bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of thermodynamics and kinetics of RNA reactions by force
Authors: Tinoco Ignacio , T. X. Li Pan , Bustamante Carlos
Published: October 2006

1. Introduction 326

2. Instrumentation 328

2.1 Instruments to study mechanical properties of RNA 328

2.1.1 AFM 328

2.1.2 Magnetic tweezers 328

2.1.3 Optical tweezers 330

2.2 Optical trap instrumentation 330

2.3 Calibrations 332

2.3.1 Calibration of trap stiffness 332

2.3.2 Calibration of force 333

2.3.3 Calibration of distance 334

2.4 Types of experiments 334

2.4.1 Force-ramp 334

2.4.2 Force-clamp or constant-force experiments 335

2.4.3 Extension-clamp or constant extension experiments 335

2.4.4 Force-jump, Force-drop 336

2.4.5 Passive mode 336

3. Thermodynamics 336

3.1 Reversibility 336

3.2 Gibbs free energy 337

3.2.1 Stretching free energy 338

3.2.1.1 Rigid molecules 338

3.2.1.2 Compliant or flexible molecules 339

3.2.2 Free energy of a reversible unfolding transition 339

3.2.3 Free energy of unfolding at zero force 340

3.2.4 Free energy of an irreversible unfolding transition 340

3.2.4.1 Jarzynski's method 341

3.2.4.2 Crooks fluctuation theorem 343

4. Kinetics 345

4.1 Measuring rate constants 345

4.1.1 Hopping 345

4.1.2 Force-jump, Force-drop 347

4.1.3 Force-ramp 348

4.1.4 Instrumental effects 350

4.2 Kinetic mechanisms 351

4.2.1 Free-energy landscapes 351

4.2.2 Kinetics of unfolding 353

5. Relating force-measured data to other measurements 354

5.1 Thermodynamics 354

5.2 Kinetics 357

6. Acknowledgements 357

7. References 358

Single-molecule methods have made it possible to apply force to an individual RNA molecule. Two beads are attached to the RNA; one is on a micropipette, the other is in a laser trap. The force on the RNA and the distance between the beads are measured. Force can change the equilibrium and the rate of any reaction in which the product has a different extension from the reactant. This review describes use of laser tweezers to measure thermodynamics and kinetics of unfolding/refolding RNA. For a reversible reaction the work directly provides the free energy; for irreversible reactions the free energy is obtained from the distribution of work values. The rate constants for the folding and unfolding reactions can be measured by several methods. The effect of pulling rate on the distribution of force-unfolding values leads to rate constants for unfolding. Hopping of the RNA between folded and unfolded states at constant force provides both unfolding and folding rates. Force-jumps and force-drops, similar to the temperature jump method, provide direct measurement of reaction rates over a wide range of forces. The advantages of applying force and using single-molecule methods are discussed. These methods, for example, allow reactions to be studied in non-denaturing solvents at physiological temperatures; they also simplify analysis of kinetic mechanisms because only one intermediate at a time is present. Unfolding of RNA in biological cells by helicases, or ribosomes, has similarities to unfolding by force.
Re-examining the Johannine Trinity: perichoresis or deification?
Authors: Crump David
Published: October 2006

Theological discussions of perichoretic trinitarianism typically turn to John's Gospel for supporting evidence despite the fact that John nowhere describes the Spirit's so-called ‘interpenetration’ (A is in B and B is in A) of either the Father or the Son. In this article, all gospel references pertinent to questions of perichoretic union among Father, Son and Spirit are examined, demonstrating that the Johannine Spirit does not share in such mutual indwelling. Rather, the Spirit is inextricably linked to Johannine ecclesiology, performing the work of regeneration and illumination as Christ's earthly alter ego. John's pneumatology is thoroughly functional and salvation-historical, offering no insight into the Spirit's eternal or essential place within the Godhead. However, John's Gospel does describe a third member of a perichoretic trinity: the disciples. As surprising as it may initially appear, believers are said to mutually indwell the Son, and to indwell the Father through the Son, thereby occupying the very position never posited of the Holy Spirit. Although John does not describe a perichoretic trinity, he does depict a perichoretic soteriology reminiscent of the Orthodox doctrine of deification. Such divine union is at the heart of Johannine salvation. It remains a crowning achievement of Johannine theology that Jesus is portrayed as the one sent from the Father to lead his people into a provocative, new terrain where the language of perichoretic union with the divine is more apropos of the believer than of the Spirit.
The large-moon hypothesis: can it be tested?
Authors: Waltham Dave
Published: October 2006

The large-moon hypothesis states that planetary habitability is enhanced by the presence of a large satellite. This controversial proposal is linked to the equally controversial idea that the axial stability of a planet also enhances habitability. Previous work has shown that, far from encouraging axial stability, large moons actually destabilize obliquity when the effects of tidal drag on the planetary spin rate are taken into account. However, our Moon's mass is remarkably close to the upper limit allowed by axial stability, suggesting that the large-moon hypothesis is actually correct but constrained by an independent requirement for axial stability. This conclusion can be tested by looking at the typical separations between large exo-planets because axial stability is more likely in planetary systems with widely spaced gas giants. Thus, if axial stability really does enhance habitability, Jupiter and Saturn should be unusually widely spaced. This can be tested using data expected from gravitational microlensing planet-search surveys. Unfortunately, in the event of a negative result from this test, it is not possible to distinguish whether this results from large moons and stable axes being unimportant for life or results from large moons and stable axes being widespread.
Oceanic hypervelocity impact events: a viable mechanism for successful panspermia?
Authors: Milner D.J. , Burchell M.J. , Creighton J.A. , Parnell J.
Published: October 2006

