bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of poling-assisted bleaching of metal-doped nanocomposite glass with poling conditions
Authors: Deparis Olivier , Kazansky Peter G. , Podlipensky Alexander , Abdolvand Amin , Seifert Gerhard , Graener Heinrich
Published: June 2005

Poling-assisted bleaching was studied with respect to poling time, voltage, and temperature in glass samples having a gradient of silver nanoparticles across the depth. The optical extinction band due to the particles’ surface plasmon resonance (around 415 nm) was measured and the Maxwell–Garnett effective medium theory was used to fit extinction spectra. Fitting allowed us to determine the evolution of the thickness of the near-surface layer where the particles’ volume filling factor has dropped to zero as a result of the bleaching process. At 280 °C, bleaching started with a voltage as low as 200 V and saturated with time after about 1 h. Tight glass-electrode contact, voltage of at least 1 kV, and temperature higher than 200 °C were required in order to obtain significant and uniform bleaching in the poled area. The results were discussed in terms of the underlying electric-field-assisted dissolution of embedded metal nanoparticles.
Voltage tunable superlattice infrared detector for mid- and long-wavelength detection
Authors: Majumdar Amlan , Choi K. K. , Reno J. L. , Tsui D. C.
Published: June 2005

We have designed and fabricated a voltage tunable superlattice (SL) infrared photodetector where the detection wavelength switches from the 3–5μm midwavelength infrared (MWIR) range under negative bias to the 8–12μm long-wavelength infrared (LWIR) range under large positive bias. The structure consists of multiple periods of two different SLs that are separated by undoped blocking barriers on one side and heavily doped layers on the other side. The background-limited temperature with F∕1.2 optics is 110 and 70 K for mid- and long-wavelength detection, respectively. This voltage tunable MWIR/LWIR detector has a performance comparable to those of one-color quantum-well infrared detectors designed for the respective wavelength ranges.
Crystallization of amorphous In2O3–10 wt % ZnO thin films annealed in air
Authors: Yaglioglu Burag , Yeom Hyo-Young , Paine David C.
Published: June 2005

We report on the crystallization of amorphous indium zinc oxide (a-IZO) with stoichiometry of In2Zn0.38O3.38 (In2O3–10 wt % ZnO) thin films deposited by dc magnetron sputtering. Transmission electron microscopy and glancing incidence x-ray diffraction were used to show that, when annealed in air at 500 °C, the product of a-IZO thin film crystallization is a compositionally modulated crystal of high-pressure corundum In2O3 phase. The composition, microstructure, resistivity, carrier density, and mobility of this new IZO phase are reported and are compared to the bixbyite ITO (In2O3–9.8wt%SnO2) deposited and annealed under identical conditions.
Resonant localized donor state above the conduction band minimum in InN
Authors: Dmowski L. H. , Plesiewicz J. A. , Suski T. , Lu Hai , Schaff W. , Kurouchi M. , Nanishi Y. , Konczewicz L. , Cimalla V. , Ambacher O.
Published: June 2005

We have studied the pressure dependence of Hall electron concentration and mobility in degenerated, not intentionally doped InN samples. The results obtained for a whole set of samples with electron concentrations from 5.4×1017cm−3 to 3.3×1018cm−3 consistently reveal the existence of a localized donor type state, resonant with the conduction band. Its energy position is estimated to be about 80–90 meV above the bottom of the conduction band. This donor state is not the only source of electrons in these not intentionally doped samples and can be entirely populated and hidden in samples with very high electron concentrations.
Enhanced tetragonality in (x)PbTiO3-(1−x)Bi(Zn1∕2Ti1∕2)O3 and related solid solution systems
Authors: Suchomel Matthew R. , Davies Peter K.
Published: June 2005

The solid solutions (x)PbTiO3-(1−x)Bi(Zn1∕2Ti1∕2)O3, (x)PbTiO3-(1−x)Bi(Zn1∕2Zn1∕2)O3, and (x)PbTiO3-(1−x)Bi(Zn1∕2Sn1∕2)O3, have been examined by x-ray diffraction, dielectric measurements, and thermal analysis. Unlike most PbTiO3-based solid solutions, these systems show enhanced tetragonality with substitution for PbTiO3. In particular, the (x)PbTiO3-(1−x)Bi(Zn1∕2Ti1∕2)O3 system exhibits a high c∕a ratio of 1.11 for x=0.60. Accordingly, the Curie temperature (TC) also increases, exceeding 700°C at the same composition. It is proposed that PbTiO3-Bi(B)O3-type solid solutions which contain only highly polarizable cations on the B site are likely to exhibit similar enhancements in tetragonality and TC.
In vacuo measurements of dangling bonds created during Ar-diluted fluorocarbon plasma etching of silicon dioxide films
Authors: Ishikawa Kenji , Okigawa Mitsuru , Ishikawa Yasushi , Samukawa Seiji , Yamasaki Satoshi
Published: June 2005

Dangling bond creation processes during fluorocarbon plasma etching of silicon dioxide (SiO2) films were studied using an in vacuo electron spin resonance technique. In a range of about 10nm underneath the interface of the SiO2 films with an amorphous fluorinated carbon film that was top-covered, a Si dangling bond in the films (E′ center, g value 2.0003) was located. Density of the E′ center was sustained during etching processes created by the illumination of vacuum ultraviolet emissions, higher photon energy than the bandgap of SiO2. The etching mechanism in this system is discussed taking into account the experimental results.
Controllable method for the preparation of metalized probes for efficient scanning near-field optical Raman microscopy
Authors: Wang J. J. , Saito Y. , Batchelder D. N. , Kirkham J. , Robinson C. , Smith D. A.
Published: June 2005

