Showing papers by "Clemson University published in 2000"

Locating blood vessels in retinal images by piecewise threshold probing of a matched filter response

Abstract: Describes an automated method to locate and outline blood vessels in images of the ocular fundus. Such a tool should prove useful to eye care specialists for purposes of patient screening, treatment evaluation, and clinical study. The authors' method differs from previously known methods in that it uses local and global vessel features cooperatively to segment the vessel network. The authors evaluate their method using hand-labeled ground truth segmentations of 20 images. A plot of the operating characteristic shows that the authors' method reduces false positives by as much as 15 times over basic thresholding of a matched filter response (MFR), at up to a 75% true positive rate. For a baseline, they also compared the ground truth against a second hand-labeling, yielding a 90% true positive and a 4% false positive detection rate, on average. These numbers suggest there is still room for a 15% true positive rate improvement, with the same false positive rate, over the authors' method. They are making all their images and hand labelings publicly available for interested researchers to use in evaluating related methods.

PVFS: a parallel file system for linux clusters

Abstract: As Linux clusters have matured as platforms for low-cost, high-performance parallel computing, software packages to provide many key services have emerged, especially in areas such as message passing and networking. One area devoid of support, however, has been parallel file systems, which are critical for high-performance I/O on such clusters. We have developed a parallel file system for Linux clusters, called the Parallel Virtual File System (PVFS). PVFS is intended both as a high-performance parallel file system that anyone can download and use and as a tool for pursuing further research in parallel I/O and parallel file systems for Linux clusters. In this paper, we describe the design and implementation of PVFS and present performance results on the Chiba City cluster at Argonne. We provide performance results for a workload of concurrent reads and writes for various numbers of compute nodes, I/O nodes, and I/O request sizes. We also present performance results for MPI-IO on PVFS, both for a concurrent read/write workload and for the BTIO benchmark. We compare the I/O performance when using a Myrinet network versus a fast-ethernet network for I/O-related communication in PVFS. We obtained read and write bandwidths as high as 700 Mbytes/sec with Myrinet and 225 Mbytes/sec with fast ethernet.

Liquefaction resistance of soils from shear-wave velocity

Abstract: A simplified procedure using shear-wave velocity measurements for evaluating the liquefaction resistance of soils is presented. The procedure was developed in cooperation with industry, researchers, and practitioners and evolved from workshops in 1996 and 1998. It follows the general format of the Seed-Idriss simplified procedure based on standard penetration test blow count and was developed using case history data from 26 earthquakes and >70 measurement sites in soils ranging from fine sand to sandy gravel with cobbles to profiles including silty clay layers. Liquefaction resistance curves were established by applying a modified relationship between the shear-wave velocity and cyclic stress ratio for the constant average cyclic shear strain suggested by R. Dobry. These curves correctly predicted moderate to high liquefaction potential for >95% of the liquefaction case histories and are shown to be consistent with the standard penetration test based curves in sandy soils. A case study is provided to illustrate application of the procedure. Additional data are needed, particularly from denser soil deposits shaken by stronger ground motions, to further validate the simplified procedure.

Cannabinoids control spasticity and tremor in a multiple sclerosis model.

Abstract: Chronic relapsing experimental allergic encephalomyelitis (CREAE) is an autoimmune model of multiple sclerosis1. Although both these diseases are typified by relapsing-remitting paralytic episodes, after CREAE induction by sensitization to myelin antigens1 Biozzi ABH mice also develop spasticity and tremor. These symptoms also occur during multiple sclerosis and are difficult to control. This has prompted some patients to find alternative medicines, and to perceive benefit from cannabis use2. Although this benefit has been backed up by small clinical studies, mainly with non-quantifiable outcomes3,4,5,6,7, the value of cannabis use in multiple sclerosis remains anecdotal. Here we show that cannabinoid (CB) receptor agonism using R(+)-WIN 55,212, Δ9-tetrahydrocannabinol, methanandamide and JWH-133 (ref. 8) quantitatively ameliorated both tremor and spasticity in diseased mice. The exacerbation of these signs after antagonism of the CB1 and CB2 receptors, notably the CB1 receptor, using SR141716A and SR144528 (ref. 8) indicate that the endogenous cannabinoid system may be tonically active in the control of tremor and spasticity. This provides a rationale for patients' indications of the therapeutic potential of cannabis in the control of the symptoms of multiple sclerosis2, and provides a means of evaluating more selective cannabinoids in the future.