The idea that life migrates naturally between planetary bodies has grown in strength in recent years. This idea (panspermia) is believed to be possible via the mechanism of impact events. Previous research on this topic has concentrated on small meteoroids (micrometres to centimetres in diameter), with giant objects (metres to kilometres in diameter) being relatively ignored. This is due to the common belief that the larger objects vaporize on impact with the Earth's surface, which in most studies is taken as rock. Here we examine experimentally whether hypervelocity impacts into water result in significant survival of the impactors. For this study the University of Kent's two-stage light gas gun was used to accelerate millimetre-sized shale projectiles obliquely into a relatively deep water layer, at approximately 5 km s−1. Two shots have been made with surviving fragments being recovered from each. The surviving fragments appear highly shocked and display clear signs of cracking. The fragments that have been isolated contribute to a significant percentage (~10%) of the original unfired projectile mass and are as large as ~20% of the original projectile diameter. This indicates that oceanic hypervelocity impact events of large asteroids may deliver significant volumes of solid material to the Earth and thus provide a possible mechanism for successful panspermia.
Intake of Vitamin A and Carotenoids from the Italian Population – Results of an Italian Total Diet Study
Authors: Lucarini Massimo , Lanzi Sabina , D’Evoli Laura , Aguzzi Altero , Lombardi-Boccia Ginevra
Published: October 2006

The present study focused on vitamin A and carotenoids (α-and β-carotene, lutein and zeaxanthin, β-cryptoxanthin, lycopene) daily intake from the Italian total diet. The input of some food groups (cereals, vegetables, fruits, milk and dairy, meat and meat products, fish) most responsible for major and minor contributions to the daily intake of these molecules was evaluated. Furthermore the contribution to the dietary intake of β-carotene and lutein of the most consumed vegetables in the market basket of the Italian total diet (beets, brassica vegetables, carrots, chicory, courgette (zucchini), green beans, lettuce, peas, pepper, spinach, tomatoes) was also investigated. Vitamin A daily intake was 855 mg/person/day. The vegetables food group made the greatest contribution (37%), followed by the meat and meat products food group (23%). The Italian total diet provided 14.3 mg/person/day of carotenoids; lycopene was the highest (7.4 mg/day), followed by lutein + zeaxanthin (4 mg/day), β-carotene (2.6 mg/day), α-carotene (0.15 mg/day), and β-cryptoxanthin (0.17 mg/day). Carrots and tomatoes were the main sources of β-carotene in the diet, otherwise the daily consumption of leafy vegetables (spinach, beets, lettuce) made the main contribution to lutein + zeaxanthin daily intake.
Dietary Calcium Supplementation Suppresses Bone Formation in Magnesium-Deficient Rats
Authors: Matsuzaki Hiroshi , Miwa Misao
Published: October 2006

The purpose of this study was to clarify the effects of dietary calcium (Ca) supplementation on bone metabolism of magnesium (Mg)-deficient rats. Male Wistar rats were randomized by weight into three groups, and fed a control diet (control group), a Mg-deficient diet (Mg- group) or a Mg-deficient diet having twice the control Ca concentrations (Mg-2Ca group) for 14 days. Trabecular bone volume was significantly lower in the Mg - and Mg-2Ca groups than in the control group. Trabecular number was also significantly lower in the Mg - and Mg-2Ca groups than in the control group. Mineralizing bone surface, mineral apposition rate (MAR), and surface referent bone formation rate (BFR/BS) were significantly lower in the Mg - and Mg-2Ca groups than in the control group. Furthermore, MAR and BFR/BS were significantly lower in the Mg-2Ca group than in the Mg - group. These results suggest that dietary Ca supplementation suppresses bone formation in Mg-deficient rats.
Plasma Resistin, Insulin Concentration in Non-Diabetic and Diabetic, Overweight/Obese Thai
Authors: Chanchay Siriporn , Tungtrongchitr Rungsunn , Harnroongroj Talabporn , Phonrat Benjaluck , Rungseesakorn Orapin , Paksanont Suporn , Pooudong Somchai , Saowakontha Sastri , Varongchayakul Chusak
Published: October 2006

This study investigated levels of fasting plasma glucose (FBS), homeostasis model of the assessment of the insulin resistance (HOMA), lipid profile, insulin, and resistin hormones in 202 individuals, divided into four groups. Two groups had type II diabetes mellitus (DM): one group had been overnourished (DM/OB) (body mass index: BMI equal or above 25) and the other had not (DM/nOB). Two additional groups not suffering from diabetes were either overnourished (nDM/OB) or of normal nutritional status (nDM/nOB). Only the DM/OB group had insulin levels elevated above the other three groups. Resistin levels had been lowest in the nDM/nOB group. When participants of the two nOB groups were pooled into one group and the subjects of the two OB groups were combined into another group, the median plasma resistin levels of the OB groups were significantly higher compared with the nOB groups. Likewise the DM groups had higher resistin levels than the nDM groups. A significant correlation of plasma resistin with BMI, waist circumference, waist-to-hip ratio, FBS, and HOMA score had been observed. The result suggests that plasma resistin has a role in linking central obesity and obesity-related insulin resistance to type II diabetes mellitus.
The Effect of Repeated Blood Donations on the Iron Status of Iranian Blood Donors Attending the Iranian Blood Transfusion Organization
Authors: Djalali Mahmoud , Neyestani Tirang R. , Bateni Jamil , Siassi Fereydoun
Published: October 2006

