bluuebunny/crossref_metadata_2025 huggingface dataset:
Rankine–Hugoniot relations for shocks in heterogeneous mixtures
Authors: GAVRILYUK S. L. , SAUREL R.
Published: March 2007

The conservation of mass, momentum and energy are not sufficient to close a system of jump relations for shocks propagating in a heterogeneous mixture of compressible fluids. We propose here a closed set of relations corresponding to a two-stage structure of shock fronts. At the first stage, microkinetic energy due to the relative motion of mixture components is produced at the shock front. At the second stage, this microkinetic energy disappears inducing strong variations in the thermodynamical states that reach mechanical equilibrium. The microkinetic energy produced at the shock front is estimated by using an idea developed earlier for turbulent shocks in compressible fluids. The relaxation zone between the shocked state and the equilibrium state is integrated over a thermodynamic path a justification of which is provided. Comparisons with experiments on shock propagation in a mixture of condensed materials confirm the proposed theory.
Dietary and genetic modulation of DNA repair in healthy human adults
Authors: Tyson J. , Mathers J. C.
Published: March 2007

The DNA in all cells of the human body is subject to damage continuously from exogenous agents, internal cellular processes and spontaneous decomposition. Failure to repair such damage is fundamental to the development of many diseases and to ageing. Fortunately, the vast majority of DNA damage is detected and repaired by one of five complementary DNA repair systems. However, recent studies have shown that even in healthy individuals there is a wide inter-individual variation in DNA repair capacity. Part of this variation can be accounted for by polymorphisms in the genes encoding DNA repair proteins. However, it is probable that environmental factors, including dietary exposure as well as diet–gene interactions, are also responsible for much of the difference in repair capacity between individuals. Whilst there is some evidence from human studies that generalised malnutrition or low intakes of specific nutrients may affect DNA repair, as yet there is limited understanding of the molecular mechanisms through which nutrients can modulate this key cellular process.
Mechanisms of the components of the metabolic syndrome that predispose to diabetes and atherosclerotic CVD
Authors: Eckel Robert H.
Published: March 2007

The metabolic syndrome represents a summation of obesity-driven risk factors for atherosclerotic CVD and type 2 diabetes. Definitions of the syndrome vary but in general agree closely in identifying subjects. The relationships between the metabolic syndrome and atherosclerotic CVD and diabetes also vary, with relative risks of approximately 1·5–3·0 and approximately 3·0–5·0 respectively. Insulin resistance appears to explain much of the pathophysiology of the syndrome. Both increased fatty acid flux and an excess of circulating pro-inflammatory cytokines are likely mediators. With increased waist circumference, increases in fatty acid delivery to the liver result in higher rates of hepatic glucose production and increases in the secretion of apoB-containing lipoproteins. Concomitant changes in HDL ensue, including a replacement of the cholesterol content with TAG, an accelerated clearance from the plasma and thus a reduced number of HDL particles. Typically also present are increases in small dense LDL. Hypertension in part relates to the insulin resistance, but may involve other mechanisms. Impaired fasting glucose often relates to defects in insulin secretion in addition to insulin resistance, and probably more than any other component of the syndrome predicts the increased incidence of type 2 diabetes. Although not included in the diagnostic criteria, increases in pro-inflammatory cytokines and pro-thrombotic factors, in addition to decreases in plasma adiponectin, may also contribute to the increased incidence of atherosclerotic CVD and diabetes. In general, the greater the number of metabolic syndrome components, the greater the risk for these outcomes. The cytokines and pro-thrombotic factors also appear to contribute.
Cues to overeat: psychological factors influencing overconsumption
Authors: Hetherington Marion M.
Published: March 2007

Human food intake is driven by necessity, but modern industrialized societies are characterized by food surfeit and an increasingly ‘obesogenic’ environment. This environment tends to discourage energy expenditure and to facilitate energy intake. The amount eaten in any given eating episode depends less on internal need state and more on environmental contextual factors such as the availability of highly-palatable energy-dense foods. In addition, the process of satiation can easily be disrupted by the introduction within a meal of different foods (variety effect), the presence of others (social context) and competing tasks (distraction). Properties of ingestants such as alcohol promote food intake and characteristics of individuals make them more or less susceptible to situational cues to overeat. In the present review the role of each of these environmental factors in promoting overconsumption are considered and the extent to which these factors might contribute to long-term weight regulation is discussed.
Brain responses to obesogenic diets and diet-induced obesity
Authors: Archer Zoë A. , Mercer Julian G.
Published: March 2007

Rodent models of diet-induced obesity (DIO) mimic common human obesity more accurately than obese single-gene mutation lines, such as the ob/ob mouse. Sprague-Dawley rats sourced in the UK develop obesity when fed a high-energy diet, but susceptibility to DIO is normally distributed, as might be anticipated for a polygenic trait in an outbred population, in contrast to reports in the literature using ostensibly the same strain of rats sourced in the USA. Nevertheless, the responses of these rats to solid and liquid obesogenic diets are very similar to those reported elsewhere, and this model of DIO has much to commend it as a vehicle for the mechanistic study of susceptibility to DIO, development and reversal of obesity on solid and liquid diets and the response of peripheral and central energy balance systems to the development of obesity and to the obesogenic diets themselves. In general, hypothalamic energy-balance-related systems respond to obesogenic diets and developing obesity with activity changes that appear designed to counter the further development of the obese state. However, these hypothalamic changes are apparently unable to maintain body weight and composition within normal limits, suggesting that attributes of the obesogenic diets either evade the normal regulatory systems and/or engage with reward pathways that override the homeostatic systems. Since diets are a risk factor in the development of obesity, it will be important to establish how obesogenic diets interact with energy-balance pathways and whether there is potential for diets to be manipulated with therapeutic benefit.
Affine functions and series with co-inductive real numbers
Authors: BERTOT YVES
Published: March 2007

