bluuebunny/crossref_metadata_2025 huggingface dataset:
A Relationship Between Rainfall and Burned Area for Portugal
Authors: Viegas DX , Viegas MT
Published: October 2005

Total area burned yearly in Portugal in the period of 1975 to 1992 is related to rainfall during particular periods of the year. Precipitation in the period of January to April, corresponding to Winter and early Spring, related to fine fuel growth and to the water reserve in the soil, shows a non monotonic relationship with burned area each year, due to the conflicting mechanisms of the these two processes. Rainfall between June and September, corresponding to the main fire season in Portugal, exhibits an inverse relation with burned area. Data of a single weather station were used in the analysis and it was demonstrated that they are representative of a wide area in the country.
Fire Regimes on Andesitic Mountain Terrain in Northeastern Yellowstone-National-Park, Wyoming
Authors: Barrett SW
Published: October 2005

A fire history investigation was conducted for three forest community types in the Absaroka Mountains of Yellowstone National Park, Wyoming. Master fire chronologies were based on fire-initiated age classes and tree fire scars. The area's major forest type, lodgepole pine (Pinus contorta Dougl. var. latifolia) ecosystems, revealed a predominant pattern of stand replacing fires with a 200 year mean interval-nearly half the length estimated in previous studies of lodgepole pine on less productive subalpine plateaus in YNP. High elevation whitebark pine (P. albicaulis Engelm.) forests had primarily stand replacing fires with >350 year mean intervals, but some stands near timberline also occasionally experienced mixed severity- or non-lethal underburns. Before nearly a century of effective fire suppression in Yellowstone's northern range, lower elevation Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco.) communities adjacent to Artemesia tridentata (Nutt.) grasslands experienced primarily non-lethal underburns at 30 year mean intervals. While short interval fire regimes have been altered by longterm fire suppression, fire exclusion apparently had only limited influence on the area's infrequently burned ecosystems prior to widespread stand replacement burning in 1988.
A Dynamic Fuel Model for Use in Managed Even-Aged Stands
Authors: Bilgili E , Methven IR
Published: October 2005

A state-dependent dynamic crown fuel model is proposed. The model is a distance-dependent tree model. The model simulates crown characteristics such as foliage weight, crown base height, crown length and crown closure. The model is based on simplified dimensional growth relationships combined with photosynthesis and respiration. Preliminary tests of the model using coefficients derived from red pine, have shown that the model effectively simulates crown characteristics under a range of sites and silvicultural interventions.
Combustion and Nutrient Losses During Laboratory Burns
Authors: Gillon D , Gomendy V , Houssard C , Marechal J , Valette JC
Published: October 2005

The aim of this study was to assess the effects on combustion characteristics, and their consequences on nutrient losses, of (1) the change in load and packing ratio of the fuel bed, and (2) the change in fuel moisture content. Eighty-one experimental burns were carried out, on a test bench in the laboratory; the fuel was composed of needles and twigs of Pinus pinaster. Two levels of fuel load an dpacking ratio (8t ha-1 needles, packing ratio of 0.040; and 16t ha-1 twigs and needles, packing ratio of 0.066) were compared at constant moisture content (6%); and four levels of moisture content(6%, 12%, 24% and 30% dry weight) were compared at constant fuel load (8t ha-1 needles). At constant moisture content, an increase in the load and packing ratio of the fuel bed led to an increase in the height of flames and in the maximum temperature 25 cm above the fuel bed, in the duration of the rise in temperatures within the fuel, and in the fireline intensity. Conversely, the rate of fire spread decreased. At constant fuel load, an increase in the moisture content of the fuel led to a decrease in the rate of fire spread, in the flame height and the maximum temperature 25 cm above the fuel bed, and in the fireline intensity. In contrast, the maximum temperatures reached within the fuel, when the flaming front was continuous, did not significantly change with varying fuel loads or fuel moisture contents. The percentage fuel consumption was always high, more than 80%, but it significantly decreased with increasing fuel load and packing ratio and with increasing moisture content. Total losses of N, S, and K significantly decreased with increasing fuel load and packing ratio, with increasing moisture content and with decreasing percentage fuel consumption. Losses in P only significantly decreased with increasing fuel load and packing ratio. Losses in Mg and Ca were not significantly affected by fuel load, moisture content. or percentage consumption. An attempt was made to separate volatile from particulate losses, based on the assumption that all the losses of Ca were in particulate form. Whereas losses in particulate form remained relatively constant, losses of nutrients in volatile form seem to have been related to the percentage fuel consumption. Even if these experimental burns were of low intensity (40 to 56 kW m-1), their impact, in terms of lethal temperatures and nutrient losses, was not negligible, particularly for N and P. The increasing fireline intensity with increasing fuel load was not accompanied by an enhancement in the proportion of nutrient losses. In the same way, the strong decrease in fireline intensity with increasing fuel moisture content led only to a slight decrease in some nutrient losses. It was through their effect on the percentage fuel consumption that fuel load or moisture content modified the nutrient losses, particularly volatile losses.
Wildland Fire and Chaparral Succession Along the California Baja-California Boundary
Authors: Minnich RA , Bahre CJ
Published: October 2005

The United States-Mexico international boundary from ElPaso, Texas to the Pacific Coast shows clear differences in plant communities that were homogeneous prior to being split by a continuous fence at the turn of the century. This study evaluates how disparate fire regimes in California (fire suppression) and northern Baja California (little or no fire control) have influenced succession in the chamise (Adenostoma fasciculatum) chaparral communities spanning the international boundary between the border towns of Jacume and Tecate. Fire history was reconstructed using U.S. Forest Service fire maps and repeat aerial photography. Once plotted onto topographic maps and dated, the burns were divided into age-classes and sampled using 50 m point-quarter transects to develop successional chronosequences. Although fires are more frequent and smaller on the Mexican side of the border, our repeat photographs of the boundary monument markers together with field samples show that chaparral succession is similar across the international boundary in species composition, stem densities, and average mass shrub height. Chamise chaparral appears to be stable under disparate fire regimes because sprouting habits and latent seed pools permit efficient stand establishment under either short or long fire intervals. Chaparral recovery during the period examined here is unrelated to fire size because recolonization of burns by long-range seed dispersal is not a trait of the majority of the local shrub species and the shrubs either resprout. or germinate from soil seed reservoirs.
Testing the Effect of Fuel Consumption on Fire Spread Rate
Authors: McAlpine RS
Published: October 2005

It has been theorized that the amount of fuel involved in a fire front can influence the rate of spread of the fire. Three data sets are examined in an attempt to prove this relationship. The first, a Canadian Forest Service database of over 400 experimental, wild, and prescribed fires showed a weak relationship in some fuel complexes. The second, a series of field experimental fires conducted to isolate the relationship, showed a small effect. The final data set, from a series of 47 small plots (3m x 3m) burned with a variety of fuel loadings, also show a weak relationship. While a relationship was shown to exist, it is debatable whether it should be included in a fire behavior prediction system. Inherent errors associated with predicting fuel consumption can be compounded, causing additional, more critical, errors with the derived fire spread rate.
Calibration of a Large Fuel Burnout Model
Authors: Albini FA , Brown JK , Reinhardt ED , Ottmar RD
Published: October 2005

A computer simulation of the burning of large woody natural fuels has been created. The model simulates flaming combustion of large woody surface fuels but includes the influence of smoldering duff on this burning. This paper describes calibration of empirical constants in the model using data from laboratory crib burns and from prescribed burns in harvest debris and in natural fuel accumulations. The calibrated model reproduced laboratory crib burning rates and natural fuel loading reductions with acceptable accuracy.
Fire Behaviour Modelling in Tasmanian Buttongrass Moorlands .I. Fuel Characteristics
Authors: Marsden-Smedley JB , Catchpole WR
Published: October 2005

As part of a program to develop fire management strategies for Tasmanian buttongrass moorlands fuel characteristics were sampled from a wide range of sites in western and southwestern Tasmania. Equations were developed to predict the total fuel loading and the dead fuel loading. These variables are shown in a subsequent paper to be correlated with fire behaviour. The best predictors of fuel loading were found to be geology, vegetation age (i.e. time since the last fire) and vegetation cover. Vegetation cover is difficult to assess consistently. It is shown that reasonable predictions can be made using age and geology alone. The dead fuel loading of a given age was found to be strongly related to the total fuel loading, independent of geology. Statistical techniques used to develop fuel models are discussed. Other fuel characteristics that could be used as inputs for the Rothermel fire behaviour model are also presented.
Seedling Regeneration of Two Cistus Species After Experimental Disturbances
Authors: Luiscalabuig E , Tárrega R , Alonso I
Published: October 2005

The regeneration process of two Cistus species (Cistus ladanifer and Cistus laurifolius) was compared during the first four years after cutting, burning and ploughing in experimental plots, in León province (NW Spain). In the burnt plots, a quicker germination, followed by a higher death rate, was observed, especially for Cistus laurifolius. The number of seedlings tended to stabilize after one year in all experimental plots. During the whole study period, the burnt plots showed a higher number of seedlings. The ploughed plot presented the lowest number, while the cut plots kept intermediate values. The differences in cover values were not so marked in the different plots and, in the fourth year, there is still a tendency to increase. Neither the cover nor the height of the seedlings have attained the values they had before disturbance. By comparing the two species for the same disturbance, we found that the cover and height values were similar, but the number of Cistus ladanifer seedlings was higher. This fact can probably not be considered as a direct consequence of disturbance, as this difference was also observed previously.
Atmospheric Properties Associated With Large Wildfires
Authors: Potter BE
Published: October 2005

Lower atmosphere moistures, temperatures, winds, and lapse rates are examined for the days of 339 fires over 400 ha in the United States from 1971 through 1984. These quantities are compared with a climatology dataset from the same 14-year period using 2-way unbalanced analysis of variance. The results show that the fire-day surface-air temperature and moisture differ from the climatology at the 0.001 significance level. Near-surface wind shear does not appear to differ significantly between fire and climatology days. Results are inconclusive for wind speed and surface lapse rate.
Legumes in the Fire-Prone Mediterranean Regions: an Example From Greece
Authors: Arianoutsou M , Thanos CA
Published: October 2005