High figure of merit in partially filled ytterbium skutterudite materials

Abstract: We present evidence of a relatively high dimensionless figure of merit (ZT) in a polycrystalline skutterudite partially filled with ytterbium ions. The small-diameter yet heavy-mass Yb atoms partially filling the voids of the host CoSb3 system exhibit low values of thermal conductivity while the quite favorable electronic properties are not substantially perturbed by the addition of Yb. This combination is ideal for thermoelectric applications exemplifying the “phonon-glass electron-crystal” concept of a thermoelectric material, resulting in ZT=0.3 at room temperature and ZT∼1 at 600 K for Yb0.19Co4Sb12.

Contigs built with fingerprints, markers, and FPC V4.7

Abstract: Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human BAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 37 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation.

Characterization of microsatellite markers in peach (Prunus persica (L.) Batsch)

Abstract: Microsatellites have emerged as an important system of molecular markers. We evaluated the potential of microsatellites for use in genetic studies of peach [Prunus persica (L.) Batsch]. Microsatellite loci in peach were identified by screening a pUC8 genomic library, a λZAPII leaf cDNA library, as well as through database searches. Primer sequences for the microsatellite loci were tested from the related Rosaceae species apple (Malus×domestica) and sour cherry (Prunus cerasus L.). The genomic library was screened for CT, CA and AGG repeats, while the cDNA library was screened for (CT)n- and (CA)n-containing clones. Estimates of microsatellite frequencies were determined from the genomic library screening, and indicate that CT repeats occur every 100 kb, CA repeats every 420 kb, and AGG repeats every 700 kb in the peach genome. Microsatellite- containing clones were sequenced, and specific PCR primers were designed to amplify the microsatellite- containing regions from genomic DNA. The level of microsatellite polymorphism was evaluated among 28 scion peach cultivars which displayed one to four alleles per primer pair. Five microsatellites were found to segregate in intraspecific peach-mapping crosses. In addition, these microsatellite markers were tested for their utility in cross-species amplification for use in comparative mapping both within the Rosaceae, and with the un- related species Arabidopsis thaliana L.

Optical Limiting Properties of Suspended and Solubilized Carbon Nanotubes

Abstract: Full and shortened single-walled and multiple-walled carbon nanotubes were suspended in water to form stable suspensions in the presence of a surfactant. Optical limiting properties of the suspensions were determined for 532-nm pulsed laser irradiation, and the results were comparable with those of carbon black aqueous suspension. Solubilization of the shortened carbon nanotubes was achieved by attaching the nanotubes to highly soluble poly(propionylethylenimine-co-ethylenimine) or by functionalizing the nanotubes with octadecylamine. The soluble carbon nanotube samples formed homogeneous solutions in room-temperature chloroform. Optical limiting properties of these solutions were also determined for 532-nm pulsed laser irradiation, and the results were found to be quite different from those of the carbon nanotube aqueous suspensions. Apparently, the carbon nanotubes exhibit significantly weaker optical limiting responses in homogeneous solutions than in suspensions. Mechanistic implications of the experi...