We extend the work of A. Ciaffaglione and P. di Gianantonio on the mechanical verification of algorithms for exact computation on real numbers, using infinite streams of digits implemented as a co-inductive type. Four aspects are studied. The first concerns the proof that digit streams correspond to axiomatised real numbers when they are already present in the proof system. The second re-visits the definition of an addition function, looking at techniques to let the proof search engine perform the effective construction of an algorithm that is correct by construction. The third concerns the definition of a function to compute affine formulas with positive rational coefficients. This is an example where we need to combine co-recursion and recursion. Finally, the fourth aspect concerns the definition of a function to compute series, with an application on the series that is used to compute Euler's number e. All these experiments should be reproducible in any proof system that supports co-inductive types, co-recursion and general forms of terminating recursion; we used the COQ system (Dowek et al. 1993; Bertot and Castéran 2004; Giménez 1994).
RealLib: An efficient implementation of exact real arithmetic
Authors: LAMBOV BRANIMIR
Published: March 2007

This paper is an introduction to the RealLib package for exact real number computations. The library provides certified accuracy, but tries to achieve this at performance close to the performance of hardware floating point for problems that do not require higher precision. The paper gives the motivation and features of the design of the library and compares it with other packages for exact real arithmetic.
Preface to the special issue: Constructive analysis, types and exact real numbers
Authors: SPITTERS BAS , GEUVERS HERMAN , NIQUI MILAD , WIEDIJK FREEK
Published: March 2007

The title Constructive analysis, types and exact real numbers covers the wide field of research dealing with ‘precise’ computationson continuous structures. The adjective ‘precise’ is used here in an informal way, referring to computations where the rounding off of the output and the approximative nature of the input are explicitly taken nto account in some way.
Implementing the cylindrical algebraic decomposition within the Coq system
Authors: MAHBOUBI ASSIA
Published: March 2007

The Coq system is a Curry–Howard based proof assistant. Therefore, it contains a full functional, strongly typed programming language, which can be used to enhance the system with powerful automation tools through the implementation of reflexive tactics. We present the implementation of a cylindrical algebraic decomposition algorithm within the Coq system, whose certification leads to a proof producing decision procedure for the first-order theory of real numbers.
Bringing home the right to food in Canada: challenges and possibilities for achieving food security
Authors: Rideout Karen , Riches Graham , Ostry Aleck , Buckingham Don , MacRae Rod
Published: March 2007

We offer a critique of Canada's approach to domestic food security with respect to international agreements, justiciability and case law, the breakdown of the public safety net, the institutionalisation of charitable approaches to food insecurity, and the need for ‘joined-up’ food and nutrition policies. We examined Canada's commitments to the right to food, as well as Canadian policies, case law and social trends, in order to assess Canada's performance with respect to the human right to food. We found that while Canada has been a leader in signing international human rights agreements, including those relating to the right to food, domestic action has lagged and food insecurity increased. We provide recommendations for policy changes that could deal with complex issues of state accountability, social safety nets and vulnerable populations, and joined-up policy frameworks that could help realise the right to adequate food in Canada and other developed nations.
Association of body mass index and dietary restraint with changes in eating behaviour throughout late childhood and early adolescence: a 5-year study
Authors: Bisset Sherri , Gauvin Lise , Potvin Louise , Paradis Gilles
Published: March 2007

Objectives

To describe patterns of dietary behaviours specific to low quality snacking, fruit and vegetable, and fast food consumption during the transition from childhood to adolescence and to examine how these behaviours are associated with tendencies towards dietary restraint and the occurrence of overweight and obesity in mid-adolescence.

Design

A 5-year follow-up of self-reported eating. Hierarchical linear modelling was utilised to explore the relationship between dietary changes and body mass index (BMI) and dietary restraint while controlling for physical activity and smoking.

Setting

The sample was derived from students participating in the Quebec Heart Health Demonstration Project, and represents rural, suburban and inner city youths.

Subjects

A sample of 561 girls and 627 boys in the fourth, sixth, seventh and ninth grades.

Results

Overall the sample was characterised by a decrease in fruit and vegetable consumption and increase in low quality snacking, and a decrease in fast food consumption over the 5-year follow-up. Dietary restraint and BMI were found to be associated with dietary behaviour. Lower than average dietary restraint was associated with a lower frequency of fast food consumption and greater increase in low quality snacking over the 5-year period. Higher than average dietary restraint was associated with lesser frequency of low quality snacking at baseline. Having a BMI in the obese range was associated with more frequent fast food consumption in the fourth grade and a more rapid drop in fast food consumption across the 5-year period.

