bluuebunny/crossref_metadata_2025 huggingface dataset:
Tracking down a critical halo mass for killing galaxies through the growth of the red sequence
Authors: Gilbank David G. , Balogh Michael L.
Published: February 2008

Red-sequence galaxies record the history of terminated star formation in the Universe and can thus provide important clues to the mechanisms responsible for this termination. We construct composite samples of published cluster and field galaxy photometry in order to study the build-up of galaxies on the red sequence, as parametrized by the dwarf-to-giant ratio (DGR). We find that the DGR in clusters is higher than that of the field at all redshifts, implying that the faint end of the red sequence was established first in clusters. We find that the DGR evolves with redshift for both samples, consistent with the ‘down-sizing’ picture of star formation. We examine the predictions of semi-analytic models for the DGR and find that neither the magnitude of its environmental dependence nor its evolution is correctly predicted in the models. Red-sequence DGRs are consistently too high in the models, the most likely explanation being that the strangulation mechanism used to remove hot gas from satellite galaxies is too efficient. Finally, we present a simple toy model including a threshold mass, below which galaxies are not strangled, and show that this can predict the observed evolution of the field DGR.
Methodology for Comparing Source and Plume Remediation Alternatives
Authors: Falta Ronald W.
Published: February 2008

It is often difficult at contaminated sites to decide whether remediation effort should be focused on the contaminant source, the dissolved plume, or on both zones. The decision process at these sites is hampered by a lack of quantitative tools for comparing remediation alternatives. A new screening‐level mass balance approach is developed for simulating the transient effects of simultaneous ground water source and plume remediation. The contaminant source model is based on a power function relationship between source mass and source discharge, and it can consider partial source remediation at any time after the initial release. The source model serves as a time‐dependent mass flux boundary condition to a new analytical plume model, where flow is assumed to be one dimensional, with three‐dimensional dispersion. The plume model simulates first‐order sequential decay and production of several species, and the decay rates and parent/daughter yield coefficients are variable functions of time and distance. This new method allows for flexible simulation of natural attenuation or remediation efforts that enhance plume degradation. The plume remediation effort may be temporary or delayed in time, limited in space, and it may have different chemical effects on different contaminant species in the decay chain.
Three‐Dimensional Geostatistical Inversion of Flowmeter and Pumping Test Data
Authors: Li Wei , Englert Andreas , Cirpka Olaf A. , Vereecken Harry
Published: February 2008

We jointly invert field data of flowmeter and multiple pumping tests in fully screened wells to estimate hydraulic conductivity using a geostatistical method. We use the steady‐state drawdowns of pumping tests and the discharge profiles of flowmeter tests as our data in the inference. The discharge profiles need not be converted to absolute hydraulic conductivities. Consequently, we do not need measurements of depth‐averaged hydraulic conductivity at well locations. The flowmeter profiles contain information about relative vertical distributions of hydraulic conductivity, while drawdown measurements of pumping tests provide information about horizontal fluctuation of the depth‐averaged hydraulic conductivity. We apply the method to data obtained at the Krauthausen test site of the Forschungszentrum Jülich, Germany. The resulting estimate of our joint three‐dimensional (3D) geostatistical inversion shows an improved 3D structure in comparison to the inversion of pumping test data only.
Forensic Isotope Analysis to Refine a Hydrologic Conceptual Model
Authors: Bassett R.L , Steinwand Aaron , Jorat Saeed , Petersen Christian , Jackson Randy
Published: February 2008

Water resources in the arid southwestern United States are frequently the subject of conflict from competing private and public interests. Legal remedies may remove impasses, but the technical analysis of the problem often determines the future success of legal solutions. In Owens Valley, California, the source of water for the Los Angeles Aqueduct (LAA) is flow diverted from the Owens River and its tributaries and ground water from valley aquifers. Future management of ground water delivered to the LAA needs technical support regarding quantity available, interconnection of shallow and confined aquifers, impact on local springs, and rate of recharge. Ground water flow models and ground water composition are tools already in use, but these have large uncertainty for local interpretations. This study conducted targeted sampling of springs and wells to evaluate the hydrologic system to corroborate conceptual and numerical models. The effort included measurement of intrinsic isotopic composition at key locations in the aquifers. The stable isotopic data of boron (δ11B), sulfur (δ34S), oxygen (δ18O), hydrogen (δD), and tritium (3H) supported by basic chemical data provided rules for characterizing the upper and the lower aquifer system, confirmed the interpretation of ground water flow near faults and flow barriers, and detected hydraulic connections between the LAA and the perennial springs at key locations along the unlined reach of the LAA. This study exemplifies the use of forensic isotopic approaches as independent checks on the consistency of interpretations of conceptual models of a ground water system and the numerical hydrologic simulations.
Screening of One‐Well Hydraulic Barrier Design Alternatives
Authors: Rubin Hillel , Shoemaker Christine A. , Köngeter Jürgen
Published: February 2008