Mediterranean climate ecosystems of the Mediterranean rim are rich in legumes, both as woody shrubs of the late successional stages and as short-lived, pioneer herbaceous plants. In a survey of the floras of numerous geographic regions of Greece, legumes in Mediterranean parts are found to contribute considerably more (11-16% of the total number of species) than in non-Mediterranean regions (6-8%). Legume presence is also notable in other Mediterranean-type ecosystems of the world; nevertheless most leguminous taxa of the Mediterranean basin are herbs in contrast to a significant contribution of shrubs in California and Chile. Due to their long-lived soil banks of hard coated seeds herbaceous legumes are usually among the early post-fire colonizers in the Mediterranean and may play a significant role in the succession of fire-prone communities.
The Sydney Australia Wildfires of January 1994 - Meteorological Conditions and High Resolution Numerical Modeling Experiments
Authors: Speer MS , Leslie LM , Colquhoun JR , Mitchell E
Published: October 2005

Southeastern Australia is particularly vulnerable to wildfires during the spring and summer months, and the threat of devastation is present most years. In January 1994, the most populous city in Australia, Sydney, was ringed by wildfires, some of which penetrated well into suburban areas and there were many other serious fires in coastal areas of New South Wales (NSW). In recent years much research activity in Australia has focussed on the development of high resolution limited area models, for eventual operational prediction of meteorological conditions associated with high levels of wildfire risk. In this study, the period January 7-8, 1994 was chosen for detailed examination, as it was the most critical period during late December 1993/early January 1994 for the greater Sydney area. Routine forecast guidance from the Australian Bureau of Meteorology's operational numerical weather prediction (NWP) models was very useful in that both the medium and short range models predicted synoptic patterns suggesting extreme fire weather conditions up to several days in advance. However, vital information of a detailed nature was lacking. A new high resolution model was run at the operational resolution of 150 km and the much higher resolutions of 25 km and 5 km. The new model showed statistically significant greater skill in predicting details of wind, relative humidity and temperature patterns both near the surface and above the boundary layer. It also produced skilful predictions of the Forest Fire Danger Index.
A Prognostic Meteorological Model Applied to the Study of a Forest Fire
Authors: Miranda AI , Borrego C
Published: October 2005

The mesoscale meteorological model MEMO was applied to a real fire situation, which occurred in the central area of Portugal, with a very complex topography. In order to numerically provide boundary values at a higher temporal and spatial resolution, a one-way nesting technique was used, and three nested domains, of resolutions 5x5 km2, 2x2 km2 and 1x1 km2, were studied. This paper includes a comparison of the model results with the-available data and a description of the calculated wind fields for the three grids. The comparison indicates that the model describes adequately the meteorological situation during the simulated period of the fire and the comparison between the different grid results enhanced the importance of using refined simulations to depict the characteristics of the flow field in an area of such complexity.
A Coupled Atmosphere-Fire Model: Role of the Convective Froude Number and Dynamic Fingering at the Fireline
Authors: Clark TL , Jenkins MA , Coen JL , Packham DR
Published: October 2005

A numerical atmospheric model is coupled with a simple dry eucalyptus forest fire model to create a wildfire simulation model. This is used to show how certain atmospheric conditions can lead to commonly observed forest fire behavior. Using short line fires, simulations show that with moderate winds, the fire line interacts with the updraft ahead of it causing the fire line to curve forward into a conical shape. Other experiments show that when ambient winds change with height, a pair of rotating updrafts at the curved fire front can touch down within the fire and break up the fire line. We also demonstrate 'dynamic fingering', in which the rotating columns near the fire front intensify to tornado strength and can result in rapid and strong increases in the fire spread rate.
Postfire Regeneration of a Mediterranean Heathland in Southern Spain
Authors: Ojeda F , Maranon T , Arroyo J
Published: October 2005

Fire is a recurrent disturbance in the vegetation of Mediterranean climate regions. Most of the woody species (16 out of 19) in a Mediterranean heathland community, in the Strait of Gibraltar region of southern Spain, sprouted from subterranean vegetative organs after a wild-fire. Dominant sprouters were the prostrated oak Quercus lusitanica, three gorses, Genista tridens, G. tridentata and Stauracanthus boivinii, and a heath, Erica scoparia. About 100 seedlings m-2 of 14 woody species were censused in the first three years after fire. The highest density of seedlings was recorded for heather (Calluna vulgaris), a rockrose (Cistus populifolius subsp. major) and a gorse (Genista triacanthos). Woody vegetation covered up to 85% of the soil surface in the third year after fire. At this stager the community was co-dominated by the sprouters Quercus lusitanica (21%), Genista tridentata (21%) and Stauracanthus boivinii (20%), and the seeder Cistus populifolius subsp. major (20%). A total of 52 herbaceous species, many of them (35) perennials, was recorded, showing a temporal change in species composition. The role of fire influencing community diversity and the consequences for the conservation of heathlands in the Strait of Gibraltar region, are discussed.
An experimental study of declining populations
Authors: Hone Jim , Caughley the late Graeme , Grice David
Published: October 2005