Conclusions

Dietary behaviours are associated with the psychological construct dietary restraint and with weight status in this population of adolescents.
The effects of dietary advice and vouchers on the intake of fruit and fruit juice by pregnant women in a deprived area: a controlled trial
Authors: Burr ML , Trembeth J , Jones KB , Geen J , Lynch LA , Roberts ZES
Published: March 2007

Objective

To examine the effectiveness of two methods of increasing fruit and fruit juice intake in pregnancy: midwives' advice and vouchers exchangeable for juice.

Design

Pregnant women were randomly allocated to three groups: a control group, who received usual care; an advice group, given advice and leaflets promoting fruit and fruit juice consumption; and a voucher group, given vouchers exchangeable for fruit juice from a milk delivery firm. Dietary questionnaires were administered at ~16, 20 and 32 weeks of pregnancy. Serum β-carotene was measured at 16 and 32 weeks.

Setting

An antenatal clinic in a deprived area.

Subjects

Pregnant women aged 17 years and over.

Results

The study comprised 190 women. Frequency of fruit consumption declined during pregnancy in all groups, but that of fruit juice increased substantially in the voucher group. Serum β-carotene concentration increased in the voucher group, from 106.2 to 141.8 μmol l− 1in women with measurements on both occasions (P = 0.003), decreased from 120.0 to 99.8 μmol l− 1in the control group (P = 0.005), and was unchanged in the advice group.

Conclusions

Pregnant women drink more fruit juice if they receive vouchers exchangeable for juice supplied by the milk delivery service. Midwives' advice to eat more fruit has no great effect. Providing vouchers for fruit juice is a simple method of increasing its intake in a deprived population and may be useful for other sections of the community.
What young Dutch adults say they do to keep from gaining weight: self-reported prevalence of overeating, compensatory behaviours and specific weight control behaviours
Authors: Wammes B , French S , Brug J
Published: March 2007

Objective

The aim of this study was to explore the prevalence of and differences in self-reported occasions of overeating (such as at celebrations and other parties), compensatory behaviours and specific weight gain prevention strategies among young Dutch adults according to sociodemographics and overweight status.

Design and subjects

Cross-sectional data were analysed from Dutch adults aged 20–40 years, recruited from an Internet research panel (n = 857, response rate = 76.6%). Using electronic questionnaires, self-report data were collected on sociodemographics, body mass index (BMI), occasions of overeating, compensatory behaviours, and diet and physical activity used as weight gain prevention strategies. Associations were tested using multiple linear and logistic regression analyses.

Results

Of the participants, 48.6% reported occasions of overeating at least once a week during the 4-week period, 44.6% reported compensating for these occasions and 72.9% reported engaging in dietary and physical activities specifically for weight gain prevention purposes. Only 32.1% of the respondents reported using the recommended combination of diet and physical activity as a weight gain prevention strategy. In addition, results showed that overweight people (BMI ≥ 25 kg m-2) and women were more likely to report overeating than people with healthy body weights (odds ratio (OR) = 1.79; 95% confidence interval (CI) 1.32–2.42) and men (OR = 1.50; 95% CI 1.14–1.97). Overweight people, women and people who regularly reported overeating were also significantly more likely to report compensatory behaviours by eating less and to report specific weight gain prevention strategies using diet and physical activity.

Conclusion

The present study suggests that people experience frequent occasions of overeating and try to compensate for such occasions in different ways. However, the combination of dietary changes and physical activity recommended by experts was seldom reported.
Flood precaution of companies and their ability to cope with the flood in August 2002 in Saxony, Germany
Authors: Kreibich Heidi , Müller Meike , Thieken Annegret H. , Merz Bruno
Published: March 2007

The German federal state of Saxony was the most affected region during the severe flood in August 2002, and damage to companies was high. A survey of 415 companies representing a variety of sectors and sizes was undertaken to identify deficits in the flood management of companies. In August 2002, preparedness and precaution of companies was low. Additionally, 45% of the companies had not received any flood warning. Consequently, many companies were unable to perform emergency measures successfully. The mean total damage to companies amounted to 1.1 million euros. However, because of relatively good flood compensation, recovery advanced quickly. After the flood, preparedness and precaution increased, but there is still significant potential for more precautionary measures. The flood warning system should be further improved. Specific incentive and communication programs should be developed for the service and financial sectors, where preparedness and precaution is weakest, as well as for the manufacturing sector, which has the highest damage potential.
Correction [to “Hydrology's efforts toward the cyberfrontier,”]
Authors: Anonymous
Published: March 2007

In the 3 January 2006 issue (Eos, 87 (1), 2006), two lines of one article appear in an adjoining article.

