bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonhelical Leash and α-Helical Structures Determine the Potency of a Peptide Antagonist of Human T-Cell Leukemia Virus Entry
Authors: Mirsaliotis Antonis , Lamb Daniel , Brighty David W.
Published: February 2008

Viral fusion proteins mediate the entry of enveloped viral particles into cells by inducing fusion of the viral and target cell membranes. Activated fusion proteins undergo a cascade of conformational transitions and ultimately resolve into a compact trimer of hairpins or six-helix bundle structure, which pulls the interacting membranes together to promote lipid mixing. Significantly, synthetic peptides based on a C-terminal region of the trimer of hairpins are potent inhibitors of membrane fusion and viral entry, and such peptides are typically extensively α-helical. In contrast, an atypical peptide inhibitor of human T-cell leukemia virus (HTLV) includes α-helical and nonhelical leash segments. We demonstrate that both the C helix and C-terminal leash are critical to the inhibitory activities of these peptides. Amino acid side chains in the leash and C helix extend into deep hydrophobic pockets at the membrane-proximal end of the HTLV type 1 (HTLV-1) coiled coil, and these contacts are necessary for potent antagonism of membrane fusion. In addition, a single amino acid substitution within the inhibitory peptide improves peptide interaction with the core coiled coil and yields a peptide with enhanced potency. We suggest that the deep pockets on the coiled coil are ideal targets for small-molecule inhibitors of HTLV-1 entry into cells. Moreover, the extended nature of the HTLV-1-inhibitory peptide suggests that such peptides may be intrinsically amenable to modifications designed to improve inhibitory activity. Finally, we propose that leash-like mimetic peptides may be of value as entry inhibitors for other clinically important viral infections.
Without Its N-Finger, the Main Protease of Severe Acute Respiratory Syndrome Coronavirus Can Form a Novel Dimer through Its C-Terminal Domain
Authors: Zhong Nan , Zhang Shengnan , Zou Peng , Chen Jiaxuan , Kang Xue , Li Zhe , Liang Chao , Jin Changwen , Xia Bin
Published: February 2008

The main protease (M
pro
) of severe acute respiratory syndrome coronavirus (SARS-CoV) plays an essential role in the extensive proteolytic processing of the viral polyproteins (pp1a and pp1ab), and it is an important target for anti-SARS drug development. It was found that SARS-CoV M
pro
exists in solution as an equilibrium of both monomeric and dimeric forms, and the dimeric form is the enzymatically active form. However, the mechanism of SARS-CoV M
pro
dimerization, especially the roles of its N-terminal seven residues (N-finger) and its unique C-terminal domain in the dimerization, remain unclear. Here we report that the SARS-CoV M
pro
C-terminal domain alone (residues 187 to 306; M
pro
-C) is produced in
Escherichia coli
in both monomeric and dimeric forms, and no exchange could be observed between them at room temperature. The M
pro
-C dimer has a novel dimerization interface. Meanwhile, the N-finger deletion mutant of SARS-CoV M
pro
also exists as both a stable monomer and a stable dimer, and the dimer is formed through the same C-terminal-domain interaction as that in the M
pro
-C dimer. However, no C-terminal domain-mediated dimerization form can be detected for wild-type SARS-CoV M
pro
. Our study results help to clarify previously published controversial claims about the role of the N-finger in SARS-CoV M
pro
dimerization. Apparently, without the N-finger, SARS-CoV M
pro
can no longer retain the active dimer structure; instead, it can form a new type of dimer which is inactive. Therefore, the N-finger of SARS-CoV M
pro
is not only critical for its dimerization but also essential for the enzyme to form the enzymatically active dimer.
Mechanism for Controlling the Dimer-Monomer Switch and Coupling Dimerization to Catalysis of the Severe Acute Respiratory Syndrome Coronavirus 3C-Like Protease
Authors: Shi Jiahai , Sivaraman J. , Song Jianxing
Published: February 2008

Unlike 3C protease, the severe acute respiratory syndrome coronavirus (SARS-CoV) 3C-like protease (3CLpro) is only enzymatically active as a homodimer and its catalysis is under extensive regulation by the unique extra domain. Despite intense studies, two puzzles still remain: (i) how the dimer-monomer switch is controlled and (ii) why dimerization is absolutely required for catalysis. Here we report the monomeric crystal structure of the SARS-CoV 3CLpro mutant R298A at a resolution of 1.75 Å. Detailed analysis reveals that Arg298 serves as a key component for maintaining dimerization, and consequently, its mutation will trigger a cooperative switch from a dimer to a monomer. The monomeric enzyme is irreversibly inactivated because its catalytic machinery is frozen in the collapsed state, characteristic of the formation of a short 310-helix from an active-site loop. Remarkably, dimerization appears to be coupled to catalysis in 3CLpro through the use of overlapped residues for two networks, one for dimerization and another for the catalysis.
pRB-E2F1 Complexes Are Resistant to Adenovirus E1A-Mediated Disruption
Authors: Seifried L. A. , Talluri S. , Cecchini M. , Julian L. M. , Mymryk J. S. , Dick F. A.
Published: February 2008