JOINTLESS is a MADS-box gene controlling tomato flower abscission zone development

Abstract: Abscission is a universal and dynamic process in plants whereby organs such as leaves, flowers and fruit are shed, both during normal development, and in response to tissue damage and stress. Shedding occurs by separation of cells in anatomically distinct regions of the plant, called abscission zones (AZs). During abscission, the plant hormone ethylene stimulates cells to produce enzymes that degrade the middle lamella between cells in the AZ. The physiology and regulation of abscission at fully developed AZs is well known, but the molecular biology underlying their development is not. Here we report the first isolation of a gene directly involved in the development of a functional plant AZ. Tomato plants with the jointless mutation fail to develop AZs on their pedicels and so abscission of flowers or fruit does not occur normally. We identify JOINTLESS as a new MADS-box gene in a distinct phylogenetic clade separate from those functioning in floral organs. We propose that a deletion in JOINTLESS accounts for the failure of activation of pedicel AZ development in jointless tomato plants.

Accumulation of heavy metals by vegetables grown in mine wastes.

Abstract: Lead, cadmium, arsenic, and zinc were quantified in mine wastes and in soils mixed with mine wastes. Metal concen- trations were found to be heterogeneous in the wastes. Iceberg lettuce, Cherry Belle radishes, Roma bush beans, and Better Boy tomatoes were cultivated in mine wastes and in waste-amended soils. Lettuce and radishes had 100% survival in the 100% mine waste treatments compared to 0% and 25% survival for tomatoes and beans, respectively. Metal concentrations were determined in plant tissues to determine uptake and distribution of metals in the edible plant parts. Individual soil samples were collected beneath each plant to assess metal content in the immediate plant environment. This analysis verified heterogeneous metal content of the mine wastes. The four plant species effectively accumulated and translocated lead, cadmium, arsenic, and zinc. Tomato and bean plants contained the four metals mainly in the roots, and little was translocated to the fruits. Radish roots accumulated less metals compared to the leaves, whereas lettuce roots and leaves accumulated similar concentrations of the four metals. Lettuce leaves and radish roots accumulated significantly more metals than bean and tomato fruits. This accumulation pattern suggests that consumption of lettuce leaves or radish roots from plants grown in mine wastes would pose greater risks to humans and wildlife than would consumption of beans or tomatoes grown in the same area. The potential risk may be mitigated somewhat in humans, as vegetables grown in mine wastes exhibited stunted growth and chlorosis.

