels.