bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetostratigraphic evidence from the Cold Creek bar for onset of ice-age cataclysmic floods in eastern Washington during the early pleistocene
Authors: Pluhar Christopher J. , Bjornstad Bruce N. , Reidel Stephen P. , Coe Robert S. , Nelson Paul B.
Published: September 2005

This study provides a detailed magnetostratigraphy of sediments composing the Cold Creek cataclysmic flood bar in the Pasco Basin, Washington. Our interpretation suggests onset of Missoula floods or similar events prior to 1.1 myr, later than previously suggested by Bjornstad et al. [Bjornstad, B.N., Fecht, K.R., Pluhar, C.J., 2001. Long history of pre-Wisconsin, Ice Age cataclysmic floods: evidence from southeastern Washington State. Journal of Geology 109 (6), 695–713]. Nonetheless these data suggest that Channeled Scabland features formed over a much longer timespan than commonly cited, that continental ice sheets of the early Pleistocene reached as far south as those of the late Pleistocene, and that similar physiography existed in eastern Washington and perhaps Montana to both generate and route Missoula-flood-like events. This study adds paleomagnetic polarity results from 213 new samples of silts and sands derived from nine new drill cores penetrating the Cold Creek cataclysmic flood bar to our previous database of 53 samples from four boreholes, resulting in a much more robust and detailed magnetostratigraphy. Rock magnetic studies on these sediments show pure magnetite to be the predominant remanence-carrying magnetic mineral, ruling out widespread remagnetization by secondary mineralization. The magnetostratigraphy at eastern Cold Creek bar is characterized by a normal polarity interval bracketed by reversed polarities. Equating the normal zone with the Jaramillo subchron (0.99–1.07 myr) affords the simplest correlation to the magnetic polarity timescale. Western Cold Creek bar was likely deposited during the Brunhes chron (0–0.78 myr) since it exhibits mainly normal polarities with only two thin reversed-polarity horizons that we interpret as magnetic excursions during the Brunhes.
Conjugate, cataclastic deformation bands in the Lower Devonian Muth Formation (Tethyan Zone, NW India): evidence for pre-Himalayan deformation structures
Authors: DRAGANITS E. , GRASEMANN B. , HAGER C.
Published: September 2005

The purpose of this study is to use the mechanisms of deformation band formation to help with interpreting the timing of phases of deformation in an area with a complex geological history. Deformation bands and zones of deformation bands are described from the quartzites of the Lower Devonian Muth Formation in the Pin Valley, NW Himalayas. Thin-section analyses show that the deformation bands in the Muth Formation formed early in the diagenetic history before porosity was lost. Deformation mechanisms involved cataclasis, translation, rotation of quartz grains and effective porosity reduction. The orientations of the deformation bands cannot be reasonably grouped with the orientations of faults related to Himalayan deformation in the Pin Valley. Additionally, the deformation bands are deformed by Eo-Himalayan (Eocene) folds, which in turn are cut by later faults. The later faults that cross-cut the Eo-Himalayan folds developed in the already-cemented Muth Formation at much higher temperature and pressure conditions by crystal plastic deformation mechanisms, indicated by quartz crystals with undulatory extinction, abundant kink bands, dislocation glide, elongated subgrains, slightly curved deformation lamellae and pronounced shape-preferred orientation. These two completely contrasting deformation mechanisms on the microstructural scale characterize two distinct fault sets that formed at different depths in the crust. Based on these differences, a pre-Himalayan origin of the deformation bands is concluded, thus representing a set of rare pre-Himalayan deformation structures. After unfolding to remove Eo-Himalayan crustal shortening, the orientation of the deformation bands and restored relative offsets of sedimentary bedding are most compatible with ∼ E–W-oriented shortening associated with N–S extension. The age of the deformation bands in the Muth Formation is bracketed by an early Devonian sedimentation age of the Muth Formation and a middle Cretaceous age of considerable cementation as deduced from compiled burial histories. Accepting a pre-middle Cretaceous age of the deformation bands, maximum conditions of about 80°C and 60 MPa lithostatic pressure during their formation are estimated from the amount of overburden during the middle Cretaceous. We suggest the deformation bands are a result of either the Neo-Tethys rifting event beginning in the early Carboniferous or the extension related to late Carnian/early Norian rapid subsidence, although a hitherto unknown deformation event cannot be excluded.
The influence of dietary carbohydrates on experimental infection withTrichuris suisin pigs
Authors: THOMSEN L. E. , PETKEVIČIUS S. , BACH KNUDSEN K. E. , ROEPSTORFF A.
Published: September 2005