Disruption of pRB-E2F interactions by E1A is a key event in the adenoviral life cycle that drives expression of early viral transcription and induces cell cycle progression. This function of E1A is complicated by E2F1, an E2F family member that controls multiple processes besides proliferation, including apoptosis and DNA repair. Recently, a second interaction site in pRB that only contacts E2F1 has been discovered, allowing pRB to control proliferation separately from other E2F1-dependent activities. Based on this new insight into pRB-E2F1 regulation, we investigated how E1A affects control of E2F1 by pRB. Our data reveal that pRB-E2F1 interactions are resistant to E1A-mediated disruption. Using mutant forms of pRB that selectively force E2F1 to bind through only one of the two binding sites on pRB, we determined that E1A is unable to disrupt E2F1's unique interaction with pRB. Furthermore, analysis of pRB-E2F complexes during adenoviral infection reveals the selective maintenance of pRB-E2F1 interactions despite the presence of E1A. Our experiments also demonstrate that E2F1 functions to maintain cell viability in response to E1A expression. This suggests that adenovirus E1A's seemingly complex mechanism of disrupting pRB-E2F interactions provides selectivity in promoting viral transcription and cell cycle advancement, while maintaining cell viability.
Sedimentation in ice-dammed Hazard Lake, Yukon
Authors: Liverman David G. E.
Published: February 2008

"Hazard Lake," located in Kluane National Park, the Yukon, is an ice-dammed lake formed in 1966 by the surge of the Steele Glacier. Since 1975 it has drained annually by means of a subglacial tunnel. During July 1979, observations were made of lake processes before drainage and of sections described in the lake bottom after drainage. Three facies associations are believed to represent prelake, stable lake, and annual draining phases. Gravel commonly found at the base of sections represents deposition in a braided fluvial system prior to 1966. Lake sediments deposited between 1966 and 1975 are dominantly graded laminated silt deposited by turbid underflow from the major inflow stream. Lamination is probably caused by diurnal underflow events or daily variation in strength of underflow. No "winter" clay component of varved sediments is observed. During drainage a regressive sequence is deposited as the lake level drops, with sand-dominated sediments overlapping laminated silt where the main inflow stream enters the lake. This is followed by local fluvial deposition along the course of the reestablished stream. During filling a transgressive sequence is deposited as the lake level rises. Sand-dominated deltaic sedimentation is followed by deposition from underflow, resulting in laminated and massive silt and clay. These fine-grained facies separate sand facies and demark individual filling events but are easily eroded. Thus it is not possible to identify the effects of each individual drainage–filling cycle in the sediments. After drainage the lake remains empty until the next melt season, during which time a braided stream is established in the lake basin, depositing sands and gravels and eroding lake sediments.
A sedimentological overview of the coal-bearing Morien Group (Pennsylvanian), Sydney Basin, Nova Scotia, Canada
Authors: Rust B. R. , Gibling M. R. , Best M. A. , Dilles S. J. , Masson A. G.
Published: February 2008

The onshore part of the Sydney Basin, Nova Scotia, contains a 2 km fining-upward coal-bearing succession, the Pennsylvanian Morien Group. Facies analysis indicates an upward change in depositional environment from mid- through distal braid-plain to meandering fluvial plain. This change occurred earliest in the southeast part of the basin, where the meandering channels were incised through penecontemporaneous duricrusts. Northeastward drainage was maintained throughout, and the basin fill records gradually decreasing slopes as source relief was worn down and rate of subsidence declined during a period of increasing tectonic quiescence. The uneconomic coals of the lower Morien Group (South Bar and Waddens Cove formations) are thin and inextensive and formed in well-drained swamps of anabranches from the active braided system or between incised meandering channels. The economic coals of the upper Morien (Sydney Mines Formation) are more extensive and formed in broad, humid swamps of large flood basins between the unconfined channels of large meandering rivers.
Éléments d'une climatostratigraphie du Pléistocène moyen et tardif dans l'est du Canada par l'analyse palynologique et isotopique du forage 84-030-003, mer du Labrador
Authors: Vernal A. de , Hillaire-Marcel C.
Published: February 2008

