bluuebunny/crossref_metadata_2025 huggingface dataset:
Diets of herring, mackerel, and blue whiting in the Norwegian Sea in relation to Calanus finmarchicus distribution and temperature conditions
Authors: Prokopchuk Irina , Sentyabov Evgeniy
Published: November 2005

Diets of Norwegian spring-spawning herring, mackerel, and blue whiting in the Norwegian Sea are investigated in relation to the distribution of plankton and hydrographic conditions. Fish stomachs and zooplankton samples were collected during summer (June and July) cruises in 2001 and 2002. Calanus finmarchicus was the principal prey of mackerel, accounting for 53–98% of total stomach content by weight. The diet composition of herring varied depending on feeding area and availability of food under various environmental conditions. C. finmarchicus was important prey for herring only in July 2001 (about 77% by weight) in the central part of the sea and in June 2002 (about 82% by weight) near the Lofotens. In July 2002 appendicularians (Oikopleura spp.), amphipods (mainly Parathemisto abissorum), and euphausiids were important in the diet of herring, and at some stations cannibalism was observed. The main prey of blue whiting were amphipods (10–34% by weight), appendicularians (11–34%), and euphausiids (8–47%), as they usually feed deep in the water column, though C. finmarchicus was important, particularly in June 2002, when blue whiting were caught in the upper layers of the sea. Higher water temperatures indirectly affect pelagic fish through accelerated development of their prey and favourable conditions for migration farther north.
Misoprostol in preventing postpartum hemorrhage: A meta‐analysis
Authors: Langenbach C.
Published: November 2005

Objective:To assess misoprostol's ability to prevent postpartum hemorrhage (PPH) where no alternatives exist. Comparison to oxytocics demonstrates how similarly misoprostol achieves a level of effectiveness–obtainable only in hospitals–in remote locations around the world.Method:Using the Mantel–Haenszel fixed‐effects model and the DerSirmonian and Laird random‐effects model, summary statistics indicated that misoprostol's excess risk of PPH was only 4% when compared to oxytocics.Result:This risk difference was well within the range of expected results for all uterotonic agents and does not warrant branding misoprostol as an inferior drug.Conclusion:Conventional uterotonic drugs should not be used to set the lowest‐accepted level of effectiveness in settings where they are entirely unsuitable. Continuing to weigh the benefits of one effective drug against another only delays the distribution of misoprostol in countries where it is the only feasible choice and must be measured against no treatment at all.
Unleashing the wild: response to Locke and Dearden's ‘rethinking protected area categories’
Authors: MARTINO DIEGO
Published: November 2005

Locke and Dearden (2005) assert that the emerging new paradigm for protected areas (PAs) risks taking the PA agenda to a ‘tragic failure,’ and the planet towards biological impoverishment. They believe the ‘new paradigm’ contributes to a persistent tendency towards giving social issues higher priority over biological considerations and is based on the promotion of PA categories V and VI of the IUCN (World Conservation Union).
Variation in fishers' attitudes within an inshore fishery: implications for management
Authors: RICHARDSON ELIZABETH A. , KAISER MICHEL J. , EDWARDS-JONES GARETH
Published: November 2005

Understanding the incentives influencing the attitudes and behaviour of resource users is a crucial input to the design of institutions for resource management. Typically fishers have been expected to exploit resources in an independent profit-maximizing manner, which is in line with common property theory, although these expectations are not always met because fishers' behaviours and attitudes are generally more heterogeneous than previously considered. Attitudinal differences between participants in the inshore commercial fishery of Wales, UK, were investigated. Semi-structured face-to-face interviews were conducted with 161 fishers from the five main sectors, namely mobile gear fishers, crustacean potters, whelk potters, line/net fishers and transient fishers. Unprompted expressions of attitudes and responses to open-ended questions underwent thematic-coding and were analysed with fishers' responses to structured questions. Investigation into whether the incentive to participate in resource stewardship varied between sectors as predicted by common property theory found attitudinal similarities across the sectors, but also certain important differences. Results suggested an attitudinal continuum, with mobile gear fishers and crustacean potters at the two extremes, and intermediate positions occupied by transient fishers, whelk potters and line/net fishers. Mobile gear fishers believed most strongly that their fishery was controlled too tightly and was impacted by other fishers and other anthropogenic influences. Crustacean potters believed most strongly that conservation of stocks was necessary and that minimum landing sizes were not overcautious. The attitudes that characterized each sector were related to the characteristics of the sector and its resource base, and generally concurred with theoretical predictions. In particular, target species' mobility and past sector experiences predicted the inclination of fishers in each sector towards resource stewardship. The observed attitudinal differences implied varying personal discount rates that may affect how respondents respond to and comply with management tools. Furthermore, attitudinal differences among sectors mean that an effective management tool in one sector may be inappropriate or counterproductive in another.
Growth and characterization of SiC epitaxial layers on Si- and C-face 4H SiC substrates by chemical-vapor deposition
Authors: Ramaiah Kodigala Subba , Bhat I. , Chow T. P. , Kim J. K. , Schubert E. F. , Johnstone D. , Akarca-Biyikli S.
Published: November 2005