In “Hydrology's Efforts Toward the Cyberfrontier,” by Christina Bandaragoda et al.,the article's concluding paragraphs on page 6 are: The HIS should include the capability to interact with other software tools, but which ones? Survey responses show that in hydrologic research,FORTRAN is the most popular programming language, Microsoft Excel is most used for data management, and Matlab is most used for mathematics and statistics work.
Outstanding student paper awards for the 2005 Fall Meeting
Authors: Anonymous
Published: March 2007

The following members received Outstanding Student Paper Awards at the 2005 Fall Meeting in San Francisco, Calif. (Winners in other sections and focus groups will be announced in subsequent issues of Eos).
In Memoriam
Authors: Anonymous
Published: March 2007

Etienne Arijs, 64,19 January 2006; Atmospheric Sciences, 1995

Stephen E. Blewett, 87; Atmospheric Sciences, 1947
Measuring Trans‐Atlantic aerosol transport from Africa
Authors: Morris Vernon , Clemente‐Colón Pablo , Nalli Nicholas R. , Joseph Everette , Armstrong Roy A. , Detrés Yasmin , Goldberg Mitchell D. , Minnett Peter J. , Lumpkin Rick
Published: March 2007

An estimated three billion metric tons of mineral aerosols are injected into the troposphere annually from the Saharan desert [Prospero et al., 1996]. Additionally, smoke from biomass burning sites in the savanna grasslands in sub‐Saharan Africa contribute significant quantities of smaller‐sized aerosols [e.g., Hobbs, 2000]. These windswept aerosols from the African continent are responsible for a variety of climate, health, and environmental impacts on both global and regional scales that span the Western Hemisphere. Unfortunately in situ measurements of aerosol evolution and transport across the Atlantic are difficult to obtain, and satellite remote sensing of aerosols can be challenging.
Rapid export of organic matter to the Mississippi Canyon
Authors: Bianchi Thomas S. , Allison Mead A. , Canuel Elizabeth A. , Corbett D. Reide , McKee Brent A. , Sampere Troy P. , Wakeham Stuart G. , Waterson Elizabeth
Published: March 2007

Coastal margins, where rivers serve as the dominant control on productivity and delivery of dissolved and particulate materials, have been understudied.The potential importance of certain river‐dominated margins (RiOMars), such as those of the Mississippi River plume, to the global carbon budget is garnering increased attention because of their disproportionate role in transporting terrigenous materials to the ocean [Dagg et al., 2004; McKee et al., 2004].

This study concludes that labile (readily open to chemical, physical, or biological change) sedimentary organic matter, produced by in situ diatom production in the Mississippi River plume, is rapidly transported to the Mississippi Canyon. Despite the notion that canyon sediments are typically unstable and lack adequate food resources to support significant macrobenthic communities, this study suggests that productive RiOMars are important conduits for transporting fixed carbon from highly productive plume waters on the shelf to deeper benthic communities.
The first accurate description of an aurora
Authors: Schröder Wilfried
Published: March 2007

As technology has advanced, the scientific study of auroral phenomena has increased by leaps and bounds. A look back at the earliest descriptions of aurorae offers an interesting look into how medieval scholars viewed the subjects that we study.

Although there are earlier fragmentary references in the literature, the first accurate description of the aurora borealis appears to be that published by the German Catholic scholar Konrad von Megenberg (1309–1374) in his book Das Buch der Natur (The Book of Nature). The book was written between 1349 and 1350.
B vitamins as regulators of phytoplankton dynamics
Authors: Panzeca Caterina , Tovar‐Sanchez Antonio , Agustí Susana , Reche Isabel , Duarte Carlos M. , Taylor Gordon T. , Sañudo‐Wilhelmy Sergio A.
Published: March 2007

Without an adequate supply of dissolved vitamins, many species of phytoplankton do not grow. Additions of inorganic nutrients like phosphorus and nitrogen, and trace metals like iron, are not alone adequate to sustain life—a practical lesson learned quickly by experimental biologists when they try to keep eukaryotic phytoplankton cultures alive in their labs. The reason is that coenzymes such as B vitamins are also required for many metabolic pathways. For example, vitamin B, serves as a cofactor for a large number of enzymatic systems, including the pyruvate dehydrogenase complex required for the metabolism of carbohydrates (glycolysis) and amino acid synthesis [Vandamme, 1989]. Vitamin B 12 is used primarily to assist two enzymes: methionine synthase, which is involved in DNA synthesis, and methylmalonyl CoA mutase, which is required for inorganic carbon assimilation [Lindemans and Abels, 1985].
NASA's plans for Moon base
Authors: Zielinski Sarah
Published: March 2007

As part of NASA's Global Exploration Strategy, the agency announced on 4 December that the United States will begin sending astronauts to the Moon again in around 2020 and plans to establish a permanent base there sometime around 2024. However, the agency has yet to determine key details of the plan, including cost and what science will be conducted.

Scott Horowitz, associate administrator for NASA's Exploration Systems Mission Directorate, said, “A lunar base will be the central theme in our…plan for going back to the Moon in preparation for going to Mars and beyond.”
Surveying the Earth's electromagnetic environment from space
Authors: Parrot Michel , Ouzounov Dimitar
Published: March 2007

The scientific objectives of DEMETER (Detection of Electro‐Magnetic Emissions Transmitted from Earthquake Regions) are the detection and characterization of the ionospheric perturbations associated with natural phenomena (such as earthquakes, volcanic eruptions, tsunamis) or with anthropogenic activities. To achieve these objectives, the microsatellite, which was launched at the end of June 2004, surveys the Earth's electromagnetic environment. DEMETER is the first in the Myriade series of microsatellites developed by the Centre National d'Etudes Spatiales (CNES, France) for lowcost science missions.
A ridgelet transform method for constraining tectonic models via abyssal‐hill morphology
Authors: Downey Nathan J. , Clayton Robert W.
Published: March 2007

