bluuebunny/crossref_metadata_2025 huggingface dataset:
MicroRaman spectroscopy of diamond and graphite in Almahata Sitta and comparison with other ureilites
Authors: ROSS Aidan J. , STEELE Andrew , FRIES Marc D. , KATER Lukas , DOWNES Hilary , JONES Adrian P. , SMITH Caroline L. , JENNISKENS Peter M. , ZOLENSKY Michael E. , SHADDAD Muawia H.
Published: March 2011

Abstract–

This work is the first detailed study of carbon phases in the ureilite Almahata Sitta (sample #7). We present microRaman data for diamond and graphite in Almahata Sitta, seven unbrecciated ureilites, and two brecciated ureilites. Diamond in Almahata Sitta was found to be distinct from that in unbrecciated and brecciated ureilites, although diamond in unbrecciated and brecciated ureilites is indistinguishable. Almahata Sitta diamond shows a peak center range of 1318.5–1330.2 cm−1 and a full width at half maximum (FWHM) range of 6.6–17.4 cm−1, representing a shock pressure of at least 60 kbar. The actual peak shock pressure may be higher than this due to postshock annealing, if shock synthesis is the source of ureilite diamonds. Diamond in unbrecciated and brecciated ureilites have peak center wave numbers closer to terrestrial kimberlite diamond, but show a wider range of FWHM than Almahata Sitta. The larger peak shift observed in Almahata Sitta may indicate the presence of lonsdaleite. Alternatively, the lower values in brecciated ureilites may be evidence of an annealing step either following the initial diamond‐generating shock or as a consequence of heating during reconsolidation of the breccia. Graphite in Almahata Sitta shows a G‐band peak center range of 1569.1–1577.1 cm−1 and a G‐band FWHM range of 24.3–41.6 cm−1 representing a formation temperature of 990 ± 120 °C. Amorphous carbon was also found. We examine the different theories for diamond formation in ureilites, such as chemical vapor deposition and shock origin from graphite, and explore explanations for the differences between Almahata Sitta and other ureilites.
Evaporite formation during weathering of Antarctic meteorites––A weathering census analysis based on the ANSMET database
Authors: LOSIAK Anna , VELBEL Michael A.
Published: March 2011

Abstract– Weathering of meteorites at the scale of the entire Antarctic Search for Meteorites program population is studied by analyzing the recent version of the online Antarctic meteorite classification database that includes information about 15,263 meteorites. This paper updates, supplements, and expands on the last Antarctic meteorite weathering census by Velbel (1988, Meteoritics 23:151–159). On average 5% of all Antarctic meteorites are indicated as evaporite bearing in the Antarctic Meteorite Database. Evaporite formation depends on compositional group. Evaporites are much more common on C chondrites than on ordinary chondrites, supporting previous findings. Ordinary chondrites of petrologic type 3 more often have evaporites on their surface than meteorites of other petrologic types. Contrary to previous findings, there is no apparent relation between evaporite formation and meteorite rustiness. Some meteorite‐bearing fields influence the frequency of evaporite‐mineral formation on meteorites. The influence of location is apparently related to differences in environmental conditions, most probably microclimate or/and hydrologic conditions. There is no relation between abundance of evaporite‐bearing meteorites and distance from the sea. Evaporite formation varies with year of collection; however, it was not possible to distinguish whether this is related to annual changes in environment or an artifact of sample categorization or curation.
Micrometer‐ and nanometer‐sized platinum group nuggets in micrometeorites from deep‐sea sediments of the Indian Ocean
Authors: RUDRASWAMI N. G. , PARASHAR K. , SHYAM PRASAD M.
Published: March 2011

Abstract– We examined 378 micrometeorites collected from deep‐sea sediments of the Indian Ocean of which 175, 180, and 23 are I‐type, S‐type, and G‐type, respectively. Of the 175 I‐type spherules, 13 contained platinum group element nuggets (PGNs). The nuggets occur in two distinct sizes and have distinctly different elemental compositions: micrometer (μm)‐sized nuggets that are >3 μm contain dominantly Ir, Os, and Ru (iridium‐platinum group element or IPGE) and sub‐μm (or nanometer)‐sized (<1 μm) nuggets, which contain dominantly Pt, Rh, and Pd (palladium—PGE or PPGE). The μm‐sized nuggets are found only one per spherule in the cross section observed and are usually found at the edge of the spherule. By contrast, there are hundreds of nanometer‐sized nuggets distributed dominantly in the magnetite phases of the spherules, and rarely in the wüstite phases. Both the nugget types are found as separate entities in the same spherule and apparently, nugget formation is a common phenomenon among I‐type micrometeorites. However, the μm‐sized nuggets are seen in fewer specimens (∼2.5% of the observed I‐type spherules). In all, we analyzed four nuggets of μm size and 213 nanometer‐sized nuggets from 13 I‐type spherules for platinum group elements. Chemically, the μm‐sized PGNs contain chondritic ratios of Os/Ir, but are depleted in the more volatile PGE (Pt, Rh, and Pd) relative to chondritic ratios. On the other hand, the nanometer‐sized nuggets contain dominantly Pt and Rh. Importantly, the refractory PGEs are conspicuous by their absence in these nanometer nuggets. Palladium, the most volatile PGE is highly depleted (<1.1%) with respect to chondritic ratios in the μm‐sized PGNs, and is observed in only 17 of 213 nanometer nuggets with concentrations that are just above the detection limit (≥0.2%). Distinct fractionation of the PGE into IPGE (Ir, Os, Ru) and PPGE seems to take place during the short span of atmospheric entry. These observations suggest several implications: (1) The observation of fractionated PGE in an Fe‐Ni system gives rise to the possibility that Earth’s core could contain fractionated PGE. (2) The present data support the processes suggested for the fractionated PGE patterns observed in the ejecta of ancient meteorite impacts. (3) Meteoric metals released in the troposphere could contain fractionated PGNs in large numbers.
Electrical Switching in Cu–As–Se Glasses
Authors: Karuppannan Ramesh , Ganesan Vijaya , Asokan Sundarrajan
Published: March 2011