High-quality Schottky junctions have been fabricated on n-type 4H SiC epitaxial layers grown by chemical-vapor deposition on C- and Si-face substrates in order to understand the effect of growth direction on the growth mechanism and formation of defects. Atomic force microscopy analysis showed dramatic differences between the surfaces of SiC epilayers grown on C and Si faces. There was a significant step bunching in the SiC grown on Si-face substrates. Current-voltage, capacitance-voltage, and deep-level transient spectroscopy (DLTS) measurements were carried out on the Schottky junctions to analyze the junction characteristics. The Schottky junctions on C-face SiC showed larger barrier heights than those on Si-face SiC, showing that each face has a different surface energy. The barrier heights of Ni Schottky junctions were found to be 1.97 and 1.54 eV for C-face and Si-face materials, respectively. However, the deep-level spectra obtained by DLTS were similar, regardless of the increased surface roughness of the Si-face 4H SiC.
Role of thermal hopping and homogeneous broadening on the spectral characteristics of quantum dot lasers
Authors: Markus A. , Rossetti M. , Calligari V. , Chen J. X. , Fiore A.
Published: November 2005

The effect of thermal hopping and homogeneous broadening on the lasing spectra and carrier distribution in quantum dot lasers is investigated by measuring the spontaneous emission spectra through a top-contact window. Two intriguing features are observed, i.e., a strong redshift of the excited-state lasing peak as compared to the spontaneous emission spectrum and the absence of population clamping at threshold. These features are interpreted on the basis of a rate-equation model taking into account energy-broadening mechanisms and thermal coupling among quantum dots. The good agreement between model and experiment allows us to estimate the homogeneous broadening and capture time, two key parameters for the understanding and proper design of quantum dot lasers.
Quantum dot decoherence measured by ensemble photoluminescence
Authors: Gurioli M. , Sanguinetti S. , Mano T. , Koguchi N. , Nötzel Richard
Published: November 2005

We propose and experimentally demonstrate that a very simple, noninvasive, and common technique, i.e., standard nonresonant photoluminescence of large ensemble of quantum dots (QDs), can be used to determine the temperature dependence of homogeneous broadening. The method can be applied to a single quantum dot layer independently of the QD density and it allows to follow the increase of the homogeneous broadening up to high T. The experimental results show that different pictures apply depending on the QD size.
Dielectric functions of AlxGa1−xSb (0.00⩽x⩽0.39) alloys from 1.5to6.0eV
Authors: Choi S. G. , Palmstrøm C. J. , Kim Y. D. , Cooper S. L. , Aspnes D. E.
Published: November 2005

Room-temperature pseudodielectric function spectra ⟨ε(ω)⟩=⟨ε1(ω)⟩+i⟨ε2(ω)⟩ of AlxGa1−xSb (0.00⩽x⩽0.39) alloys were measured from 1.5to6.0eV by spectroscopic ellipsometry. Effects of surface overlayers on the measured spectra have been minimized as far as possible by performing in situ chemical etching on samples immediately before the measurements rather than correcting the measured data mathematically for the presence of overlayers. Analysis of second energy derivatives numerically calculated from the measured data yielded the critical-point energies of the E1, E1+Δ1, E0′, E2, and E1′ interband transitions. Dependence of the critical-point energies on composition x is obtained.
Effects of double filling of La and Ce on thermoelectric properties of CemLanFe1.0Co3.0Sb12 compounds by spark plasma sintering
Authors: Lu Q. M. , Zhang J. X. , Zhang X. , Liu Y. Q. , Liu D. M. , Zhou M. L.
Published: November 2005

Double-filled skutterudite compounds CemLanFeCo3Sb12 with (m+n)=0.2–0.4 were synthesized by spark plasma sintering using powders of Co, Sb, Fe, and rare-earth Ce and La as starting materials, and the thermoelectric properties were studied in detail. The dominant phases of all the samples are the skutterudite with small amount of Sb as an impurity phase, and the amount of Sb decreases in double-filled compound. The lattice constant is enhanced linearly up to (m+n)=0.30 with increasing filling fraction and then unchanged. The Seebeck coefficient and thermal conductivity of double-filled compounds are generally higher than single-filled samples whatever the filling fraction is. Among all the samples, Ce0.1La0.2FeCo3Sb12 shows the highest Seebeck coefficient of 150μVK−1 at 773K and the lowest thermal conductivity of 1.81W∕mK at 673K, and the maximum ZT value reaches 0.60 at 773K due to its lower thermal conductivity.
Brittle dynamic fracture of crystalline cubic silicon carbide (3C-SiC) via molecular dynamics simulation
Authors: Kikuchi Hideaki , Kalia Rajiv K. , Nakano Aiichiro , Vashishta Priya , Branicio Paulo S. , Shimojo Fuyuki
Published: November 2005

Brittle fracture dynamics for three low-index crack surfaces, i.e., (110), (111), and (100), in crystalline cubic silicon carbide (3C-SiC) is studied using molecular dynamics simulation. The results exhibit significant orientation dependence: (110) fracture propagates in a cleavage manner; (111) fracture involves slip in the {111¯} planes; and crack branching is observed in (001) fracture. Calculated critical energy release rates, which characterize fracture toughness, are compared with available experimental and ab initio calculation data.
Hydrogen termination of Si(110) surfaces upon wet cleaning revealed by highly resolved scanning tunneling microscopy
Authors: Arima Kenta , Katoh Jun , Horie Shinya , Endo Katsuyoshi , Ono Tomoya , Sugawa Shigetoshi , Akahori Hiroshi , Teramoto Akinobu , Ohmi Tadahiro
Published: November 2005