The piston and gravity cores 84-030-003, collected in the southern Labrador Sea, have been sampled for detailed palynological and isotopic analyses. The δ18O record on foraminifera (Neogloboquadrina pachyderma, left-coiling) indicates a stratigraphy spanning isotopic stages 8 to 1, i.e., over ca. 300 000 years. The isotopic record allows the calculation of a mean sedimentation rate of approximately 5 cm/ka.The pollen and spore contents of the sediments are low. The low pollen influxes (generally less than 1 grain/cm2 per year) and the dominance of Pinus suggest aeolian transport over long distances with southwest–northeast to south-southwest–north-northeast trends. Dinoflagellate cyst concentrations are relatively low, indicating a low regional phytoplanktonic productivity. The assemblages are, however, diversified. They reflect influences from the North Atlantic Drift and from the Labrador Current. The occurrence of warm-temperate to tropical Impagidinium species in deposits suggests an almost permanent penetration of North Atlantic water masses into the Labrador Sea during the middle and Late Pleistocene. This divergence was apparently interrupted during the last glacial maximum of isotopic stage 2. Increases in the concentration of dinocysts such as Operculodinium centrocarpum, Nematosphaeropsis labyrinthea, and Bitectatodinium tepikiense were recorded during interglacial maxima of stages 7, 5, and 1. These dinocyst peaks indicate a high primary productivity and cool-temperate to subarctic conditions in surficial water masses offshore eastern Canada. In addition, they are probably related to a strong hydrodynamic regime of the Labrador Current. Fluctuations in the dinocyst concentrations are in most cases synchronous with the δ18O changes of foraminifera, indicating a strong relationship between the paleo-oceanography of the Labrador Sea and the Quaternary glaciations.
EXISTENCE OF SPECTRAL GAPS, COVERING MANIFOLDS AND RESIDUALLY FINITE GROUPS
Authors: LLEDÓ FERNANDO , POST OLAF
Published: February 2008

In the present paper we consider Riemannian coverings (X,g) → (M,g) with residually finite covering group Γ and compact base space (M,g). In particular, we give two general procedures resulting in a family of deformed coverings (X,gε) → (M,gε) such that the spectrum of the Laplacian Δ(Xε,gε) has at least a prescribed finite number of spectral gaps provided ε is small enough.

If Γ has a positive Kadison constant, then we can apply results by Brüning and Sunada to deduce that spec Δ(X,gε) has, in addition, band-structure and there is an asymptotic estimate for the number [Formula: see text] of components of spec Δ(X,gε) that intersect the interval [0,λ]. We also present several classes of examples of residually finite groups that fit with our construction and study their interrelations. Finally, we mention several possible applications for our results.
KAON CONTRIBUTIONS TO THE GERASIMOV–DRELL–HEARN INTEGRALS ON THE PROTON
Authors: MART T.
Published: February 2008

Using KAON-MAID, an operator for kaon photo- and electro-production on the nucleon, we calculate contributions of kaon–hyperon final states to the Gerasimov–Drell–Hearn (GDH) integrals on the proton. We also calculate the corresponding contributions to the forward spin polarizability γ0 of the proton. By extending the operator to the finite Q2 region we then calculate kaon contributions to the generalized GDH integrals, as well as to the longitudinal-transverse polarizability δ0. Our results show relatively small but still sizable contributions.
TENSOR SELF-ENERGY IN A VECTOR-TENSOR MODEL
Authors: BUCHEL A. , CHISHTIE F. A. , GAGNÉ-PORTELANCE M. , HOMAYOUNI S. , MCKEON D. G. C.
Published: February 2008

The tensor self-energy is computed at one-loop order in a model in which a vector and tensor interact in a way that eliminates all tensor degrees of freedom. Divergencies arise which cannot be eliminated without introducing a kinetic term for the tensor field which does not appear in the classical action. A field redefinition serves to eliminate these divergences.
RESIDUAL RESISTIVITY OF DILUTE ALLOYS
Authors: VORA ADITYA M.
Published: February 2008

The residual resistivity for 156 dilute alloys of 19 hosts of different groups of the periodic table has been studied on the basis of the single parametric model potential formalism. Ashcroft's empty core model (EMC) potential is explored for the first time with five different local field correction functions, viz, Hartree (H), Taylor (T), Ichimaru–Utsumi (IU), Farid et al. (F), and Sarkar et al. (S) to investigate the effect of the exchange and correlation on the aforesaid properties. The comparison of the presently computed outcomes with the available theoretical and experimental data is highly encouraging. The investigation of residual resistivity is found to be quite sensitive to the selection of local field correction function, showing a significant variation with the change in the function.
DIELECTRIC RESPONSE OF ANISOTROPIC GRADED CYLINDRICAL COMPOSITES WITH A GENERAL POWER-LAW PROFILE
Authors: WEI EN-BO , GU G. Q. , YU K. W.
Published: February 2008

The effective dielectric response of composites containing anisotropic graded cylindrical inclusions whose graded profile along the radial direction is different from that along the tangential direction in cylindrical coordinates, has been investigated. As an example, we have studied composites of anisotropic graded cylindrical inclusions with general power-law profiles, [Formula: see text] and [Formula: see text], where r is the distance of a point in the cylindrical inclusion from the origin. Analytical solutions of the local electric potentials are derived in terms of the hyper-geometric function and the formulas for calculating the effective response of anisotropic graded composites are given in the dilute limit. Furthermore, we have validated the anisotropic differential effective dipole approximation (ADEDA) by comparing with our exact results, and obtained excellent agreement.
Planar landforms as markers of denudation chronology: an inversion of East Pyrenean tectonics based on landscape and sedimentary basin analysis
Authors: Calvet Marc , Gunnell Yanni
Published: February 2008

