bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limitations of Boltzmann's kinetic equation
Authors: Woods L.C 
Published: April 2008

It is often assumed that Boltzmann's kinetic equation (BKE) for the evolution of the velocity distribution function
f
(

r

,

w

,
t
) in a gas is valid regardless of the magnitude of the Knudsen number defined by
ϵ
≡
τ
d ln
ϕ
/d
t
, where
ϕ
is a macroscopic variable like the fluid velocity

v

or temperature
T
, and
τ
is the collision interval. Almost all accounts of transport theory based on BKE are limited to terms in
O
(
ϵ
)≪1, although there are treatments in which terms in
O
(
ϵ
2
) are obtained, classic examples being due to Burnett and Grad. The
mathematical
limitations that arise are discussed, for example, by Kreuzer and Cercignani. However, as we shall show, the
physical
limitation to BKE is that it is
not
valid for the terms of order higher than
ϵ
because the assumption of ‘molecular chaos’, which is the basis of Boltzmann's collision integral, is an approximation that applies only up to first order in
ϵ
.

Another difficulty with Boltzmann's collision integral is that it is defined at a point, so that the varying ambient conditions upon which transport depends must be found by Taylor series expansions along particle trajectories. This fails in a strong-field magnetoplasma where, in a single collision interval, the trajectories are almost infinitely repeating gyrations; we shall illustrate this by deriving a dominant
O
(
ϵ
2
) transport equation for a magnetoplasma that
cannot
be found from Boltzmann's equation.

A further problem that sometimes arises in BKE occurs when an external force is present, the equilibrium state being constrained by the stringent Maxwell–Boltzmann conditions. Unless this is removed by a transformation of coordinates, confusion between convection and diffusion is probable. A mathematical theory for transport in tokamaks, termed
neoclassical transport
, is shown to be invalid, one of several errors being the retention of an electric field component in the drift kinetic equation.
Identification and Regulation of TPS04/GES, anArabidopsisGeranyllinalool Synthase Catalyzing the First Step in the Formation of the Insect-Induced Volatile C16-Homoterpene TMTT
Authors: Herde Marco , Gärtner Katrin , Köllner Tobias G. , Fode Benjamin , Boland Wilhelm , Gershenzon Jonathan , Gatz Christiane , Tholl Dorothea 
Published: April 2008

AbstractVolatile secondary metabolites emitted by plants contribute to plant–plant, plant–fungus, and plant–insect interactions. The C16-homoterpene TMTT (for 4,8,12-trimethyltrideca-1,3,7,11-tetraene) is emitted after herbivore attack by a wide variety of plant species, including Arabidopsis thaliana, and is assumed to play a role in attracting predators or parasitoids of herbivores. TMTT has been suggested to be formed as a degradation product of the diterpene alcohol (E,E)-geranyllinalool. Here, we report the identification of Terpene Synthase 04 (TPS04; At1g61120) as a geranyllinalool synthase (GES). Recombinant TPS04/GES protein expressed in Escherichia coli catalyzes the formation of (E,E)-geranyllinalool from the substrate geranylgeranyl diphosphate. Transgenic Arabidopsis lines carrying T-DNA insertions in the TPS04 locus are deficient in (E,E)-geranyllinalool and TMTT synthesis, a phenotype that can be complemented by expressing the GES gene under the control of a heterologous promoter. GES transcription is upregulated under conditions that induce (E,E)-geranyllinalool and TMTT synthesis, including infestation of plants with larvae of the moth Plutella xylostella and treatment with the fungal peptide alamethicin or the octadecanoid mimic coronalon. Induction requires jasmonic acid but is independent from salicylic acid or ethylene. This study paves the ground to address the contribution of TMTT in ecological interactions and to elucidate the signaling network that regulates TMTT synthesis.
Thylakoid Membrane Remodeling during State Transitions inArabidopsis
Authors: Chuartzman Silvia G. , Nevo Reinat , Shimoni Eyal , Charuvi Dana , Kiss Vladimir , Ohad Itzhak , Brumfeld Vlad , Reich Ziv 
Published: April 2008