Wildlife population declines have been attributed to predation, habitat change, and other agents of decline. An experimental study applied predation (at three levels) and habitat (at two levels) treatments over two years and measured the patterns of decline of populations of a medium-sized mammal (European rabbits). A model of population dynamics and effects of the treatments predicted negative effects of both treatments and an interaction of the treatments. All populations declined during the study including the experimental controls. During the first seven months (first phase of the study) the rate of decline, as estimated by the observed monthly instantaneous rate of increase (r), was more negative (P < 0.05) with increasing predation levels but there was no effect (P > 0.05) of habitat manipulation on r. There were no significant effects of treatments on rabbit abundance, or density, during the first phase of the study. During the second phase of the study, of 12 months’ duration, there were no significant (P > 0.05) effects of treatments on rabbit abundance, density, or r. There were no significant (P > 0.05) interactions of treatments on any response variable during either phase of the study. The interaction predicted by the theoretical model was not supported. Estimated abundance at the end of the study was not related (P > 0.05) to initial abundance (correlation = 0.023). The implications of the results are that such experimental studies can be used to evaluate theoretical models, though such studies may require a larger number of treatment replicates, and treatments at more extreme levels, to more clearly detect the effects of agents of population decline and their interactions.
Sodium fluoroacetate residues and carcass degradation of free-ranging feral pigs poisoned with 1080
Authors: Twigg Laurie E. , Lowe Tim , Martin Gary
Published: October 2005

Sodium fluoroacetate (1080) residues in muscle and liver of free-ranging feral pigs, poisoned with 1080-treated grain in a range of habitats, were determined. The incidence of vomiting, and the degradation of poisoned carcasses were also monitored. The maximum recorded concentrations in muscle (n = 79) and liver (n = 16) were 2.42 and 4.28 µg g–1 tissue, respectively. Mean (±s.d.) concentrations were 0.702 ± 0.535 and 0.635 ± 1.091 µg g–1, respectively. Muscle concentration in pigs sampled within 24 h of death were similar between those pigs poisoned with wheat (0.993 µg g–1, n = 21) and malted barley (1.012 µg g–1, n = 20) (P > 0.05), but muscle residues may have been lower in those pigs poisoned with lupin bait (0.178 µg g–1, n = 3). Muscle concentrations were also lower in those pigs sampled 24–48 h after death (0.481 µg g–1, n = 13) (P = 0.004). There were no differences between the sexes (northern rangeland: mean, females 0.883, males 0.869 µg g–1; agricultural: mean, 0.420 and 0.324 µg g–1) (P > 0.05), but adult pigs had lower muscle concentrations than did non-adult pigs (P < 0.001). There was no evidence of vomiting by any recovered poisoned pigs (n = 85), and all but one stomach contained substantial amounts of bait and other foods. Scavengers (mainly raptors) rapidly consumed poisoned pigs weighing <16 kg, within 2 days with no apparent ill-effects. Poisoned adults (≥25 kg) were scavenged less frequently but, because of microbial action and the activity of invertebrates (e.g. fly larvae), these pigs were degraded within 7–10 days (i.e. no longer represented a potential food source for vertebrates). The levels of residues recorded were such that 1080-poisoned pig carcasses pose little potential risk to the long-term viability of non-target species.
Polyglutamine aggregation nucleation: Thermodynamics of a highly unfavorable protein folding reaction
Authors: Bhattacharyya Anusri M. , Thakur Ashwani K. , Wetzel Ronald
Published: October 2005

Polyglutamine (polyGln) aggregation is implicated in the disease progression of Huntington's disease and other expanded CAG repeat diseases. PolyGln aggregationin vitrofollows a simple nucleated growth polymerization pathway without apparent complications such as populated intermediates, alternative assembly pathways, or secondary nucleation phenomena. Previous analysis of the aggregation of simple polyGln peptides revealed that the critical nucleus (the number of monomeric units involved in the formation of an energetically unfavorable aggregation nucleus) is equal to one, suggesting that polyGln nucleation can be viewed as an unfavorable protein folding reaction. We provide here a method for experimentally determining the number of elongation growth sites per unit weight for any polyGln aggregate preparation, a key parameter required for completion of the nucleation kinetics analysis and determination of the thermodynamics of nucleation. We find that, for the polyGln peptide Q47, the second-order rate constant for fibril elongation is 11,400 liters/mol per s, whereasKn*, the equilibrium constant for nucleation of aggregation, is remarkably small, equal to 2.6 × 10-9. The latter value corresponds to a free energy of nucleus formation of +12.2 kcal/mol, a value consistent with a highly unfavorable folding reaction. The methods introduced here should allow further analysis of the energetics of polyGln nucleus formation and accurate comparisons of the seeding capabilities of different fibril preparations, a task of increasing importance in the amyloid field.
A maize resistance gene functions against bacterial streak disease in rice
Authors: Zhao Bingyu , Lin Xinghua , Poland Jesse , Trick Harold , Leach Jan , Hulbert Scot
Published: October 2005