Objective: Blood donation leads to substantial iron loss, as about 0.5 mg iron is lost per each milliliter of blood donated. If not compensated for efficiently, the iron loss may eventually lead to anemia, though non-anemic iron deficiency per se may be problematic. The aim of this study was to evaluate the effects of blood donation, and its frequency over a year’s time, on iron status of Iranian male blood donors attended blood transfusion stations of the Iranian Blood Transfusion Organization (IBTO). Design and setting: A cross-sectional, descriptive, and analytic study was conducted. 91 male volunteer blood donors aged from 20 to 50 years attending three IBTO stations located in central areas of Tehran, and 63 apparently healthy controls that were matched for age, gender, monthly income, height, and weight, were included in the study. Blood donors were divided into 4 groups according to the frequency of blood donation per year; i.e. 1, 2, 3, and 4 with 20, 30, 26, and 15 persons in each group, respectively. Just before blood donation, 10 mL venous blood sample was taken and divided into heparinized and non-heparinized tubes for determination of hemoglobin (Hb), hematocrit (Hct), serum iron (SI), total iron binding capacity (TIBC), ferritin, transferrin saturation (TS), and mean corpuscular hemoglobin concentration (MCHC). Dietary assessment was also done using 3 different questionnaires; i.e. general health, food frequency, and 24hr recall. Results: The levels of Hb, Hct, and iron status indices were all significantly lower in the subjects than in controls and a gradual but significant decrease in iron status indices in each time of blood donation was found. Serum ferritin showed significant correlations with age (r = 0.33, p < 0.001) and body-mass index (BMI) (r = 0.26, p = 0.03) only in the control group. Frequency of blood donation per year was also inversely correlated with Hb (r = -0.67, p < 0.001), Hct (r = -0.65, p < 0.001), MCHC (r = -0.56, p < 0.001), serum ferritin (r = -0.38, p < 0.001), SI (r = -0.62, p < 0.001), and TS (r = -0.61, p < 0.001), but was directly correlated with TIBC (r = 0.56, p < 0.001). Interestingly in blood donors, but not in healthy controls, serum ferritin levels showed weak but statistically significant correlations with daily intake of iron (r = 0.17, p < 0.05) and energy (r = 0.20, p = 0.03). Conclusion: Though repeated blood donations might diminish iron status, it could be safe to donate 2–3 U/year without an appreciable incidence of iron deficiency, provided that the pre-donation Hb and ferritin values are ≥ 14.7 g/dL and 58.9 μg/L, respectively. The male volunteers with Hb ≥ 14.2 g/dL and serum ferritin ≥ 57.2 μg/L could donate 1–2 U/year and those with Hb ≥ 13.1 g/dL and serum ferritin ≥ 35.3 μg/L could donate just once a year. Volunteers who undergo (repeated) blood donation should receive special nutritional care, especially in terms of iron and energy.
Differential Effects of Pyrazinamide and Clofibrate on Gene Expression of Rat Hepatic a-Amino-b-Carboxymuconate-e-Semialdehyde Decarboxylase, a Key Enzyme of the Tryptophan-NAD Pathway
Authors: Egashira Yukari , Sato Makiko , Sato Mayuki , Sugawara Ryoko , Tanabe Atsushi , Shin Mariko , Sanada Hiroo
Published: October 2006

Hepatic α-amino-β-carboxymuconate-e-semialdehyde decarboxylase (ACMSD) [EC4.1.1.45] plays a key role in regulating NAD biosynthesis from tryptophan. The aim of this study was to evaluate the ACMSD mRNA expression after pyrazinamide or peroxisome proliferators ingestion. When rats were fed a control (pyrazinamide- and clofibrate-free) diet, 1% pyrazinamide- or 0.24% clofibrate-containing diets for 8 days, hepatic ACMSD activity and mRNA in rats consuming the clofibrate-containing diet was strongly suppressed, as compared with those fed the control and pyrazinamide diet. Pyrazinamide suppressed liver and kidney ACMSD activities, but did not affect ACMSD mRNA. Blood NAD was increased in the clofibrate and pyrazinamide groups. Shifting from the control diet to a clofibrate diet suppressed ACMSD mRNA strongly at day 1 and continued through day 4. However ACMSD activity decreased gradually. In rats fed with several kinds of peroxisome-proliferator-containing diets such as phthalate ester, bezafibrate, Wy-14,643, 2-(-4-chlorophenoxy) propionic acid, or dehydroisoandrosterone for 8 days, hepatic ACMSD mRNA was drastically decreased by all the peroxisome proliferators. These results suggest that the transcription level of hepatic ACMSD is modulated by peroxisome proliferators, and the fluctuation of the hepatic ACMSD mRNA expression was followed by that of the ACMSD activity. However, pyrazinamide does not affect the transcription level of hepatic ACMSD.
A new method to investigate hyperspectral image cubes: An application of the wavelet transform
Authors: Gendrin Aline , Langevin Yves , Bibring Jean‐Pierre , Forni Olivier
Published: October 2006