For over half a century the Pyrenees were considered to be a mountain range in which compressional structures were ancient (pre-Oligocene) but topography was young due to late Neogene tectonic uplift. Sufficient time had been afforded for a ‘peneplain’ to form at low elevations, undergo vertical uplift and remain partially preserved at high elevations until present times. This model of topographic growth has since been challenged by alternative theories. One of these postulates that topography in active orogens is in a steady-state, hence mountain ranges must be monocyclic and their ‘peneplains’ must have formed at high altitudes during continental convergence as a result of raised foreland base levels. Here we investigate Pyrenean denudation chronology using a range of evidence including provenance stratigraphy, the cross-cutting relations between topographic and tectonic features, and the age of regolith based on fossil faunas and floras. We find that the Eastern Pyrenees underwent a punctuated topographic evolution until recent times driven primarily by tectonic forcing, including kilometre-scale rock and surface uplift after 12 Ma. Climatic and eustatic inputs were subsidiary driving mechanisms.
Time scales of tectonic landscapes and their sediment routing systems
Authors: Allen Philip A.
Published: February 2008

In regions undergoing active tectonics, the coupling between the tectonic displacement field, the overlying landscape and the redistribution of mass at the Earth's surface in the form of sediment routing systems, is particularly marked and variable. Coupling between deformation and surface processes takes place at a range of scales, from the whole orogen to individual extensional fault blocks or contractional anticlines. At the large scale, the attainment of a steady-state between the overlying topography and the prevailing tectonic conditions in active contractional orogens requires an efficient erosional system, with a time scale dependent on the vigour of the erosional system, generally in the range 10
6
–10
7
years. The catchment–fan systems associated with extensional fault blocks and basins of the western USA are valuable natural examples to study the coupling between tectonic deformation, landscape and sediment routing systems. Even relatively simple coupled systems such as an extensional fault block and its associated basin margin fans have a range of time scales in response to a tectonic perturbation. These response times originate from the development of uniform (steady-state) relief during the accumulation of displacement on a normal fault (
c
. 10
6
years), the upstream propagation of a bedrock knickpoint in transverse catchments following a change in tectonic uplift rate (
c
. 10
6
years), or the relaxation times of the integrated catchment–fan system in response to changes in climatic and tectonic boundary conditions (10
5
–10
6
years). The presence of extensive bedrock or alluvial piedmonts increases response times significantly. The sediment efflux of a mountain catchment is a boundary condition for far-field fluvial transport, but the fluvial system is much more than a simple transmitter of the sediment supply signal to a neighbouring depocentre. Fluvial systems appear to act as buffers to incoming sediment supply signals, with a diffusive time scale (
c
. 10
5
–10
6
years) dependent on the length of the system and the extent of its floodplains, stream channels and proximal gravel fans. The vocabulary for explaining landscapes would benefit from a greater recognition of the importance of the repeat time and magnitude of perturbations in relation to the response and relaxation times of the landscape and its sediment routing systems. Landscapes are best differentiated as ‘buffered’ or ‘reactive’ depending on the ratio of the response time to the repeat time of the perturbation. Furthermore, landscapes may be regarded as ‘steady’ or ‘transient’ depending on the ratio of the response time to the time elapsed since the most recent change in boundary conditions. The response of tectonically and climatically perturbed landscapes has profound implications for the interpretation of stratigraphic architecture.
Limits to resolving catastrophic events in the Quaternary fluvial record: a case study from the Nene valley, Northamptonshire, UK
Authors: Briant Rebecca M. , Gibbard Philip L. , Boreham Steve , Coope G. Russell , Preece Richard C.
Published: February 2008

Flood events within rivers are responsible for much erosion and deposition. Thus, deposits laid down during floods could potentially comprise the bulk of the Quaternary fluvial record. However, it is difficult to detect individual flood events, as effectively illustrated by the Middle Devensian (Weichselian) to Holocene fluvial sequence from the Nene Valley, Northamptonshire, described in this paper. This is due to limits in the resolution of sedimentological, palaeontological and geochronological techniques. Geochronological techniques have the highest resolution, but error bars of
c
. 50 years (radiocarbon) and up to 2 ka (optically stimulated luminescence) in the Late-glacial do not allow detection of floods lasting only a few weeks or less. Geochronology is, however, essential for linking periods of fluvial deposition to climatic phases at the marine isotope substage scale. Thus, multiple age determinations show remnant Middle Devensian deposits within a facies association mainly of Younger Dryas age, showing similar fluvial response to climate during both time periods. Palaeontological assemblages suggest that climate was also similar, although with some subtle differences. Determining ‘average’ fluvial activity in response to broad climate phases improves understanding of how rivers behave over long time periods, even though determination of the role of flood events in the Quaternary fluvial record remains elusive.
Content and quality
Authors: Radun Jenni , Leisti Tuomas , Häkkinen Jukka , Ojanen Harri , Olives Jean-Luc , Vuori Tero , Nyman Göte
Published: February 2008