This study develops a robust method for screening one‐well hydraulic barrier design alternatives that can be easily computed without a numerical simulation model. The paper outlines the general method and shows its implementation with hydraulic barriers using a single pumping well. For such barriers, the method is easily computable with spreadsheets and/or charts depicted within the paper and posted online. The method applies the potential flow theory, which leads to using a curvilinear coordinate system for all types of calculations. For contaminant transport calculations, the method applies the boundary layer theory. For calculations of aquifer remediation, the method refers to bulk characteristics of the domain. As an example, the method has been applied to calculate the possible containment of a wide part of the coastal plain aquifer in Israel, which is contaminated by entrapped kerosene (a light nonaqueous phase liquid).
Importance of Unsaturated Zone Flow for Simulating Recharge in a Humid Climate
Authors: Hunt Randall J. , Prudic David E. , Walker John F. , Anderson Mary P.
Published: February 2008

Transient recharge to the water table is often not well understood or quantified. Two approaches for simulating transient recharge in a ground water flow model were investigated using the Trout Lake watershed in north‐central Wisconsin: (1) a traditional approach of adding recharge directly to the water table and (2) routing the same volume of water through an unsaturated zone column to the water table. Areas with thin (less than 1 m) unsaturated zones showed little difference in timing of recharge between the two approaches; when water was routed through the unsaturated zone, however, less recharge was delivered to the water table and more discharge occurred to the surface because recharge direction and magnitude changed when the water table rose to the land surface. Areas with a thick (15 to 26 m) unsaturated zone were characterized by multimonth lags between infiltration and recharge, and, in some cases, wetting fronts from precipitation events during the fall overtook and mixed with infiltration from the previous spring snowmelt. Thus, in thicker unsaturated zones, the volume of water infiltrated was properly simulated using the traditional approach, but the timing was different from simulations that included unsaturated zone flow. Routing of rejected recharge and ground water discharge at land surface to surface water features also provided a better simulation of the observed flow regime in a stream at the basin outlet. These results demonstrate that consideration of flow through the unsaturated zone may be important when simulating transient ground water flow in humid climates with shallow water tables.
Ligand‐independent Regulation of the hairless Promoter by Vitamin D Receptor†
Authors: Engelhard Andrew , Bauer Robert C. , Casta Alexandre , Djabali Karima , Christiano Angela M.
Published: February 2008

The characteristic alopecia associated with mutations in the hairless (hr) and vitamin D receptor (VDR) genes defines the resulting genetic disorders, known as atrichia and VDRRIIa rickets, as phenocopies. In both cases, the separation of the dermal papilla from the regressing hair follicle at the onset of the first catagen phase of the hair cycle and the development of dermal cysts and utricules subsequent to mutation of either gene suggests that their activities affect the same regulatory pathways. VDR functions as a hormonally activated transcription factor, and a role in transcription has been postulated for Hr due in part to its nuclear localization and homology with the GATA‐1 zinc‐finger domain. Therefore, we examined the hypothesis that VDR and Hr have a direct regulatory effect on each other via a transcriptional mechanism. Ectopic expression of the VDR repressed hr promoter activity in HaCaT cells and primary human keratinocytes (PHKs). While this repression occurs in the absence of 1,25 dihydroxyvitamin D3 (D3), the addition of ligand greatly augments the effect. However, we also demonstrate the rare phenomenon of ligand‐independent promoter transactivation by VDR. We show that the full‐length promoter is transactivated by VDR in a ligand‐independent and cell type‐specific manner, suggesting that direct transcriptional regulation of hr by the VDR accounts in part for the phenotypic overlap between atrichia and VDRRIIa rickets.
Use of Synthetic Aperture Radar for Selecting Alaskan Lakes for Winter Water Use1
Authors: White D.M. , Prokein P. , Chambers M.K. , Lilly M.R. , Toniolo H.
Published: February 2008

Abstract:  Water resources are limited in many areas of the North Slope, Alaska, particularly during winter. Water is used by the oil industry for ice road construction and maintenance, drilling and facility operations, and potable water supplies. The coastal plain between Teshekpuk Lake, in the National Petroleum Reserve‐Alaska (NPR‐A) and the Colville River has numerous shallow lakes, but further south in the northern foothills of the Brooks Range, and east to the Canning River, lakes are fewer. While many oil and gas lease sales have been conducted, or are proposed, access to the leases may be limited because of the lack of available water for ice road construction. Ice roads are the main means by which exploration is conducted in the Arctic, putting a stress on freshwater bodies that do not freeze to the lakebed in winter. Lakes that do not freeze to the lakebed also serve as overwintering habitat for fish. The purpose of this paper is to report on the potential distribution of water bodies that may provide overwinter water in selected areas from Teshekpuk Lake to the Canning River. The project used synthetic aperture radar (SAR) imagery to search for the presence of water in lakes in March 2006. In the Kuparuk and Canning SAR images, 52 and 61% of lakes were frozen to their beds by March 2006, accounting for 49 and 57% of the lake area in these study regions. Conversely, only 2% of the lakes in the Teshekpuk region were frozen to the bottom by March 2006. Unfrozen water was more available because of deeper and more numerous lakes in the Teshekpuk Lake region (west) than in the Canning River area (east). While only specific SAR tiles were analyzed herein, the method will be a useful tool for land managers who seek to evaluate the potential for ice road construction across the Arctic.
Effects of Water Withdrawal From Ice‐Covered Lakes on Oxygen, Temperature, and Fish1
Authors: Cott Peter A. , Sibley Paul K. , Gordon Andrew M. , Bodaly R.A. (Drew) , Mills Kenneth H. , Somers W. Murray , Fillatre Gerald A.
Published: February 2008