Lyapunov-Based Control of Mechanical Systems

Abstract: 1 Introduction- 11 Lyapunov-Based Control- 12 Rigid Mechanical Systems- 13 Flexible Mechanical Systems- 14 Real-Time Control Implementation- References- 2 Control Techniques for Friction Compensation- 21 Introduction- 22 Reduced-Order Friction Model- 23 Control Designs for Reduced-Order Model- 231 Standard Adaptive Control- 232 Modular Adaptive Control- 233 Adaptive Setpoint Control- 234 Experimental Evaluation- 24 Full-Order Friction Model- 25 Control Designs for Full-Order Model- 251 Model-Based Control: Asymptotic Tracking- 252 Model-Based Control: Exponential Tracking- 253 Adaptive Control: Case- 254 Adaptive Control: Case- 255 Experimental Evaluation- 26 Notes- References- 3 Full-State Feedback Tracking Controllers- 31 Introduction- 32 System Model- 33 Problem Statement- 34 Standard Adaptive Control- 341 Controller Formulation- 342 Stability Result- 35 Desired Trajectory-Based Adaptive Control- 351 Controller Formulation- 352 Stability Results- 353 Experimental Results- 354 Nonadaptive Extensions- 36 Control/Adaptation Law Modularity- 361 Input-to-State Stability Result- 362 Position Tracking Result- 363 Experimental Results- 364 Discussion of Results- 37 Notes- References- 4 Output Feedback Tracking Controllers- 41 Introduction- 42 Problem Statement- 43 Model-Based Observer/Control- 431 Velocity Observer Formulation- 432 Controller Formulation- 433 Composite Stability Result- 434 Experimental Results- 44 Linear Filter-Based Adaptive Control- 441 Filter Formulation- 442 Controller Formulation- 443 Composite Stability Result- 444 Experimental Results- 445 Nonadaptive Extensions- 45 Nonlinear Filter-Based Adaptive Control- 451 Filter/Controller Formulation- 452 Composite Stability Result- 453 OFB Form of Filter/Controller- 454 Simulation Results- 455 Extensions- 46 Notes- References- 5 Strings and Cables- 51 Introduction- 52 Actuator-String System- 521 System Model- 522 Problem Statement- 523 Model-Based Control Law- 524 Adaptive Control Law- 525 Extensions- 526 Experimental Evaluation- 53 Cable System- 531 System Model- 532 Problem Statement- 533 Model-Based Control Law- 534 Adaptive Control Law- 535 Experimental Evaluation- 54 Notes- References- 6 Cantilevered Beams- 61 Introduction- 62 Euler-Bernoulli Beam- 621 System Model- 622 Problem Statement- 623 Model-Based Control Law- 624 Adaptive Control Law- 625 Extensions- 626 Experimental Evaluation- 63 Timoshenko Beam- 631 System Model- 632 Problem Statement- 633 Model-Based Control Law- 634 Adaptive Control Law- 635 Simulation Results- 64 Notes- References- 7 Boundary Control Applications- 71 Introduction- 72 Axially Moving String System- 721 System Model- 722 Problem Statement- 723 Model-Based Control Law - 724 Adaptive Control Law- 725 Experimental Evaluation- 73 Flexible Link Robot Arm- 731 System Model- 732 Problem Statement- 733 Model-Based Control Law- 734 Adaptive Control Law- 735 Experimental Evaluation- 74 Flexible Rotor System- 741 System Model- 742 Problem Statement- 743 Model-Based Control Law- 744 Adaptive Control Law- 745 Experimental Evaluation- 75 Notes- References- Appendices- A Mathematical Background- References- B Bounds for General Rigid Mechanical System- References- C Bounds for the Puma Robot- References- D Control Programs- D1 DCAL Controller- D2 Flexible Rotor

Rice Transposable Elements: A Survey of 73,000 Sequence-Tagged-Connectors

Abstract: Transposable elements (TEs) are ubiquitous in all organisms (Burge and Howe 1989; Xiong and Eickbush 1990). In plants, TEs are classified into two main classes (Flavell et al. 1994). Retrotransposons comprise Class I and transpose via an RNA intermediate. Class I TEs include retrotransposons with long terminal repeats (LTRs) such as Ty1/Copia-like and Ty3/Gypsy-like, as well as non-LTR retrotransposons. The class II TEs transpose via a DNA intermediate and in plants have been found mainly in maize. Class II TEs include Ac/Ds, En/Spm, and Mutator (Federoff 1989). MITEs, that is, miniature inverted-repeat transposable elements, such as maize Tourist and Stowaway, fall into a newly described third class of TEs (Bureau and Wessler 1992, 1994a,b, 1996). The mechanism of transposition of MITEs is still unclear, although they have received considerable attention recently due to their high copy numbers and tendency to be associated with genes in maize (Wessler et al. 1995; Zhang et al. 2000). Rice (Oryza sativa) is the main staple food for more than half of the world's population and is of great economic importance. Among the cereal grasses, rice has the smallest genome size (430 Mb) and, as revealed by comparative mapping, has substantial conservation of synteny with other cereal crops such as maize, sorghum, and wheat (Gale and Devos 1998). Consequently, rice is an ideal representative for cereal genomics studies and is the focus of an international effort to completely sequence its genome. Although numerous TEs have been reported in rice, no comprehensive investigation has been carried out on a genome-wide scale, because the majority of rice TEs were uncovered by chance or by limited assays using conserved regions such as reverse transcriptase of retrotransposons (Hirochika et al. 1992; Motohashi et al. 1996; Kumekawa et al. 1999). As part of the International Rice Genome Sequencing Project (IRGSP), a rice BAC library was constructed from a partial HindIII digest of the genome of the rice variety Nipponbare (Budiman 1999), and the ends of BAC clone inserts have been sequenced. BAC end sequences will serve as sequence-tagged-connectors (STCs) for selecting minimum overlapping clones for genome sequencing (Venter et al. 1996). The generation of >73,000 Nipponbare STCs also provides an opportunity to preview TE content and distribution in rice genome. The current STC library contains ∼48 Mb of rice genomic DNA after vector removal, with an average sequence read of 707 nucleotides. With an average insert of 128.5 kb, the CUGI rice BAC library is expected to cover ∼10 rice genome equivalents. Preliminary efforts to confirm the coverage of the library based strictly on sequence comparison of the STCs to finished rice BACs have shown that the estimated coverage is ∼10.4 genome equivalents (data not shown). Assuming that the HindIII sites are evenly distributed, our 73,000 STCs should be distributed one STC every 9 kb across the 430-Mb rice genome. TEs are one of the major sources of repetitive sequences in cereal plants and have been a concern of the IRGSP as a potential source of problems in completing the rice genome sequence. Here, we report the TE content of the STC database and show that the rice genome probably contains a small fraction of TEs in comparison with other cereal genomes, such as maize. The small amount of TEs confirms rice as a well-chosen model crop genome. We note the discovery of several potentially novel TEs, and we investigate the location of TE–STCs on the current physical map of the CUGI rice BAC library. We find that the TEs appear to be randomly distributed with respect to potential genes, identified by similarity to rice ESTs.