Data analysis of the Observatoire pour la Minéralogie, l'Eau, les Glaces, et l'Activité (OMEGA), the imaging spectrometer aboard Mars Express, necessitates the use of techniques able to extract the relevant information of large data sets. Numerous efficient algorithms have already been developed for similar purposes for terrestrial imaging spectrometers such as the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS). We propose here a complementary method based on the wavelet transform. Our algorithm allows the detection of the absorption bands in each spectrum and returns their position, width, and depth. We use it either to study separately the properties of each absorption band or as a classification method, grouping together the pixels whose spectra contain the same absorption bands. We test our algorithm on an AVIRIS observation of Mauna Kea, Hawaii. The method identifies the dominant mineralogy of this area: variability in the ferric and ferrous mineralogy and several types of phyllosilicates. We also study six Martian observation sessions acquired by the Infrared Spectrometer for Mars onboard Phobos 2. We identify ferric and ferrous absorption bands in the data set and variations in the ferrous mineralogy corresponding to different proportions of high and low calcium pyroxene. Finally, we apply our technique to the first 6 months of Mars surface observation by OMEGA/Mars Express, resampled on a 1° × 1° grid. We thus retrieve the global large‐scale variability of the OMEGA data set and identify a global spectral discrepancy inside Martian dark regions which corresponds to the spectral difference between type I and type II terrains previously identified by the Thermal Emission Spectrometer.
What determines altocumulus dissipation time?
Authors: Larson Vincent E. , Smith Adam J. , Falk Michael J. , Kotenberg Kurt E. , Golaz Jean‐Christophe
Published: October 2006

This paper asks what factors influence the dissipation time of altocumulus clouds. The question is addressed using three‐dimensional, large‐eddy simulations of a thin, midlevel cloud that was observed by aircraft. The cloud might be aptly described as “altostratocumulus” because it was overcast and contained radiatively driven turbulence. The simulations are used to construct a budget equation of cloud water. This equation allows one to directly compare the four processes that diminish liquid: diffusional growth of ice crystals, large‐scale subsidence, radiative heating, and turbulent mixing of dry air into the cloud. Various sensitivity studies are used to find the “equivalent sensitivity” of cloud decay time to changes in various parameters. A change from no sunlight to direct overhead sunlight decreases the lifetime of our simulated cloud as much as increasing subsidence by 1.2 cm s−1, increasing ice number concentration by 780 m−3, or decreasing above‐cloud total water mixing ratio by 0.60 g kg−1. Finally, interactions among the terms in the cloud water budget are summarized in a “budget term feedback matrix.” It is able to diagnose, for instance, that in our particular simulations, the diffusional growth of ice is a negative feedback.
Dynamic error estimation for radio occultation bending angles retrieved by the full spectrum inversion technique
Authors: Lohmann Martin S.
Published: October 2006

Application of any measurement requires reliable error estimates; this is particularly the case when meteorological observations are assimilated into numerical weather prediction models. Radio occultation measurement errors vary considerably between different observations. It is therefore desirable to estimate these errors dynamically on a profile‐to‐profile basis. In this study it is demonstrated that fluctuations in the full spectrum inversion (FSI) log amplitude can be mapped into profiles of error standard deviations for FSI retrieved bending angles on a profile‐to‐profile basis without using any external data. The performance of this technique is assessed by applying it to simulated GPS radio occultation signals sampled at 50 Hz with both severe additive noise and significant phase noise. In both cases, good agreement between predicted error profiles and the “true” error profiles is achieved. Comparisons between power spectra of predicted errors and “true” errors also show good agreement. However, a small part of the simulated signals is distorted by aliasing due to the downsampling to 50 Hz, which affects bending angles retrieved for a narrow range of impact parameters. For these bending angles, the predicted errors are too small as compared with the “true” errors. This shows that the proposed technique cannot predict errors related to poor signal acquisition.
Particle lifting at the soil‐air interface by atmospheric pressure excursions in dust devils
Authors: Balme Matthew , Hagermann Axel
Published: October 2006

Dust devils, small‐scale convective vortices found on Earth and on Mars, can transfer substantial quantities of dust from the ground into the atmosphere. It has been proposed that the low‐pressure region found at the center of dust devil vortices provides a lift (the ‘ΔP’ effect) that ‘sucks up’ material from the surface. Two simple models are compared to investigate the physics behind the ΔP effect and the relevance of competing processes. The first considers an impermeable bed of particles where lifting is by vertical pressure gradients, the second considers a permeable bed where lifting is by drag forces on the particles as gas is sucked from the bed. Pressure gradient lifting appears to be far more efficient than drag force lifting. We describe conditions that favor lifting by the ΔP effect and make qualitative predictions that might be tested in the laboratory, the field, or through observations from Mars Landers.
Recent trends in sea level pressure in the Indian Ocean region
Authors: Copsey Dan , Sutton Rowan , Knight Jeff R.
Published: October 2006

During the second half of the twentieth century the Indian Ocean exhibited a rapid rise in sea surface temperatures (SST). It has been argued ‐ largely on the basis of experiments with atmospheric GCMs ‐ that this rapid warming was an important cause of remote changes in climate, in particular an increasing trend in the North Atlantic Oscillation Index and decreases in African rainfall. Here however we present evidence that the Indian Ocean warming was associated with local increases in sea level pressure (SLP). These increases are inconsistent with results from experiments in which an atmospheric GCM is forced by historical SST, which show robust decreases in SLP. The clear discrepancy between the observed and simulated trends in SLP suggests that the response of some atmospheric GCMs to the Indian Ocean warming may not provide a reliable guide to the behaviour of the real world.
Streamflow trends in western Britain
Authors: Dixon Harry , Lawler Damian M. , Shamseldin Asaad Y.
Published: October 2006