Abstract:  In northern regions, large volumes of water are needed for activities such as winter road construction. Such withdrawals, particularly from small lakes, can reduce oxygen concentrations and water levels, potentially affecting aquatic organisms. Withdrawal limits have been developed by regulatory agencies, but are largely theoretical. Water withdrawal thresholds were tested in two small lakes by removing 10% and 20% of their respective under‐ice volumes and comparing oxygen parameters, temperature, over‐wintering habitat, and northern pike (Esox lucius) abundance to reference conditions. Because of a milder winter, oxygen parameters were elevated in reference lakes in the period following withdrawal compared to the prewithdrawal period. The 10% withdrawal resulted in a −0.2 m shift in the oxygen concentration profile at 4 mg/l in that lake, but had no effect on total volume‐weighted oxygen, or volume of over‐wintering habitat. In contrast, the 20% withdrawal caused 0.7 m reduction in the oxygen concentration profile at 4 mg/l compared to the previous year, a 26% decline in the volume‐weighted oxygen concentration, and a 23% reduction in the volume of over‐wintering habitat compared to prewithdrawal conditions. Water temperatures were slightly (≤ 10%) colder in the upper strata in the year following the withdrawal in both withdrawal and reference lakes. Northern pike abundance was not impacted by water withdrawals in either of the lakes. The results of this study show that the effects of water withdrawal on the parameters investigated reflected the characteristics of the lakes, and would therefore be expected to vary from lake to lake. Policy development to mitigate impacts must therefore reflect the site‐specific nature of water withdrawal.
Evaluation of 65% Permethrin Spot‐on and Deltamethrin‐impregnated Collars for Canine Leishmania infantum Infection Prevention
Authors: Ferroglio E. , Poggi M. , Trisciuoglio A.
Published: February 2008

During the 2004 and 2005 sand fly seasons, we evaluated the efficacy of a 65% spot‐on solution of permethrin (Exspot, Schering & Plough) and deltamethrin‐impregnated collar (Scalibor, Intervet) in reducing Leishmania infantum infection, in a canine leishmaniasis (CanL) endemic region (Liguria) in Italy. Immunofluorescent assay (IFA) revealed that three of 120 dogs (2.5%) treated with a 65% spot‐on solution of permethrin, as three of 119 dogs (2.5%) treated with deltamethrin‐impregnated collar have shown seroconversion after sand fly season. On the contrary, seroconversion was 15% in 188 untreated control dogs. Treatment reduced the risk of infection by 84%. The difference in treated dogs and control ones is highly significant (χ2 = 12.4; P = 0.0004). Our results show that treatment with 65% spot‐on solution of permethrin and the deltamethrin‐impregnated collar are effective in reducing the risk of acquiring L. infantum infection.
Prevalence of Gastrointestinal Bacterial Pathogens in a Population of Zoo Animals
Authors: Stirling J. , Griffith M. , Blair I. , Cormican M. , Dooley J. S. G. , Goldsmith C. E. , Glover S. G. , Loughrey A. , Lowery C. J. , Matsuda M. , McClurg R. , McCorry K. , McDowell D. , McMahon A. , Cherie Millar B. , Nagano Y. , Rao J. R. , Rooney P. J. , Smyth M. , Snelling W. J. , Xu J. , Moore J. E.
Published: February 2008

Faecal prevalence of gastrointestinal bacterial pathogens, including Campylobacter, Escherichia coli O157:H7, Salmonella, Shigella, Yersinia, as well as Arcobacter, were examined in 317 faecal specimens from 44 animal species in Belfast Zoological Gardens, during July–September 2006. Thermophilic campylobacters including Campylobacter jejuni, Campylobacter coli and Campylobacter lari, were the most frequently isolated pathogens, where members of this genus were isolated from 11 animal species (11 of 44; 25%). Yersinia spp. were isolated from seven animal species (seven of 44; 15.9%) and included, Yersinia enterocolitica (five of seven isolates; 71.4%) and one isolate each of Yersinia frederiksenii and Yersinia kristensenii. Only one isolate of Salmonella was obtained throughout the entire study, which was an isolate of Salmonella dublin (O 1,9,12: H g, p), originating from tiger faeces after enrichment. None of the animal species found in public contact areas of the zoo were positive for any gastrointestinal bacterial pathogens. Also, water from the lake in the centre of the grounds, was examined for the same bacterial pathogens and was found to contain C. jejuni. This study is the first report on the isolation of a number of important bacterial pathogens from a variety of novel host species, C. jejuni from the red kangaroo (Macropus rufus), C. lari from a maned wolf (Chrysocyon brachyurus), Y. kristensenii from a vicugna (Vicugna vicugna) and Y. enterocolitica from a maned wolf and red panda (Ailurus fulgens). In conclusion, this study demonstrated that the faeces of animals in public contact areas of the zoo were not positive for the bacterial gastrointestinal pathogens examined. This is reassuring for the public health of visitors, particularly children, who enjoy this educational and recreational resource.
Human Seroprevalence to Coxiella burnetii (Q fever) in Northern Ireland
Authors: McCaughey C. , McKenna J. , McKenna C. , Coyle P. V. , O’Neill H. J. , Wyatt D. E. , Smyth B. , Murray L. J.
Published: February 2008