AbstractAdaptability of oxygenic photosynthetic organisms to fluctuations in light spectral composition and intensity is conferred by state transitions, short-term regulatory processes that enable the photosynthetic apparatus to rapidly adjust to variations in light quality. In green algae and higher plants, these processes are accompanied by reversible structural rearrangements in the thylakoid membranes. We studied these structural changes in the thylakoid membranes of Arabidopsis thaliana chloroplasts using atomic force microscopy, scanning and transmission electron microscopy, and confocal imaging. Based on our results and on the recently determined three-dimensional structure of higher-plant thylakoids trapped in one of the two major light-adapted states, we propose a model for the transitions in membrane architecture. The model suggests that reorganization of the membranes involves fission and fusion events that occur at the interface between the appressed (granal) and nonappressed (stroma lamellar) domains of the thylakoid membranes. Vertical and lateral displacements of the grana layers presumably follow these localized events, eventually leading to macroscopic rearrangements of the entire membrane network.
Cryptococcus neoformans inhibits nitric oxide synthesis caused by CpG‐oligodeoxynucleotide‐stimulated macrophages in a fashion independent of capsular polysaccharides
Authors: Xiao Gang , Miyazato Akiko , Inden Ken , Nakamura Kiwamu , Shiratori Kohei , Nakagawa Kiyotaka , Miyazawa Teruo , Suzuki Kazuo , Kaku Mitsuo , Kawakami Kazuyoshi 
Published: April 2008

ABSTRACT Cryptococcus neoformans is eradicated by macrophages via production of NO. Unmethylated CpG‐ODN protect mice from infection with this fungal pathogen by inducing IFN‐γ. The present study was designed to elucidate the effect of C. neoformans on the synthesis of NO by alveolar macrophages. For this purpose, MH‐S, an alveolar macrophage cell line, was stimulated with CpG‐ODN in the presence of IFN‐γ. A highly virulent strain of C. neoformans with thick capsule suppressed the production of NO. Capsular polysaccharides were not essential for this suppression, because there was no difference between acapsular mutant (Cap67) and its parent strain. Physical or close interaction of Cap67 with MH‐S was necessary, as shown by the loss of such effect when direct contact was interfered by nitrocellulose membrane. Similar effects were observed by disrupted as well as intact Cap67. Whereas the inhibitory effect of intact Cap67 was completely abrogated by heat treatment, disrupted Cap67 did not receive such influence. Finally, disrupted Cap67 did not show any inhibitory effect on the TLR9‐mediated activation of NF‐κB in a luciferase reporter assay with HEK293T cells, although the TLR4‐mediated activation was suppressed. These results revealed that C. neoformans suppressed the synthesis of NO by CpG‐ODN and IFN‐γ‐stimulated macrophages in a fashion independent of capsular polysaccharides, although the precise mechanism remains to be elucidated.
Epidemiological characteristics of tsutsugamushi disease in Oita Prefecture, Japan: Yearly and monthly occurrences of its infections and serotypes of its causative agent, Orientia tsutsugamushi, during 1984–2005
Authors: Ogawa Masao , Ono Testuro 
Published: April 2008

ABSTRACTUsing indirect immunofluorescence assay, we examined the sera of 561 patients from November 1984 to February 2005 to determine the incidence of tsutsugamushi disease (scrub typhus) in Oita Prefecture, Japan. The results obtained were positive in 384 individuals (68.4%). Municipalities where patients were presumed to have been infected with Orientia tsutsugamushi were Taketa City (41.7%), Oyama Town (13.5%), and Ogi Town (8.3%). Infections occurred most often in October, November, and December. A small number of cases occurred from January to May. The serotypes Kuroki (47.5%), Kawasaki (42.5%), and Karp (10.0%) were detected by genetic analysis of O. tsutsugamushi DNA extracted from the blood of 120 patients. The gene sequences of the Kuroki type were highly homologous to that of the Nishino strain. The gene sequences of the Kawasaki type were identical to that of the Kawasaki strain. The gene sequence of the Karp type was highly homologous to that of the JP‐2 type. To determine the distribution of vector mites, 558 wild rodents were captured and 72 010 mites attached to these rodents were collected from 1982 to 1998. Six genera and 16 species of trombiculid mites were collected. Leptotrombidium pallidum and L. scutellare, which are known to be mite vectors for tsutsugamushi disease, accounted for 20.5% and 5.9%, respectively, of all trombiculid mites collected. The geographical distribution of cases roughly coincided with the distribution of L. scutellare. In Oita Prefecture, L. scutellare is presumed to primarily transmit tsutsugamushi disease. In addition, our results also suggest that L. pallidum transmits the Karp type of the causative rickettsia in some municipalities.
Efficacy of Clostridium butyricum preparation concomitantly with Helicobacter pylori eradication therapy in relation to changes in the intestinal microbiota
Authors: Imase Kyoto , Takahashi Motomichi , Tanaka Akifumi , Tokunaga Kengo , Sugano Hajime , Tanaka Mamoru , Ishida Hitoshi , Kamiya Shigeru , Takahashi Shin'ichi 
Published: April 2008

ABSTRACTAntibiotic associated diarrhea due to human intestinal microbiota abnormalities is a side effect of H. pylori eradication therapy. We examined intestinal microbiota changes during H. pylori eradication therapy and the preventive effect of CBM588 as a probiotic agent. Nineteen patients with gastro‐duodenal ulcer were randomly divided into three groups: group A (without probiotics), group B (with regular doses of CBM588) and group C (with double doses of CBM588). The incidence of diarrhea and soft stools during H. pylori eradication therapy was 43% in group A and 14% in group B, while none of the patients in group C reported diarrhea or soft stools. Both bacterial counts and detection rates of bifidobacteria and/or obligate anaerobe were decreased by eradication therapy. However, bacterial counts of obligate anaerobes in group C were significantly higher than in group A (P < 0.05). Additionally, during eradication therapy C. difficile toxin A was detected in both group A and group B but not in group C.In conclusion, these results indicate that H. pylori eradication therapy induces antibiotic associated diarrhea due to abnormalities in intestinal microbiota and/or C. difficile. However, these side effects might be prevented by probiotics.
Decline in a dominant invertebrate species contributes to altered carbon cycling in a low‐diversity soil ecosystem
Authors: BARRETT J. E. , VIRGINIA ROSS A. , WALL DIANA H. , ADAMS BYRON J. 
Published: April 2008

AbstractLow‐diversity ecosystems cover large portions of the Earth's land surface, yet studies of climate change on ecosystem functioning typically focus on temperate ecosystems, where diversity is high and the effects of individual species on ecosystem functioning are difficult to determine. We show that a climate‐induced decline of an invertebrate species in a low‐diversity ecosystem could contribute to significant changes in carbon (C) cycling. Recent climate variability in the McMurdo Dry Valleys of Antarctica is associated with changes in hydrology, biological productivity, and community composition of terrestrial and aquatic ecosystems. One of the greatest changes documented in the dry valleys is a 65% decrease in the abundance of the dominant soil invertebrate (Scottnema lindsayae, Nematoda) between 1993 and 2005, illustrating sensitivity of biota in this ecosystem to small changes in temperature. Globally, such declines are expected to have significant influences over ecosystem processes such as C cycling. To determine the implications of this climate‐induced decline in nematode abundance on soil C cycling we followed the fate of a 13C tracer added to soils in Taylor Valley, Antarctica. Carbon assimilation by the dry valley nematode community contributed significantly to soil C cycling (2–7% of the heterotrophic C flux). Thus, the influence of a climate‐induced decline in abundance of a dominant species may have a significant effect on ecosystem functioning in a low‐diversity ecosystem.
Modeling analysis of primary controls on net ecosystem productivity of seven boreal and temperate coniferous forests across a continental transect
Authors: YUAN FENGMING , ARAIN M. ALTAF , BARR ALAN G. , BLACK T. ANDREW , BOURQUE CHARLES P.‐A. , COURSOLLE CAROLE , MARGOLIS HANK A. , McCAUGHEY J. HARRY , WOFSY STEVEN C. 
Published: April 2008