Electrical switching in CuxAs40Se60−x glasses has been studied over a wide composition range for 0≤x≤32. The glasses with lower Cu concentrations (x<15) do not exhibit switching, whereas glasses in the range 15≤x≤25 show a threshold type switching. The glasses in the range 26≤x≤29 exhibited an unusual switching from low‐resistance to high‐resistance state. For x≥30, the glasses are found to show a memory switching. The thermally crystallized samples indicate that the structural network is characterized by Cu3AsSe4 and As2Se3 for x<15 and by Cu3AsSe4 and Cu2As3 for x≥25. The composition range 15≤x≤20 is characterized only by Cu3AsSe4 structural units. The samples cooled from their melt show only the ternary Cu3AsSe4 for x≤20. For x>20, precipitates of “As” have also been observed along with Cu3AsSe4 and Cu2As3 phases. The present studies provided a unique way to understand the electrical switching exhibited by chalcogenide glasses based on the thermal model and the filament formation.
ON THE VERY IDEA OF CRITERIA FOR PERSONHOOD
Authors: Chappell Timothy
Published: March 2011

abstract

I examine the familiar criterial view of personhood, according to which the possession of personal properties such as self‐consciousness, emotionality, sentience, and so forth is necessary and sufficient for the status of a person. I argue that this view confuses criteria for personhood with parts of an ideal of personhood. In normal cases, we have already identified a creature as a person before we start looking for it to manifest the personal properties, indeed this pre‐identification is part of what makes it possible for us to see and interpret the creature as a person in the first place. This pre‐identification is typically based on biological features. Except in some interesting special or science‐fiction cases, some of which I discuss, it is human animals that we identify as persons.
KNOWLEDGE HAPPENS: WHY ZAGZEBSKI HAS NOT SOLVED THE MENO PROBLEM
Authors: Dougherty Trent
Published: March 2011

abstract

I argue that Linda Zagzebski's proposed solution to the Meno Problem faces serious challenges. The Meno Problem, roughly, is how to explain the value that knowledge, as such, has over mere true belief. Her proposed solution is that believings—when thought of more like actions—can have value in virtue of their motivations. This meshes nicely with her theory that knowledge is, essentially, virtuously motivated true belief. Her solution fails because it entails that, necessarily, all knowledge is motivated in a way that resembles the motivation of actions. Crucially, Zagzebski says the value derived from motivation comes from certain laudable feelings—like love of truth (she is explicit that love is a feeling). But there are possible cases of knowledge—probably some of which are actual—in which subjects do not or cannot experience these feelings.
Field effect controlled lateral field emission triode
Authors: Palma John , Mil’shtein Samson
Published: March 2011

Lateral field emission transistors show promise for many high frequency and high power applications. Typical lateral devices place a gate roughly in between the cathode tip and the anode. While effective, such devices require large gate voltages for device control. This study proposes relocating the gate on top of the semiconductor cathode stem, behind its emitting tip, allowing field effect transistor based control of the transistor. Both enhancement and depletion mode are possible, and the gate bias range needed for control becomes an easily designed parameter. Example structures are modeled where this range is about 1 V. Relocation of the gate has the additional benefit of simplifying the region between the anode and the cathode tip, thus opening up the possibility of shrinking their spacing.
Novel approach for the synthesis of rutile titania nanotubes at very low temperature
Authors: Seo Hyung-Kee , Elliott C. Michael , Shin Hyung-Shik , Suh Eun-Kyung
Published: March 2011

A novel method is presented to synthesize crystalline rutile titania nanotube at comparatively lower temperature than reported previously. A conversion from commercial titania nanoparticles to nanotubes was achieved by hydrothermal method with 10M NaOH, at 70 °C for 48 h. The mixture of titania and NaOH was sonicated for at different times before loading into a hydrothermal reactor. With increasing sonication time a phase transition from anatase to rutile was observed with structural transition from spherical particles to nanotubes. A gradual reduction in x-ray diffraction peak intensities of anatase with a new peak corresponding to the layered titanate is observed. With increasing sonication time, the observed Raman bands are significantly different from that of the commercial TiO2 powder, indicating the changes in the phase with treatment time. Specific surface area is found to increase with the sonication times. The mechanical energy from sonication appears to be helpful in increased dispersion of the nanoparticles in NaOH solution aiding the phase transition from anatase to rutile.
Multiplex Immunoassay for Lyme Disease Using VlsE1-IgG and pepC10-IgM Antibodies: Improving Test Performance through Bioinformatics
Authors: Porwancher Richard B. , Hagerty C. Greg , Fan Jianqing , Landsberg Lisa , Johnson Barbara J. B. , Kopnitsky Mark , Steere Allen C. , Kulas Karen , Wong Susan J.
Published: March 2011