Two experiments (Exps 1 and 2) were carried out to study the effect of dietary carbohydrates on the establishment ofTrichuris suisin pigs. Two experimental diets based on barley flour were used; Diet 1 was supplemented with non-fermentable carbohydrates from oat hull meal, while Diet 2 was supplemented with fermentable carbohydrates from sugar beet fibre and inulin. In Exp. 1, thirty-two pigs were allocated randomly into 4 groups. Two groups were fed Diet 1 and 2 groups were fed Diet 2. Pigs from one of each diet group were inoculated with 2000 infectiveT. suiseggs each and the other two groups were uninfected controls. All pigs were slaughtered 8 weeks post-inoculation (p.i.). In Exp. 2, twenty-four pigs were allocated randomly into 2 groups and fed Diet 1 or Diet 2, respectively. All the pigs were inoculated with 2000 infectiveT. suiseggs. Six pigs from each group were slaughtered 8 weeks p.i. and the remaining 6 pigs from each group were slaughtered 12 weeks p.i. Infections were followed by faecal egg counts and worm burdens were assessed at necropsy. Pigs fed Diet 2 had lower egg counts in both experiments; in Exp. 2 the difference was significant (P<0·05). No differences were found in worm burdens 8 weeks p.i. in both experiments, however, worms from pigs on Diet 2 were significantly shorter (P<0·0001). Pigs fed Diet 2 and slaughtered 12 weeks p.i. had significantly lower worm counts (P<0·01) compared to pigs fed Diet 1. The results indicate that fermentable carbohydrates do not affect the establishment ofT. suisin naïve pigs, but result in earlier expulsion and reduced growth of the established worms. Thus, diets with highly fermentable carbohydrates may be used in the control ofT. suis.
Global warming and temperature-mediated increases in cercarial emergence in trematode parasites
Authors: POULIN R.
Published: September 2005

Global warming can affect the world's biota and the functioning of ecosystems in many indirect ways. Recent evidence indicates that climate change can alter the geographical distribution of parasitic diseases, with potentially drastic consequences for their hosts. It is also possible that warmer conditions could promote the transmission of parasites and raise their local abundance. Here I have compiled experimental data on the effect of temperature on the emergence of infective stages (cercariae) of trematode parasites from their snail intermediate hosts. Temperature-mediated changes in cercarial output varied widely among trematode species, from small reductions to 200-fold increases in response to a 10 °C rise in temperature, with a geometric mean suggesting an almost 8-fold increase. Overall, the observed temperature-mediated increases in cercarial output are much more substantial than those expected from basic physiological processes, for which 2- to 3-fold increases are normally seen. Some of the most extreme increases in cercarial output may be artefacts of the methods used in the original studies; however, exclusion of these extreme values has little impact on the preceding conclusion. Across both species values and phylogenetically independent contrasts, neither the magnitude of the initial cercarial output nor the shell size of the snail host correlated with the relative increase in cercarial production mediated by rising temperature. In contrast, the latitude from which the snail-trematode association originated correlated negatively with temperature-mediated increases in cercarial production: within the 20 ° to 55 ° latitude range, trematodes from lower latitudes showed more pronounced temperature-driven increases in cercarial output than those from higher latitudes. These results suggest that the small increases in air and water temperature forecast by many climate models will not only influence the geographical distribution of some diseases, but may also promote the proliferation of their infective stages in many ecosystems.
Effect of temperature onWolbachiadensity and impact on cytoplasmic incompatibility
Authors: MOUTON L. , HENRI H. , BOULETREAU M. , VAVRE F.
Published: September 2005

The outcome and the evolution of host-symbiont associations depend on environmental constraints, but responses are difficult to predict since they arise from a complex interaction between the host, the parasite and the environment. The situation can be even more complex when multiple parasite genotypes, with potentially different responses to environmental changes, coexist within a single host. In this paper, we investigated the effect of the temperature (from 14 to 26 °C) during the host development on the density of 3 strains of the intracellular bacteriumWolbachiathat coexist within the waspLeptopilina heterotoma. In this species,Wolbachiainduces cytoplasmic incompatibility, a sperm-egg incompatibility that allows it to spread and persist in host populations. Using real-time quantitative PCR we found that (i)Wolbachiadensity is temperature-specific and highest at 26 °C; (ii) the order of the abundance of the 3Wolbachiastrains does not vary with temperature changes; (iii) the response of bacterial density to temperature occurs within a single insect generation, during the egg-to-adult developmental period; (iv) in this species, temperature-related changes inWolbachiadensity do not influence cytoplasmic incompatibility.
Triadic model of the neurobiology of motivated behavior in adolescence
Authors: ERNST MONIQUE , PINE DANIEL S. , HARDIN MICHAEL
Published: September 2005

Background. Risk-taking behavior is a major cause of morbidity and mortality in adolescence. In the context of decision theory and motivated (goal-directed) behavior, risk-taking reflects a pattern of decision-making that favors the selection of courses of action with uncertain and possibly harmful consequences. We present a triadic, neuroscience systems-based model of adolescent decision-making.

Method. We review the functional role and neurodevelopmental findings of three key structures in the control of motivated behavior, i.e. amygdala, nucleus accumbens, and medial/ventral prefrontal cortex. We adopt a cognitive neuroscience approach to motivated behavior that uses a temporal fragmentation of a generic motivated action. Predictions about the relative contributions of the triadic nodes to the three stages of a motivated action during adolescence are proposed.

Results. The propensity during adolescence for reward/novelty seeking in the face of uncertainty or potential harm might be explained by a strong reward system (nucleus accumbens), a weak harm-avoidant system (amygdala), and/or an inefficient supervisory system (medial/ventral prefrontal cortex). Perturbations in these systems may contribute to the expression of psychopathology, illustrated here with depression and anxiety.