Abyssal‐hill shape and orientation are related to the direction and spreading rate of paleo‐spreading centers. Therefore analyzing abyssal‐hill shape and trend is useful for constraining tectonic models of regions devoid of magnetic reversal anomalies. Detecting systematic changes of abyssal‐hill shapes or trends, due to changes in spreading rate or direction, is not straightforward, which makes it difficult to determine appropriate regions over which to average abyssal‐hill parameters. Often, however, detecting these systematic changes, where they occur, and the scale over which they occur, is of primary importance for tectonic reconstructions. We present a new method of abyssal‐hill analysis that is based on the ridgelet transform, a relative of the two‐dimensional wavelet transform. Our method is capable of locally estimating the width, azimuth, and root‐mean‐square (RMS) amplitude of abyssal‐hill fabric and highlights changes in these parameters across a survey area, making it possible to identify regions created with a constant spreading rate and direction. We use three multibeam swaths, one crossing the Osbourn Trough in the southwest Pacific Basin, one crossing the East Pacific Rise, and one crossing the Mid‐Atlantic Ridge, to demonstrate the utility and performance of our method.
Variability of Adriatic Sea coastal turbid waters from SeaWiFS imagery
Authors: Bignami F. , Sciarra R. , Carniel S. , Santoleri R.
Published: March 2007

The objective of this work is to gain new insight on the variability and offshore export of turbid coastal waters in the Adriatic Sea, which are optically classified as Case 2 waters. This is done by means of the 1998–2004 SeaWiFS ocean color products (chlorophyll, Case 2 flags and light attenuation coefficient at 490 nm, k490) and NOAA AVHRR sea surface temperature. The role of wind‐driven circulation in the redistribution of the above ocean color features is also analyzed both at seasonal and interannual time scales and in the light of particular wind and current situations occurring in 2003, via scatterometer wind data as well as atmospheric and marine circulation medium and high resolution model output. Results indicate that turbid (Case 2) waters are exported offshore at the Po delta and Ancona headland during the colder months, in concomitance of Bora wind events and when the 2003 daily Po river discharge is above about 500 m3 s−1 and 1000 m3 s−1, respectively. Southeasterly Sirocco events do not to originate extensive offshore transport, but only locally modify the shape of the WAC front. Mistral episodes enhance the WAC flow into the Ionian Sea. Finally, estimates of coastal current width and length from Case 2 flag distribution follow the Po discharge pattern, confirming this forcing to be the main responsible for WAC width seasonal modulation. Experimental WAC widths agree reasonably with theoretical analyses, while underestimation of WAC length suggests the necessity to include the other Italian rivers in the freshwater discharge evaluation.
Observed and simulated microphysical composition of arctic clouds: Data properties and model validation
Authors: Sandvik A. , Biryulina M. , Kvamstø N. G. , Stamnes J. J. , Stamnes K.
Published: March 2007

Data from two different sensors measuring ice particles were combined to establish an improved data series for ice water content. Together with liquid water measurements this new data set was used to evaluate arctic cloud properties, simulated with a state‐of‐the‐art mesoscale atmospheric model. Dependent on the method used for comparison, the mean cloud fraction was found to lie between 51 and 58% in the observations and 53% in the simulations. The hit rate for the total water content was estimated to be between 65 and 71% and the systematic error to a few percent. On the basis of in‐cloud observations only, the model was able to reproduce cloudy conditions in 74% of the data points. On the other hand, the model underestimated the occurrence of the liquid phase by about 80% and slightly overestimated the occurrence of the ice phase. Also, in the temperature range from 255 K to 230 K, where considerable amounts of supercooled water were observed, the model failed to produce the liquid phase. Our results confirm the previous finding that despite high forecast skill with respect to cloudy or cloud‐free events, the model underpredicts the occurrence of liquid phase in arctic clouds. This shortcoming will have a large influence on precipitation forecasts, as well as on climate predictions. Despite some improvements in recent years, more research is needed to improve the parameterization of arctic cloud properties in fine‐scale weather prediction models. For climate models, which have to employ a much cruder parameterization of the microphysics, we face a number of challenges.
Analyses and comparisons of variations of 7Be, 210Pb, and 7Be/210Pb with ozone observations at two Global Atmosphere Watch stations from high mountains
Authors: Lee H. N. , Tositti L. , Zheng X. , Bonasoni P.
Published: March 2007