Despite the widespread prevalence of infection with Coxiella burnetii, there have been few large population‐based studies examining the epidemiology of this infection. The aim of this study was to examine the distribution and determinants of C. burnetii past infection in Northern Ireland (NI). Coxiella burnetii phase II specific IgG antibodies were measured by enzyme‐linked immunosorbent assay in stored serum from 2394 randomly selected subjects, aged 12–64, who had participated in population‐based surveys of cardiovascular risk factors performed in 1986 and 1987. The overall prevalence of C. burnetii antibody positivity was 12.8%. The prevalence of sero‐positivity was slightly higher in males than that in females (14.3% versus 11.2%, P = 0.02). Sero‐positivity was low in children (<10%), increasing to 19.5% and 16.4% in males and females, respectively, in the 25–34 age group and subsequently remaining fairly steady with increasing age. Sero‐positivity among farmers, at 48.8%, was significantly higher than the general population. More sero‐positive than sero‐negative women had a history of a miscarriage or still‐birth (19.5% versus 9.8%, P < 0.001). In conclusion, this study demonstrated a high prevalence of evidence of past C. burnetii infection in NI. Associations between past C. burnetii infection and age, sex, social class, occupation and reproductive history were seen. We estimate that 20% of Q fever infections in NI occur in farmers.
The Euler multiplicity and addition–deletion theorems for multiarrangements
Authors: Abe Takuro , Terao Hiroaki , Wakefield Max
Published: February 2008

The addition–deletion theorems for hyperplane arrangements, which were originally shown by Terao [J. Fac. Sci. Univ. Tokyo Sect. IA Math. 27 (1980) 293–320.], provide useful ways to construct examples of free arrangements. In this article, we prove addition–deletion theorems for multiarrangements. A key to the generalization is the definition of a new multiplicity, called the Euler multiplicity, of a restricted multiarrangement. We compute the Euler multiplicities in many cases. Then we apply the addition–deletion theorems to various arrangements, including supersolvable arrangements and the Coxeter arrangement of type A3, to construct free and non‐free multiarrangements.
‘Dynamic’ Starling mechanism: effects of ageing and physical fitness on ventricular–arterial coupling
Authors: Shibata Shigeki , Hastings Jeff L. , Prasad Anand , Fu Qi , Okazaki Kazunobu , Palmer M. Dean , Zhang Rong , Levine Benjamin D.
Published: February 2008

Cardiovascular diseases increase with advancing age, associated with left ventricular and arterial stiffening in humans. In contrast, daily exercise training prevents and/or improves both ventricular and arterial stiffening with ageing. We propose a new approach to quantify the dynamics of the Starling mechanism, namely the beat‐to‐beat modulation of stroke volume (SV) caused by beat‐to‐beat alterations in left ventricular filling, which we propose reflects the complex interaction between ventricular and arterial stiffness. We hypothesized that the dynamic Starling mechanism would be impaired with ageing, and that this impairment would be prevented and restored by daily exercise training. Two different approaches were employed: (1) a cross‐sectional study to assess the effects of ageing and life‐long exercise training; and (2) a longitudinal study to assess the effects of one‐year endurance training in the elderly. Spectral transfer function gain between beat‐to‐beat changes in left ventricular end‐diastolic pressure and SV was used as an index of the dynamic Starling mechanism. Gain was significantly lower in the sedentary elderly (70 ± 3 years) than in both young individuals (27 ± 6 years) and Masters athletes (68 ± 3 years), and it was significantly lower in Masters athletes than in young controls (elderly: 0.37 ± 0.11; Masters athletes: 0.96 ± 0.55; young: 1.52 ± 0.42 ml m−2 mmHg−1, mean ±s.d.). Gain increased by 65% after one‐year exercise training in the elderly, although the response was quite variable (P= 0.108). These findings suggest that the dynamic Starling mechanism is impaired with human ageing possibly due to ventricular–arterial stiffening. Life‐long daily exercise training may minimize this impairment, although the effect may be limited particularly when started later in life.
Differential effects of hydrocortisone and TNFα on tight junction proteins in an in vitro model of the human blood–brain barrier
Authors: Förster Carola , Burek Malgorzata , Romero Ignacio A. , Weksler Babette , Couraud Pierre‐Olivier , Drenckhahn Detlev
Published: February 2008

