bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Ezrin-Radixin-Moesin Family Member Ezrin Regulates Stable Microtubule Formation and Retroviral Infection
Authors: Haedicke Juliane , de los Santos Kenia , Goff Stephen P. , Naghavi Mojgan H. 
Published: February 2008

ABSTRACT
We recently identified the cytoskeletal regulatory protein moesin as a novel gene that inhibits retroviral replication prior to reverse transcription by downregulation of stable microtubule formation. Here, we provide evidence that overexpression of ezrin, another closely related ezrin-radixin-moesin (ERM) family member, also blocks replication of both murine leukemia viruses and human immunodeficiency virus type 1 (HIV-1) in Rat2 fibroblasts before reverse transcription, while knockdown of endogenous ezrin increases the susceptibility of human cells to HIV-1 infection. Together, these results suggest that ERM proteins may be important determinants of retrovirus susceptibility through negative regulation of stable microtubule networks.
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

ABSTRACT
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

ABSTRACT

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

ABSTRACTUnlike 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

ABSTRACT
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.
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.
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

Abstract
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

Abstract

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

Abstract

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.
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.
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].
Common Fixed Point Theorems on Weakly Contractive and Nonexpansive Mappings
Authors: Xiao Jian-Zhong , Zhu Xing-Hua 
Published: February 2008

AbstractA family of commuting nonexpansive self-mappings, one of which is weakly contractive, are studied. Some convergence theorems are established for the iterations of types Krasnoselski-Mann, Kirk, and Ishikawa to approximate a common fixed point. The error estimates of these iterations are also given.
Effect of Cavities on the Optical Properties of Bullet Rosettes: Implications for Active and Passive Remote Sensing of Ice Cloud Properties
Authors: Yang Ping , Zhang Zhibo , Kattawar George W. , Warren Stephen G. , Baum Bryan A. , Huang Hung-Lung , Hu Yong X. , Winker David , Iaquinta Jean 
Published: February 2008

AbstractBullet rosette particles are common in ice clouds, and the bullets may often be hollow. Here the single-scattering properties of randomly oriented hollow bullet rosette ice particles are investigated. A bullet, which is an individual branch of a rosette, is defined as a hexagonal column attached to a hexagonal pyramidal tip. For this study, a hollow structure is included at the end of the columnar part of each bullet branch and the shape of the hollow structure is defined as a hexagonal pyramid. A hollow bullet rosette may have between 2 and 12 branches. An improved geometric optics method is used to solve for the scattering of light in the particle. The primary optical effect of incorporating a hollow end in each of the bullets is to decrease the magnitude of backscattering. In terms of the angular distribution of scattered energy, the hollow bullets increase the scattering phase function values within the forward scattering angle region from 1° to 20° but decrease the phase function values at side- and backscattering angles of 60°–180°. As a result, the presence of hollow bullets tends to increase the asymmetry factor. In addition to the scattering phase function, the other elements of the phase matrix are also discussed. The backscattering depolarization ratios for hollow and solid bullet rosettes are found to be very different. This may have an implication for active remote sensing of ice clouds, such as from polarimetric lidar measurements. In a comparison of solid and hollow bullet rosettes, the effect of the differences on the retrieval of both the ice cloud effective particle size and optical thickness is also discussed. It is found that the presence of hollow bullet rosettes acts to decrease the inferred effective particle size and to increase the optical thickness in comparison with the use of solid bullet rosettes.
Convective–Stratiform Precipitation Variability at Seasonal Scale from 8 Yr of TRMM Observations: Implications for Multiple Modes of Diurnal Variability
Authors: Yang Song , Smith Eric A. 
Published: February 2008

AbstractThis study investigates the variability of convective and stratiform rainfall from 8 yr (1998–2005) of Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR) and TRMM Microwave Imager (TMI) measurements, focusing on seasonal diurnal variability. The main scientific goals are 1) to understand the climatological variability of these two dominant forms of precipitation across the four cardinal seasons and over continents and oceans separately and 2) to understand how differences in convective and stratiform rainfall variations ultimately determine how the diurnal variability of the total rainfall is modulated into multiple modes.There are distinct day–night differences for both convective and stratiform rainfall. Oceanic (continental) convective rainfall is up to 25% (50%) greater during nighttime (daytime) than daytime (nighttime). The seasonal variability of convective rainfall’s day–night difference is relatively small, while stratiform rainfall exhibits very apparent day–night variations with seasonal variability. There are consistent late evening diurnal peaks without obvious seasonal variations over ocean for convective, stratiform, and total rainfall. Over continents, convective and total rainfall exhibit consistent dominant afternoon peaks with little seasonal variations—but with late evening secondary peaks exhibiting seasonal variations. Stratiform rainfall over continents exhibits a consistent strong late evening peak and a weak afternoon peak, with the afternoon mode undergoing seasonal variability. Thus, the diurnal characteristics of stratiform rainfall appear to control the afternoon secondary maximum of oceanic rainfall and the late evening secondary peak of continental rainfall. Even at the seasonal–regional scale spatially or the interannual global scale temporally, the secondary mode can become very pronounced, but only on an intermittent basis. Overall, the results presented here demonstrate the importance of partitioning the total rainfall into convective and stratiform components and suggest that diurnal modes largely arise from distinct diurnal stratiform variations modulating convective variations.
Beliefs About Schizophrenia and Its Treatment in Kota Kinabalu, Malaysia
Authors: Swami Viren , Furnham Adrian , Kannan Kumaraswami , Sinniah Dhachayani 
Published: February 2008

Background: Lay beliefs about schizophrenia have been extensively studied in cross-cultural settings, but research on ethnic differences are currently lacking. Aims: This study examined beliefs about the manifestations, causes and cures of schizophrenia in a multi-ethnic sample from Malaysia. Methods: In this study, 561 Malay, Chinese and Kadazan-Dusun participants rated 72 statements about schizophrenia on a 7-point scale. Results: Results showed that Malaysians tended to favour social-environmental explanations for schizophrenia. There were also ethnic and sex differences in these results. Specifically, Malay participants more strongly agreed that schizophrenia has a social cause, that treatment should affect changes at a societal level, that schizophrenic behaviour is sinful and that mental hospitals do not provide effective treatments. Conclusions: Lay beliefs about schizophrenia may serve different functions for different ethno-cultural groups, which have an influence on help-seeking behaviour.