Simultaneous measurements of 7Be and 210Pb and the analyses of activity ratio, i.e., 7Be/210Pb, offer another useful analytical tool for improving our understanding of ozone variability occurring at high altitude because they can provide diagnostic indicators of horizontal and vertical transport processes. Generally, the increase (decrease) of 7Be with decrease (increase) of 210Pb in association with high (low) values of 7Be/210Pb indicates the mechanisms associated with vertical (for being favorable to the horizontal) transport processes. For the purpose of demonstrating these mechanisms for ozone transport, we have presented the distinct transport processes of ozone and background conditions for two Global Atmosphere Watch (GAW) stations: Mount Cimone station (44.18°N, 10.7°E, 2165 m asl) and Mount Waliguan station (36.29°N, 100.90°E, 3816 m asl), located high in the mountains of Italy and China, respectively. We have performed the frequency distribution analyses and various comparisons of variations of 7Be with 210Pb and variations of 7Be, 210Pb, and 7Be/210Pb with surface ozone. The maximum ozone levels occur in the summer, and minimum levels occur in the winter at these two high mountain stations. Our analyses suggest that the processes of the stratospheric intrusions/upper tropospheric transport combined with the long‐range transport from polluted areas over eastern central China are the mechanisms that cause the ozone summer peak at the Mount Waliguan station. The ozone summer peak at the Mount Cimone station is mainly the result of photochemical production in the lower atmosphere associated with the transport of polluted air masses on regional and continental scales. Frequency distributions of 7Be, 210Pb, 7Be/210Pb, and surface ozone can be well represented by the lognormal distributions. Strikingly, we have found that the similarities of bimodal distributions for 7Be/210Pb at these two stations are clearly exhibited except for the magnitude, although the lognormal distributions of 7Be and 210Pb, with the noteworthy difference in altitude of these two stations, are significantly different. The measurements of 7Be and 210Pb combined with the analyses using 7Be/210Pb activity ratio can enhance our understanding of the transport processes in the atmosphere.
Refinements to the Köhler's theory of aerosol equilibrium radii, size spectra, and droplet activation: Effects of humidity and insoluble fraction
Authors: Khvorostyanov Vitaly I. , Curry Judith A.
Published: March 2007

Hygroscopic growth of mixed aerosol particles and activation of cloud condensation nuclei (CCN) are considered using Köhler theory without the assumption of a dilute solution and accounting for the effect of insoluble fraction. New analytical expressions are derived for the equilibrium wet radius of the wet aerosol and for the critical radii and supersaturations for CCN activation for both volume‐distributed soluble fraction and a soluble shell on the surface of an insoluble core (e.g., mineral dust particle). These expressions generalize the known equations of the Köhler theory, and the accuracy and applicability of the classical expressions are clarified. On the basis of these new expressions, a general but simple method is derived for calculation of the wet size spectrum and the CCN activity spectrum from the dry aerosol size spectrum. The method is applicable for any arbitrary shape of the dry aerosol spectra. Some applications for evaluation of aerosol extinction and homogeneous ice nucleation in a polydisperse aerosol are briefly considered. The method described here can be used in cloud and climate models, in particular, for evaluation of the aerosol direct and indirect effects.
Scaling tidal channel geometry with marsh island area: A tool for habitat restoration, linked to channel formation process
Authors: Hood W. Gregory
Published: March 2007

Hydraulic geometry and related analyses are often used to investigate tidal channel geometry and evolution and inform marsh restoration. An alternative approach is presented that avoids calculating tidal prism and allows analysis of additional channel metrics. It relies on scaling relationships between marsh island surface area and various metrics of the set of tidal channels draining each island. In the Skagit Delta marshes (Washington, United States), total channel surface area and length and surface area of the largest channel draining an island scaled disproportionately with island area, suggesting restoration of a 100‐ha site would be preferable to restoration of 10 separate 10‐ha sites to maximize channel length and area. A model of channel formation through random island conglomeration replicated observed scaling patterns, linking channel scaling to blind channel evolution from river distributaries. Channel size and complexity varied spatially, with significant deficits in an eroding marsh isolated from river distributaries and riverine sediments.
Role of segregating impurities in grain-boundary diffusion
Authors: Kansuwan P. , Rickman J. M.
Published: March 2007

The impact of segregating impurities on grain-boundary diffusion is investigated using a kinetic Monte Carlo simulation of boundary transport on a lattice that is appropriate for both slab and pipe geometries. More specifically, the grain-boundary diffusivity is determined as a function of impurity concentration using an analog of the experimental sectioning method. The retardation of diffusion that results from segregation is interpreted in terms of site-blocking models that reflect the local free volume available to a diffusing tracer. Finally, the results of this investigation are interpreted in the context of experimental determinations of grain-boundary diffusivity in doped ceramic oxides.
Ringlike cores of cylindrically confined nematic point defects
Authors: De Luca Gino , Rey Alejandro D.
Published: March 2007

Nematic liquid crystals confined in a cylindrical capillary and subjected to strong homeotropic anchoring conditions is a long-studied fundamental problem that uniquely incorporates nonlinearity, topological stability, defects, and texture physics. The observed and predicted textures that continue to be investigated include escape radial, radial with a line defect, planar polar with two line defects, and periodic array of point defects. This paper presents theory and multiscale simulations of global and fine scale textures of nematic point defects, based on the Landau–de Gennes tensor order parameter equations. The aim of this paper is to further investigate the ringlike nature of point defect cores and its importance on texture transformation mechanisms and stability. The paper shows that the ringlike cores can be oriented either along the cylinder axis or along the radial direction. Axial rings can partially expand but are constrained by the capillary sidewalls. Radial rings can deform into elliptical structures whose major axis is along the capillary axis. The transformation between several families of textures under capillary confinement as well as their stability is discussed in terms of defect ring distortions. A unified view of nematic textures found in the cylindrical cavities is provided.
Relationship between the structure of SET/TAF-Iβ/INHAT and its histone chaperone activity
Authors: Muto Shinsuke , Senda Miki , Akai Yusuke , Sato Lui , Suzuki Toru , Nagai Ryozo , Senda Toshiya , Horikoshi Masami
Published: March 2007