Homeostasis of the central nervous system (CNS) microenvironment is maintained by the blood–brain barrier (BBB) which regulates the transport of molecules from blood into brain and back. Many disorders change the functionality and integrity of the BBB. Glucocorticoids are being used sucessfully in the treatment of some disorders while their effects on others are questionable. In addition, conflicting results between clinical and experimental experience using animal models has arisen, so that the results of molecular studies in animal models need to be revisited in an appropriate in vitro model of the human BBB for more effective treatment strategies. Using the human brain microvascular endothelial cell line hCMEC/D3, the influence of glucocorticoids on the expression of barrier constituting adherens junction and tight junction transmembrane proteins (VE‐cadherin, occludin, claudins) was investigated and compared to other established BBB models. In hCMEC/D3 cells the administration of glucocorticoids induced expression of the targets occludin 2.75 ± 0.04‐fold and claudin‐5 up to 2.32 ± 0.11‐fold, which is likely to contribute to the more than threefold enhancement of transendothelial electrical resistance reflecting barrier tightness. Our analyses further provide direct evidence that the GC hydrocortisone prevents endothelial barrier breakdown in response to pro‐inflammatory stimuli (TNFα administration), which could be demonstrated to be partly based on maintenance of occludin levels. Our studies strongly suggest stabilization of BBB function as a mode of GC action on a molecular level in the human brain vasculature.
Action potential initiation and propagation in hippocampal mossy fibre axons
Authors: Schmidt‐Hieber Christoph , Jonas Peter , Bischofberger Josef
Published: February 2008

Dentate gyrus granule cells transmit action potentials (APs) along their unmyelinated mossy fibre axons to the CA3 region. Although the initiation and propagation of APs are fundamental steps during neural computation, little is known about the site of AP initiation and the speed of propagation in mossy fibre axons. To address these questions, we performed simultaneous somatic and axonal whole‐cell recordings from granule cells in acute hippocampal slices of adult mice at ∼23°C. Injection of short current pulses or synaptic stimulation evoked axonal and somatic APs with similar amplitudes. By contrast, the time course was significantly different, as axonal APs had a higher maximal rate of rise (464 ± 30 V s−1 in the axon versus 297 ± 12 V s−1 in the soma, mean ±s.e.m.). Furthermore, analysis of latencies between the axonal and somatic signals showed that APs were initiated in the proximal axon at ∼20–30 μm distance from the soma, and propagated orthodromically with a velocity of 0.24 m s−1. Qualitatively similar results were obtained at a recording temperature of ∼34°C. Modelling of AP propagation in detailed cable models of granule cells suggested that a ∼4 times higher Na+ channel density (∼1000 pS μm−2) in the axon might account for both the higher rate of rise of axonal APs and the robust AP initiation in the proximal mossy fibre axon. This may be of critical importance to separate dendritic integration of thousands of synaptic inputs from the generation and transmission of a common AP output.
Synaptic Protein Degradation Underlies Destabilization of Retrieved Fear Memory
Authors: Lee Sue-Hyun , Choi Jun-Hyeok , Lee Nuribalhae , Lee Hye-Ryeon , Kim Jae-Ick , Yu Nam-Kyung , Choi Sun-Lim , Lee Seung-Hee , Kim Hyoung , Kaang Bong-Kiun
Published: February 2008

Reactivated memory undergoes a rebuilding process that depends on de novo protein synthesis. This suggests that retrieval is dynamic and serves to incorporate new information into preexisting memories. However, little is known about whether or not protein degradation is involved in the reorganization of retrieved memory. We found that postsynaptic proteins were degraded in the hippocampus by polyubiquitination after retrieval of contextual fear memory. Moreover, the infusion of proteasome inhibitor into the CA1 region immediately after retrieval prevented anisomycin-induced memory impairment, as well as the extinction of fear memory. This suggests that ubiquitin- and proteasome-dependent protein degradation underlies destabilization processes after fear memory retrieval. It also provides strong evidence for the existence of reorganization processes whereby preexisting memory is disrupted by protein degradation, and updated memory is reconsolidated by protein synthesis.
Use of U.S. Croplands for Biofuels Increases Greenhouse Gases Through Emissions from Land-Use Change
Authors: Searchinger Timothy , Heimlich Ralph , Houghton R. A. , Dong Fengxia , Elobeid Amani , Fabiosa Jacinto , Tokgoz Simla , Hayes Dermot , Yu Tun-Hsiang
Published: February 2008

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.
Land Clearing and the Biofuel Carbon Debt
Authors: Fargione Joseph , Hill Jason , Tilman David , Polasky Stephen , Hawthorne Peter
Published: February 2008