Concerns about recent river flow changes are increasing, given their importance for water management, flooding, drought mitigation, and geomorphological and ecological processes. For the first time, this paper develops a full picture of recent streamflow trends over the period 1962–2001 for western Britain across the entire flow spectrum, at annual and seasonal resolutions, for 56 gauging stations and three study periods. Annual and seasonal trends are calculated and mapped using the non‐parametric Mann‐Kendall test with bootstrap resampling. Several significant, mainly positive, trends are observed at high and low flows, while mean flows are relatively stable. A marked east‐west gradient of streamflow trend emerges, with more significant and positive trends in the mountainous west, particularly for autumn and winter high flows. Positive annual low flow trends are found across western Wales, largely driven by increasing summer base flow. Many trends are consistent with previously observed rainfall and North Atlantic Oscillation (NAO) changes.
Estimating canopy snow unloading timescales from daily observations of albedo and precipitation
Authors: MacKay Murray D. , Bartlett Paul A.
Published: October 2006

A method is proposed to estimate canopy snow unloading timescales from conventional daily observations of precipitation and above canopy albedo. If the unloading process is assumed to be purely exponential in time, then the Laplace convolution theorem can be exploited to obtain the timescale without the necessity of solving an inverse transform. The method is illustrated with a simple analytic example, and then used to evaluate the unloading timescales of mature stands of Jack Pine and Black Spruce in the Canadian boreal forest. Simulations of these stands with a land surface model for a single winter season yielded better results with the new observed estimates of about 2 days, compared with the model's default value of 10 days.
When and where might climate change be detectable in UK river flows?
Authors: Wilby R. L.
Published: October 2006

The Mann‐Kendall statistic is used to investigate trends in homogeneous rainfall and river flow records since the 1860s for 15 basins in the UK. The relationship between the strength of trend and detection time is then explored for seasonal and annual flows. Here it is shown that, under widely assumed climate change scenarios, expected trends in UK summer river flows will seldom be detectable within typical planning horizons (the 2020s). Even where climate driven changes may already be underway, losses in deployable resources will have to be factored into long‐term water plans long before they are statistically detectable. Rather than an excuse for inaction, such insights should inform more sophisticated approaches to environmental monitoring, climate change detection and adaptation.
Multimodel simulations of carbon monoxide: Comparison with observations and projected near‐future changes
Authors: Shindell D. T. , Faluvegi G. , Stevenson D. S. , Krol M. C. , Emmons L. K. , Lamarque J.‐F. , Pétron G. , Dentener F. J. , Ellingsen K. , Schultz M. G. , Wild O. , Amann M. , Atherton C. S. , Bergmann D. J. , Bey I. , Butler T. , Cofala J. , Collins W. J. , Derwent R. G. , Doherty R. M. , Drevet J. , Eskes H. J. , Fiore A. M. , Gauss M. , Hauglustaine D. A. , Horowitz L. W. , Isaksen I. S. A. , Lawrence M. G. , Montanaro V. , Müller J.‐F. , Pitari G. , Prather M. J. , Pyle J. A. , Rast S. , Rodriguez J. M. , Sanderson M. G. , Savage N. H. , Strahan S. E. , Sudo K. , Szopa S. , Unger N. , van Noije T. P. C. , Zeng G.
Published: October 2006

We analyze present‐day and future carbon monoxide (CO) simulations in 26 state‐of‐the‐art atmospheric chemistry models run to study future air quality and climate change. In comparison with near‐global satellite observations from the MOPITT instrument and local surface measurements, the models show large underestimates of Northern Hemisphere (NH) extratropical CO, while typically performing reasonably well elsewhere. The results suggest that year‐round emissions, probably from fossil fuel burning in east Asia and seasonal biomass burning emissions in south‐central Africa, are greatly underestimated in current inventories such as IIASA and EDGAR3.2. Variability among models is large, likely resulting primarily from intermodel differences in representations and emissions of nonmethane volatile organic compounds (NMVOCs) and in hydrologic cycles, which affect OH and soluble hydrocarbon intermediates. Global mean projections of the 2030 CO response to emissions changes are quite robust. Global mean midtropospheric (500 hPa) CO increases by 12.6 ± 3.5 ppbv (16%) for the high‐emissions (A2) scenario, by 1.7 ± 1.8 ppbv (2%) for the midrange (CLE) scenario, and decreases by 8.1 ± 2.3 ppbv (11%) for the low‐emissions (MFR) scenario. Projected 2030 climate changes decrease global 500 hPa CO by 1.4 ± 1.4 ppbv. Local changes can be much larger. In response to climate change, substantial effects are seen in the tropics, but intermodel variability is quite large. The regional CO responses to emissions changes are robust across models, however. These range from decreases of 10–20 ppbv over much of the industrialized NH for the CLE scenario to CO increases worldwide and year‐round under A2, with the largest changes over central Africa (20–30 ppbv), southern Brazil (20–35 ppbv) and south and east Asia (30–70 ppbv). The trajectory of future emissions thus has the potential to profoundly affect air quality over most of the world's populated areas.
Latitudinal dependency in dust devil activity on Mars
Authors: Whelley Patrick L. , Greeley Ronald
Published: October 2006

There are more dust devils (dd; inferred from dust devil tracks, or ddt) in the southern hemisphere than in the north. Ddt suggest that the dd season starts in late spring (Ls = 60° and 240°, northern and southern hemispheres, respectively) and continues through the summer into mid fall (Ls = 210° and 30°, northern and southern hemispheres, respectively). However, the ddt density in the southern hemisphere averages ∼0.6 ddt/km2, while the northern hemisphere averages ∼0.06 ddt/km2, or an order of magnitude less. This is attributed to the observation that in southern summer the surface receives 40% more solar energy for atmospheric motion and dd formation than the surface in the northern summer, due to the eccentricity of Mars' orbit.
Size and shape effects on excitons and biexcitons in single InAs∕InP quantum dots
Authors: Chauvin N. , Salem B. , Bremond G. , Guillot G. , Bru-Chevallier C. , Gendry M.
Published: October 2006