Histone chaperones assemble and disassemble nucleosomes in an ATP-independent manner and thus regulate the most fundamental step in the alteration of chromatin structure. The molecular mechanisms underlying histone chaperone activity remain unclear. To gain insights into these mechanisms, we solved the crystal structure of the functional domain of SET/TAF-Iβ/INHAT at a resolution of 2.3 Å. We found that SET/TAF-Iβ/INHAT formed a dimer that assumed a “headphone”-like structure. Each subunit of the SET/TAF-Iβ/INHAT dimer consisted of an N terminus, a backbone helix, and an “earmuff” domain. It resembles the structure of the related protein NAP-1. Comparison of the crystal structures of SET/TAF-Iβ/INHAT and NAP-1 revealed that the two proteins were folded similarly except for an inserted helix. However, their backbone helices were shaped differently, and the relative dispositions of the backbone helix and the earmuff domain between the two proteins differed by ≈40°. Our biochemical analyses of mutants revealed that the region of SET/TAF-Iβ/INHAT that is engaged in histone chaperone activity is the bottom surface of the earmuff domain, because this surface bound both core histones and double-stranded DNA. This overlap or closeness of the activity surface and the binding surfaces suggests that the specific association among SET/TAF-Iβ/INHAT, core histones, and double-stranded DNA is requisite for histone chaperone activity. These findings provide insights into the possible mechanisms by which histone chaperones assemble and disassemble nucleosome structures.
Impaired FGF signaling contributes to cleft lip and palate
Authors: Riley Bridget M. , Mansilla M. Adela , Ma Jinghong , Daack-Hirsch Sandra , Maher Brion S. , Raffensperger Lisa M. , Russo Erilynn T. , Vieira Alexandre R. , Dodé Catherine , Mohammadi Moosa , Marazita Mary L. , Murray Jeffrey C.
Published: March 2007

Nonsyndromic cleft lip and palate (NS CLP) is a complex birth defect resulting from a combination of genetic and environmental factors. Several members of the FGF and FGFR families are expressed during craniofacial development and can rarely harbor mutations that result in human clefting syndromes. We hypothesized that disruptions in this pathway might also contribute to NS CLP. We sequenced the coding regions and performed association testing on 12 genes (FGFR1,FGFR2,FGFR3,FGF2,FGF3,FGF4,FGF7,FGF8,FGF9,FGF10,FGF18, andNUDT6) and used protein structure analyses to predict the function of amino acid variants. Seven likely disease-causing mutations were identified, including: one nonsense mutation (R609X) in FGFR1, ade novomissense mutation (D73H) in FGF8, and other missense variants in FGFR1, FGFR2, and FGFR3. Structural analysis of FGFR1, FGFR2, and FGF8 variants suggests that these mutations would impair the function of the proteins, albeit through different mechanisms. Genotyping of SNPs in the genes found associations between NS CLP and SNPs inFGF3,FGF7,FGF10,FGF18, andFGFR1. The data suggest that the FGF signaling pathway may contribute to as much as 3–5% of NS CLP and will be a consideration in the clinical management of CLP.
EDEM1 reveals a quality control vesicular transport pathway out of the endoplasmic reticulum not involving the COPII exit sites
Authors: Zuber Christian , Cormier James H. , Guhl Bruno , Santimaria Roger , Hebert Daniel N. , Roth Jürgen
Published: March 2007

Immature and nonnative proteins are retained in the endoplasmic reticulum (ER) by the quality control machinery. Folding-incompetent glycoproteins are eventually targeted for ER-associated protein degradation (ERAD). EDEM1 (ER degradation-enhancing α-mannosidase-like protein 1), a putative mannose-binding protein, targets misfolded glycoproteins for ERAD. We report that endogenous EDEM1 exists mainly as a soluble glycoprotein. By high-resolution immunolabeling and serial section analysis, we find that endogenous EDEM1 is sequestered in buds that form along cisternae of the rough ER at regions outside of the transitional ER. They give rise to ≈150-nm vesicles scattered throughout the cytoplasm that are lacking a recognizable COPII coat. About 87% of the immunogold labeling was over the vesicles and ≈11% over the ER lumen. Some of the EDEM1 vesicles also contain Derlin-2 and the misfolded Hong Kong variant of α-1-antitrypsin, a substrate for EDEM1 and ERAD. Our results demonstrate the existence of a vesicle budding transport pathway out of the rough ER that does not involve the canonical transitional ER exit sites and therefore represents a previously unrecognized passageway to remove potentially harmful misfolded luminal glycoproteins from the ER.
Systemic inflammation and neurodegeneration in a mouse model of multiple sulfatase deficiency
Authors: Settembre Carmine , Annunziata Ida , Spampanato Carmine , Zarcone Daniela , Cobellis Gilda , Nusco Edoardo , Zito Ester , Tacchetti Carlo , Cosma Maria Pia , Ballabio Andrea
Published: March 2007