Test image contents affect subjective image-quality evaluations. Psychometric methods might show that contents have an influence on image quality, but they do not tell what this influence is like, i.e., how the contents influence image quality. To obtain a holistic description of subjective image quality, we have used an interpretation-based quality (IBQ) estimation approach, which combines qualitative and quantitative methodology. The method enables simultaneous examination of psychometric results and the subjective meanings related to the perceived image-quality changes. In this way, the relationship between subjective feature detection, subjective preferences, and interpretations are revealed. We report a study that shows that different impressions are conveyed in five test image contents after similar sharpness variations. Thirty naïve observers classified and freely described the images after which magnitude estimation was used to verify that they distinguished the changes in the images. The data suggest that in the case of high image quality, the test image selection is crucial. If subjective evaluation is limited only to technical defects in test images, important subjective information of image-quality experience is lost. The approach described here can be used to examine image quality and it will help image scientists to evaluate their test images.
Application-aware snoop filtering for low-power cache coherence in embedded multiprocessors
Authors: Zhou Xiangrong , Yu Chenjie , Dash Alokika , Petrov Peter
Published: February 2008

Maintaining local caches coherently in shared-memory multiprocessors results in significant power consumption. The customization methodology we propose exploits the fact that in embedded systems, important knowledge is available to the system designers regarding memory sharing between tasks. We demonstrate how the snoop-induced cache probings can be significantly reduced by identifying and exploiting in a deterministic way the shared memory regions between the processors. Snoop activity is enabled only for the accesses referring to known shared regions. The hardware support is not only cost efficient, but also software programmable, which allows for reprogrammability and customization across different tasks and applications.
Mobile gaming
Authors: Soh Jason O. B. , Tan Bernard C. Y.
Published: February 2008

Tens of millions of users worldwide play games, as well as make phone calls, on their cell phones and other handheld devices.
The illusion of security
Authors: Wright David , Friedewald Michael , Schreurs Wim , Verlinden Michiel , Gutwirth Serge , Punie Yves , Maghiros Ioannis , Vildjiounaite Elena , Alahuhta Petteri
Published: February 2008

A fictional scenario of daily life in a world networked with ambient intelligence illustrates the dark side of the technology and the need for appropriate safeguards.
Requirements engineering in new product development
Authors: Safayeni Frank , Duimering P. Robert , Zheng Kimberley , Derbentseva Natalia , Poile Christopher , Ran Bing
Published: February 2008

How effective are the socio-technical interactions in developing new products?
Sensor localization in concave environments
Authors: Wang Chen , Xiao Li
Published: February 2008

In sensor network localization, multihop based approaches have been proposed to approximate the shortest paths to Euclidean distances between pairwise sensors. A good approximation can be achieved when sensors are densely deployed in a convex area, where the shortest paths are close to straight lines connecting pairwise sensors. However, in a concave network, the shortest paths may deviate far away from straight lines, which leads to erroneous distance estimation and inaccurate localization results. To solve this problem, we propose an improved multihop algorithm that can recognize and filter out the erroneous distance estimation, and therefore achieve accurate localization results even in a concave network.
Cluster-based congestion control for sensor networks
Authors: Karenos Kyriakos , Kalogeraki Vana , Krishnamurthy Srikanth V.
Published: February 2008

In wireless sensor networks, multiple flows from data collecting sensors to an aggregating sink could traverse paths that are largely interference coupled. These interference effects manifest themselves as congestion, and cause the flows to experience high packet loss and arbitrary packet delays. This is particularly problematic in event-based sensor networks (such as those in disaster recovery missions) where some flows are of greater importance than others and require a higher fidelity in terms of packet delivery and timeliness. In this paper we present COMUT (COngestion control for MUlti-class Traffic), a distributed cluster-based mechanism for supporting multiple classes of traffic in sensor networks. COMUT is based on the self-organization of the network into
clusters
, each of which autonomously and
proactively
monitors congestion within its localized scope. The clusters then exchange appropriate information to facilitate system wide rate control where, each data source, depending on the relative importance of its data flow and the experienced congestion en route the sink, is coerced into controlling its rate. Our simulation results demonstrate that (i) our techniques are highly effective in dealing with multiple, interfering flows and in achieving high delivery ratios and low delays compared to traditional approaches, (ii) operate successfully over multiple underlying routing protocols, (iii) provide higher throughput to higher importance flows, (iv) are responsive to failures and, finally, (v) achieve substantial energy savings due to the considerable reduction in packet drops via the effective regulation of the network load.
A utility-based unified disk scheduling framework for shared mixed-media services
Authors: Verma Akshat , Jain Rohit , Ghosal Sugata
Published: February 2008

We present a new disk scheduling framework to address the needs of a shared multimedia service that provides differentiated multilevel quality-of-service for mixed-media workloads. In such a shared service, requests from different users have different associated performance objectives and utilities, in accordance with the negotiated service-level agreements (SLAs). Service providers typically provision resources only for average workload intensity, so it becomes important to handle workload surges in a way that maximizes the utility of the served requests.