AbstractProcess‐based models are effective tools to synthesize and/or extrapolate measured carbon (C) exchanges from individual sites to large scales. In this study, we used a C‐ and nitrogen (N)‐cycle coupled ecosystem model named CN‐CLASS (Carbon Nitrogen‐Canadian Land Surface Scheme) to study the role of primary climatic controls and site‐specific C stocks on the net ecosystem productivity (NEP) of seven intermediate‐aged to mature coniferous forest sites across an east–west continental transect in Canada. The model was parameterized using a common set of parameters, except for two used in empirical canopy conductance–assimilation, and leaf area–sapwood relationships, and then validated using observed eddy covariance flux data. Leaf Rubisco‐N dynamics that are associated with soil–plant N cycling, and depend on canopy temperature, enabled the model to simulate site‐specific gross ecosystem productivity (GEP) reasonably well for all seven sites. Overall GEP simulations had relatively smaller differences compared with observations vs. ecosystem respiration (RE), which was the sum of many plant and soil components with larger variability and/or uncertainty associated with them. Both observed and simulated data showed that, on an annual basis, boreal forest sites were either carbon‐neutral or a weak C sink, ranging from 30 to 180 g C m−2 yr−1; while temperate forests were either a medium or strong C sink, ranging from 150 to 500 g C m−2 yr−1, depending on forest age and climatic regime. Model sensitivity tests illustrated that air temperature, among climate variables, and aboveground biomass, among major C stocks, were dominant factors impacting annual NEP. Vegetation biomass effects on annual GEP, RE and NEP showed similar patterns of variability at four boreal and three temperate forests. Air temperature showed different impacts on GEP and RE, and the response varied considerably from site to site. Higher solar radiation enhanced GEP, while precipitation differences had a minor effect. Magnitude of forest litter content and soil organic matter (SOM) affected RE. SOM also affected GEP, but only at low levels of SOM, because of low N mineralization that limited soil nutrient (N) availability. The results of this study will help to evaluate the impact of future climatic changes and/or forest C stock variations on C uptake and loss in forest ecosystems growing in diverse environments.
Long‐term impact of a stand‐replacing fire on ecosystem CO2 exchange of a ponderosa pine forest
Authors: DORE S. , KOLB T. E. , MONTES‐HELU M. , SULLIVAN B. W. , WINSLOW W. D. , HART S. C. , KAYE J. P. , KOCH G. W. , HUNGATE B. A. 
Published: April 2008

AbstractPonderosa pine (Pinus ponderosa) forests of the southwestern United States are a mosaic of stands where undisturbed forests are carbon sinks, and stands recovering from wildfires may be sources of carbon to the atmosphere for decades after the fire. However, the relative magnitude of these sinks and sources has never been directly measured in this region, limiting our understanding of the role of fire in regional and US carbon budgets. We used the eddy covariance technique to measure the CO2 exchange of two forest sites, one burned by fire in 1996, and an unburned forest. The fire was a high‐intensity stand‐replacing burn that killed all trees. Ten years after the fire, the burned site was still a source of CO2 to the atmosphere [109±6 (SEM) g C m−2 yr−1], whereas the unburned site was a sink (−164±23 g C m−2 yr−1). The fire reduced total carbon storage and shifted ecosystem carbon allocation from the forest floor and living biomass to necromass. Annual ecosystem respiration was lower at the burned site (480±5 g C m−2 yr−1) than at the unburned site (710±54 g C m−2 yr−1), but the difference in gross primary production was even larger (372±13 g C m−2 yr−1 at the burned site and 858±37 g C m−2 yr−1at the unburned site). Water availability controlled carbon flux in the warm season at both sites, and the burned site was a source of carbon in all months, even during the summer, when wet and warm conditions favored respiration more than photosynthesis. Our study shows that carbon losses following stand‐replacing fires in ponderosa pine forests can persist for decades due to slow recovery of the gross primary production. Because fire exclusion is becoming increasingly difficult in dry western forests, a large US forest carbon sink could shift to a decadal‐scale carbon source.
Long‐term ozone effects on vegetation, microbial community and methane dynamics of boreal peatland microcosms in open‐field conditions
Authors: MÖRSKY SAMI K. , HAAPALA JAANA K. , RINNAN RIIKKA , TIIVA PÄIVI , SAARNIO SANNA , SILVOLA JOUKO , HOLOPAINEN TOINI , MARTIKAINEN PERTTI J. 
Published: April 2008