Conclusions. A triadic model, integrated in a temporally organized map of motivated behavior, can provide a helpful framework that suggests specific hypotheses of neural bases of typical and atypical adolescent behavior.
Neuregulin 1 gene and variations in perceptual aberration of schizotypal personality in adolescents
Authors: LIN HSIAO-FAN , LIU YU-LI , LIU CHIH-MIN , HUNG SHUEN-IU , HWU HAI-GWO , CHEN WEI J.
Published: September 2005

Background. We test the hypothesis that the neuregulin 1 (NRG1) gene at chromosome 8p22-p12, which has been implicated as a susceptibility gene to schizophrenia, is associated with variations in schizotypal personality in non-clinical populations.

Method. A randomly selected sample of 905 adolescents were assessed for their personality features using the Perceptual Aberration Scale (PAS) and the Schizotypal Personality Questionnaire (SPQ) and genotyped for three single nucleotide polymorphisms (SNP8NRG221533, rs3924999, and rs2954041) at the NRG1 gene. Relations between the three genetic variants and continuous schizotypal personality scores were evaluated using ANOVA for single-locus analyses and haplotype trend regression test for multi-locus analyses.

Results. Single locus analysis showed that the A allele of rs3924999, a functional polymorphism in exon 2, had the largest effect size and exhibited a prominent allele–dose trend effect for the PAS score. Haplotype analyses using the haplotype trend regression test indicated that the A allele of rs3924999 was mainly responsible for the association with the PAS but not with the SPQ or its three factors, and the magnitude of significance was not strengthened by the combination of this allele with adjacent locus.

Conclusions. Our study provides the first evidence for the association of NRG1 with schizotypal personality and indicates a possible role of NRG1 in the genetic etiology of schizophrenia through perceptual aberrations.
occupational activity and risk of prostate cancer in ireland
Authors: flinton d. m. , walters n. j.
Published: September 2005

study objective: the study intended to investigate the possible relationship between physical activity and prostate cancer risk on a previously unexamined population set.

design: a population-based study was conducted on males entered on the irish cancer registry between the years 1994 to 1997 to investigate if physical activity affected the risk of prostate cancer. activity was coded for three levels of occupational activity and the odds ratios were calculated together with 95% confidence limits.

results: despite limitations in the data, an elevated risk (odds ratio 2.13, 95% confidence interval 1.29–3.52) was seen in working subjects with low levels of activity compared with the high activity group. in the retired group there was a slight elevation of risk, although it was not statistically significant.

conclusion: the study suggests that physical activity offers a small but significant reduction in prostate cancer risk for those people in work.
the production of a best practice statement in the skincare of patients receiving radiotherapy
Authors: hornsby c. , fletcher j. , blyth c. m.
Published: September 2005

radiotherapy skin care is a contentious issue surrounded by myth, damaging and frightening stories and unfounded guidance. this is compounded by the fact that, when seeking information, patients, relatives and staff are faced with a barrage of conflicting, poorly researched data. each of the five scottish cancer centres worked together to produce guidance for all health professionals who are involved in the care of patients with radiotherapy skin reactions. as a result, a “best practice statement” has been produced to give an overall view of radiotherapy skin reactions and their recommended care. this will guide best practice and dispel the many myths of care, which are still in existence, thus ensuring that equity of best practice care is available to all patients.
disaster planning and recovery – the caribbean experience
Authors: hewison hazel
Published: September 2005

hazel hewison, biall chair, reports on her experiences at the carall conference workshop on disaster planning, following the disastrous 2004 atlantic hurricane season and the devastating asian tsunami tragedy in december 2004.
letter from carol clark in south africa …
Authors: clark carol
Published: September 2005

it was in an e-mail from christine miskin discussing what i could write about in this article that i learnt of the death of gillian sands. i was saddened by this news as although i never met her in person, we did “meet” via e-mail. only a couple of weeks before her death she responded to a request we had sent out on the listserve for an obscure english case. her friendliness and willingness to assist a colleague were immediately apparent. her name was also familiar to me from articles she had written for legal information management and i know that the librarian in our london office had contact with her when she worked at the institute of advanced legal studies. to gillian's family, friends and colleagues we extend our deepest sympathy.
Effects of parameter uncertainties on the modeling of terrestrial biosphere dynamics
Authors: Zaehle S. , Sitch S. , Smith B. , Hatterman F.
Published: September 2005

Dynamic global vegetation models (DGVMs) have been shown to broadly reproduce seasonal and interannual patterns of carbon exchange, as well as realistic vegetation dynamics. To assess the uncertainties in these results associated with model parameterization, the Lund‐Potsdam‐Jena‐DGVM (LPJ‐DGVM) is analyzed in terms of model robustness and key sensitive parameters. Present‐day global land‐atmosphere carbon fluxes are relatively well constrained, despite considerable uncertainty in global net primary production mainly propagating from uncertainty in parameters controlling assimilation rate, plant respiration and plant water balance. In response to climate change, water‐use efficiency driven increases in net carbon assimilation by plants, transient changes in vegetation composition and global warming effects on soil organic matter dynamics are robust model results. As a consequence, long‐term trends in land‐atmosphere fluxes are consistently modeled despite an uncertainty range of −3.35 ± 1.45 PgC yr−1 at the end of the twenty‐first century for the specific scenario used.
Response of the bottom boundary layer over a sloping shelf to variations in alongshore wind
Authors: Perlin A. , Moum J. N. , Klymak J. M.
Published: September 2005