We capture the performance objectives and utilities associated with these multiclass diverse workloads in a unified framework and formulate the disk scheduling problem as a reward maximization problem. We map the reward maximization problem to a minimization problem on graphs and, by novel use of graph-theoretic techniques, design a scheduling algorithm that is computationally efficient and optimal in the class of seek-optimizing algorithms. Comprehensive experimental studies demonstrate that the proposed algorithm outperforms other disk schedulers under all loads, with the performance improvement approaching 100% under certain high load conditions. In contrast to existing schedulers, the proposed scheduler is extensible to new performance objectives (workload type) and utilities by simply altering the reward functions associated with the requests.
Shared heap management for memory-limited java virtual machines
Authors: Choi Yoonseo , Han Hwansoo
Published: February 2008

One scarce resource in embedded systems is memory. Multitasking makes the lack of memory problem even worse. Most current embedded systems, which do not provide virtual memory, simply divide physical memory and evenly assign contiguous memory chunks to multiple applications. Such simple memory management can frequently cause the lack of available memory for some applications, while others are not using the full amount of assigned memory. To overcome inefficiency in current memory management, we present an efficient heap management scheme that allows multiple applications to share heap space. To reduce overall heap memory usage, applications adaptively acquire subheaps out of shared pool of memory and release surplus subheaps to shared pool. As a result, applications see noncontiguous multiple subheaps as a heap in their address space. We target Java applications to implement our heap-sharing scheme in the KVM from Sun Microsystems. To protect fragmented heap space with a limited number of regions in memory protection unit (MPU), we maintain only a limited number of subheaps. We experimentally evaluate our heap management scheme with J2ME MIDP applications. Our static and dynamic schemes reduce heap memory usage, on average, by 30 and 27%, respectively. For both schemes, overheads are kept low. The execution times in our schemes are increased only by 0.01% for static scheme and 0.35% for dynamic scheme, on average.
Fast exploration of bus-based communication architectures at the CCATB abstraction
Authors: Pasricha Sudeep , Dutt Nikil , Ben-Romdhane Mohamed
Published: February 2008

Currently, system-on-chip (SoC) designs are becoming increasingly complex, with more and more components being integrated into a single SoC design. Communication between these components is increasingly dominating critical system paths and frequently becomes the source of performance bottlenecks. It, therefore, becomes imperative for designers to explore the communication space early in the design flow. Traditionally, system designers have used Pin-Accurate Bus Cycle Accurate (PA-BCA) models for early communication space exploration. These models capture all of the bus signals and strictly maintain cycle accuracy, which is useful for reliable performance exploration but results in slow simulation speeds for complex, designs, even when they are modeled using high-level languages. Recently, there have been several efforts to use the Transaction-Level Modeling (TLM) paradigm for improving simulation performance in BCA models. However, these transaction-based BCA (T-BCA) models capture a lot of details that can be eliminated when exploring communication architectures. In this paper, we extend the TLM approach and propose a new transaction-based modeling abstraction level (CCATB) to explore the communication design space. Our abstraction level bridges the gap between the TLM and BCA levels, and yields an average performance speedup of 120% over PA-BCA and 67% over T-BCA models, on average. The CCATB models are not only faster to simulate, but also extremely accurate and take less time to model compared to both T-BCA and PA-BCA models. We describe the mechanisms that produce the speedup in CCATB models and also analyze how the achieved simulation speedup scales with design complexity. To demonstrate the effectiveness of using CCATB for exploration, we present communication space exploration case studies from the broadband communication and multimedia application domains.
An ethnocentric look at the law and technology interface
Authors: Fass Leona F.
Published: February 2008

We often conduct ethnocentric research, observing everyday citizen end-users in their own environments to assess their access, technological and policy concerns. Our recent research has revealed that many end-user concerns are on the interface of Law and Technology. Such interface issues also have become apparent throughout our own interactions with software and the Web, as well as within our specific research into eCommerce; Link Analysis and Data Mining; and the Semantic Web applied to eGovernment and Homeland Security. Among the relevant areas we now address are information security and integrity; barriers (intentional or otherwise) to access; security-privacy trade-offs; the need for user education; and importance of cooperation among stakeholders, policymakers and experts in Technology-related Law. We illustrate that in many policy areas of evolving Law related to Technology there may be no general decision procedure; many decisions can only be made case-by-case. We strongly support ethnocentric studies by practitioners of Software Engineering, experts in Technology Law and policymakers. This can identify specific critical deployment issues that might otherwise be overlooked within traditional research venues. We believe that many end-user concerns on the Law and Technology interface, once recognized, can be alleviated by Software Engineering professionals.
Mechanism design for stochastic optimization problems
Authors: Ieong Samuel , Sundararajan Mukund , So Anthony Man-Cho
Published: February 2008