The Centers for Disease Control and Prevention currently recommends a 2-tier serologic approach to Lyme disease laboratory diagnosis, comprised of an initial serum enzyme immunoassay (EIA) for antibody toBorrelia burgdorferifollowed by supplementary IgG and IgM Western blotting of EIA-positive or -equivocal samples. Western blot accuracy is limited by subjective interpretation of weakly positive bands, false-positive IgM immunoblots, and low sensitivity for detection of early disease. We developed an objective alternative second-tier immunoassay using a multiplex microsphere system that measures VlsE1-IgG and pepC10-IgM antibodies simultaneously in the same sample. Our study population comprised 79 patients with early acute Lyme disease, 82 patients with early-convalescent-phase disease, 47 patients with stage II and III disease, 34 patients post-antibiotic treatment, and 794 controls. A bioinformatic technique called partial receiver-operator characteristic (ROC) regression was used to combine individual antibody levels into a single diagnostic score with a single cutoff; this technique enhances test performance when a high specificity is required (e.g., ≥95%). Compared to Western blotting, the multiplex assay was equally specific (95.6%) but 20.7% more sensitive for early-convalescent-phase disease (89.0% versus 68.3%, respectively; 95% confidence interval [95% CI] for difference, 12.1% to 30.9%) and 12.5% more sensitive overall (75.0% versus 62.5%, respectively; 95% CI for difference, 8.1% to 17.1%). As a second-tier test, a multiplex assay for VlsE1-IgG and pepC10-IgM antibodies performed as well as or better than Western blotting for Lyme disease diagnosis. Prospective validation studies appear to be warranted.
A Critical Threshold of Meningococcal Factor H Binding Protein Expression Is Required for Increased Breadth of Protective Antibodies Elicited by Native Outer Membrane Vesicle Vaccines
Authors: Koeberling Oliver , Delany Isabel , Granoff Dan M.
Published: March 2011

Native outer membrane vesicles (NOMV) (not detergent treated), which are prepared from recombinant strains with attenuated endotoxin activity and overexpressed factor H binding protein (fHbp), elicited broad serum bactericidal antibody responses in mice. The amount of overexpressed fHbp required for optimal immunogenicity is not known. In this study we prepared NOMV vaccines from LpxL1 knockout (ΔLpxL1) mutants with penta-acylated lipooligosaccharide and attenuated endotoxin activity. The recombinant strains had wild-type (1×) fHbp expression or were engineered for 3-fold- or 10-fold-increased fHbp expression (3× or 10× fHbp). Control vaccines included NOMV from ΔLpxL1/ΔfHbp mutants or recombinant fHbp. In mice, only the 10× fHbp NOMV vaccine elicited significantly higher serum IgG anti-fHbp antibody titers than the corresponding 1× fHbp NOMV or recombinant fHbp vaccine. The 10× fHbp NOMV vaccine also elicited higher bactericidal responses (P< 0.05) against five group B strains with heterologous PorA than the recombinant fHbp or 1× fHbp NOMV vaccine. The 3× fHbp NOMV vaccine gave higher bactericidal titers against only one strain. Serum bactericidal titers in mice immunized with the control ΔfHbp NOMV vaccines were <1:10, and bactericidal titers in mice immunized with the 10× fHbp NOMV vaccine were <1:10 after adsorption of anti-fHbp antibodies. Mixing antiserum to NOMV vaccines from fHbp knockout mutants with antiserum to recombinant fHbp did not increase anti-fHbp bactericidal titers. Thus, a critical threshold of increased fHbp expression is required for NOMV vaccines to elicit broad serum bactericidal responses, and the antibodies conferring protection are directed primarily at fHbp.
Safety, Tolerability, and Immunogenicity of a Recombinant, Genetically Engineered, Live-Attenuated Vaccine against Canine Blastomycosis
Authors: Wüthrich Marcel , Krajaejun Theerapong , Shearn-Bochsler Valerie , Bass Chris , Filutowicz Hanna I. , Legendre Alfred M. , Klein Bruce S.
Published: March 2011

Blastomycosis is a severe, commonly fatal infection caused by the dimorphic fungusBlastomyces dermatitidisin dogs that live in the United States, Canada, and parts of Africa. The cost of treating an infection can be expensive, and no vaccine against this infection is commercially available. A genetically engineered live-attenuated strain ofB. dermatitidislacking the major virulence factor BAD-1 successfully vaccinates against lethal experimental infection in mice. Here we studied the safety, toxicity, and immunogenicity of this strain as a vaccine in dogs, using 25 beagles at a teaching laboratory and 78 foxhounds in a field trial. In the beagles, escalating doses of live vaccine ranging from 2 × 104to 2 × 107yeast cells given subcutaneously were safe and did not disseminate to the lung or induce systemic illness, but a dose of <2 × 106yeast cells induced less fever and local inflammation. A vaccine dose of 105yeast cells was also well tolerated in vaccinated foxhounds who had never had blastomycosis; however, vaccinated dogs with prior infection had more local reactions at the vaccine site. The draining lymph node cells and peripheral blood lymphocytes from vaccinated dogs demonstrated gamma interferon (IFN-γ), tumor necrosis factor alpha (TNF-α), and granulocyte-macrophage colony-stimulating factor (GM-CSF) specifically in response to stimulation withBlastomycesantigens. Thus, the live-attenuated vaccine against blastomycosis studied here proved safe, well tolerated, and immunogenic in dogs and merits further studies of vaccine efficacy.
First Report of a Hip Prosthetic and Joint Infection Caused by Lactococcus garvieae in a Woman Fishmonger
Authors: Aubin G. G. , Bémer P. , Guillouzouic A. , Crémet L. , Touchais S. , Fraquet N. , Boutoille D. , Reynaud A. , Lepelletier D. , Corvec S.
Published: March 2011