The surface structure of the hydrogen-saturated Si(110) surfaces after wet cleaning is studied on an atomic scale by means of scanning tunneling microscopy. When a surface oxide layer is stripped using a HF-containing solution, the surface consists of nanometer-scaled terraces and atomic steps along various directions. Coupled monohydride lines are formed inside a small terrace, as predicted by infrared spectra. The Si(110) surface after subsequent rinsing for a short period is occupied by a long terrace along the [1¯10] direction in which the ideal 1×1 structure is formed. Atomic arrangements around step edges are determined in detail based on atomic images and first-principles calculations. A ridge-shaped structure is observed after excess rinsing with water, and infrared spectra indicate that the slope is composed of (111) microfacets. From these results, we present the mechanism underlying the formation of the hydrogen-terminated Si(110) surfaces during wet cleaning processes.
Importance of coherence for electron transport in terahertz quantum cascade lasers
Authors: Callebaut Hans , Hu Qing
Published: November 2005

A density matrix approach is used in combination with a tight-binding model to describe electron transport in terahertz quantum cascade lasers and is incorporated into a Monte Carlo simulation. Scattering events, including LO-phonon, electron-electron, and ionized impurity scattering, are treated semiclassically but contribute to dephasing scattering. In addition, a phenomenological “pure dephasing rate” was introduced to take into account dephasing caused by interface roughness scattering. This model was used to investigate the influence of dephasing on electron transport through a barrier. Additionally, current densities, populations and electron temperatures were calculated for a simple three-level structure and a five-level structure that achieved lasing at 3.2THz, and the results were compared to a semiclassical simulation. We find that the inclusion of coherent transport and dephasing in the calculations is essential when transport is dominated by transitions between weakly coupled states.
Growth mechanism of second harmonic generation of optically poled disperse red 1∕polymer films
Authors: Wang Yuxiao , Wang C. H.
Published: November 2005

The writing process in the formation of χ(2) gratings for disperse red 1 (DR1)∕polymethylmethacrylate film at room temperature is investigated. The writing laser power and film thickness dependence for the growth of the second harmonic generation (SHG) intensity in optically poled films is delineated. The effective growth rate of the SHG intensity is shown to be proportional to the fourth power of the fundamental laser intensity. This result is not in agreement with the existing theory. A model to account for the experimental result associated with the writing process is proposed. The dependence of the induced SHG intensity on the film thickness dependence is also studied. An equation that can adequately describe the dependence on the fundamental laser intensity and the film thickness for the effective growth rate of the SHG intensity is provided.
Effect of oxygen deprivation on soil hydrophobicity during heating
Authors: Bryant R. , Doerr S. H. , Helbig M.
Published: November 2005

Previous studies of the effects of heating on soil hydrophobicity have been conducted under free availability of oxygen. Under fire, however, soils may be deprived of oxygen due to its consumption at the heat source and inadequate replenishment in the soil. In the present study, effects of heating on soil hydrophobicity are examined for three initially hydrophobic Australian eucalypt forest soils under standard and oxygen-deprived atmospheres for temperatures (T) of 250–600°C and durations (tE) 2–180 min. Hydrophobicity assessments using water droplet penetration time (WDPT) tests indicate substantial differences between the absence and presence of oxygen. Heating to 250–300°C enhanced hydrophobicity from initial respective WDPTs of 2029 s, 361 s and 15 s to > 18 000 s for all samples under both atmospheres. Depending on heating duration, hydrophobicity was eliminated (WDPTs ~0 s) in air between 210 and 340°C, but under oxygen-deprived conditions between 400 and 510°C. Relationships between the destruction temperature for hydrophobicity TD and tE provide temperature–duration thresholds below which hydrophobicity persists under oxygen concentrations <21%. As established temperature–duration thresholds for hydrophobicity destruction are based on the free availability of oxygen, caution is advised in their applicability to field situations where heating under burning may occur in oxygen-depleted conditions.
Age classes of the greater bilby (Macrotis lagotis) based on track and faecal pellet size
Authors: Southgate R. I.
Published: November 2005

The gait length and width and faecal pellet diameter of bilbies were examined to determine whether these measures could be used to accurately identify different age classes of individuals in the field. There was a good relationship between gait width+length and animal size that allowed the identification of three age classes: immature–independent individuals <500 g, mature females and small males 500–1200 g, and large males >1700 g. The relationship between pellet diameter and animal size was not as strong and faecal pellet diameter was suitable to identify only immature–independent individuals. An application of these measurements to a bilby population in the Tanami Desert indicated that immature individuals were limited to the central half of their current distribution whereas medium-sized individuals were distributed throughout.
Fecundity, egg size and the influence of rainfall in an isolated population of malleefowl (Leipoa ocellata)
Authors: Priddel David , Wheeler Robert
Published: November 2005