We identify and address algorithmic and game-theoretic issues arising from welfare maximization in the well-studied two-stage stochastic optimization framework. In contrast, prior work in algorithmic mechanism design has focused almost exclusively on optimization problems without uncertainty. We show both positive results, by demonstrating a mechanism that implements the social welfare maximizer in sequential ex post equilibrium, and also negative results, by showing the impossibility of dominant-strategy implementation. In this letter, we describe the relationship between mechanism design and stochastic optimization, and highlight our key technical results. An extended abstract will appear in WINE 2007, and a journal version is under preparation.
Mixed multi-unit combinatorial auctions for supply chain management
Authors: Giovannucci Andrea , Rodriguez-Aguilar Juan A. , Vinyals Meritxell , Cerquides Jesus , Endriss Ulle
Published: February 2008

Mixed Multi-Unit Combinatorial Auctions (MMUCAs) allow agents to bid for bundles of goods to buy, goods to sell, and transformations of goods. In particular, MMUCAs offer a high potential to be employed for the automated assembly of supply chains of agents offering goods and services, and in general MMUCAs extend and generalise several types of combinatorial auctions. In this letter, we summarise our current research on MMUCAs and highlight lines for future research.
Combinatorial exchanges for coordinating grid services
Authors: Schnizler Björn , Neumann Dirk
Published: February 2008

In this paper, two combinatorial exchange mechanisms MACE and GreedEx are introduced that are suitable for resource allocation in service-oriented environments such as Grids. MACE provides users with a fairly complex bidding language offering flexibility in the bidding process. This flexibility comes at the expense of computational tractability. GreedEx tremendously restricts the bidding language and thereby reduces the problem complexity considerably. As with any practical mechanism design effort, the designed artifact does not implement desirable allocations in dominant strategies. In this short paper we also introduced jCase as tool for evaluating the market outcome when agents are acting strategically on the market for Grids.
Update on the IS model curriculum revision project
Authors: Topi Heikki
Published: February 2008

In my previous
inroads
IS Education column I described the first steps that had been taken toward the launch of a process to revise the undergraduate Information Systems model curriculum. The main purpose of this follow-up column is to give you an update of the status of the project and discuss the next steps.
Reflections on distance learning
Authors: Gal-Ezer Judith
Published: February 2008

Distance learning (DL) provides conditions that meet the constraints of individuals who work, raise a family, manage a household or serve in the military. Basically, DL is not space or time dependent and usually is not based on a central campus where lecturers and students gather, and in many cases no prerequisites are needed before enrolling. Thus, DL makes higher education available to those who wish to study but cannot do so in traditional universities.
Resist and persist (productively)
Authors: Kaczmarczyk Lisa
Published: February 2008

Sometimes a brilliantly percolated pedagogical idea results in poisoning and death. Such was the case last fall, when my colleague Matt Boutell and I decided to overhaul an introductory computing honors class. You may think that being asked to teach small sections of technically well prepared and occasionally even brilliant freshmen would be a gleeful and satisfying relief. Indeed, the faculty members at Rose-Hulman often celebrate, and justifiably so, how well the students respond to being "fire-hosed" with technical content. In this case, our self-appointed task was to excite, challenge, motivate and above all push the limits of new students.
Society in transition
Authors: Popyack Jeffrey
Published: February 2008

Greetings! This year has marked some transitions for Upsilon Pi Epsilon -- both in operations and constitutionally. It also marked another year of outstanding student achievement and awards.
Alternating accumulation
Authors: Ginat David
Published: February 2008

The current issue's new challenge involves the development of a seemingly simple task of collecting integers from a given list. Yet one has to be careful. The more intuitive solution and its various patches may not be "safe". In our experience, this task is yet another example where one should be very careful with correctness and efficiency.
Novices' knowledge construction of difficult concepts in CS1
Authors: Yuen Timothy T.
Published: February 2008

This cognitive study examines how students come to know and apply what they learn in a CS1 course. Students were asked to solve problems involving three difficult concepts in CS1 in clinical interviews. Data show diverse forms of knowledge (automatic, associate, and conceptual) and their application (need to code, generalizing, and efficiency) in problem solving. This study was funded by the SIGCSE Special Projects grant.
Humans under bombardment
Authors: Eshet-Alkalai Yoram
Published: February 2008

In present-day technologies, such as computer games, multimedia simulators, educational animations, chatrooms and, and synchronous teaching platforms, the performance of users depends on their ability to process simultaneously large volumes and various types of stimuli that "bombard" their cognition in real-time and at a high speed. Real-time thinking is described here as a cognitive skill that helps users to work effectively in real-time environments. The paper describes the major dimensions of real-time thinking (i.e. simultaneous processing, responding to high-speed stimuli, attention management and multi-tasking, handling multiple perspectives and multiple representations effectively and managing real-time feedback), and discusses the challenges it poses for online teachers and designers of multimedia learning environments.
Dear Dorothy
Authors: Edmondson Carol
Published: February 2008