Although cereal crops all belong to the grass family (
Poacea
), most of their diseases are specific to a particular species. Thus, a given cereal species is typically resistant to diseases of other grasses, and this nonhost resistance is generally stable. To determine the feasibility of transferring nonhost resistance genes (R genes) between distantly related grasses to control specific diseases, we identified a maize R gene that recognizes a rice pathogen,
Xanthomonas oryzae
pv.
oryzicola
, which causes bacterial streak disease. Bacterial streak is an important disease of rice in Asia, and no simply inherited sources of resistance have been identified in rice. Although
X. o
. pv.
oryzicola
does not cause disease on maize, we identified a maize gene,
Rxo1
, that conditions a resistance reaction to a diverse collection of pathogen strains. Surprisingly,
Rxo1
also controls resistance to the unrelated pathogen
Burkholderia andropogonis
, which causes bacterial stripe of sorghum and maize. The same gene thus controls resistance reactions to both pathogens and nonpathogens of maize.
Rxo1
has a nucleotide-binding site-leucine-rich repeat structure, similar to many previously identified R genes. Most importantly,
Rxo1
functions after transfer as a transgene to rice, demonstrating the feasibility of nonhost R gene transfer between cereals and providing a valuable tool for controlling bacterial streak disease.
Synergistic action of E74B and ecdysteroid receptor in activating a 20-hydroxyecdysone effector gene
Authors: Sun GuoQiang , Zhu Jinsong , Chen Li , Raikhel Alexander S.
Published: October 2005

A number of insect effector genes activated by the steroid hormone 20-hydroxyecdysone (20E) are dually controlled by the ecdysteroid receptor (EcR/USP) and products of ecdysteroid early responsive genes (
E74
,
E75
, and
Broad
). However, the molecular mechanism of this dual action is poorly understood. Here we examined transcriptional activation of the
vitellogenin
(
Vg
) gene in the yellow fever mosquito,
Aedes aegypti
, by EcR/USP and E74 in response to an elevation of 20E titers. There are two isoforms of the
Aedes E74
gene, AaE74A and AaE74B, which have a common C-terminal Ets DNA-binding domain and isoform-specific N termini in the female mosquito. Inhibiting expression of AaE74B but not AaE74A by RNA interference led to substantial reduction in the
Vg
gene expression. AaE74B and the ecdysteroid receptor synergistically enhanced 20E-induced transcription of the
Vg
promoter. This action required the E74-binding sites and the ecdysone response elements in the
Vg
5′ regulatory region. Two-hybrid assays and coimmunoprecipitation analyses demonstrated direct interaction between AaE74B and AaEcR/AaUSP. Moreover, disruption of this interaction by a dominant negative E74 mutant abolished the enhanced activation of
Vg
. Therefore, the cooperative interaction between AaE74B and the ecdysteroid receptor is required for high-level expression of the
Vg
gene
in vivo
. The synergistic activation is accomplished through their 20E-dependent protein-protein interaction on the gene promoter. This study reveals how the 20E direct-indirect regulation of an effector gene is achieved at the molecular level.
Rostral and dorsal anterior cingulate cortex make dissociable contributions during antisaccade error commission
Authors: Polli Frida E. , Barton Jason J. S. , Cain Matthew S. , Thakkar Katharine N. , Rauch Scott L. , Manoach Dara S.
Published: October 2005

The anterior cingulate cortex (ACC) participates in both performance optimization and evaluation, with dissociable contributions from dorsal (dACC) and rostral (rACC) regions. Deactivation in rACC and other default-mode regions is important for performance optimization, whereas increased rACC and dACC activation contributes to performance evaluation. Errors activate both rACC and dACC. We propose that this activation reflects differential error-related involvement of rACC and dACC during both performance optimization and evaluation, and that these two processes can be distinguished by the timing of their occurrence within a trial. We compared correct and error antisaccade trials. We expected errors to correlate with an early failure of rACC deactivation and increased activation of both rACC and dACC later in the trial. Eighteen healthy subjects performed a series of prosaccade and antisaccade trials during event-related functional MRI. We estimated the hemodynamic responses for error and correct antisaccades using a finite impulse-response model. We examined ACC activity by comparing error and correct antisaccades with a fixation baseline and error to correct antisaccades directly. Compared with correct antisaccades, errors were characterized by an early bilateral failure of deactivation of rACC and other default-mode regions. This difference was significant in rACC. Errors also were associated with increased activity in both rACC and dACC later in the trial. These results show that accurate performance involves deactivation of the rACC and other default mode regions and suggest that both rACC and dACC contribute to the evaluation of error responses.
Asymptotically scale-invariant occupancy of phase space makes the entropy

S
q

extensive
Authors: Tsallis Constantino , Gell-Mann Murray , Sato Yuzuru
Published: October 2005

Phase space can be constructed for
N
equal and distinguishable subsystems that could be probabilistically either
weakly
correlated or
strongly
correlated. If they are locally correlated, we expect the Boltzmann-Gibbs entropy
S
BG
≡ -
k
Σ

i
p
i

ln

p
i

to be
extensive
, i.e.,
S
BG
(
N
) ∝
N
for
N
→ ∞. In particular, if they are independent,
S
BG
is
strictly additive
, i.e.,
S
BG
(
N
) =
NS
BG
(1), ∀
N
. However, if the subsystems are globally correlated, we expect, for a vast class of systems, the entropy

S
q

≡
k
[1 - Σ

i
p
q
i

]/(
q
- 1) (with
S
1
=
S
BG
) for some special value of
q
≠ 1 to be the one which is extensive [i.e.,