A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes

Abstract: Modern cultivated barley is an important cereal crop with an estimated genome size of 5000 Mb. To develop the resources for positional cloning and structural genomic analyses in barley, we constructed a bacterial artificial chromosome (BAC) library for the cultivar Morex using the cloning enzyme HindIII. The library contains 313344 clones (816 384-well plates). A random sampling of 504 clones indicated an average insert size of 106 kbp (range=30–195 kbp) and 3.4% empty vectors. Screening the colony filters for chloroplast DNA content indicated an exceptionally low 1.5% contamination with chloroplast DNA. Thus, the library provides 6.3 haploid genome equivalents allowing a >99% probability of recovering any specific sequence of interest. High-density filters were gridded robotically using a Genetix Q-BOT in a 4×4 double-spotted array on 22.5-cm2 filters. Each set of 17 filters allows the entire library to be screened with 18432 clones represented per filter. Screening the library with 40 single copy probes identified an average 6.4 clones per probe, with a range of 1–13 clones per probe. A set of resistance-gene analog (RGA) sequences identified 121 RGA-containing BAC clones representing 20 different regions of the genome with an average of 6.1 clones per locus. Additional screening of the library with a P-loop disease resistance primer probe identified 459 positive BAC clones. These data indicate that this library is a valuable resource for structural genomic applications in barley.

Phase transformations in Ti-Nb-Ta and Ti-Nb-Ta-Zr alloys

Abstract: Phase transformations in solution treated and quenched Ti-(13-26) Nb-(22-38) Ta (wt.%) and Ti-(13-35.5) Nb-(5-22) Ta-(4-7.2) Zr alloys have been studied. It has been observed that phase transformations in these alloys are sensitive to both composition and cooling rate. In ternary alloys, water and oil quenching resulted in the formation of orthorhombic martensite (α′′) in a retained β + ωathermal matrix, whereas slower cooling showed evidence of fine α and ωisothermal formation within the β matrix. Increase of Nb + Ta content decreases the volume percentage of martensite. Moreover, addition of Zr stabilized the β phase, lowered the martensite start temperature and suppressed ω formation. Finally, dynamic moduli of air cooled quaternary alloys showed that the modulus was sensitive to the composition, a minima at Nb/Ta ratio of 12.0 and 5 at% Zr being observed, this minimum in dynamic modulus being consistent with ω phase suppression.

Environmental Scanning Behavior in a Transitional Economy: Evidence from Russia

Abstract: We examined the effects of perceived strategic uncertainty in seven environmental sectors on the scanning behavior of Russian executives. Strategic uncertainty was highest in sectors influenced by ...