Single InAs quantum dots grown on an InP vicinal substrate are studied using polarized microphotoluminescence. The study of electron-hole exchange energy splitting reveals that the energy splitting is influenced by quantum confinement. The biexciton binding energies found for single dots grown on the vicinal substrate (around 2.4meV) are high as compared to those of dots grown on an InP(001) substrate and this is attributed to a difference in spatial confinement. Moreover, the quantum dot size is shown to influence directly the biexciton binding energy.
Full characterization and analysis of a terahertz heterodyne receiver based on a NbN hot electron bolometer
Authors: Hajenius M. , Baselmans J. J. A. , Baryshev A. , Gao J. R. , Klapwijk T. M. , Kooi J. W. , Jellema W. , Yang Z. Q.
Published: October 2006

We present a complete experimental characterization of a quasioptical twin-slot antenna coupled small area (1.0×0.15μm2) NbN hot electron bolometer (HEB) mixer compatible with currently available solid state tunable local oscillator (LO) sources. The required LO power absorbed in the HEB is analyzed in detail and equals only 25nW. Due to the small HEB volume and wide antenna bandwidth, an unwanted direct detection effect is observed which decreases the apparent sensitivity. Correcting for this effect results in a receiver noise temperature of 700K at 1.46THz. The intermediate frequency (IF) gain bandwidth is 2.3GHz and the IF noise bandwidth is 4GHz. The single channel receiver stability is limited to 0.2–0.3s in a 50MHz bandwidth.
Potential energy surfaces for small alcohol dimers I: Methanol and ethanol
Authors: Rowley Richard L. , Tracy Christopher M. , Pakkanen Tapani A.
Published: October 2006

Potential energy landscapes for homogeneous dimers of methanol and ethanol were calculated using counterpoise (CP) corrected energies at the MP2∕6-311+G(2df,2pd) level. The landscapes were sampled at approximately 15 dimer separation distances for different relative monomer geometries, or routes, given in terms of a relative monomer yaw, pitch, and roll and the spherical angles between the monomer centers (taken as the C atom attached to the O). The 19 different routes studied for methanol and the 22 routes examined for ethanol include 607 CP corrected energies. Both landscapes can be adequately represented by site-site, pairwise-additive models, suitable for use in molecular simulations. A modified Morse potential is used for the individual pair interactions either with or without point charges to represent the monomer charge distribution. A slightly better representation of the methanol landscape is obtained using point charges, while the potential energy landscape of ethanol is slightly better without point charges. This latter representation may be computationally advantageous for molecular simulations because it avoids difficulties associated with long-range effects of point-charge-type models.
Nanoscale resolution microchannel flow velocimetry by atomic force microscopy
Authors: Piorek Brian , Mechler Ádám , Lal Ratnesh , Freudenthal Patrick , Meinhart Carl , Banerjee Sanjoy
Published: October 2006

The velocity of a microchannel flow was determined by atomic force microscopy (AFM) using a 50nm wide “whisker,” which was partially submerged and scanned transverse to the flow while drag was recorded. A peaked, near parabolic, flow velocity profile was found. Particle image velocity (PIV) measurements using 70nm diameter quantum-dot-coated polystyrene spheres confirmed the shape of the AFM-measured velocity profile. AFM-based nanometer resolution velocimetry confirms that the drag-velocity relationship for the whisker remains consistent over a wide range of shear values and appears to successfully resolve submicron scale flows, which are beyond the limits of conventional PIV measurements.
Adsorption of diblock copolymers on stripe-patterned surfaces
Authors: Sumithra K. , Straube E.
Published: October 2006

We present the results of extensive Monte Carlo simulations of diblock copolymers adsorbed on stripe-patterned surfaces of various widths. We have found that the width of the stripe pattern is an important parameter which dictates favorable recognition on the surface. For certain stripe widths, the adsorption of diblock copolymers to striped surfaces exhibits two transitions. The process involves recognition of the surface pattern by the diblock copolymer which follows a two step process in which the first block getting adsorbed to the appropriate pattern on the surface, without any recognition of the surface pattern, followed by the adsorption of the second block, where a reorganization process happens. For small widths and also for higher widths, the chain behaves just like a homopolymer where the twofold adsorbing process changes to the typical homopolymer adsorption. We have also found that there exists an optimal width of the stripes, independent of the chain length, where the recognition on the surface pattern is most favored. The characteristic temperature of the adsorption of the second block with weaker interactions is found to be independent of the chain length at this optimal width, proving that only local rearrangements take place after the first step. Some of our results describing the thermodynamics compare very well with the recent semianalytical approach of Kriksin et al. [J. Chem. Phys. 122, 114703 (2005)] on multiblock copolymers on heterogeneous surfaces. We also present some interesting conformational properties of the copolymer chain near the stripe-patterned surface.
Te marine algae of Lord Howe Island (NSW): The dictyotales and Cutleriales (Phaeophyta).
Authors: Allender BM , Kraft GT
Published: October 2006