S
q

(
N
) ∝
N
for
N
→ ∞]. Another concept which is relevant is strict or asymptotic
scale-freedom
(or
scale-invariance
), defined as the situation for which all marginal probabilities of the
N
-system coincide or asymptotically approach (for
N
→ ∞) the joint probabilities of the (
N
- 1)-system. If each subsystem is a binary one, scale-freedom is guaranteed by what we hereafter refer to as the
Leibnitz rule
, i.e., the sum of two successive joint probabilities of the
N
-system coincides or asymptotically approaches the corresponding joint probability of the (
N
- 1)-system. The kinds of interplay of these various concepts are illustrated in several examples. One of them justifies the title of this paper. We conjecture that these mechanisms are deeply related to the very frequent emergence, in natural and artificial complex systems, of scale-free structures and to their connections with nonextensive statistical mechanics. Summarizing, we have shown that, for asymptotically scale-invariant systems, it is

S
q

with
q
≠ 1, and not
S
BG
, the entropy which matches standard, clausius-like, prescriptions of classical thermodynamics.
Hairpin folding rates reflect mutations within and remote from the turn region
Authors: Olsen Katherine A. , Fesinmeyer R. Matthew , Stewart James M. , Andersen Niels H.
Published: October 2005

Hairpins play a central role in numerous protein folding and misfolding scenarios. Prior studies of hairpin folding, many conducted with analogs of a sequence from the B1 domain of protein G, suggest that faster folding can be achieved only by optimizing the turn propensity of the reversing loop. Based on studies using dynamic NMR, the native GB1 sequence is a slow folding hairpin

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\begin{equation*}(k_{{\mathrm{F}}}^{278}=1.5{\times}10^{4}/{\mathrm{s}})\end{equation*}\end{document}

. GB1 hairpin analogs spanning a wide range of thermodynamic stabilities

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\begin{equation*}({\Delta}G_{{\mathrm{U}}}^{298}=-3.09{\;}{\mathrm{to}}+3.25{\;}{\mathrm{kJ}}/{\mathrm{mol}})\end{equation*}\end{document}

were examined. Fold-stabilizing changes in the reversing loop can act either by accelerating folding or retarding unfolding; we present examples of both types. The introduction of an attractive side-chain/side-chain Coulombic interaction at the chain termini further stabilizes this hairpin. The 1.9-fold increase in folding rate constant observed for this change at the chain termini implies that this Coulombic interaction contributes before or at the transition state. This observation is difficult to rationalize by “zipper” folding pathways that require native turn formation as the sole nucleating event; it also suggests that Coulombic interactions should be considered in the design of systems intended to probe the protein folding speed limit.
Single-stranded DNA mimicry in the p53 transactivation domain interaction with replication protein A
Authors: Bochkareva Elena , Kaustov Lilia , Ayed Ayeda , Yi Gwan-Su , Lu Ying , Pineda-Lucena Antonio , Liao Jack C. C. , Okorokov Andrei L. , Milner Jo , Arrowsmith Cheryl H. , Bochkarev Alexey
Published: October 2005

One of many protein–protein interactions modulated upon DNA damage is that of the single-stranded DNA-binding protein, replication protein A (RPA), with the p53 tumor suppressor. Here we report the crystal structure of RPA residues 1–120 (RPA70N) bound to the N-terminal transactivation domain of p53 (residues 37–57; p53N) and, by using NMR spectroscopy, characterize two mechanisms by which the RPA/p53 interaction can be modulated. RPA70N forms an oligonucleotide/oligosaccharide-binding fold, similar to that previously observed for the ssDNA-binding domains of RPA. In contrast, the N-terminal p53 transactivation domain is largely disordered in solution, but residues 37–57 fold into two amphipathic helices, H1 and H2, upon binding with RPA70N. The H2 helix of p53 structurally mimics the binding of ssDNA to the oligonucleotide/oligosaccharide-binding fold. NMR experiments confirmed that both ssDNA and an acidic peptide mimicking a phosphorylated form of RPA32N can independently compete the acidic p53N out of the binding site. Taken together, our data suggest a mechanism for DNA damage signaling that can explain a threshold response to DNA damage.
Potential theory for shock reflection by a large-angle wedge
Authors: Chen Gui-Qiang , Feldman Mikhail
Published: October 2005

When a plane shock hits a wedge head on, it experiences a reflection, and then a self-similar reflected shock moves outward as the original shock moves forward in time. Experimental, computational, and asymptotic analysis has shown that various patterns of reflected shocks may occur, including regular and Mach reflection. However, most fundamental issues for shock reflection phenomena have not been understood, such as the transition among the different patterns of shock reflection; therefore, it is essential to establish a global existence and stability theory for shock reflection. On the other hand, there has been no rigorous mathematical result on the global existence and stability of solutions to shock reflection, especially for potential flow, which has widely been used in aerodynamics. The theoretical problems involve several challenging difficulties in the analysis of nonlinear partial differential equations including elliptic-hyperbolic mixed type, free-boundary problems, and corner singularity, especially when an elliptic degenerate curve meets a free boundary. Here we develop a potential theory to overcome these difficulties and to establish the global existence and stability of solutions to shock reflection by a large-angle wedge for potential flow. The techniques and ideas developed will be useful to other nonlinear problems involving similar difficulties.
Insights into the organization and dynamics of bacterial chemoreceptor clusters through
in vivo
crosslinking studies
Authors: Studdert Claudia A. , Parkinson John S.
Published: October 2005