We describe the first case of hip prosthetic infection due to
Lactococcus garvieae
. The patient, a 71-year-old woman fishmonger, developed a hip infection 7 years after total hip arthroplasty. The origin of infection was possibly due to the manipulation or intake of seafood or fish contaminated with
Lactococcus garvieae
.
Multicenter, Prospective Clinical Evaluation of Respiratory Samples from Subjects at Risk for Pneumocystis jirovecii Infection by Use of a Commercial Real-Time PCR Assay
Authors: Hauser Philippe M. , Bille Jacques , Lass-Flörl Cornelia , Geltner Christian , Feldmesser Marta , Levi Michael , Patel Hitesh , Muggia Victoria , Alexander Barbara , Hughes Martin , Follett Sarah A. , Cui Xiaohui , Leung Flora , Morgan Gillian , Moody Adrian , Perlin David S. , Denning David W.
Published: March 2011

Pneumocystis jirovecii
pneumonia (PCP) is a common opportunistic infection. Microscopic diagnosis, including diagnosis using the Merifluor-Pneumocystis direct fluorescent antigen (MP-DFA) test, has limitations. Real-time PCR may assist in diagnosis, but no commercially validated real-time PCR assay has been available to date. MycAssay Pneumocystis is a commercial assay that targets the
P. jirovecii
mitochondrial large subunit (analytical detection limit, ≤3.5 copies/μl of sample). A multicenter trial recruited 110 subjects: 54 with transplants (40 with lung transplants), 32 with nonmalignant conditions, 13 with leukemia, and 11 with solid tumors; 9 were HIV positive. A total of 110 respiratory samples (92% of which were bronchoalveolar lavage [BAL] specimens) were analyzed by PCR. Performance was characterized relative to investigator-determined clinical diagnosis of PCP (including local diagnostic tests), and PCR results were compared with MP-DFA test results for 83 subjects. Thirteen of 14 subjects with PCP and 9/96 without PCP (including 5 undergoing BAL surveillance after lung transplantation) had positive PCR results; sensitivity, specificity, and positive and negative predictive values (PPV and NPV, respectively) were 93%, 91%, 59%, and 99%, respectively. Fourteen of 83 subjects for whom PCR and MP-DFA test results were available had PCP; PCR sensitivity, specificity, PPV, and NPV were 93%, 90%, 65%, and 98%, respectively, and MP-DFA test sensitivity, specificity, PPV, and NPV were 93%, 100%, 100%, and 98%. Of the 9 PCR-positive subjects without PCP, 1 later developed PCP. The PCR diagnostic assay compares well with clinical diagnosis using nonmolecular methods. Additional positive results compared with the MP-DFA test may reflect low-level infection or colonization.
HIV Coreceptor Tropism in Paired Plasma, Peripheral Blood Mononuclear Cell, and Cerebrospinal Fluid Isolates from Antiretroviral-Naïve Subjects
Authors: Parisi S. G. , Andreoni C. , Sarmati L. , Boldrin C. , Buonomini A. R. , Andreis S. , Scaggiante R. , Cruciani M. , Bosco O. , Manfrin V. , d'Ettorre G. , Mengoli C. , Vullo V. , Palù G. , Andreoni M.
Published: March 2011

A survey of HIV coreceptor usage in cerebrospinal fluid (CSF) samples, peripheral blood mononuclear cells (PBMCs), and plasma samples from naïve seropositive patients was conducted. One hundred patients were enrolled in this study. Of the 100 patients, 36 had a primary or recent infection (P-RI), 31 had an early chronic infection (>350 CD4 cells) (ECI), and 33 had a late chronic infection (LCI). All 3 compartments were sampled in a subset of 33 participants, while the remaining 67 patients provided plasma samples and PBMCs only. Seventy-seven patients harbored the R5 virus in plasma samples and had a significantly higher median and percentage of CD4+T cells than patients with X4 virus (437 and 281 cells/μl, respectively;P= 0.0086; 20.6% and 18.6%, respectively). The X4 strain was detected more frequently in patients with LCI than in patients with P-RI or ECI (39.3%, 19.4%, and 9.6%, respectively;P= 0.0063). PBMC and plasma tropism was concordant in 90 patients, and 73 had the R5 strain. Among patients with discordant results, 4 had the R5 virus in their plasma and the X4 virus in PBMCs; 6 showed the opposite profile. Plasma, PBMC, and CSF tropism determinations were concordant in 26/33 patients (21 patients had R5, and 5 had X4). The tropism was discordant in 5/33 patients, with the X4 virus in plasma and R5 in CSF; the HIV tropism in PBMCs was X4 in 3 patients. The remaining 2/33 patients had the R5 virus in plasma and PBMCs and the X4 virus in CSF; one of these patients had a P-RI. The discordant tropism in CSF and blood may have implications for chemokine (C-C motif) receptor 5 (CCR5) antagonist use in patients with limited response to antiretroviral therapy (ART) or in responding patients evaluated for simplification of treatment.
A report of the medical team activity at the 2009 Special Olympics GB
Authors: Wheeler Patrick C , Williamson Tim , Stephens Catherine , Ferguson Mike
Published: March 2011

Objective

To quantify and categorise medical workload from the 2009 Special Olympics GB (SOL GB) which involved 2500 athletes with learning disabilities across 21 different sports supported by nearly 9000 family members, volunteers and staff over a 7-day period.