Increasing energy use, climate change, and carbon dioxide (CO
2
) emissions from fossil fuels make switching to low-carbon fuels a high priority. Biofuels are a potential low-carbon energy source, but whether biofuels offer carbon savings depends on how they are produced. Converting rainforests, peatlands, savannas, or grasslands to produce food crop–based biofuels in Brazil, Southeast Asia, and the United States creates a “biofuel carbon debt” by releasing 17 to 420 times more CO
2
than the annual greenhouse gas (GHG) reductions that these biofuels would provide by displacing fossil fuels. In contrast, biofuels made from waste biomass or from biomass grown on degraded and abandoned agricultural lands planted with perennials incur little or no carbon debt and can offer immediate and sustained GHG advantages.
Visualizing graphs in three dimensions
Authors: Ware Colin , Mitchell Peter
Published: February 2008

It has been known for some time that larger graphs can be interpreted if laid out in 3D and displayed with stereo and/or motion depth cues to support spatial perception. However, prior studies were carried out using displays that provided a level of detail far short of what the human visual system is capable of resolving. Therefore, we undertook a graph comprehension study using a very high resolution stereoscopic display. In our first experiment, we examined the effect of stereoscopic display, kinetic depth, and using 3D tubes versus lines to display the links. The results showed a much greater benefit for 3D viewing than previous studies. For example, with both motion and stereoscopic depth cues, unskilled observers could see paths between nodes in 333 node graphs with less than a 10% error rate. Skilled observers could see up to a 1000-node graph with less than a 10% error rate. This represented an order of magnitude increase over 2D display. In our second experiment, we varied both nodes and links to understand the constraints on the number of links and the size of graph that can be reliably traced. We found the difference between number of links and number of nodes to best account for error rates and suggest that this is evidence for a “perceptual phase transition.” These findings are discussed in terms of their implications for information display.
Enhancing air traffic displays via perceptual cues
Authors: Palmer Evan M. , Clausner Timothy C. , Kellman Philip J.
Published: February 2008

We examined graphical representations of aircraft altitude in simulated air traffic control (ATC) displays. In two experiments, size and contrast cues correlated with altitude improved participants' ability to detect future aircraft collisions (conflicts). Experiment 1 demonstrated that, across several set sizes, contrast and size cues to altitude improved accuracy at identifying conflicts. Experiment 2 demonstrated that graphical cues for representing altitude both improved accuracy and reduced search time for finding conflicts in large set size displays. The addition of size and contrast cues to ATC displays may offer specific benefits in aircraft conflict detection.
Epidemic thresholds in real networks
Authors: Chakrabarti Deepayan , Wang Yang , Wang Chenxi , Leskovec Jurij , Faloutsos Christos
Published: February 2008

How will a virus propagate in a real network? How long does it take to disinfect a network given particular values of infection rate and virus death rate? What is the single best node to immunize? Answering these questions is essential for devising network-wide strategies to counter viruses. In addition, viral propagation is very similar in principle to the spread of rumors, information, and “fads,” implying that the solutions for viral propagation would also offer insights into these other problem settings. We answer these questions by developing a nonlinear dynamical system (NLDS) that accurately models viral propagation in anyarbitrarynetwork, including real and synthesized network graphs. We propose a general epidemic threshold condition for theNLDSsystem: we prove that the epidemic threshold for a network is exactly the inverse of the largest eigenvalue of its adjacency matrix. Finally, we show that below the epidemic threshold, infections die out at an exponential rate. Our epidemic threshold model subsumes many known thresholds for special-case graphs (e.g., Erdös--Rényi, BA powerlaw, homogeneous). We demonstrate the predictive power of our model with extensive experiments on real and synthesized graphs, and show that our threshold condition holds for arbitrary graphs. Finally, we show how to utilize our threshold condition for practical uses: It can dictate which nodes to immunize; it can assess the effects of a throttling policy; it can help us design network topologies so that they are more resistant to viruses.
Formal foundations for hybrid hierarchies in GTRBAC
Authors: Joshi James B. D. , Bertino Elisa , Ghafoor Arif , Zhang Yue
Published: February 2008

A role hierarchy defines permission acquisition and role-activation semantics through role--role relationships. It can be utilized for efficiently and effectively structuring functional roles of an organization having related access-control needs. The focus of this paper is the analysis of hybrid role hierarchies in the context of the
generalized temporal role-based access control
(GTRBAC) model that allows specification of a comprehensive set of temporal constraints on role, user-role, and role-permission assignments. We introduce the notion of
uniquely activable set
(UAS) associated with a role hierarchy that indicates the access capabilities of a user resulting from his membership to a role in the hierarchy. Identifying such a role set is essential, while making an authorization decision about whether or not a user should be allowed to activate a particular combination of roles in a single session. We formally show how UAS can be determined for a hybrid hierarchy. Furthermore, within a hybrid hierarchy, various hierarchical relations may be derived between an arbitrary pair of roles. We present a set of inference rules that can be used to generate all the possible derived relations that can be inferred from a specified set of hierarchical relations and show that it is
sound
and
complete
. We also present an analysis of hierarchy transformations with respect to role addition, deletion, and partitioning, and show how various cases of these transformations allow the original permission acquisition and role-activation semantics to be managed. The formal results presented here provide a basis for developing efficient security administration and management tools.
Papiercraft
Authors: Liao Chunyuan , Guimbretière François , Hinckley Ken , Hollan Jim
Published: February 2008