An isolated population of malleefowl (Leipoa ocellata) at Yalgogrin in New South Wales, Australia, was studied intensively between 1986–87 and 1998–99. During this period the population produced 124 clutches, comprising a total of 1705 eggs. The number of clutches per annum varied between 5 and 15. Eggs were laid between mid-August and mid-February, with 90% laid between the last week of September and the first week of January. The mean date of laying of the first egg of each clutch (±s.d.) was 21 September ± 13 days and the mean date of the last egg was 23 December ± 19 days. The mean duration of egg laying varied significantly between years (range 70–117 days) and was negatively correlated with the daily maximum ambient temperature in December. Cool temperatures and rain in early summer prolonged the laying season. The mean interval between laying was 6.4 ± 1.1 days (range 3–12 days), with eggs laid at a faster rate during the first half of the laying period. Overall, mean clutch size was 14.1 ± 5.8 (range 1–28). Large clutches were the result of an extended period of laying rather than an increase in the rate of laying. Mean clutch size was greatest when laying extended into mid-February. The best predictor of clutch size was rainfall between May and December – the interval spanning both nest construction and egg laying. The mean volume of all measured eggs (n = 1362) was 162.1 ± 9.0 mL (range 99–200 mL). Egg volume varied during the laying period, with those eggs laid early or late in the breeding season being smaller. Eggs at Yalgogrin were, on average, 10.5% smaller than those recorded at nearby Pulletop.
Effectiveness of the eastern grey kangaroo foot thump for deterring conspecifics
Authors: Bender Helena
Published: November 2005

Overabundant wild populations of herbivores often present challenges to primary industry, competing with stock, and damaging crops and property. Eastern grey kangaroos (Macropus giganteus) are one of seven macropodid species that are considered a problem in agriculture in Australia. Most deterrent devices available commercially use sounds that do not occur in nature (i.e. artificial sounds), which often have a short-lived or no effect on the target species, whereas trials with biologically significant sounds are often more effective and provide greater resistance to habituation. I used a playback trial of an eastern grey kangaroo foot thump, a biologically significant signal that is given in response to a predator and is usually followed by flight. I determined its effectiveness compared with a recording of background noise (control) for deterring kangaroos over a seven-week period. Kangaroos significantly increased their vigilance levels in response to the foot thump, but not in response to the control signal. Just over 60% of kangaroos took flight in response to the foot thump and the control signals, but more kangaroos took flight in the first 3 s when the foot thump was played. The foot thump shows potential as a deterrent of eastern grey kangaroos for primary industry, and is less likely to suffer from habituation because it is a natural sound.
Home ranges of feral cats (Felis catus) in central-western New South Wales, Australia
Authors: Molsher Robyn , Dickman Chris , Newsome Alan , Müller Warren
Published: November 2005

Twenty-one feral cats were radio-tracked using direct sighting and triangulation techniques (amassing 730 location fixes) during winter in an agricultural landscape in central-western New South Wales. Factors affecting home-range size, home-range overlap and habitat use were assessed. Mean home-range size was 248 ha (s.e. = 34.9, n = 15 cats, 598 location fixes). Home-range size and habitat use were not influenced by sex or age of adult cats, prey abundance or time of day. However, cat weight significantly influenced range size, with heavier cats having larger ranges than smaller cats. Although the cats are apparently solitary, their home ranges overlapped considerably, particularly between young adults and old adult cats. Cats were active both by day and night and did not occupy permanent dens. Home ranges encompassed mixed habitat types that provided both shelter and prey. Open woodland and open forest were the main habitat types covered by home ranges, but within these areas cats showed a preference for grassland, where rabbits were more abundant. The results recorded in this study indicate that cat-control programs should concentrate in mixed habitat areas, where both shelter and food are available, and over widely dispersed areas. The absence of group living suggests that the effectiveness of virally vectored fertility or biological control agents would be limited.
Differential habitat use by a local population of subadult common dunnarts, Sminthopsis murina, following wildfire in coastal wet heath, New South Wales, Australia
Authors: Monamy Vaughan , Fox Barry J.
Published: November 2005

Little has been published about Sminthopsis murina, a small insectivorous marsupial encountered infrequently during trapping studies. Individuals favour vegetation associations found in recently burnt heathlands and forests; however, individuals rarely remain in such areas long enough for repeated capture. We report an unusual occurrence of habitat fidelity by a dense population of subadult S. murina in coastal wet heath, New South Wales, Australia. Individuals were captured repeatedly in the first 16 months following wildfire (30 subadults trapped 154 times: recapture rate = 80%). Densities peaked 10 months after fire at 3.75 individuals ha–1. More males than females were captured (23 males, 7 females). Habitat analyses revealed differential use of regenerating coastal wet heathland by S. murina. Significantly more captures were made in areas of high soil moisture in the first six months following fire. Captures then decreased in these areas but increased where soil moisture had been lower and where vegetation had been growing more slowly. Beyond the 1995/96 breeding season, regenerating vegetation became increasingly dense and less patchy and captures of S. murina ultimately declined to zero. This paper records a rare opportunity to examine habitat preferences of a single cohort of subadult S. murina. Habitat use may have been determined by the presence of a narrow range of vegetation structure.
Microhabitat use and foraging behaviour of Sminthopsis youngsoni (Marsupialia:Dasyuridae) in arid central Australia
Authors: Haythornthwaite Adele S.
Published: November 2005