Sportscasting and Sports Reporting: The Power of Gender Bias

Abstract: Comparison of the sportscasting on ESPN and CNN and sports reporting in The New York Times and USA Today revealed the very high degree of embedded favoritism toward men’s sports and men athletes, e...

The Stigma of Psychological Problems in a Work Environment: Evidence From the Screening of Service Members Returning From Bosnia1

Abstract: The present research examined the stigma associated with psychological problems among service members returning from the United States peacekeeping mission to Bosnia. The results show that admitting a psychological problem in the military is perceived as muchmore stigmatizing than admitting a medical problem. Service members had more concerns about stigmatization and felt more uncomfortable discussing psychological problems than medical problems, and these feelings were magnified when service members were being screened with their units rather than alone. Service members also reported a lesser likelihood of following through with a psychological referral than with a medical referral. However, participants who discussed psychological issues with a therapist felt the screening was more beneficial than those who did not discuss their responses. The results address the neglected topic of the stigma associated with psychological problems in the workplace.

A Uniform Analysis of the Ly-alpha forest at z = 0 - 5: II. Measuring the mean intensity of the extragalactic ionizing background using the proximity effect

Abstract: A homogeneous sample of 99 moderate resolution QSO spectra at z > 1.7 were presented in Paper I, including 39 previously unpublished spectra from the Multiple Mirror Telescope. The statistics of the Lyman alpha forest were discussed. In this analysis, we demonstrate that a proximity effect is present in the data, ie. there exists a significant (5.5$\sigma$) deficit of lines at $z_{abs} \approx z_{em}$. Within 1.5 $h^{-1}$ Mpc of the QSO emission redshift, the significance does depend on QSO luminosity, in accordance with the theory that this effect is caused by enhanced ionization of hydrogen in the vicinity of the QSO from UV photons from the QSO itself. The photoionization model of Bajtlik, Duncan, and Ostriker (1988) permits an estimate of the mean intensity of the extragalactic background radiation at the Lyman limit. We compare the results of this standard analysis with those obtained using a maximum likelihood technique. The best fit value for $J( u_{0})$ is 7.0$^{+3.4}_{-4.4}$ x 10$^{-22}$ ergs/s/cm$^{2}$/Hz/sr, over the redshift range 1.7 < z < 3.8, using QSO redshifts based on narrow emission lines. The best fit value for the HI ionization rate is 1.9$^{+1.2}_{-1.0}$ x 10$^{-12}$ s$^{-1}$, in good agreement with models of the background which incorporate QSOs only. This large absorption line sample and these techniques for measuring the background and understanding the systematics involved allow us to place what we believe are are the firmest limits on the background at these redshifts.

Recounting the Rationals

Abstract: (2000). Recounting the Rationals. The American Mathematical Monthly: Vol. 107, No. 4, pp. 360-363.

A Uniform Analysis of the Lyα Forest at z = 0-5. II. Measuring the Mean Intensity of the Extragalactic Ionizing Background Using the Proximity Effect