Paper persists as an integral component of
active reading
and other knowledge-worker tasks because it provides ease of use unmatched by digital alternatives. Paper documents are light to carry, easy to annotate, rapid to navigate, flexible to manipulate, and robust to use in varied environments. Interactions with paper documents create rich webs of annotation, cross reference, and spatial organization. Unfortunately, the resulting webs are confined to the physical world of paper and, as they accumulate, become increasingly difficult to store, search, and access. XLibris [Schilit et al. 1998] and similar systems address these difficulties by simulating paper with tablet PCs. While this approach is promising, it suffers not only from limitations of current tablet computers (e.g., limited screen space) but also from loss of invaluable paper affordances.

In this article, we describe PapierCraft, a gesture-based command system that allows users to manipulate digital documents using paper printouts as proxies. Using an Anoto [Anoto 2002] digital pen, users can draw command gestures on paper to tag a paragraph, e-mail a selected area, copy selections to a notepad, or create links to related documents. Upon pen synchronization, PapierCraft executes the commands and presents the results in a digital document viewer. Users can then search the tagged information and navigate the web of annotated digital documents resulting from interactions with the paper proxies. PapierCraft also supports real time interactions across mix-media, for example, letting users copy information from paper to a Tablet PC screen. This article presents the design and implementation of the PapierCraft system and describes user feedback from initial use.
Comparing usability of one-way and multi-way constraints for diagram editing
Authors: Wybrow Michael , Marriott Kim , Mciver Linda , Stuckey Peter J.
Published: February 2008

We investigate the usability of constraint-based alignment and distribution placement tools in diagram editors. Currently one-way constraints are used to provide alignment and distribution tools in many commercial editors. We believe the limitations of these constraints lead to serious usability issues, and thus suggest that such tools be implemented using multi-way constraints. We have conducted two usability studies, the first studies we are aware of that examine the relative usefulness of interactive graphical tools based on one-way and multi-way constraints. They provide strong evidence that multi-way constraint-based alignment and distribution tools are more usable than one-way constraint-based alignment and distribution tools.
Block variants of Hammarling's method for solving Lyapunov equations
Authors: Kressner Daniel
Published: February 2008

This article is concerned with the efficient numerical solution of the Lyapunov equation
A

T

X
+
XA
= -
C
with a stable matrix
A
and a symmetric positive semidefinite matrix
C
of possibly small rank. We discuss the efficient implementation of Hammarling's method and propose among other algorithmic improvements a block variant, which is demonstrated to perform significantly better than existing implementations. An extension to the discrete-time Lyapunov equation
A

T

XA
-
X
= -
C
is also described.
Algorithm 872
Authors: Chernikov Andrey N. , Chrisochoides Nikos P.
Published: February 2008

Delaunay refinement is a widely used method for the construction of guaranteed quality triangular and tetrahedral meshes. We present an algorithm and a software for the parallel constrained Delaunay mesh generation in two dimensions. Our approach is based on the decomposition of the original mesh generation problem into
N
smaller subproblems which are meshed in parallel. The parallel algorithm is asynchronous with small messages which can be aggregated and exhibits low communication costs. On a heterogeneous cluster of more than 100 processors our implementation can generate over one billion triangles in less than 3 minutes, while the single-node performance is comparable to that of the fastest to our knowledge sequential guaranteed quality Delaunay meshing library (the Triangle).
A clustering framework based on subjective and objective validity criteria
Authors: Halkidi M. , Gunopulos D. , Vazirgiannis M. , Kumar N. , Domeniconi C.
Published: February 2008

Clustering, as an unsupervised learning process is a challenging problem, especially in cases of high-dimensional datasets. Clustering result quality can benefit from user constraints and objective validity assessment. In this article, we propose a semisupervised framework for learning the weighted Euclidean subspace, where the best clustering can be achieved. Our approach capitalizes on: (i) user constraints; and (ii) the quality of intermediate clustering results in terms of their structural properties. The proposed framework uses the clustering algorithm and the validity measure as its parameters. We develop and discuss algorithms for learning and tuning the weights of contributing dimensions and defining the “best” clustering obtained by satisfying user constraints. Experimental results on benchmark datasets demonstrate the superiority of the proposed approach in terms of improved clustering accuracy.
High-level synthesis of digital microfluidic biochips
Authors: Su Fei , Chakrabarty Krishnendu
Published: February 2008