In this study, fluorescent pigment tracking was used to determine the microhabitat use and foraging behaviour of a small insectivorous marsupial, Sminthopsis youngsoni (the lesser hairy-footed dunnart), in the dunefields of the Simpson Desert, south-western Queensland. In total, 25 successful trails were traced over the duration of this study, between March 1996 and April 1998. Nocturnal foraging trails were identified, then the distance travelled by the dunnart through each microhabitat type (nine in all) was measured and accumulated for each trail and compared with surrounding available microhabitats along control trails. This provided an index of selectivity of microhabitat use. Terrestrial invertebrates were collected from both actual and control trails to measure food availability. Dunnarts strongly selected open microhabitats when foraging, with the periphery of spinifex hummocks (up to 20 cm from the edge of a spinifex hummock) being favoured. Spinifex itself was avoided unless shelter was sought (i.e. immediately after release). Potential invertebrate prey captured along the actual trails travelled by dunnarts tended to occur in greater numbers and were larger than those captured along the control trails, indicating that dunnarts can accurately locate resource-rich areas in which to forage. Clearly, the foraging strategies used by this species enable it to successfully exploit patchy and unpredictable food resources, thereby ensuring its continued persistence and relative abundance in an unstable environment.
Predicting the effect of immunocontraceptive recombinant murine cytomegalovirus on population outbreaks of house mice (Mus musculus domesticus) in mallee wheatlands
Authors: Arthur A. D. , Pech R. P. , Singleton G. R.
Published: November 2005

Virally vectored immunocontraception using a modified murine cytomegalovirus (MCMV) is being developed for the control of house mice in Australia. In this paper, we develop disease–host models using a combination of laboratory and field data. We then combine these models with a model of a previous mouse population outbreak to explore the likely effectiveness of modified MCMV for controlling mice. Models of homogeneous mixing with and without vertical/pseudovertical transmission provided reasonable fits to field serological data collected during the onset and development of a mouse population outbreak in south-eastern Australia. Both models include the high transmission rate of MCMV suggested by the data. We found no strong support for non-linear contact rates or heterogeneous mixing. When applied to a past outbreak of mice both models gave similar results and suggested that immunocontraceptive MCMV could be effective at reducing agricultural damage to acceptable levels. Successful control was still possible when lags in the development of infertility of up to 10 weeks were added to the model, provided high levels of infertility were achieved. These lags were added because mice can become pregnant just before becoming infertile – the resultant litter would not emerge for 6–7 weeks. Trade-offs between two parameters that could be altered by engineering strains of MCMV – the level of infertility in infected mice and the virus transmission rate – were explored and suggest that a variety of parameter combinations could produce successful control. Our results are encouraging for the future development of virally vectored immunocontraception control of house mice, but future work will need to consider some of the assumptions of these single-strain models.
Perfusion functional MRI reveals cerebral blood flow pattern under psychological stress
Authors: Wang Jiongjiong , Rao Hengyi , Wetmore Gabriel S. , Furlan Patricia M. , Korczykowski Marc , Dinges David F. , Detre John A.
Published: November 2005

Despite the prevalence of stress in everyday life and its impact on happiness, health, and cognition, little is known about the neural substrate of the experience of everyday stress in humans. We use a quantitative and noninvasive neuroimaging technique, arterial spin-labeling perfusion MRI, to measure cerebral blood flow (CBF) changes associated with mild to moderate stress induced by a mental arithmetic task with performance monitoring. Elicitation of stress was verified by self-report of stress and emotional state and measures of heart rate and salivary-cortisol level. The change in CBF induced by the stress task was positively correlated with subjective stress rating in the ventral right prefrontal cortex (RPFC) and left insula/putamen area. The ventral RPFC along with right insula/putamen and anterior cingulate showed sustained activation after task completion in subjects reporting a high stress level during arithmetic tasks. Additionally, variations of baseline CBF in the ventral RPFC and right orbitofrontal cortex were found to correlate with changes in salivary-cortisol level and heart rate caused by undergoing stress tasks. We further demonstrated that the observed right prefrontal activation could not be attributed to increased cognitive demand accompanying stress tasks and extended beyond neural pathways associated with negative emotions. Our results provide neuroimaging evidence that psychological stress induces negative emotion and vigilance and that the ventral RPFC plays a key role in the central stress response.
Coupled protein domain motion inTaqpolymerase revealed by neutron spin-echo spectroscopy
Authors: Bu Zimei , Biehl Ralf , Monkenbusch Michael , Richter Dieter , Callaway David J. E.
Published: November 2005