Sulfatases are involved in several biological functions such as degradation of macromolecules in the lysosomes. In patients with multiple sulfatase deficiency, mutations in theSUMF1gene cause a reduction of sulfatase activities because of a posttranslational modification defect. We have generated a mouse line carrying a null mutation in theSumf1gene. Sulfatase activities are completely absent inSumf1−/−mice, indicating that Sumf1 is indispensable for sulfatase activation and that mammals, differently from bacteria, have a single sulfatase modification system. Similarly to multiple sulfatase deficiency patients,Sumf1−/−mice display frequent early mortality, congenital growth retardation, skeletal abnormalities, and neurological defects. All examined tissues showed progressive cell vacuolization and significant lysosomal storage of glycosaminoglycans.Sumf1−/−mice showed a generalized inflammatory process characterized by a massive presence of highly vacuolated macrophages, which are the main site of lysosomal storage. Activated microglia were detected in the cerebellum and brain cortex associated with remarkable astroglyosis and neuronal cell loss. Between 4 and 6 months of age, we detected a strong increase in the expression levels of inflammatory cytokines and of apoptotic markers in both the CNS and liver, demonstrating that inflammation and apoptosis occur at the late stage of disease and suggesting that they play an important role in both the systemic and CNS phenotypes observed in lysosomal disorders. This mouse model, in which the function of an entire protein family has been silenced, offers a unique opportunity to study sulfatase function and the mechanisms underlying lysosomal storage diseases.
Chemical genetics reveals the requirement for Polo-like kinase 1 activity in positioning RhoA and triggering cytokinesis in human cells
Authors: Burkard Mark E. , Randall Catherine L. , Larochelle Stéphane , Zhang Chao , Shokat Kevan M. , Fisher Robert P. , Jallepalli Prasad V.
Published: March 2007

Polo-like kinases (Plks) play crucial roles in mitosis and cell division. Whereas lower eukaryotes typically contain a single Plk, mammalian cells express several closely related but functionally distinct Plks. We describe here a chemical genetic system in which a single Plk family member, Plk1, can be inactivated with high selectivity and temporal resolution by using an allele-specific, small-molecule inhibitor, as well as the application of this system to dissect Plk1's role in cytokinesis. To do this, we disrupted both copies of the
PLK1
locus in human cells through homologous recombination and then reconstituted Plk1 activity by using either the wild-type kinase (Plk1
wt
) or a mutant version whose catalytic pocket has been enlarged to accommodate bulky purine analogs (Plk1
as
). When cultured in the presence of these analogs, Plk1
as
cells accumulate in prometaphase with defects that parallel those found in
PLK1
Δ/Δ
cells. In addition, acute treatment of Plk1
as
cells during anaphase prevents recruitment of both Plk1 itself and the Rho guanine nucleotide exchange factor (RhoGEF) Ect2 to the central spindle, abolishes RhoA GTPase localization to the equatorial cortex, and suppresses cleavage furrow formation and cell division. Our studies define and illuminate a late mitotic function of Plk1 that, although difficult or impossible to detect in Plk1-depleted cells, is readily revealed with chemical genetics.
De novopeptide sequencing using ion peak intensity and amino acid cleavage intensity ratio
Authors: Kanazawa Mitsuhiro , Anyoji Hisae , Ogiwara Atsushi , Nagashima Umpei
Published: March 2007

Motivation: Peptide-sequencing methods by mass spectrum use the following two approaches: database searching and de novo sequencing. The database-searching approach is convenient; however, in cases wherein the corresponding sequences are not included in the databases, the exact identification is difficult. On the other hand, in the case of de novo sequencing, no preliminary information is necessary; however, continuous amino acid sequence peaks and the differentiation of these peaks are required. It is, however, very difficult to obtain and differentiate the peaks of all amino acids by using an actual spectrum.

We propose a novel de novo sequencing approach using not only mass-to-charge ratio but also ion peak intensity and amino acid cleavage intensity ratio (CIR).

Results: Our method compensates for any undetectable amino acid peak intervals by estimating the amino acid set and the probability of peak expression based on amino acid CIR. It provides more accurate identification of sequences than the existing methods, by which it is usually difficult to sequence.

Contact:  kanazawa@reifycs.com
AMPer: a database and an automated discovery tool for antimicrobial peptides
Authors: Fjell Christopher D. , Hancock Robert E.W. , Cherkasov Artem
Published: March 2007

Motivation: Increasing antibiotics resistance in human pathogens represents a pressing public health issue worldwide for which novel antibiotic therapies based on antimicrobial peptides (AMPs) may offer one possible solution. In the current study, we utilized publicly available data on AMPs to construct hidden Markov models (HMMs) that enable recognition of individual classes of antimicrobials peptides (such as defensins, cathelicidins, cecropins, etc.) with up to 99% accuracy and can be used for discovering novel AMP candidates.

Results: HMM models for both mature peptides and propeptides were constructed. A total of 146 models for mature peptides and 40 for propeptides have been developed for individual AMP classes. These were created by clustering and analyzing AMP sequences available in the public sources and by consequent iterative scanning of the Swiss-Prot database for previously unknown gene-coded AMPs. As a result, an additional 229 additional AMPs have been identified from Swiss-Prot, and all but 34 could be associated with known antimicrobial activities according to the literature. The final set of 1045 mature peptides and 253 propeptides have been organized into the open-source AMPer database.

Availability: The developed HMM-based tools and AMP sequences can be accessed through the AMPer resource at http://www.cnbi2.com/cgi-bin/amp.pl

Contact:  cfjell@interchange.ubc.ca

Supplementary information: Supplementary data are available at Bioinformatics online.