Lord Howe Island (31�33'S., lat.; 159�05'E. long.) lies c. 600 km east of the Australian
mainland and is fringed by the world's southernmost coral reefs. It possesses a rich
marine flora which is heavily dominated by brown algae of the order Dictyotales, of
which 22 species in 11 genera occur on the island. Most species show tropical affinities,
although several have restricted occurrences on the central eastern seaboard of the
continent in addition to Lord Howe, and a few are recorded from the Kermadec Islands
some 2150 km further east. Two species (Distromium didymothrix; Pachydictyon
aegerrime) and two varieties (Stypopodium flabelliforme var. rhabdoides; Dictyota
bartayresii var. plectens) are described as new and are at present known only from the
island, while Padina boergesenii has been erected for a well known Caribbean species
also found at Lord Howe and which, following examination of type material, can no
longer be properly referred to P. gymnospora (Kuetz.) Vickers. Two new combinations
[Stypopodium australasicum (Zan.) Allender & Kraft; Dilophus intermedius (Zan.)
Allender & Kraft] are also made. The order Cutleriales is represented at Lord Howe by
a single newly described species, Cutleria mollis, whose abundant sporophytic
(Aglaozonia) stage is very Zonaria-like in habit.
The genomic landscape of histone modifications in human T cells
Authors: Roh Tae-Young , Cuddapah Suresh , Cui Kairong , Zhao Keji
Published: October 2006

To understand the molecular basis that supports the dynamic gene expression programs unique to T cells, we investigated the genomic landscape of activating histone modifications, including histone H3 K9/K14 diacetylation (H3K9acK14ac), H3 K4 trimethylation (H3K4me3), and the repressive histone modification H3 K27 trimethylation (H3K27me3) in primary human T cells. We show that H3K9acK14ac and H3K4me3 are associated with active genes required for T cell function and development, whereas H3K27me3 is associated with silent genes that are involved in development in other cell types. Unexpectedly, we find that 3,330 gene promoters are associated with all of these histone modifications. The gene expression levels are correlated with both the absolute and relative levels of the activating H3K4me3 and the repressive H3K27me3 modifications. Our data reveal that rapidly inducible genes are associated with the H3 acetylation and H3K4me3 modifications, suggesting they assume a chromatin structure poised for activation. In addition, we identified a subpopulation of chromatin regions that are associated with high levels of H3K4me3 and H3K27me3 but low levels of H3K9acK14ac. Therefore, these regions have a distinctive chromatin modification pattern and thus may represent a distinct class of chromatin domains.
T cell receptor for antigen induces linker for activation of T cell–dependent activation of a negative signaling complex involving Dok-2, SHIP-1, and Grb-2
Authors: Dong Shen , Corre Béatrice , Foulon Eliane , Dufour Evelyne , Veillette André , Acuto Oreste , Michel Frédérique
Published: October 2006

Adaptor proteins positively or negatively regulate the T cell receptor for antigen (TCR) signaling cascade. We report that after TCR stimulation, the inhibitory adaptor downstream of kinase (Dok)-2 and its homologue Dok-1 are involved in a multimolecular complex including the lipid phosphatase Src homology 2 domain–containing inositol polyphosphate 5′-phosphatase (SHIP)-1 and Grb-2 which interacts with the membrane signaling scaffold linker for activation of T cells (LAT). Knockdown of LAT and SHIP-1 expression indicated that SHIP-1 favored recruitment of Dok-2 to LAT. Knockdown of Dok-2 and Dok-1 revealed their negative control on Akt and, unexpectedly, on Zap-70 activation. Our findings support the view that Dok-1 and -2 are critical elements of a LAT-dependent negative feedback loop that attenuates early TCR signal. Dok-1 and -2 may therefore exert a critical role in shaping the immune response and as gatekeepers for T cell tolerance.
The Hsp70 member, Ssa1, acts as a DNA‐binding transcriptional co‐activator of laccase in Cryptococcus neoformans
Authors: Zhang Shirong , Hacham Moshe , Panepinto John , Hu Guowu , Shin Soowan , Zhu Xudong , Williamson Peter R.
Published: October 2006

Hsp70 proteins are a well‐known class of chaperones that have also been described to have roles in cellular regulation. Here, we show that a Cryptococcus neoformans Hsp70 homologue Ssa1 acts as a DNA‐binding transcriptional co‐activator of the fungal virulence factor, laccase, via binding to a GC‐rich element within the 5′‐UAS in response to glucose starvation, iron, copper, calcium and temperature. In addition, Ssa1 forms a regulatory complex with heat shock transcription factor and TATA‐binding protein during laccase induction. Furthermore, deletion of Ssa1 results in reduced laccase and attenuated virulence using a mouse model. These results indicate that Hsp70 functions as a stress‐related transcriptional co‐activator required for fungal virulence.
Integration of omics data: how well does it work for bacteria?
Authors: De Keersmaecker Sigrid C. J. , Thijs Inge M. V. , Vanderleyden Jos , Marchal Kathleen
Published: October 2006

In the current omics era, innovative high‐throughput technologies allow measuring temporal and conditional changes at various cellular levels. Although individual analysis of each of these omics data undoubtedly results into interesting findings, it is only by integrating them that gaining a global insight into cellular behaviour can be aimed at. A systems approach thus is predicated on data integration. However, because of the complexity of biological systems and the specificities of the data‐generating technologies (noisiness, heterogeneity, etc.), integrating omics data in an attempt to reconstruct signalling networks is not trivial. Developing its methodologies constitutes a major research challenge. Besides for their intrinsic value towards health care, environment and industry, prokaryotes are ideal model systems to further develop these methods because of their lower regulatory complexity compared with eukaryotes, and the ease with which they can be manipulated. Several successful examples outlined in this review already show the potential of the systems approach for both fundamental and industrial applications, which would be time‐consuming or impossible to develop solely through traditional reductionist approaches.
Evaluation of adhesion to buccal epithelial cells in Candida species obtained from denture wearers after exposure to fluconazole
Authors: Pereira Lyon Juliana , De Resende Maria Aparecida
Published: October 2006