Design and participants

Prospective survey of all medical contacts that took place at the 2009 SOL GB with subsequent analysis of consultation rates, medical problems and medical activity.

Results

581 medical consultations occurred during the 2009 SOL GB, with 95% of these for athletes. The majority of the athlete consultations were for musculoskeletal disorders, followed by skin wound care. Most athletes were judged fit to participate following their consultation.

Conclusion

A large multisport event for athletes with learning disabilities carries a significant medical workload that has not been studied previously, with different sports having different individual risks and demands. The vast majority of consultations are for systemically well athletes that can be managed locally without necessity for hospital admission. This study identifies the quantity and nature of medical consultations undertaken during this event in an attempt to inform planning for future events.
Trends in hospitalisations associated with paediatric burns
Authors: Bowman Stephen M , Aitken Mary E , Maham Sabrina A , Sharar Sam R
Published: March 2011

Background

In the United States, burns are the third leading cause of unintentional injury death in children aged 1–14 years, accounting for more than 600 deaths per year in children aged 0–19 years.

Objective

To describe trends in paediatric burn hospitalisations in the United States and provide national benchmarks for state and regional comparisons.

Methods

Analysis of existing data (1993–2006) from the Nationwide Inpatient Sample—the largest, longitudinal, all-payer inpatient care database in the United States. Children aged 0–19 years were included. Main outcome measures: estimated national annual rates of burn-related hospitalisations, stratified by age, gender, and in-hospital mortality.

Results

From 1993 to 2006, the estimated annual incidence rate of paediatric hospitalisations associated with burns declined 40% from 27.3 (1993–94) to 16.1 per 100 000 (p<0.001). The rates declined for all age groups and for both boys and girls. Boys were consistently more likely to be hospitalised than girls (20.3 vs 11.7 hospitalisations per 100 000 during 2004–06, p<0.001). For children less than 5 years of age, burn hospitalisations decreased 46% from 65.2 per 100 000 in 1993–94 to 35.1 per 100 000 in 2004–06 (p<0.001). Fatal hospitalisation rates also declined from 0.3 deaths per 100 000 in 1993–94 to 0.1 in 2004–06 (p<0.001).

Conclusion

Paediatric hospitalisation rates for burns have decreased over the past 14 years. The study also provides national estimates of paediatric burn hospitalisations that can be used as benchmarks to further injury prevention effectiveness through targeting of effective strategies.
Solving Very Sparse Rational Systems of Equations
Authors: Cook William , Steffy Daniel E.
Published: March 2011

Efficient methods for solving linear-programming problems in exact precision rely on the solution of sparse systems of linear equations over the rational numbers. We consider a test set of instances arising from exact-precision linear programming and use this test set to compare the performance of several techniques designed for symbolic sparse linear-system solving. We compare a direct exact solver based on LU factorization, Wiedemann’s method for black-box linear algebra, Dixon’s
p
-adic-lifting algorithm, and the use of iterative numerical methods and rational reconstruction as developed by Wan.
SelInv---An Algorithm for Selected Inversion of a Sparse Symmetric Matrix
Authors: Lin Lin , Yang Chao , Meza Juan C. , Lu Jianfeng , Ying Lexing , E Weinan
Published: March 2011

We describe an efficient implementation of an algorithm for computing selected elements of a general sparse symmetric matrix
A
that can be decomposed as
A
=
LDLT
, where
L
is lower triangular and
D
is diagonal. Our implementation, which is called
SelInv
, is built on top of an efficient supernodal left-looking
LDLT
factorization of
A
. We discuss how computational efficiency can be gained by making use of a relative index array to handle indirect addressing. We report the performance of SelInv on a collection of sparse matrices of various sizes and nonzero structures. We also demonstrate how SelInv can be used in electronic structure calculations.
Costas Arrays
Authors: Taylor Ken , Rickard Scott , Drakakis Konstantinos
Published: March 2011

A Costas array is an arrangement of
N
dots on an
N
-by-
N
grid, one per row, one per column, such that no two dots share the same displacement vector with any other pair. Costas arrays have applications in SONAR/RADAR systems, communication systems, cryptography, and other areas. We present a standardization of notation and language which can be used to discuss Costas array generation techniques and array manipulations. Using this standardization we can concisely and clearly state various theorems about Costas arrays, including several new theorems about the symmetries of Costas arrays. We also define labels for each array (generated, emergent, and sporadic), which describe whether the array is generated using a known technique, generated using a semiempirical variation of a known technique, or of unexplained origin. A new method for obtaining emergent Costas arrays, the DRT expansion, is also given here for the first time. A MATLAB Costas array toolbox has also been developed which implements the proposed standardization. The toolbox contains a comprehensive set of functions covering Costas array generation, manipulation and classification.
An Optimal Iterative Solver for Symmetric Indefinite Systems Stemming from Mixed Approximation
Authors: Silvester David J. , Simoncini Valeria
Published: March 2011