AbstractTo study the effects of elevated ozone concentration on methane dynamics and a sedge species, Eriophorum vaginatum, we exposed peatland microcosms, isolated by coring from an oligotrophic pine fen, to double ambient ozone concentration in an open‐air ozone exposure field for four growing seasons. The field consists of eight circular plots of which four were fumigated with elevated ozone concentration and four were ambient controls. At the latter part of the first growing season (week 33, 2003), the methane emission was 159±14 mg CH4 m−2 day−1 (mean±SE) in the ozone treatment and 214±8 mg CH4 m−2 day−1 under the ambient control. However, towards the end of the experiment the ozone treatment slightly, but consistently, enhanced the methane emission. At the end of the third growing season (2005), microbial biomass (estimated by phospholipid fatty acid biomarkers) was higher in peat exposed to ozone (1975±108 nmol g−1 dw) than in peat of the control microcosms (1589±115 nmol g−1 dw). The concentrations of organic acids in peat pore water showed a similar trend. Elevated ozone did not affect the shoot length or the structure of the sedge E. vaginatum leaves but it slightly increased the total number of sedge leaves towards the end of the experiment. Our results indicate that elevated ozone concentration enhances the general growth conditions of microbes in peat by increasing their substrate availability. However, the methane production did not reflect the increase in the concentration of organic acids, probably because hydrogenotrophic methane production dominated in the peat studied. Although, we used isolated peatland microcosms with limited size as study material, we did not find experimental factors that could have hampered the basic conclusions on the effects of ozone.
Sixty years of environmental change in the world's largest freshwater lake – Lake Baikal, Siberia
Authors: HAMPTON STEPHANIE E. , IZMEST'EVA LYUBOV R. , MOORE MARIANNE V. , KATZ STEPHEN L. , DENNIS BRIAN , SILOW EUGENE A. 
Published: April 2008

AbstractHigh‐resolution data collected over the past 60 years by a single family of Siberian scientists on Lake Baikal reveal significant warming of surface waters and long‐term changes in the basal food web of the world's largest, most ancient lake. Attaining depths over 1.6 km, Lake Baikal is the deepest and most voluminous of the world's great lakes. Increases in average water temperature (1.21 °C since 1946), chlorophyll a (300% since 1979), and an influential group of zooplankton grazers (335% increase in cladocerans since 1946) may have important implications for nutrient cycling and food web dynamics. Results from multivariate autoregressive (MAR) modeling suggest that cladocerans increased strongly in response to temperature but not to algal biomass, and cladocerans depressed some algal resources without observable fertilization effects. Changes in Lake Baikal are particularly significant as an integrated signal of long‐term regional warming, because this lake is expected to be among those most resistant to climate change due to its tremendous volume. These findings highlight the importance of accessible, long‐term monitoring data for understanding ecosystem response to large‐scale stressors such as climate change.
Effects of temperature and fertilization on nitrogen cycling and community composition of an urban lawn
Authors: BIJOOR NEETA S. , CZIMCZIK CLAUDIA I. , PATAKI DIANE E. , BILLINGS SHARON A. 
Published: April 2008

AbstractWe examined the influence of temperature and management practices on the nitrogen (N) cycling of turfgrass, the largest irrigated crop in the United States. We measured nitrous oxide (N2O) fluxes, and plant and soil N content and isotopic composition with a manipulative experiment of temperature and fertilizer application. Infrared lamps were used to increase surface temperature by 3.5±1.3 °C on average and control and heated plots were split into high and low fertilizer treatments. The N2O fluxes increased following fertilizer application and were also directly related to soil moisture. There was a positive effect of warming on N2O fluxes. Soils in the heated plots were enriched in nitrogen isotope ratio (δ15N) relative to control plots, consistent with greater gaseous losses of N. For all treatments, C4 plant C/N ratio was negatively correlated with plant δ15N, suggesting that low leaf N was associated with the use of isotopically depleted N sources such as mineralized organic matter. A significant and unexpected result was a large, rapid increase in the proportion of C4 plants in the heated plots relative to control plots, as measured by the carbon isotope ratio (δ13C) of total harvested aboveground biomass. The C4 plant biomass was dominated by crabgrass, a common weed in C3 fescue lawns. Our results suggest that an increase in temperature caused by climate change as well as the urban heat island effect may result in increases in N2O emissions from fertilized urban lawns. In addition, warming may exacerbate weed invasions, which may require more intensive management, e.g. herbicide application, to manage species composition.