The team signaling model for bacterial chemoreceptors proposes that receptor dimers of different detection specificities form mixed trimers of dimers that bind the cytoplasmic proteins CheA and CheW to form ternary signaling complexes clustered at the cell poles. We used a trifunctional crosslinking reagent targeted to cysteine residues in the aspartate (Tar) and serine (Tsr) receptors to obtain
in vivo
snapshots of trimer composition in the receptor population. To analyze the dynamics of trimer formation, we followed the appearance of mixed trimers when cells expressing Tar were induced for the expression of Tsr and treated with the crosslinker shortly after the onset of induction. In the absence of CheA or CheW, preformed Tar trimers exchanged partners readily with newly made Tsr. Conversely, in the presence of CheA and CheW, receptor trimers seldom exchanged partners, irrespective of the presence or absence of attractants. The C-terminal receptor-coupling domain of the CheA kinase, which contains binding determinants for the CheW protein, was essential for conferring low exchangeability to the preformed trimers of dimers. CheW also was required for this effect, but, unlike CheA, overexpression of CheW interfered with trimer formation and chemotactic behavior. The CheW effect probably occurs through binding interactions that mask the receptor sites needed for trimer formation. We propose that clustered receptors are organized in mixed trimers of dimers through binding interactions with CheA and CheW, which play distinctly different architectural roles. Moreover, once complete signaling teams have formed, they no longer undergo dynamic exchange of receptor members.
The copper-iron connection in biology: Structure of the metallo-oxidase Fet3p
Authors: Taylor Alexander B. , Stoj Christopher S. , Ziegler Lynn , Kosman Daniel J. , Hart P. John
Published: October 2005

Fet3p is a multicopper-containing glycoprotein localized to the yeast plasma membrane that catalyzes the oxidation of Fe(II) to Fe(III). This ferrous iron oxidation is coupled to the reduction of O
2
to H
2
O and is termed the ferroxidase reaction. Fet3p-produced Fe(III) is transferred to the permease Ftr1p for import into the cytosol. The posttranslational insertion of four copper ions into Fet3p is essential for its activity, thus linking copper and iron homeostasis. The mammalian ferroxidases ceruloplasmin and hephaestin are homologs of Fet3p. Loss of the Fe(II) oxidation catalyzed by these proteins results in a spectrum of pathological states, including death. Here, we present the structure of the Fet3p extracellular ferroxidase domain and compare it with that of human ceruloplasmin and other multicopper oxidases that are devoid of ferroxidase activity. The Fet3p structure delineates features that underlie the unique reactivity of this and homologous multicopper oxidases that support the essential trafficking of iron in diverse eukaryotic organisms. The findings are correlated with biochemical and physiological data to cross-validate the elements of Fet3p that define it as both a ferroxidase and cuprous oxidase.
Aldosterone acts via an ATP autocrine/paracrine system: The Edelman ATP hypothesis revisited
Authors: Gorelik Julia , Zhang Yanjun , Sánchez Daniel , Shevchuk Andrew , Frolenkov Gregory , Lab Max , Klenerman David , Edwards Christopher , Korchev Yuri
Published: October 2005

Aldosterone, the most important sodium-retaining hormone, was first characterized >50 years ago. However, despite numerous studies including the classical work of Isidore S. “Izzy” Edelman showing that aldosterone action depended on ATP production, the mechanism by which it activates sodium reabsorption via the epithelial sodium channel remains unclear. Here, we report experiments that suggest that one of the key steps in aldosterone action is via an autocrine/paracrine system. The hormone stimulates ATP release from the basolateral side of the target kidney cell. Prevention of ATP accumulation or its removal blocks aldosterone action. ATP then acts via a purinergic mechanism to produce contraction of small groups of adjacent epithelial cells. Patch clamping demonstrates that it is these contracted cells that have channel activity. With progressive recruitment of contracting cells, there is then a parallel increase in transepithelial electrical conductance. In common with other stimuli of sodium transport, this pathway involves phosphatidylinositol 3-kinase. Inhibition of phosphatidylinositol 3-kinase blocks both cell contraction and conductance. We put forward the hypothesis that redistribution of the cell volume caused by the lateral contraction results in apical swelling and that this change, in turn, disrupts the epithelial sodium channel interaction with the F-actin cytoskeleton, opening the channel and hence increasing sodium transport.
Population distribution and redistribution of the baby-boom cohort in the United States: Recent trends and implications
Authors: Rogerson Peter A. , Kim Daejong
Published: October 2005

Over 70 million people were born into the baby-boom cohort between 1946 and 1964. Over 65 million of these individuals are presently alive, and thus the cohort continues to exert a powerful influence on regional population change in the United States. In this article, we examine the recent and current geographic distribution of the baby-boom cohort. In 1990, the members of the cohort comprised a particularly high proportion of the population in a small number of dynamic metropolitan areas. We also highlight the recent migration trends exhibited by this cohort; these trends are potentially important early indicators of the retirement-related migration patterns that the cohort might follow. The spatial redistribution of the cohort has many implications, including potentially significant consequences for intergenerational relationships and caregiving. Also highlighted in the article are the temporal and geographical implications for intergenerational caregiving. There has been much attention given to the “sandwich” generation, with its members having dual caregiving responsibilities to both parents and children. A more appropriate designation may be the “stretched” generation, because caregiving seems to extend over a long period. In particular, many members of the baby-boom cohort are beginning to care for their aging parents just as they finish child rearing.
NMDA antagonist inhibits the extracellular signal-regulated kinase pathway and suppresses cancer growth
Authors: Stepulak Andrzej , Sifringer Marco , Rzeski Wojciech , Endesfelder Stefanie , Gratopp Alexander , Pohl Elena E. , Bittigau Petra , Felderhoff-Mueser Ursula , Kaindl Angela M. , Bührer Christoph , Hansen Henrik H. , Stryjecka-Zimmer Marta , Turski Lechoslaw , Ikonomidou Chrysanthy
Published: October 2005