Long-range conformational changes in proteins are ubiquitous in biology for the transmission and amplification of signals; such conformational changes can be triggered by small-amplitude, nanosecond protein domain motion. Understanding how conformational changes are initiated requires the characterization of protein domain motion on these timescales and on length scales comparable to protein dimensions. Using neutron spin-echo spectroscopy (NSE), normal mode analysis, and a statistical-mechanical framework, we reveal overdamped, coupled domain motion within DNA polymerase I fromThermus aquaticus(Taqpolymerase). This protein utilizes correlated domain dynamics over 70 Å to coordinate nucleotide synthesis and cleavage during DNA synthesis and repair. We show that NSE spectroscopy can determine the domain mobility tensor, which determines the degree of dynamical coupling between domains. The mobility tensor defines the domain velocity response to a force applied to it or to another domain, just as the sails of a sailboat determine its velocity given the applied wind force. The NSE results provide insights into the nature of protein domain motion that are not appreciated by conventional biophysical techniques.
Salmonella inhibit T cell proliferation by a direct, contact-dependent immunosuppressive effect
Authors: van der Velden Adrianus W. M. , Copass Michael K. , Starnbach Michael N.
Published: November 2005

Dendritic cells (DC) are of central importance in the initiation of T cell-mediated adaptive immunity because these professional phagocytes internalize, process, and present microbial antigens to T lymphocytes. T lymphocytes have a pivotal role in controlling and clearing infection with intracellular pathogens through cytokine production. T lymphocytes also can mediate direct lysis of infected cells or activate B and T cells. In this article, we report that DC, when cocultured withSalmonella, fail to efficiently stimulate T cells for proliferation. We show that the failure of T lymphocytes to respond toSalmonella-infected DC is not simply due toSalmonella-induced programmed DC death or interference with up-regulation of costimulatory molecules CD80 and CD86. We cocultured bacteria with purified T lymphocytes, and we demonstrate here thatSalmonellahave a direct, contact-dependent inhibitory effect on the T cells, even in the absence of DC. This direct,Salmonella-induced inhibitory effect reduces the ability of T cells to proliferate and produce cytokines in response to stimulation and appears to require live bacteria. Cumulatively, these results are evidence thatSalmonellamay interfere with the development of acquired immunity, providing insights into the complex nature of this hostpathogen interaction.
Brain signals for spatial attention predict performance in a motion discrimination task
Authors: Sapir Ayelet , d'Avossa Giovanni , McAvoy Mark , Shulman Gordon L. , Corbetta Maurizio
Published: November 2005

The reliability of visual perception is thought to reflect the quality of the sensory information. However, we show that subjects' performance can be predicted, trial-by-trial, by neural activity that precedes the onset of a sensory stimulus. Using functional MRI (fMRI), we studied how neural mechanisms that mediate spatial attention affect the accuracy of a motion discrimination judgment. The amplitude of blood oxygen level-dependent (BOLD) signals after a cue directing spatial attention predicted subjects' accuracy on 60-75% of the trials. Widespread predictive signals, which included dorsal parietal, visual extra-striate, prefrontal and sensory-motor cortex, depended on whether the cue correctly specified the stimulus location. Therefore, these signals indicate the degree of utilization of the cued information and play a role in the control of spatial attention. We conclude that variability in perceptual performance can be partly explained by the variability in endogenous, preparatory processes and that BOLD signals can be used to forecast human behavior.
A cysteine-rich motif confers hypoxia sensitivity to mammalian large conductance voltage- and Ca-activated K (BK) channel α-subunits
Authors: McCartney Claire E. , McClafferty Heather , Huibant Jean-Marc , Rowan Edward G. , Shipston Michael J. , Rowe Iain C. M.
Published: November 2005

Cellular responses to hypoxia are tissue-specific and dynamic. However, the mechanisms that underlie this differential sensitivity to hypoxia are unknown. Large conductance voltage- and Ca-activated K (BK) channels are important mediators of hypoxia responses in many systems. Although BK channels are ubiquitously expressed, alternative pre-mRNA splicing of the single gene encoding their pore-forming α-subunits provides a powerful mechanism for generating functional diversity. Here, we demonstrate that the hypoxia sensitivity of BK channel α-subunits is splice-variant-specific. Sensitivity to hypoxia is conferred by a highly conserved motif within an alternatively spliced cysteine-rich insert, the stress-regulated exon (STREX), within the intracellular C terminus of the channel. Hypoxic inhibition of the STREX variant is Ca-sensitive and reversible, and it rapidly follows the change in oxygen tension by means of a mechanism that is independent of redox or CO regulation. Hypoxia sensitivity was abolished by mutation of the serine (S24) residue within the STREX insert. Because STREX splice-variant expression is tissue-specific and dynamically controlled, alternative splicing of BK channels provides a mechanism to control the plasticity of cellular responses to hypoxia.
Bacterial DNA segregation by dynamic SopA polymers
Authors: Lim Grace E. , Derman Alan I. , Pogliano Joe
Published: November 2005