We discuss the design and implementation of a suite of functions for solving symmetric indefinite linear systems associated with mixed approximation of systems of PDEs. The novel feature of our iterative solver is the incorporation of error control in the natural “energy” norm in combination with an a posteriori estimator for the PDE approximation error. This leads to a robust and optimally efficient stopping criterion: the iteration is terminated as soon as the algebraic error is insignificant compared to the approximation error. We describe a “proof of concept” MATLAB implementation of this algorithm, which we callEST_MINRES, and we illustrate its effectiveness when integrated into the Incompressible Flow Iterative Solution Software (IFISS) package (cf. ACM Transactions on Mathematical Software 33, Article 14, 2007).
Algorithm 909
Authors: Le Digabel Sébastien
Published: March 2011

NOMAD is software that implements the Mesh Adaptive Direct Search (MADS) algorithm for blackbox optimization under general nonlinear constraints. Blackbox optimization is about optimizing functions that are usually given as costly programs with no derivative information and no function values returned for a significant number of calls attempted. NOMAD is designed for such problems and aims for the best possible solution with a small number of evaluations. The objective of this article is to describe the underlying algorithm, the software’s functionalities, and its implementation.
Algorithm 910
Authors: Kormanyos Christopher
Published: March 2011

This article presents a portable C++ system for multiple precision calculations of special functions called
e_float
. It has an extendable architecture with a uniform C++ layer which can be used with any suitably prepared MP type. The system implements many high-precision special functions and extends some of these to very large parameter ranges. It supports calculations with 30 ⋯ 300 decimal digits of precision. Interoperabilities with Microsoft’s® CLR, Python, and Mathematica® are supported. The e_float system and its usage are described in detail. Implementation notes, testing results, and performance measurements are provided.
Algorithm 911
Authors: Smith David M.
Published: March 2011

This article describes a collection of Fortran-95 routines for evaluating the exponential integral function, error function, sine and cosine integrals, Fresnel integrals, Bessel functions, and related mathematical special functions using the FM multiple-precision arithmetic package.
The Case for Pair Programming in the Computer Science Classroom
Authors: Braught Grant , Wahls Tim , Eby L. Marlin
Published: March 2011

Previous studies indicate that the use of pair programming has beneficial effects on student learning. In this article, we present a controlled study that directly measured students’ acquisition of individual programming skills using laboratory practica (in which students programmed individually under exam conditions). Additionally, we analyzed other measures of student performance, attitudes, and retention. Our results provide direct evidence that pair programming improves the individual programming skills of lower SAT students, and that students who pair program are more confident in their work and are more likely to successfully complete the course. Results from the four other major studies of the effects of pair programming are reviewed and compared with those presented here in order to draw broader conclusions.
On the Quality of Examples in Introductory Java Textbooks
Authors: Börstler Jürgen , Nordström Marie , Paterson James H.
Published: March 2011

Example programs play an important role in the teaching and learning of programming. Students as well as teachers rank examples as the most important resources for learning to program. Example programs work as role models and must therefore always be consistent with the principles and rules we are teaching.

However, it is difficult to find or develop examples that are fully faithful to all principles and guidelines of the object-oriented paradigm and also follow general pedagogical principles and practices. Unless students are able to engage with good examples, they will not be able to tell desirable from undesirable properties in their own and others’ programs.

In this article we report on a study in which experienced educators evaluated the quality of object-oriented example programs for novices from popular Java textbooks. The evaluation was accomplished using an online checklist that elicited responses on the technical, object-oriented, and didactic quality of examples.

In total 25 reviewers contributed 215 reviews to our dataset, based on 38 example programs from 13 common introductory programming textbooks. Results show that the evaluation instrument is reliable in terms of inter-rater agreement. Overall, example quality was not as good as one might expect from common textbooks, in particular regarding certain object-oriented properties.

We conclude that educators should be careful when taking examples straight out of a textbook.
Extensive Evaluation of Using a Game Project in a Software Architecture Course
Authors: Wang Alf Inge
Published: March 2011

This article describes an extensive evaluation of introducing a game project to a software architecture course. In this project, university students have to construct and design a type of software architecture, evaluate the architecture, implement an application based on the architecture, and test this implementation. In previous years, the domain of the software architecture project has been a robot controller for navigating a maze. In 2008, the students on the software architecture course chose between the two domains: Khepera robot simulation in Java and XNA game development in C#. Independent of the domain chosen, the students had to go through the same phases, produce the same documents based on the same templates, and follow exactly the same process. This article describes an evaluation where we wanted to investigate if a game development project could successfully be used to teach software architecture. Specifically in the evaluation, the effect of the choice of COTS (Commercial Off-The-Shelf) and domain is compared in relation to popularity of the project type, how the students perceive the project, the complexity of the software architectures produced, the effort put into the project, and the grades achieved for the project and the written examination. The main conclusion is that game development projects can successfully be used to teach software architecture. Further, the results of the evaluation show among other things that students who chose the Game project produced software architecture with higher complexity, and put more effort into the project than the Robot project students. No significant statistical differences were found in final grades awarded to the Game project students vs. Robot project students. However, the Game project students obtained a higher grade in their project than in the written examination, whereas the Robot project students scored higher in the written examination than in their project. Finally compared to the Robot project students, those that chose the Game project had fewer problems with COTS hindering the architecture design and introducing technical challenges.
Robust Record Linkage Blocking Using Suffix Arrays and Bloom Filters
Authors: de Vries Timothy , Ke Hui , Chawla Sanjay , Christen Peter
Published: March 2011