Rapidly repeated transects of currents, density, and turbulence through the bottom boundary layer across a relatively uniform stretch of the continental shelf off Oregon reveal the response to a sequence of strong upwelling followed by relaxation and thence a resumption of upwelling. Several definitions of boundary layer thickness are employed to describe the evolution of the bottom boundary layer. Well‐mixed and turbulent layers were typically confined to 10 m from the bottom. However, boundary layer thicknesses were greatest during relaxation from upwelling (when mixed layer and turbulent layer thicknesses exceeded 20 m), and turbulence in the bottom boundary layer was most intense at this time. Dense, near‐bottom fluid was observed to move upslope with upwelling and back down the slope with relaxation from upwelling. By tracking the intersection of near‐bottom isopycnals with the bottom over successive transects, we estimate the cross‐shore speed of fluid in the bottom boundary layer. Cross‐shore speed agrees well with dynamical estimates of cross‐shore velocity in the bottom Ekman layer derived from bottom stress measurements. This leads to a confirmation of the Ekman balance of alongshore momentum in the bottom boundary layer across the full width of the shelf. Good correlation exists between alongshore velocity at the top of the bottom boundary layer and cross‐shore velocity of dense fluid in the bottom boundary layer. Application of a derived proxy for bottom stress to moored velocity observations indicates Ekman balance of alongshore momentum at a midshelf location (81 m depth) for a 3 month period in spring/summer 2001.
Eddy diffusivity near bubble plumes
Authors: Wain Danielle J. , Rehmann Chris R.
Published: September 2005

Profiles of eddy diffusivity and the rate of dissipation of temperature variance were inferred from temperature microstructure measurements near a bubble plume at the center of a tank with a diameter of 13.7 m and a maximum depth of 8.3 m. Measurements occurred outside the bubbly part of the flow. Profiles of eddy diffusivity were estimated with two methods: one based on the equation for turbulent kinetic energy and one based on the equation for temperature variance. The eddy diffusivities showed nonmonotonic behavior with distance from the plume axis, as in numerical simulations. Eddy diffusivities estimated with the two methods match well, except for one data set with strong turbulence and weak stratification. The estimates of the eddy diffusivity allow two empirical formulas for the bulk, or tank‐averaged, effective diffusivity to be evaluated; the bulk diffusivity is within the range of values predicted by the models.
Nonlinear dynamics in Tomlinson’s model for atomic-scale friction and friction force microscopy
Authors: Conley W. G. , Raman A. , Krousgrill C. M.
Published: September 2005

Tomlinson’s model is often used to describe the friction of a single asperity or of a scanning force probe sliding over an atomic lattice. We present results on the complex dynamic behavior found in this model using a combination of continuation methods, perturbation techniques, and numerical simulations. Specifically, periodic stick-slip motions and their bifurcations and stability are investigated in the slow-sliding speed range and in higher speed ranges at which fundamental and parametric resonances set in. The results predict a complex range of bifurcations, superharmonic and subharmonic motions, and possibly chaotic dynamics which bear significant implications for understanding single-asperity friction or the dynamic response in friction force microscopy.
Electron diffraction from free-standing, metal-coated transmission gratings
Authors: Gronniger Glen , Barwick Brett , Batelaan Herman , Savas Tim , Pritchard Dave , Cronin Alex
Published: September 2005

Electron diffraction from a free-standing nanofabricated transmission grating was demonstrated, with energies ranging from 125 eV to 25 keV. Observation of 21 diffraction orders highlights the quality of the gratings. The image charge potential due to one electron was measured by rotating the grating. These gratings may pave the way to low-energy electron interferometry.
Multilayer and functional coatings on carbon nanotubes using atomic layer deposition
Authors: Herrmann C. F. , Fabreguette F. H. , Finch D. S. , Geiss R. , George S. M.
Published: September 2005

Atomic layer deposition (ALD) can be used to deposit ultra-thin and conformal films on flat substrates, high aspect ratios structures and particles. In this paper, we demonstrate that insulating, multilayered and functionalized ALD coatings can also be deposited conformally on carbon nanotubes. Multilayered coatings consisting of alternating layers of dielectric and conductive materials, such as Al2O3 and W, respectively, are deposited on conductive multi-walled carbon nanotubes. This coated carbon nanotube can function as a nanoscale coaxial cable. Thin layers of Al2O3 ALD are also used as a seed layer to functionalize nanotubes. A carbon nanotube was made highly hydrophobic using an Al2O3 ALD seed layer followed by the attachment of perfluorinated molecules.
Season of prescribed burn in ponderosa pine forests in eastern Oregon: impact on pine mortality
Authors: Thies Walter G. , Westlind Douglas J. , Loewen Mark
Published: September 2005

A study of the effects of season of prescribed burn on tree mortality was established in mixed-age ponderosa pine (Pinus ponderosa Dougl. ex Laws.) at the south end of the Blue Mountains near Burns, Oregon. Each of six previously thinned stands was subdivided into three experimental units and one of three treatments was randomly assigned to each: fall 1997 burn, spring 1998 burn, and no burning (control). Burns were conducted as operational prescribed burns. Trees within six 0.2-ha circular plots on each experimental unit were observed for four post-burn growing seasons to determine fire damage and to detect immediate and delayed mortality and occurrence of black stain root disease (BSRD). There were 5321 tagged ponderosa pines alive at the time of the burns. The percentage of ponderosa pine dying was higher after fall burns than after spring burns. Differences in percentages of fire-caused mortality may be because fall burns are inherently more severe than spring burns. Although present in many trees, BSRD appeared to have little impact on mortality. The lion’s-tail appearance, thought to be a symptom of BSRD, was found to be an unreliable indicator of BSRD in the six test stands.
Fire history and stand structure of two ponderosa pine-mixed conifer sites: San Francisco Peaks, Arizona, USA
Authors: Heinlein Thomas A. , Moore Margaret M. , Fulé Peter Z. , Covington W. Wallace
Published: September 2005