Many bacterial plasmids and chromosomes rely on ParA ATPases for proper positioning within the cell and for efficient segregation to daughter cells. Here we demonstrate that the F-plasmid-partitioning protein SopA polymerizes into filaments in an ATP-dependent manner
in vitro
, and that the filaments elongate at a rate that is similar to that of plasmid separation
in vivo
. We show that SopA is a dynamic protein within the cell, undergoing cycles of polymerization and depolymerization, and shuttling back and forth between nucleoprotein complexes that are composed of the SopB protein bound to
sopC
-containing plasmids (SopB/
sopC
). The dynamic behavior of SopA is critical for Sop-mediated plasmid DNA segregation; mutations that lock SopA into a static polymer in the cell inhibit plasmid segregation. We show that SopA colocalizes with SopB/
sopC
in the cell and that SopB/
sopC
nucleates the assembly of SopA and is required for its dynamic behavior. When SopA is polymerized
in vitro
in the presence of SopB and
sopC
-containing DNA, SopA filaments emanate from the plasmid DNA in radial asters. We propose a mechanism in which plasmid separation is driven by the polymerization of SopA, and we speculate that the radial assembly of SopA polymers is responsible for positioning plasmids both before and after segregation.
Rerouting lipoprotein nanoparticles to selected alternate receptors for the targeted delivery of cancer diagnostic and therapeutic agents
Authors: Zheng Gang , Chen Juan , Li Hui , Glickson Jerry D.
Published: November 2005

We report that a lipoprotein-based nanoplatform generated by conjugating tumor-homing molecules to the protein components of naturally occurring lipoproteins reroutes them from their normal lipoprotein receptors to other selected cancer-associated receptors. Multiple copies of these targeting moieties may be attached to the same nanoparticle, or a variety of different targeting moieties can be attached. Such a diverse set of tumor-homing molecules could be used to create a variety of conjugated lipoproteins as multifunctional, biocompatible nanoplatforms with a broad application to both cancer imaging and treatment. The same principle can be applied to imaging and treatment of other diseases and for monitoring specific tissues. To validate this concept, we prepared a low-density lipoprotein (LDL)-based folate receptor (FR)-targeted agent by conjugating folic acid to the Lys residues of the apolipoprotein B (apoB)-100 protein. To demonstrate the ability of the lipoprotein-based nanoplatform to deliver surfaceloaded and core-loaded payloads, the particles were labeled either with the optical reporter 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine that was intercalated in the phospholipid monolayer or with the lipophilic photodynamic therapy agent, tetra-
t
-butyl-silicon phthalocyanine bisoleate, that was reconstituted into the lipid core. Cellular localization of the labeled LDL was monitored by confocal microscopy and flow cytometry in FR-overexpressing KB cells, in FR-nonexpressing CHO and HT-1080 cells, and in LDL receptor-overexpressing HepG
2
cells. These studies demonstrate that the folic acid conjugation to the Lys side-chain amino groups blocks binding to the normal LDL receptor and reroutes the resulting conjugate to cancer cells through their FRs.
Crystal structure of Bacillus subtilis anti-TRAP protein, an antagonist of TRAP/RNA interaction
Authors: Shevtsov Mikhail B. , Chen Yanling , Gollnick Paul , Antson Alfred A.
Published: November 2005

In
Bacillus subtilis
the anti-TRAP protein (AT) is produced in response to the accumulation of uncharged tRNA
Trp
. AT regulates expression of genes involved in tryptophan biosynthesis and transport by binding to the tryptophan-activated
trp
RNA-binding attenuation protein (TRAP) and preventing its interaction with several mRNAs. Here, we report the x-ray structure of AT at 2.8 Å resolution, showing that the protein subunits assemble into tight trimers. Four such trimers are further associated into a 12-subunit particle in which individual trimers are related by twofold and threefold symmetry axes. Twelve DnaJ-like, cysteine-rich zinc-binding domains form spikes on the surface of the dodecamer. Available data suggest several possible ways for AT to interact with the 11-subunit TRAP. Interaction between the two symmetry-mismatching molecules could be assisted by the flexible nature of AT zinc-binding domains.
Dynamics of hepatitis B virus clearance in chimpanzees
Authors: Murray John M. , Wieland Stefan F. , Purcell Robert H. , Chisari Francis V.
Published: November 2005

Mathematical modeling was performed to test the extent to which cytopathic and noncytopathic T cell effector functions contribute to resolution of hepatitis B virus (HBV) infection in three acutely infected chimpanzees. Simulations based exclusively on cytopathic functions show a poor fit to the data and would require the destruction and regeneration of ≈11 livers for clearance to occur. In contrast, a simulation based on a combination of cytopathic and noncytopathic functions provided a significantly better fit to the data (P< 0.001) and required as much as 5-fold less destruction to clear the virus from the liver. The best fit simulation supports the notion that during the early phase of HBV clearance, noncytopathic T cell effector mechanisms inhibit viral replication and greatly shorten the half-life of the long lived covalently closed circular viral DNA transcriptional template, thereby limiting the extent to which cytopathic T cell effector functions and tissue destruction are required to terminate acute HBV infection.
Simple model for tuberculosis in cattle and badgers
Authors: Cox D. R. , Donnelly Christl A. , Bourne F. John , Gettinby George , McInerney John P. , Morrison W. Ivan , Woodroffe Rosie
Published: November 2005

As an aid to the study of bovine tuberculosis (TB), a simple model has been developed of an epidemic involving two species, cattle and badgers. Each species may infect the other. The proportion of animals affected is assumed relatively small so that the usual nonlinear aspects of epidemic theory are avoided. The model is used to study the long-run and transient effect on cattle of culling badgers and the effect of a period without routine testing for TB, such as occurred during the 2001 epidemic of foot-and-mouth disease in Great Britain. Finally, by examining the changes in cattle TB over the last 15 years, and with some other working assumptions, it is estimated that the net reproduction number of the epidemic is ≈1.1. The implications for controlling the disease are discussed.
Fast noninvasive activation and inhibition of neural and network activity by vertebrate rhodopsin and green algae channelrhodopsin
Authors: Li Xiang , Gutierrez Davina V. , Hanson M. Gartz , Han Jing , Mark Melanie D. , Chiel Hillel , Hegemann Peter , Landmesser Lynn T. , Herlitze Stefan
Published: November 2005