Microfluidic biochips offer a promising platform for massively parallel DNA analysis, automated drug discovery, and real-time biomolecular recognition. Current techniques for full-custom design of droplet-based “digital” biochips do not scale well for concurrent assays and for next-generation system-on-chip (SOC) designs that are expected to include microfluidic components. We propose a system design methodology that attempts to apply classical high-level synthesis techniques to the design of digital microfluidic biochips. We focus here on the problem of scheduling bioassay functions under resource constraints. We first develop an optimal scheduling strategy based on integer linear programming. However, because the scheduling problem is NP-complete, we also develop two heuristic techniques that scale well for large problem instances. A clinical diagnostic procedure, namely multiplexed in-vitro diagnostics on human physiological fluids, is first used to illustrate and evaluate the proposed method. Next, the synthesis approach is applied to a protein assay, which serves as a more complex bioassay application. The proposed synthesis approach is expected to reduce human effort and design cycle time, and it will facilitate the integration of microfluidic components with microelectronic components in next-generation SOCs.
Synthesis of reversible sequential elements
Authors: Chuang Min-Lun , Wang Chun-Yao
Published: February 2008

To construct a reversible sequential circuit, reversible sequential elements are required. This work presents novel designs of reversible sequential elements such as the D latch, JK latch, and T latch. Based on these reversible latches, we construct the designs of the corresponding flip-flops. Then we further discuss the physical implementations of our designs based on electron waveguide Y-branch switch technology. Test costs, including test generation and test application, of reversible sequential circuits with these reversible flip-flops are also discussed. Compared with previous work, the implementation cost of our new designs, including the number of gates and the number of garbage outputs, is significantly reduced. The number of gates in our designs is 47.4% of the designs in previous work on average. The number of garbage outputs in our designs is 25% of the designs in previous work on average.
Efficient architectural design space exploration via predictive modeling
Authors: Ipek Engin , McKee Sally A. , Singh Karan , Caruana Rich , Supinski Bronis R. de , Schulz Martin
Published: February 2008

Efficiently exploring exponential-size architectural design spaces with many interacting parameters remains an open problem: the sheer number of experiments required renders detailed simulation intractable. We attack this via an automated approach that builds accurate predictive models. We simulate sampled points, using results to teach our models the function describing relationships among design parameters. The models can be queried and are very fast, enabling efficient design tradeoff discovery. We validate our approach via two uniprocessor sensitivity studies, predicting IPC with only 1--2% error. In an experimental study using the approach, training on 1% of a 250-K-point CMP design space allows our models to predict performance with only 4--5% error. Our predictive modeling combines well with techniques that reduce the time taken by each simulation experiment, achieving net time savings of three-four orders of magnitude.
Multidocument Summary Generation
Authors: Kuo June-Jei , Chen Hsin-Hsi
Published: February 2008

Summary generation for multiple documents poses a number of issues including sentence selection, sentence ordering, and sentence reduction over single-document summarization. In addition, the temporal resolution among extracted sentences is also important. This article considers informative words and event words to deal with multidocument summarization. These words indicate the important concepts and relationships in a document or among a set of documents, and can be used to select salient sentences. We present a temporal resolution algorithm, using focusing time and coreference chains, to convert Chinese temporal expressions in a document into calendrical forms. Moreover, we consider the last calendrical form of a sentence as a sentence time stamp to address sentence ordering. Informative words, event words, and temporal words are introduced to a sentence reduction algorithm, which deals with both length constraints and information coverage. Experiments on Chinese-news data sets show significant improvements of both information coverage and readability.
The Traust Authorization Service
Authors: Lee Adam J. , Winslett Marianne , Basney Jim , Welch Von
Published: February 2008

In recent years, trust negotiation has been proposed as a novel authorization solution for use in open-system environments, in which resources are shared across organizational boundaries. Researchers have shown that trust negotiation is indeed a viable solution for these environments by developing a number of policy languages and strategies for trust negotiation that have desirable theoretical properties. Further, existing protocols, such as TLS, have been altered to interact with prototype trust negotiation systems, thereby illustrating the utility of trust negotiation. Unfortunately, modifying existing protocols is often a time-consuming and bureaucratic process that can hinder the adoption of this promising technology.

In this paper, we present Traust, a third-party authorization service that leverages the strengths of existing prototype trust negotiation systems. Traust acts as an authorization broker that issues access tokens for resources in an open system after entities use trust negotiation to satisfy the appropriate resource access policies. The Traust architecture was designed to allow Traust to be integrated either directly with newer trust-aware applications or indirectly with existing legacy applications; this flexibility paves the way for the incremental adoption of trust negotiation technologies without requiring widespread software or protocol upgrades. We discuss the design and implementation of Traust, the communication protocol used by the Traust system, and its performance. We also discuss our experiences using Traust to broker access to legacy resources, our proposal for a Traust-aware version of the GridFTP protocol, and Traust's resilience to attack.
Open source as a foundation for systems research
Authors: Ben-Yehuda Muli , Van Hensbergen Eric
Published: February 2008

You are a systems researcher at a corporate research lab. The corporation you work for deals with both proprietary and open source software. You have an exciting new idea that will undoubtedly revolutionize the field, but first you need to build a working system to validate it. Before embarking on your exploratory research project, you must decide: Do you start from scratch, or do you build upon a mature system? And if the latter---should the system be proprietary or open source?