We reconstructed historical fire regimes and contemporary and historical stand structures in two stands of ponderosa pine–mixed conifer forests on the San Francisco Peaks in northern Arizona, USA. Thirty-four fire-scarred specimens recorded 256 fires from the EAST and WEST study sites. Fires were recorded between 1739 and 1903 for the EAST site and between 1548 and 1947 for the WEST site. The mean fire return interval (MFI: ≥25% scarred) for the period 1690–1892 was 10 years with a range of 3–21 years for the EAST site. The WEST site MFI (period 1612–1876) was 9 years with a range of 3–21 years. Seasonal patterns of fire occurrence showed that the majority of fires burned during the summer months. Fire interval (years) means, variances and distributions between the EAST and WEST sites were not statistically different from one another for the common analysis period of 1690–1876. Historically, both the EAST and WEST sites were dominated by ponderosa pine, with scattered individuals of Douglas-fir, limber pine and white fir, with tree densities that ranged from 43 to 60 trees per hectare (TPH). Current forest composition has shifted from fire-tolerant ponderosa pine to less fire-tolerant, more shade-tolerant species, with tree densities ranging from 928 to over 1700 TPH. We suggest that the dramatic structural changes recorded at our study sites occurred since fire regime disruption.
Effect of fire shelters on perceived fire danger: implications for risk compensation
Authors: Braun Curt C. , Fouts Jason , Silver N. Clayton , Putnam Ted
Published: September 2005

The fire shelter is an integral part of wildland firefighting Personal Protective Equipment (PPE). There is growing concern, however, that firefighters may accept greater levels of risk while carrying them. Such concerns are consistent with Risk Homeostasis Theory, which postulates that behavior is regulated by an internal stabilizing process that balances target and perceived risk and the effects of safety interventions. When any one of the three components changes, the resulting disequilibrium is compensated for by changes in behavior. As a safety intervention, fire shelters may alter the equilibrium of this system producing a behavior change that negates any safety improvements it produced. Two experiments were conducted to assess how PPE affects the behavior of athletes and how fire shelters affect wildland firefighters’ perceptions of fire danger. In Experiment 1, 53% of participants demonstrated behavior that offset gains in safety produced by PPE. The results from Experiment 2 revealed that the presence of fire shelters significantly reduced perceived hazard levels associated with three different fire scenarios. Although neither experiment actually measured the behavior of firefighters, the combined results suggest that firefighters might not be immune to the effects of risk compensation.
Fire history of the San Francisco East Bay region and implications for landscape patterns
Authors: Keeley Jon E.
Published: September 2005

The San Francisco East Bay landscape is a rich mosaic of grasslands, shrublands and woodlands that is experiencing losses of grassland due to colonization by shrubs and succession towards woodland associations. The instability of these grasslands is apparently due to their disturbance-dependent nature coupled with 20th century changes in fire and grazing activity. This study uses fire history records to determine the potential for fire in this region and for evidence of changes in the second half of the 20th century that would account for shrubland expansion. This region has a largely anthropogenic fire regime with no lightning-ignited fires in most years. Fire suppression policy has not excluded fire from this region; however, it has been effective at maintaining roughly similar burning levels in the face of increasing anthropogenic fires, and effective at decreasing the size of fires. Fire frequency parallels increasing population growth until the latter part of the 20th century, when it reached a plateau. Fire does not appear to have been a major factor in the shrub colonization of grasslands, and cessation of grazing is a more likely immediate cause. Because grasslands are not under strong edaphic control, rather their distribution appears to be disturbance-dependent, and natural lightning ignitions are rare in the region, I hypothesize that, before the entrance of people into the region, grasslands were of limited extent. Native Americans played a major role in creation of grasslands through repeated burning and these disturbance-dependent grasslands were maintained by early European settlers through overstocking of these range lands with cattle and sheep. Twentieth century reduction in grazing, coupled with a lack of natural fires and effective suppression of anthropogenic fires, have acted in concert to favor shrubland expansion.
The antimalarial drug artemisinin alkylates heme in infected mice
Authors: Robert Anne , Benoit-Vical Françoise , Claparols Catherine , Meunier Bernard
Published: September 2005

Heme alkylation by the antimalarial drug artemisinin is reported
in vivo
, within infected mice that have been treated at pharmacologically relevant doses. Adducts resulting from the alkylation of heme by the drug were characterized in the spleen of treated mice, and their glucuroconjugated derivatives were present in the urine. Because these heme-artemisinin adducts were not observed in noninfected mice, this report confirms that the alkylating activity of this antimalarial drug is related to the presence of the parasite in infected animals. The identification of heme-artemisinin adducts in mice should be considered as the signature of the alkylation capacity of artemisinin
in vivo
.
Ensemble versus single-molecule protein unfolding
Authors: Day Ryan , Daggett Valerie
Published: September 2005