Record linkage is an important data integration task that has many practical uses for matching, merging and duplicate removal in large and diverse databases. However, quadratic scalability for the brute force approach of comparing all possible pairs of records necessitates the design of appropriate indexing or blocking techniques. The aim of these techniques is to cheaply remove candidate record pairs that are unlikely to match. We design and evaluate an efficient and highly scalable blocking approach based on suffix arrays. Our suffix grouping technique exploits the ordering used by the index to merge similar blocks at marginal extra cost, resulting in a much higher accuracy while retaining the high scalability of the base suffix array method. Efficiently grouping similar suffixes is carried out with the use of a sliding window technique. We carry out an in-depth analysis of our method and show results from experiments using real and synthetic data, which highlight the importance of using efficient indexing and blocking in real-world applications where datasets contain millions of records. We extend our disk-based methods with the capability to utilise main memory based storage to construct Bloom filters, which we have found to cause significant speedup by reducing the number of costly database queries by up to 70% in real data. We give practical implementation details and show how Bloom filters can be easily applied to Suffix Array based indexing.
Clustering Large Attributed Graphs
Authors: Cheng Hong , Zhou Yang , Yu Jeffrey Xu
Published: March 2011

Social networks, sensor networks, biological networks, and many other information networks can be modeled as a large graph. Graph vertices represent entities, and graph edges represent their relationships or interactions. In many large graphs, there is usually one or more attributes associated with every graph vertex to describe its properties. In many application domains, graph clustering techniques are very useful for detecting densely connected groups in a large graph as well as for understanding and visualizing a large graph. The goal of graph clustering is to partition vertices in a large graph into different clusters based on various criteria such as vertex connectivity or neighborhood similarity. Many existing graph clustering methods mainly focus on the topological structure for clustering, but largely ignore the vertex properties, which are often heterogenous. In this article, we propose a novel graph clustering algorithm,
SA-Cluster
, which achieves a good balance between structural and attribute similarities through a unified distance measure. Our method partitions a large graph associated with attributes into
k
clusters so that each cluster contains a densely connected subgraph with homogeneous attribute values. An effective method is proposed to automatically learn the degree of contributions of structural similarity and attribute similarity. Theoretical analysis is provided to show that SA-Cluster is converging quickly through iterative cluster refinement. Some optimization techniques on matrix computation are proposed to further improve the efficiency of SA-Cluster on large graphs. Extensive experimental results demonstrate the effectiveness of SA-Cluster through comparisons with the state-of-the-art graph clustering and summarization methods.
The PowerNap Server Architecture
Authors: Meisner David , Gold Brian T. , Wenisch Thomas F.
Published: March 2011

Data center power consumption is growing to unprecedented levels: the EPA estimates U.S. data centers will consume 100 billion kilowatt hours annually by 2011. Much of this energy is wasted in idle systems: in typical deployments, server utilization is below 30%, but idle servers still consume 60% of their peak power draw. Typical idle periods---though frequent---last seconds or less, confounding simple energy-conservation approaches.

In this article, we propose PowerNap, an energy-conservation approach where the entire system transitions rapidly between a high-performance active state and a near-zero-power idle state in response to instantaneous load. Rather than requiring fine-grained power-performance states and complex load-proportional operation from individual system components, PowerNap instead calls for minimizing idle power and transition time, which are simpler optimization goals. Based on the PowerNap concept, we develop requirements and outline mechanisms to eliminate idle power waste in enterprise blade servers. Because PowerNap operates in low-efficiency regions of current blade center power supplies, we introduce the Redundant Array for Inexpensive Load Sharing (RAILS), a power provisioning approach that provides high conversion efficiency across the entire range of PowerNap’s power demands. Using utilization traces collected from enterprise-scale commercial deployments, we demonstrate that, together, PowerNap and RAILS reduce average server power consumption by 74%.
Productive tensions
Authors: Hirsch Tad
Published: March 2011

"Community + Culture" features practitioner perspectives on designing technologies for and with communities. We highlight compelling projects and provocative points of view that speak to both community technology practice and the interaction design field as a whole.

Tad Hirsch, Editor
UNDER DEVELOPMENTWhile the meter is running
Authors: Chetty Marshini , Banks Richard , Bernheim Brush A. J. , Donner Jonathan , Grinter Rebecca E.
Published: March 2011

This forum looks at how the fields of interaction design and HCI can extend to cover "developing" communities around the world, ones that are gaining access to digital technology for the first time.

Gary Marsden, Editor | gaz@acm.org
Universal interactions
Authors: Hourcade Juan Pablo , Bullock-Rest Natasha E.
Published: March 2011

In this forum we will celebrate research that helps to successfully bring the benefits of computing technologies to children, older adults, people with disabilities, and other populations that are often ignored in the design of mass-marketed products.