Techniques for fast noninvasive control of neuronal excitability will be of major importance for analyzing and understanding neuronal networks and animal behavior. To develop these tools we demonstrated that two light-activated signaling proteins, vertebrate rat rhodopsin 4 (RO4) and the green algae channelrhodospin 2 (ChR2), could be used to control neuronal excitability and modulate synaptic transmission. Vertebrate rhodopsin couples to the Gi/o, pertussis toxin-sensitive pathway to allow modulation of G protein-gated inward rectifying potassium channels and voltage-gated Ca
2+
channels. Light-mediated activation of RO4 in cultured hippocampal neurons reduces neuronal firing within ms by hyperpolarization of the somato-dendritic membrane and when activated at presynaptic sites modulates synaptic transmission and paired-pulse facilitation. In contrast, somato-dendritic activation of ChR2 depolarizes neurons sufficiently to induce immediate action potentials, which precisely follow the ChR2 activation up to light stimulation frequencies of 20 Hz. To demonstrate that these constructs are useful for regulating network behavior in intact organisms, embryonic chick spinal cords were electroporated with either construct, allowing the frequency of episodes of spontaneous bursting activity, known to be important for motor circuit formation, to be precisely controlled. Thus light-activated vertebrate RO4 and green algae ChR2 allow the antagonistic control of neuronal function within ms to s in a precise, reversible, and noninvasive manner in cultured neurons and intact vertebrate spinal cords.
Gene expression profiling differentiates germ cell tumors from other cancers and defines subtype-specific signatures
Authors: Juric Dejan , Sale Sanja , Hromas Robert A. , Yu Ron , Wang Yan , Duran George E. , Tibshirani Robert , Einhorn Lawrence H. , Sikic Branimir I.
Published: November 2005

Germ cell tumors (GCTs) of the testis are the predominant cancer among young men. We analyzed gene expression profiles of 50 GCTs of various subtypes, and we compared them with 443 other common malignant tumors of epithelial, mesenchymal, and lymphoid origins. Significant differences in gene expression were found among major histological subtypes of GCTs, and between them and other malignancies. We identified 511 genes, belonging to several critical functional groups such as cell cycle progression, cell proliferation, and apoptosis, to be significantly differentially expressed in GCTs compared with other tumor types. Sixty-five genes were sufficient for the construction of a GCT class predictor of high predictive accuracy (100% training set, 96% test set), which might be useful in the diagnosis of tumors of unknown primary origin. Previously described diagnostic and prognostic markers were found to be expressed by the appropriate GCT subtype (
AFP
,
POU5F1
,
POV1
,
CCND2
, and
KIT
). Several additional differentially expressed genes were identified in teratomas (
EGR1
and
MMP7
), yolk sac tumors (
PTPN13
and
FN1
), and seminomas (
NR6A1
,
DPPA4
, and
IRX1
). Dynamic computation of interaction networks and mapping to existing pathways knowledge databases revealed a potential role of EGR1 in p21-induced cell cycle arrest and intrinsic chemotherapy resistance of mature teratomas.
RETURNS TO SKILLS AND PERSONNEL MANAGEMENT: U.S. DEPARTMENT OF DEFENSE SCIENTISTS AND ENGINEERS
Authors: GIBBS MICHAEL
Published: November 2005

Personnel records are used to examine compensation, recruitment, and retention of a group of highly skilled workers: civilian scientists and engineers in U.S. Department of Defense laboratories. In contrast to those of the private sector, returns to skills were largely flat for this group from 1982 to 1996. Despite this, quality and performance of recruits relative to earlier cohorts, and of those retained relative to those who left, remained stable. One explanation is the importance of defense industry–specific human capital. These results hold for three different pay plans, including the federal government's primary plan and two intended to introduce greater flexibility in personnel management. (JEL J31, J44, J45, M52)
Dynamic Models for Dynamic Theories: The Ins and Outs of Lagged Dependent Variables
Authors: Keele Luke , Kelly Nathan J.
Published: November 2005

A lagged dependent variable in an OLS regression is often used as a means of capturing dynamic effects in political processes and as a method for ridding the model of autocorrelation. But recent work contends that the lagged dependent variable specification is too problematic for use in most situations. More specifically, if residual autocorrelation is present, the lagged dependent variable causes the coefficients for explanatory variables to be biased downward. We use a Monte Carlo analysis to assess empirically how much bias is present when a lagged dependent variable is used under a wide variety of circumstances. In our analysis, we compare the performance of the lagged dependent variable model to several other time series models. We show that while the lagged dependent variable is inappropriate in some circumstances, it remains an appropriate model for the dynamic theories often tested by applied analysts. From the analysis, we develop several practical suggestions on when and how to use lagged dependent variables on the right-hand side of a model.