Molecular dynamics (MD) simulations are the classic single-molecule “experiments,” providing atomic-resolution structural and dynamic information. However, the single-molecule nature of the technique has also been its shortcoming, with frequent criticisms of sampling inadequacies and questions regarding the ensemble behavior of large numbers of molecules. Given the increase in computer power, we now address this issue by performing a large number of simulations and comparing individual and ensemble properties. One hundred independent MD simulations of the protein chymotrypsin inhibitor 2 were carried out for 20 ns each at 498 K in water to more fully describe the potentially diverse routes of protein unfolding and investigate how representative a single trajectory can be. Rapid unfolding was observed in all cases with the trajectories distributed about an average “ensemble” path in which secondary and tertiary structure was lost concomitantly, with tertiary structure loss occurring slightly faster. Individual trajectories did, however, sample conformations far from the average path with very heterogeneous time-dependent properties. Nevertheless, all of the simulations but one followed the average ensemble pathway, such that a small number of simulations (
5
-
10
) are sufficient to capture the average properties of these states and the unfolding pathway.
Statistical signals in bioinformatics
Authors: Karlin Samuel
Published: September 2005

The Arthur M. Sackler Colloquium of the National Academy of Sciences, “Frontiers in Bioinformatics: Unsolved Problems and Challenges,” organized by David Eisenberg, Russ Altman, and myself, was held October 15-17, 2004, to provide a forum for discussing concepts and methods in bioinformatics serving the biological and medical sciences. The deluge of genomic and proteomic data in the last two decades has driven the creation of tools that search and analyze biomolecular sequences and structures. Bioinformatics is highly interdisciplinary, using knowledge from mathematics, statistics, computer science, biology, medicine, physics, chemistry, and engineering.
Structural models for the protein family characterized by gamete surface protein Pfs230 ofPlasmodium falciparum
Authors: Gerloff Dietlind L. , Creasey Alison , Maslau Siarhei , Carter Richard
Published: September 2005

Ps230 is the largest representative of a 10-member family of proteins found in allPlasmodiumspecies. The family is defined by partially conserved, cysteine-rich double domains that are ≈350 aa in length and have one to three predicted disulfide bridges in each half. InPlasmodium falciparum, the most dangerous human malaria, Pf12 is the smallest member of the family, comprising just one double domain. Pfs230, with 7 double domains, and Pfs48/45 and Pfs47, with 1.5 double domains each, are found on the gamete surfaces and are thus potential candidates for a transmission-blocking vaccine. Fold prediction analyses of the double domains in Pfs230 reveal structural resemblance to SAG1 (surface antigen 1), a surface protein with a double β-sandwich structure from another apicomplexan parasite,Toxoplasma gondii. Template-directed modeling onto SAG1 clearly establishes the structural link between SAG1 and Pfs230 and produces positions for the cysteines that accord with the disulfide-bonding arrangement predicted for the Pfs230 family in earlier work. A highly clustered region of polymorphisms within the second double domain in Pfs230 maps to one side of the sandwich surface. This observation suggests that this region may be functional and reinforces the validity of these molecular models for the core domains of the Pfs230 family of proteins.
Viral targeting of the interferon-β-inducing Traf family member-associated NF-κB activator (TANK)-binding kinase-1
Authors: Unterstab Gunhild , Ludwig Stephan , Anton Aline , Planz Oliver , Dauber Bianca , Krappmann Daniel , Heins Gudrun , Ehrhardt Christina , Wolff Thorsten
Published: September 2005

Expression of the antiviral cytokines IFN-α/β is among the most potent innate defenses of higher vertebrates to virus infections, which is controlled by the inducible transcription factor IFN regulatory factor (IRF)3. Borna disease virus (BDV) establishes persistent noncytolytic infections in animals and tissue culture cells, indicating that it can circumvent this antiviral reaction by an unexplained activity. In this study, we identify the BDV P protein as microbial gene product that associates with and inhibits the principal regulatory kinase of IRF3, Traf family member-associated NF-κB activator (TANK)-binding kinase 1 (TBK-1). We demonstrate that the P protein counteracts TBK-1-dependent IFN-β expression in cells and, hence, the establishment of an antiviral state. Furthermore, our data show that the BDV P protein itself is phosphorylated by TBK-1, suggesting that P functions as a viral decoy substrate that prevents activation of cellular target proteins of TBK-1. Thus, our findings provide evidence for a previously undescribed mechanism by which a viral protein interferes with the induction of the antiviral IFN cascade.
Reversal of amyloid-induced heart disease in desmin-related cardiomyopathy
Authors: Sanbe Atsushi , Osinska Hanna , Villa Chet , Gulick James , Klevitsky Raisa , Glabe Charles G. , Kayed Rakez , Robbins Jeffrey
Published: September 2005