Students who are new to tertiary study may be confused about the way things are done at university. Students who fared well at secondary school by doing what they were told, and students who view education as a process of collecting the correct answers, are particularly prone to being disoriented by first year programming courses. This paper uses humour, in the form of fake letters to a mythical agony aunt, to inform students without admonishing them for their lack of understanding.
A survey of literature on the teaching of introductory programming
Authors: Pears Arnold , Seidman Stephen , Malmi Lauri , Mannila Linda , Adams Elizabeth , Bennedsen Jens , Devlin Marie , Paterson James
Published: February 2008

Three decades of active research on the teaching of introductory programming has had limited effect on classroom practice. Although relevant research exists across several disciplines including education and cognitive science, disciplinary differences have made this material inaccessible to many computing educators. Furthermore, computer science instructors have not had access to a comprehensive survey of research in this area. This paper collects and classifies this literature, identifies important work and mediates it to computing educators and professional bodies.

We identify research that gives well-supported advice to computing academics teaching introductory programming. Limitations and areas of incomplete coverage of existing research efforts are also identified. The analysis applies publication and research quality metrics developed by a previous ITiCSE working group [74].
Visual analysis of dynamic group membership in temporal social networks
Authors: Kang Hyunmo , Getoor Lise , Singh Lisa
Published: February 2008

C-Group is a tool for analyzing dynamic group membership in temporal social networks over time. Unlike most network visualization tools, which show the group structure within an entire network, or the group membership for a single actor, C-Group allows users to focus their analysis on a pair of individuals. While C-Group allows for viewing the addition and deletion of nodes (actors) and edges (relationships) over time, its major contribution is its focus on changing group memberships over time. By doing so, users can investigate the context of temporal group memberships for the pair. C-Group provides users with a flexible interface for defining (and redefining) groups interactively, and supports two novel visual representations of the evolving group memberships. This flexibility gives users alternate views that are appropriate for different network sizes and provides users with different insights into the grouping behavior. We demonstrate the utility of the tool on a scientific publication network.
KDD Cup and workshop 2007
Authors: Bennett James , Elkan Charles , Liu Bing , Smyth Padhraic , Tikk Domonkos
Published: February 2008

The KDD Cup is the oldest of the many data mining competitions that are now popular [1]. It is an integral part of the annual ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD). In 2007, the traditional KDD Cup competition was augmented with a workshop with a focus on the concurrently active Netflix Prize competition [2]. The KDD Cup itself in 2007 consisted of a prediction competition using Netflix movie rating data, with tasks that were different and separate from those being used in the Netflix Prize itself. At the workshop, participants in both the KDD Cup and the Netflix Prize competition presented their results and analyses, and exchanged ideas.
Major components of the gravity recommendation system
Authors: Takács Gábor , Pilászy István , Németh Bottyán , Tikk Domonkos
Published: February 2008

The Netflix Prize is a collaborative filtering problem. This subfield of machine learning became popular in the late 1990s with the spread of online services that used recommendation systems (e.g. Amazon, Yahoo! Music, and of course Netflix). The aim of such a system is to predict what items a user might like based on his/her and other users' previous ratings. The Netflix Prize dataset is much larger than former benchmark datasets, therefore the scalability of the algorithms is a must. This paper describes the major components of our blending based solution, called the Gravity Recommendation System (GRS). In the Netflix Prize contest, it attained RMSE 0.8743 as of November 2007. We now compare the effectiveness of some selected individual and combined approaches on a particular subset of the Prize dataset, and discuss their important features and drawbacks.
More bang for their bucks
Authors: Lambert Diane , Pregibon Daryl
Published: February 2008

Online search systems that display ads continually offer new features that advertisers can use to fine-tune and enhance their ad campaigns. An important question is whether a new feature actually helps advertisers. In an ideal world for statisticians, we would answer this question by running a statistically designed experiment. But that would require randomly choosing a set of advertisers and forcing them to use the feature, which is not realistic. Accordingly, in the real world, new features for advertisers are seldom evaluated with a traditional experimental protocol. Instead, customer service representatives select advertisers who are invited to be among the first to test a new feature (i.e., white-listed), and then each white-listed advertiser chooses whether or not to use the new feature. Neither the customer service representative nor the advertiser chooses at random. This paper addresses the problem of drawing valid inferences from whitelist trials about the effects of new features on advertiser happiness. We are guided by three principles. First, statistical procedures for whitelist trials are likely to be applied in an automated way, so they should be robust to violations of modeling assumptions. Second, standard analysis tools should be preferred over custom-built ones, both for clarity and for robustness. Standard tools have withstood the test of time and have been thoroughly debugged. Finally, it should be easy to compute reliable confidence intervals for the estimator. We review an estimator that has all these attributes, allowing us to make valid inferences about the effects of a new feature on advertiser happiness.