The aim of this study was to assess the adhesion ability by Candida spp. obtained from denture wearer patients with and without denture stomatitis and the possible reduction in adhesion after exposure to fluconazole. Nine C. tropicalis, five C. glabrata and two C. parapsilosis obtained from the oral cavity of patients with denture stomatitis and 11 C. tropicalis, nine C. glabrata and six C. parapsilosis obtained from the oral cavity of denture wearers with normal palatal mucosa were compared for adhesion ability to buccal epithelial cells (BEC) and reduction in adhesion after exposure to fluconazole. Candida spp. obtained from denture stomatitis patients were more adherent to BEC, and there was a reduction in adhesion after exposure to fluconazole in all the species tested. Our results demonstrated that exposure to fluconazole reduces Candida spp. adherence to BEC. These results also suggest that adhesion, even in non‐albicans species, could be factors that, along with predisposing conditions related to the host, determine if an individual will develop disease or remain as a healthy carrier and confirm that fluconazole has an impact in the adherence ability in Candida spp.
Efficacy and safety of a new single‐dose terbinafine 1% formulation in patients with tinea pedis (athlete's foot): a randomized, double‐blind, placebo‐controlled study
Authors: Ortonne JP , Korting HC , Viguié‐Vallanet C , Larnier C , Savaluny E
Published: October 2006

Background  Tinea pedis is a common dermatophyte infection with frequent recurrences. Terbinafine (presently used as a 1‐week topical treatment of tinea pedis) is now available in a novel topical solution (film‐forming solution – FFS), developed to allow single application.

Objectives  To demonstrate the efficacy and safety of terbinafine 1% FFS in a randomized, double‐blind, placebo‐controlled, phase III trial, and to determine relapse or re‐infection rate of tinea pedis at 12 weeks.

Patients/methods  Fifty‐four centres (27 in France; 27 in Germany) enrolled 273 evaluable patients (2 : 1 randomization). Patients applied terbinafine 1% FFS or placebo only once between, under and over the toes, soles and sides of both feet. Efficacy assessments included direct microscopy, mycological culture, and clinical signs and symptoms at baseline, and at weeks 1, 6 and 12 after the single drug application.

Results  Effective treatment (negative mycology plus absent/minimal symptoms) at week 6 in the terbinafine 1% FFS group was 63%; vehicle was 17% (P  0.0001). Mycological cure was 72% in the terbinafine group and 21% in the placebo (P  0.0001) at week 6. Clinical signs/symptoms decreased significantly in the active group compared to the placebo. The self‐assessment of itching and burning sensation by the patient showed a clear reduction in symptoms starting 15 min after treatment application (this could be attributed to the cooling effect of the FFS). Recurrence (positive culture at 3 months) occurred in 12.5% of the effectively treated patients at week 6 in the terbinafine group. FFS was well tolerated.

Conclusion  Terbinafine 1% FFS, single dose application is an effective, safe and convenient treatment for tinea pedis. The relapse/re‐infection rate 3 months after the end of single‐dose therapy is similar to that previously demonstrated in a study using terbinafine 1% cream for 7 days.
Binding areas of urokinase‐type plasminogen activator–plasminogen activator inhibitor‐1 complex for endocytosis receptors of the low‐density lipoprotein receptor family, determined by site‐directed mutagenesis
Authors: Skeldal Sune , Larsen Jakob V. , Pedersen Katrine E. , Petersen Helle H. , Egelund Rikke , Christensen Anni , Jensen Jan K. , Gliemann Jørgen , Andreasen Peter A.
Published: October 2006

Some endocytosis receptors related to the low‐density lipoprotein receptor, including low‐density lipoprotein receptor‐related protein‐1A, very‐low‐density lipoprotein receptor, and sorting protein‐related receptor, bind protease‐inhibitor complexes, including urokinase‐type plasminogen activator (uPA), plasminogen activator inhibitor‐1 (PAI‐1), and the uPA–PAI‐1 complex. The unique capacity of these receptors for high‐affinity binding of many structurally unrelated ligands renders mapping of receptor‐binding surfaces of serpin and serine protease ligands a special challenge. We have mapped the receptor‐binding area of the uPA–PAI‐1 complex by site‐directed mutagenesis. Substitution of a cluster of basic residues near the 37‐loop and 60‐loop of uPA reduced the receptor‐binding affinity of the uPA–PAI‐1 complex approximately twofold. Deletion of the N‐terminal growth factor domain of uPA reduced the affinity 2–4‐fold, depending on the receptor, and deletion of both the growth factor domain and the kringle reduced the affinity sevenfold. The binding affinity of the uPA–PAI‐1 complex to the receptors was greatly reduced by substitution of basic and hydrophobic residues in α‐helix D and α‐helix E of PAI‐1. The localization of the implicated residues in the 3D structures of uPA and PAI‐1 shows that they form a continuous receptor‐binding area spanning the serpin as well as the A‐chain and the serine protease domain of uPA. Our results suggest that the 10–100‐fold higher affinity of the uPA–PAI‐1 complex compared with the free components depends on the bonus effect of bringing the binding areas on uPA and PAI‐1 together on the same binding entity.