Amyloid oligomers, similar to the toxic entities found in Alzheimer's disease patients and in other amyloid-based diseases, are present in cardiomyocytes derived from human heart-failure patients and in animal models of desmin-related cardiomyopathy (DRM). The R120G mutation in α-B-crystallin (CryAB) causes DRM and is characterized by aggresomes containing CryAB
R120G
and amyloid oligomer. In this study, we show that aggresome levels do not correlate with disease. Blocking aggresome formation results in increased levels of toxic amyloid oligomer and decreased cardiomyocyte viability. We confirmed the primary toxicity of intrasarcoplasmic amyloid accumulation in the cardiomyocytes by ectopic expression of the amyloidogenic peptide PQ81, which consists of multiple repeats of a polyglutamine tract. We then addressed the issue of disease reversibility by placing CryAB
R120G
under inducible cardiomyocyte-specific expression in transgenic mice. The mice developed aggresomes and contained high concentrations of amyloid oligomer in the heart, resulting in cardiac disease. Cessation of CryAB
R120G
expression in symptomatic mice improved cardiac function and rescued all of the animals from premature death. Rescue was accompanied by significant decreases in amyloid oligomer without a significant reduction in aggresomes. Blocking cardiac amyloid oligomer formation, even after cardiac dysfunction presents, may be a therapeutic strategy in DRM as well as in other types of cardiac disease in which significant amyloid accumulation occurs.
AtFtsH6 is involved in the degradation of the light-harvesting complex II during high-light acclimation and senescence
Authors: Żelisko Agnieszka , García-Lorenzo Maribel , Jackowski Grzegorz , Jansson Stefan , Funk Christiane
Published: September 2005

Degradation of the most abundant membrane protein on earth, the light-harvesting complex of Photosystem II (LHC II), is highly regulated under various environmental conditions, e.g., light stress, to prevent photochemical damage to the reaction center. We identified the LHC II degrading protease in
Arabidopsis thaliana
as a Zn
2+
-dependent metalloprotease, activated by the removal of unknown extrinsic factors, similar to the proteolytic activity directed against Lhcb3 in barley. By using a reversed genetic approach, the chloroplast-targeted protease FtsH6 was identified as being responsible for the degradation. T-DNA KO
A. thaliana
mutants, lacking
ftsH6
, were unable to degrade either Lhcb3 during dark-induced senescence or Lhcb1 and Lhcb3 during highlight acclimation. The
A. thaliana ftsH6
gene has a clear orthologue in the genome of
Populus trichocarpa
. It is likely that FtsH6 is a general LHC II protease and that FtsH6-dependent LHC II proteolysis is a feature of all higher plants.
Cdc42GAP regulates c-Jun N-terminal kinase (JNK)-mediated apoptosis and cell number during mammalian perinatal growth
Authors: Wang Lei , Yang Linda , Burns Kevin , Kuan Chia-Yi , Zheng Yi
Published: September 2005

Rho family GTPase Cdc42 is known to regulate polarity and growth in lower eukaryotes, but its physiologic function in mammals has yet to be determined. Here we have disrupted
cdc42gap
, a ubiquitously expressed negative regulator of Cdc42, in mice. Cdc42GAP
-/-
embryonic fibroblasts and various organs displayed significantly elevated Cdc42 activity. The embryonic and neonatal homozygous mice were reduced in size by ≈25-40% and suffered severe growth retardation. Major organs from Cdc42GAP
-/-
mice were proportionally smaller because of decreased cell number. Basal apoptosis was increased in Cdc42GAP
-/-
cells and tissues, and this was attributed to altered c-Jun N-terminal kinase apoptotic signals. These results reveal a role of Cdc42GAP in mammalian perinatal growth and implicate the c-Jun N-terminal kinase-mediated apoptosis machinery as a Cdc42 effector pathway
in vivo
.
Inactivation of
Drosophila
DJ-1 leads to impairments of oxidative stress response and phosphatidylinositol 3-kinase/Akt signaling
Authors: Yang Yufeng , Gehrke Stephan , Haque Md. Emdadul , Imai Yuzuru , Kosek Jon , Yang Lichuan , Beal M. Flint , Nishimura Isao , Wakamatsu Kazumasa , Ito Shosuke , Takahashi Ryosuke , Lu Bingwei
Published: September 2005

Parkinson's disease (PD) is the most common movement disorder characterized by dopaminergic dysfunction and degeneration. The cause of most PD cases is unknown, although postmortem studies have implicated the involvement of oxidative stress. The identification of familial PD-associated genes offers the opportunity to study mechanisms of PD pathogenesis in model organisms. Here, we show that DJ-1A, a
Drosophila
homologue of the familial PD-associated gene DJ-1, plays an essential role in oxidative stress response and neuronal maintenance. Inhibition of DJ-1A function through RNA interference (RNAi) results in cellular accumulation of reactive oxygen species, organismal hypersensitivity to oxidative stress, and dysfunction and degeneration of dopaminergic and photoreceptor neurons. To identify other genes that may interact with DJ-1A in regulating cell survival, we performed genetic interaction studies and identified components of the phosphatidylinositol 3-kinase (PI3K)/Akt-signaling pathway as specific modulators of DJ-1A RNAi-induced neurodegeneration. PI3K signaling suppresses DJ-1A RNAi phenotypes at least in part by reducing cellular reactive oxygen species levels. Consistent with the genetic interaction results, we also found reduced phosphorylation of Akt in DJ-1A RNAi animals, indicating an impairment of PI3K/Akt signaling by DJ-1A down-regulation. Together with recent findings in mammalian systems, these results implicate impairments of PI3K/Akt signaling and oxidative stress response in DJ-1-associated disease pathogenesis. We also observed impairment of PI3K/Akt signaling in the fly
parkin
model of PD, hinting at a common molecular event in the pathogenesis of PD. Manipulation of PI3K/Akt signaling may therefore offer therapeutic benefits for the treatment of PD.
Imaging input and output of neocortical networks
in vivo
Authors: Kerr Jason N. D. , Greenberg David , Helmchen Fritjof
Published: September 2005