Abstract: Moderate-resolution data for 40 quasi-stellar objects (QSOs) at z ≈ 2 were combined with spectra of comparable resolution of 59 QSOs with redshifts greater than 1.7 found in the literature to form a large, homogeneous sample of moderate-resolution (~1 A) QSO spectra. These spectra were presented and the statistics of the Lyα forest were discussed in Paper I. In this analysis, we demonstrate that a proximity effect is present in the data; i.e., there exists a significant (5.5 σ) deficit of lines at zabs ≈ zem. Within 1.5 h-1 Mpc of the QSO emission redshift, the significance does depend on QSO luminosity, in accordance with the theory that this effect is caused by enhanced ionization of hydrogen in the vicinity of the QSO from UV photons from the QSO itself. The photoionization model of Bajtlik, Duncan, & Ostriker permits an estimate of the mean intensity of the extragalactic background radiation at the Lyman limit. We compare the results of this standard analysis with those obtained using a maximum likelihood technique. If the spectrum of the background is assumed to be identical to that of each individual QSO, and if this background is assumed to be constant over the redshift range 1.7 < z < 3.8, then the best-fit value for J(ν0) is found to be 1.4 × 10-21 ergs s-1 cm-2 Hz-1 sr-1, using QSO redshifts based on the Lyα emission line. Systemic QSO redshifts based on the [O III] λ5007 emission line for 19 objects in our sample show an average redshift of ~400 km s-1 with respect to Lyα emission. Using redshifts based on [O III] or Mg II for the 35 objects for which they are measured and adding 400 km s-1 to the remaining QSO Lyα redshifts gives a lower value of J(ν0), 7.0 × 10-22 ergs s-1 cm-2 Hz-1 sr-1. This value is in reasonable agreement with the predictions of various models of the ionizing background based on the integrated quasar luminosity function. Allowing for the fact that individual QSOs have different spectral indices that may also be different from that of the background, we use the standard methods to solve for the H I photoionization rate, Γ, and the parameters describing its evolution with redshift. The best-fit value for the H I ionization rate we derive is 1.9 × 10-12 s-1, in good agreement with models of the background that incorporate QSOs only. Finally, we use simulated Lyα forest spectra including the proximity effect to investigate curve-of-growth effects in the photoionization model used in the analysis. We find that the presence of lines on the saturated part of the curve of growth could cause our estimates of the background intensity to be overestimated by a factor of 2-3. This large absorption-line sample and these techniques for measuring the background and understanding the systematics involved allow us to place what we believe are the firmest limits on the background at these redshifts.

The Impact of Airport Noise and Proximity on Residential Property Values

Abstract: The hedonic price method is used to estimate the relationship between residential property values and airport noise and proximity to the airport in the Reno-Sparks area. Empirical results suggest there is a statistically significant negative relationship between airport noise and residential property values, with the average home in areas where noise levels are 65 decibels or high selling for about $2400 less than equivalent homes in quieter areas. However, in direct contrast to the study by Tomkins et al.(1998) who found proximity to the Manchester airport to be an amenity, this study finds proximity to the Reno-Sparks airport to have a significant negative value.

A deep-coverage tomato BAC library and prospects toward development of an STC framework for genome sequencing.

Abstract: Recently a new strategy using BAC end sequences as sequence-tagged connectors (STCs) was proposed for whole-genome sequencing projects. In this study, we present the construction and detailed characterization of a 15.0 haploid genome equivalent BAC library for the cultivated tomato, Lycopersicon esculentum cv. Heinz 1706. The library contains 129,024 clones with an average insert size of 117.5 kb and a chloroplast content of 1.11%. BAC end sequences from 1490 ends were generated and analyzed as a preliminary evaluation for using this library to develop an STC framework to sequence the tomato genome. A total of 1205 BAC end sequences (80.9%) were obtained, with an average length of 360 high-quality bases, and were searched against the GenBank database. Using a cutoff expectation value of <10(-6), and combining the results from BLASTN, BLASTX, and TBLASTX searches, 24.3% of the BAC end sequences were similar to known sequences, of which almost half (48.7%) share sequence similarities to retrotransposons and 7% to known genes. Some of the transposable element sequences were the first reported in tomato, such as sequences similar to maize transposon Activator (Ac) ORF and tobacco pararetrovirus-like sequences. Interestingly, there were no BAC end sequences similar to the highly repeated TGRI and TGRII elements. However, the majority (70.3%) of STCs did not share significant sequence similarities to any sequences in GenBank at either the DNA or predicted protein levels, indicating that a large portion of the tomato genome is still unknown. Our data demonstrate that this BAC library is suitable for developing an STC database to sequence the tomato genome. The advantages of developing an STC framework for whole-genome sequencing of tomato are discussed.