Glutamate antagonists limit the growth of human cancersin vitro. The mechanism of anticancer action of NMDA antagonists is not known, however. In this article, we report that the NMDA antagonist dizocilpine inhibits the extracellular signal-regulated kinase 1/2 pathway, an intracellular signaling cascade that is activated by growth factors and controls the proliferation of cancer cells. Dizocilpine reduces the phosphorylation of cAMP-responsive element binding protein, suppresses the expression of cyclin D1, up-regulates the cell cycle regulators and tumor suppressor proteins p21 and p53, and increases the number of lung adenocarcinoma cells in the G2and S phases of the cell cycle. Silencing of the tumor suppressor protein p21 abolishes antiproliferative action of dizocilpine. Consistent with inhibition of the extracellular signal-regulated kinase 1/2-signaling cascade, dizocilpine reverses the stimulation of proliferation induced by epidermal, insulin, and basic fibroblast growth factors in lung adenocarcinoma cells. Furthermore, dizocilpine prolongs the survival of mice with metastatic lung adenocarcinoma and slows the growth of neuroblastoma and rhabdomyosarcoma in mice. These findings reveal the mechanism of antiproliferative action of dizocilpine and indicate that it may be useful in the therapy of human cancers.
Sustainability of irrigated agriculture in the San Joaquin Valley, California
Authors: Schoups Gerrit , Hopmans Jan W. , Young Chuck A. , Vrugt Jasper A. , Wallender Wesley W. , Tanji Ken K. , Panday Sorab
Published: October 2005

The sustainability of irrigated agriculture in many arid and semiarid areas of the world is at risk because of a combination of several interrelated factors, including lack of fresh water, lack of drainage, the presence of high water tables, and salinization of soil and groundwater resources. Nowhere in the United States are these issues more apparent than in the San Joaquin Valley of California. A solid understanding of salinization processes at regional spatial and decadal time scales is required to evaluate the sustainability of irrigated agriculture. A hydro-salinity model was developed to integrate subsurface hydrology with reactive salt transport for a 1,400-km
2
study area in the San Joaquin Valley. The model was used to reconstruct historical changes in salt storage by irrigated agriculture over the past 60 years. We show that patterns in soil and groundwater salinity were caused by spatial variations in soil hydrology, the change from local groundwater to snowmelt water as the main irrigation water supply, and by occasional droughts. Gypsum dissolution was a critical component of the regional salt balance. Although results show that the total salt input and output were about equal for the past 20 years, the model also predicts salinization of the deeper aquifers, thereby questioning the sustainability of irrigated agriculture.
Kinesin crouches to sprint but resists pushing
Authors: Fisher Michael E. , Kim Young C.
Published: October 2005

Recent optical trap experiments have applied resisting, assisting, and sideways loads to conventional kinesin moving on microtubules at fixed [ATP]. To gain insight into intermediate motions when the motor protein takes its 8.2-nm steps, the velocity and randomness data have been analyzed by using discrete-state stochastic models with a three-dimensional “energy landscape.” The bead size and tether angle play a crucial role. The analysis implies that on binding ATP the motor “crouches,” the point of attachment of the tether at the necklinker junction moving downward toward the microtubule by 0.5–0.7 nm, while inching forward by only 0.1–0.2 nm, before completing the step from a transition state by a unitary “sprint” of ∼7.8 nm. These inferences accord with high-resolution observations that exclude a previously predicted substep of 1.8–2.1 nm. Assisting and leftward loads are opposed in that the perpendicular component of the tension in the tether is enhanced by ∼2 pN, which reduces the velocity, but sideways lurching is not supported.
Delayed resistance to transgenic cotton in pink bollworm
Authors: Tabashnik Bruce E. , Dennehy Timothy J. , Carrière Yves
Published: October 2005

Transgenic crops producing
Bacillus thuringiensis
(Bt) toxins kill some key insect pests and thus can reduce reliance on insecticides. Widespread planting of such Bt crops increased concerns that their usefulness would be cut short by rapid evolution of resistance to Bt toxins by pests. Pink bollworm (
Pectinophora gossypiella
) is a major pest that has experienced intense selection for resistance to Bt cotton in Arizona since 1997. We monitored pink bollworm resistance to Bt toxin for 8 years with laboratory bioassays of strains derived annually from 10-17 cotton fields statewide. Bioassay results show no net increase from 1997 to 2004 in the mean frequency of pink bollworm resistance to Bt toxin. A synthesis of experimental and modeling results suggests that this delay in resistance can be explained by refuges of cotton without Bt toxin, recessive inheritance of resistance, incomplete resistance, and fitness costs associated with resistance.