Neural activity manifests itself as complex spatiotemporal activation patterns in cell populations. Even for local neural circuits, a comprehensive description of network activity has been impossible so far. Here we demonstrate that two-photon calcium imaging of bulk-labeled tissue permits dissection of local input and output activities in rat neocortex
in vivo
. Besides astroglial and neuronal calcium transients, we found spontaneous calcium signals in the neuropil that were tightly correlated to the electrocorticogram. This optical encephalogram (OEG) is shown to represent bulk calcium signals in axonal structures, thus providing a measure of local input activity. Simultaneously, output activity in local neuronal populations could be derived from action potential-evoked calcium transients with single-spike resolution. By using these OEG and spike activity measures, we characterized spontaneous activity during cortical Up states. We found that (
i
) spiking activity is sparse (<0.1 Hz); (
ii
) on average, only ≈10% of neurons are active during each Up state; (
iii
) this active subpopulation constantly changes with time; and (
iv
) spiking activity across the population is evenly distributed throughout the Up-state duration. Furthermore, the number of active neurons directly depended on the amplitude of the OEG, thus optically revealing an input-output function for the local network. We conclude that spontaneous activity in the neocortex is sparse and heterogeneously distributed in space and time across the neuronal population. The dissection of the various signal components in bulk-loaded tissue as demonstrated here will enable further studies of signal flow through cortical networks.
An interaction between αvβ8 integrin and Band 4.1B via a highly conserved region of the Band 4.1 C-terminal domain
Authors: McCarty Joseph H. , Cook Aaron A. , Hynes Richard O.
Published: September 2005

αvβ8 integrin is highly expressed in the vertebrate CNS, and mice lacking the αv or β8 genes develop cerebral hemorrhage due to defective interactions between blood vessels and αvβ8-expressing neural cells. Although αvβ8 binds many of the same extracellular matrix protein ligands as other integrins, very little is known about the intracellular signal transduction events used by αvβ8 to regulate CNS development. Here we identify Band 4.1B as an intracellular factor that interacts selectively with the β8 cytoplasmic tail. The association with αvβ8 occurs via the band 4.1B C-terminal domain, a region highly conserved among the various Band 4.1 family members. Indeed, we show that β8 integrin interacts directly with the C-terminal domains of several Band 4.1 proteins and colocalizes with them in cultured astrocytes and in the brain. These data identify a previously uncharacterized interaction between an integrin and Band 4.1 family members and suggest an important functional role for αvβ8-Band 4.1 interactions in the development and maintenance of the CNS.
Defined DNA/nanoparticle conjugates
Authors: Ackerson Christopher J. , Sykes Michael T. , Kornberg Roger D.
Published: September 2005

Glutathione monolayer-protected gold clusters were reacted by place exchange with 19- or 20-residue thiolated oligonucleotides. The resulting DNA/nanoparticle conjugates could be separated on the basis of the number of bound oligonucleotides by gel electrophoresis and assembled with one another by DNA-DNA hybridization. This approach overcomes previous limitations of DNA/nanoparticle synthesis and yields conjugates that are precisely defined with respect to both gold and nucleic acid content.
l
-citrulline and
l
-arginine supplementation retards the progression of high-cholesterol-diet-induced atherosclerosis in rabbits
Authors: Hayashi Toshio , Juliet Packiasamy A. R. , Matsui-Hirai Hisako , Miyazaki Asaka , Fukatsu Akiko , Funami Jun , Iguchi Akihisa , Ignarro Louis J.
Published: September 2005

The objective of this study was to evaluate the influence of ingested
l
-arginine,
l
-citrulline, and antioxidants (vitamins C and E) on the progression of atherosclerosis in rabbits fed a high-cholesterol diet. The fatty diet caused a marked impairment of endothelium-dependent vasorelaxation in isolated thoracic aorta and blood flow in rabbit ear artery
in vivo
, the development of atheromatous lesions and increased superoxide anion production in thoracic aorta, and increased oxidation-sensitive gene expression [Elk-1 and phosphorylated cAMP response element-binding protein]. Rabbits were treated orally for 12 weeks with
l
-arginine,
l
-citrulline, and/or antioxidants.
l
-arginine plus
l
-citrulline, either alone or in combination with antioxidants, caused a marked improvement in endothelium-dependent vasorelaxation and blood flow, dramatic regression in atheromatous lesions, and decrease in superoxide production and oxidation-sensitive gene expression. These therapeutic effects were associated with concomitant increases in aortic endothelial NO synthase expression and plasma

\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
\begin{equation*}{\mathrm{N}}{\mathrm{O}}_{2}^{-}+{\mathrm{N}}{\mathrm{O}}_{3}^{-}\end{equation*}\end{document}

and cGMP levels. These observations indicate that ingestion of certain NO-boosting substances, including
l
-arginine,
l
-citrulline, and antioxidants, can abrogate the state of oxidative stress and reverse the progression of atherosclerosis. This approach may have clinical utility in the treatment of atherosclerosis in humans.