Juan Pablo Hourcade, Editor
The BioCassava Plus Program: Biofortification of Cassava for Sub-Saharan Africa
Authors: Sayre Richard , Beeching John R. , Cahoon Edgar B. , Egesi Chiedozie , Fauquet Claude , Fellman John , Fregene Martin , Gruissem Wilhelm , Mallowa Sally , Manary Mark , Maziya-Dixon Bussie , Mbanaso Ada , Schachtman Daniel P. , Siritunga Dimuth , Taylor Nigel , Vanderschuren Herve , Zhang Peng
Published: March 2011

More than 250 million Africans rely on the starchy root crop cassava (Manihot esculenta) as their staple source of calories. A typical cassava-based diet, however, provides less than 30% of the minimum daily requirement for protein and only 10%–20% of that for iron, zinc, and vitamin A. The BioCassava Plus (BC+) program has employed modern biotechnologies intended to improve the health of Africans through the development and delivery of genetically engineered cassava with increased nutrient (zinc, iron, protein, and vitamin A) levels. Additional traits addressed by BioCassava Plus include increased shelf life, reductions in toxic cyanogenic glycosides to safe levels, and resistance to viral disease. The program also provides incentives for the adoption of biofortified cassava. Proof of concept was achieved for each of the target traits. Results from field trials in Puerto Rico, the first confined field trials in Nigeria to use genetically engineered organisms, and ex ante impact analyses support the efficacy of using transgenic strategies for the biofortification of cassava.
Determination of Symmetric and Asymmetric Division Planes in Plant Cells
Authors: Rasmussen Carolyn G. , Humphries John A. , Smith Laurie G.
Published: March 2011

The cellular organization of plant tissues is determined by patterns of cell division and growth coupled with cellular differentiation. Cells proliferate mainly via symmetric division, whereas asymmetric divisions are associated with initiation of new developmental patterns and cell types. Division planes in both symmetrically and asymmetrically dividing cells are established through the action of a cortical preprophase band (PPB) of cytoskeletal filaments, which is disassembled upon transition to metaphase, leaving behind a cortical division site (CDS) to which the cytokinetic phragmoplast is later guided to position the cell plate. Recent progress has been made in understanding PPB formation and function as well as the nature and function of the CDS. In asymmetrically dividing cells, division plane establishment is governed by cell polarity. Recent work is beginning to shed light on polarization mechanisms in asymmetrically dividing cells, with receptor-like proteins and potential downstream effectors emerging as important players in this process.
The Epigenome and Plant Development
Authors: He Guangming , Elling Axel A. , Deng Xing Wang
Published: March 2011

The epigenomic regulation of chromatin structure and genome stability is essential for the interpretation of genetic information and ultimately the determination of phenotype. High-resolution maps of plant epigenomes have been obtained through a combination of chromatin technologies and genomic tiling microarrays and through high-throughput sequencing-based approaches. The transcriptomic activity of a plant at a certain stage of development is controlled by genome-wide combinatorial interactions of epigenetic modifications. Tissue- or environment-specific epigenomes are established during plant development. Epigenomic reprogramming triggered by the activation and movement of small RNAs is important for plant gametogenesis. Genome-wide loss of DNA methylation in the endosperm and the accompanying endosperm-specific gene expression during seed development provide a genomic insight into epigenetic regulation of gene imprinting in plants. Global changes of histone modifications during plant responses to different light environments play an important regulatory role in a sophisticated light-regulated transcriptional network. Epigenomic natural variation that developed during evolution is important for phenotypic diversity and can potentially contribute to the molecular mechanisms of complex biological phenomena such as heterosis in plants.
Germline Specification and Function in Plants
Authors: Berger Frédéric , Twell David
Published: March 2011

The flowering plant germline is produced during the haploid gametophytic stage. Defining the germline is complicated by the extreme reduction of the male and female gametophytes, also referred to as pollen and embryo sac, respectively. Both male and female gamete progenitors are segregated by an asymmetric cell division, as is the case for the germline in animals. Genetic studies and access to the transcriptome of isolated gametes have provided a regulatory framework for the mechanisms that define the male germline. What specifies female germline identity remains unknown. Recent evidence indicates that an auxin gradient provides positional information and plays a role in defining the identity of the female gamete lineage. The animal germline is also marked by production of small RNAs, and recent evidence indicates that this trait might be shared with the plant gamete lineage.
In Vivo Imaging of Ca2+, pH, and Reactive Oxygen Species Using Fluorescent Probes in Plants
Authors: Swanson Sarah J. , Choi Won-Gyu , Chanoca Alexandra , Gilroy Simon
Published: March 2011

Changes in the levels of Ca2+, pH, and reactive oxygen species (ROS) are recognized as key cellular regulators involved in diverse physiological and developmental processes in plants. Critical to understanding how they exert such widespread control is an appreciation of their spatial and temporal dynamics at levels from organ to organelle and from seconds to many hours. With appropriate controls, fluorescent sensors can provide a robust approach with which to quantify such changes in Ca2+, pH, and ROS in real time, in vivo. The fluorescent cellular probes available for visualization split into two broad classes: (a) dyes and (b) an increasingly diverse set of genetically encoded sensors based around green fluorescent proteins (GFPs). The GFP probes in particular can be targeted to well-defined subcellular locales, offering the possibility of high-resolution mapping of these signals within the cell.