A modification of the mirror reaction method has been used to metalize atomic force microscope (AFM) probes for apertureless near-field optical microscopy. The method produces a single silver particle of controllable size at the apex of the AFM tip with no detrimental effects on the AFM probe. A particle of the order 80nm in diameter appears to provide the best tip-enhanced Raman signal using 488nm excitation. The near-field Raman spatial resolution of one such probe was shown to be as high as 24nm using single-walled carbon nanotubes as a test sample.
Differential seed ecology in the shrubs Kunzea rupestris, K. capitata and associated hybrids (Myrtaceae): the function of thin-walled fruit in a fire-prone vegetation
Authors: Tierney David A. , Wardle Glenda M.
Published: June 2005

In fire-prone vegetation many plants bear thick woody fruits that retains seeds and insulate these seeds from heat. However, in the same vegetation, some plants retain seeds in thin indehiscent fruits that offer little protection from heat. The function of these thin indehiscent fruits is unknown. We investigated two closely related Kunzea species that occur together in fire-prone vegetation, namely eucalypt woodland. We also studied naturally occurring hybrids of these two species. K. rupestris bears indehiscent thin-walled fruit, whereas K. capitata bears fruit that dehisce to release seed on maturity. Hybrid fruits partly dehisce but retain seed. Studies of seed viability, dormancy and germination demonstrate a distinct combination of these traits for both species. Hybrid seed also has a unique combination of these traits, having some characteristics of both species. The indehiscent capsules impart dormancy to retained seed. However, K. capitata seed, which is not retained in fruit, also displays dormancy. In K. capitata, dormancy is associated with a water-impermeable seed coat. Surprisingly, seed retained in indehiscent capsules was found to have lower viability when exposed to heat than seed that had been released from capsules and exposed to heat.
The evaluation of indices of animal abundance using spatial simulation of animal trapping
Authors: Ramsey Dave , Efford Murray , Ball Steve , Nugent Graham
Published: June 2005

We apply a new algorithm for spatially simulating animal trapping that utilises a detection function and allows for competition between animals and traps. Estimates of the parameters of the detection function from field studies allowed us to simulate realistically the expected range of detection probabilities of brushtail possums caught in traps. Using this model we evaluated a common index of population density of brushtail possums based on the percentage of leg-hold traps catching possums. Using field estimates of the parameters of the detection function, we simulated the relationship between the trap-catch index and population density. The relationship was linear up to densities of 10 possums ha–1. We also investigated the accuracy (bias and precision) of the trap-catch index for possums to estimate relative changes in population density (relative abundance) under conditions of varying detection probability, and compared these results with those obtained using a removal estimate of the population in the vicinity of trap lines. The ratio of trap-catch indices was a more precise estimator of relative abundance than the ratio of removal estimates but was positively biased (i.e. overestimated relative abundance). In contrast, the ratio of removal estimates was relatively unbiased but imprecise. Despite the positive bias, the trap-catch index had a higher power to determine the correct ranking between population densities than the removal estimate. Although varying detection probability can bias estimates of relative abundance using indices, we show that the potential for bias to lead to an incorrect result is small for indices of brushtail possum density based on trapping.
Correcting wildlife counts using detection probabilities
Authors: White Gary C.
Published: June 2005

One of the most pervasive uses of indices of wildlife populations is uncorrected counts of animals. Two examples are the minimum number known alive from capture and release studies, and aerial surveys where the detection probability is not estimated from a sightability model, marked animals, or distance sampling. Both the mark–recapture and distance-sampling estimators are techniques to estimate the probability of detection of an individual animal (or cluster of animals), which is then used to correct a count of animals. However, often the number of animals in a survey is inadequate to compute an estimate of the detection probability and hence correct the count. Modern methods allow sophisticated modelling to estimate the detection probability, including incorporating covariates to provide additional information about the detection probability. Examples from both distance and mark–recapture sampling are presented to demonstrate the approach.
A method for estimating wildlife detection probabilities in relation to home-range use: insights from a field study on the common brushtail possum (Trichosurus vulpecula)
Authors: Ball Stephen J. , Ramsey David , Nugent Graham , Warburton Bruce , Efford Murray
Published: June 2005

Using field data from brushtail possums (Trichosurus vulpecula), we present a method for modelling wildlife detection probabilities. Whereas detection functions typically (e.g. for distance sampling) describe the probability of direct human observations of animal subjects, we adapted this approach for cryptic species where observation depends on animals being caught in traps. Specifically, we characterised the probability of individual brushtail possums being caught by leg-hold traps in an area of farmland and native forest in New Zealand. Detection probability was defined as the per-individual, per-trap, per-night probability of a possum being captured, and was modelled as a function of home-range utilisation. Radio-telemetry was used to define the home-range distributions of 18 possums, and a combination of scanning radio-receivers and movement-activated video-cameras recorded instances when radio-collared possums encountered and stepped on the trigger of leg-hold traps (inactivated by being wired open). We estimated a 5% chance of trapping individual possums with a single leg-hold trap located in the centre of their home range for one night (median value across possums). Furthermore, this probability decreased rapidly as a function of distance, so that at 120 m from the centre of the home range there was less than a 1% chance of trapping success per possum per night. The techniques developed in this study could be applied to a wide variety of species and sampling methods.
Does variable probability of detection compromise the use of indices in aerial surveys of medium-sized mammals?
Authors: Tracey John P. , Fleming Peter J. S. , Melville Gavin J.
Published: June 2005

Although aerial surveys are an effective and commonly used method of monitoring wildlife populations, variable detection probability may result in unreliable indices or biased estimates of absolute abundance. Detection probability can vary between sites, sampling periods, species, group sizes, vegetation types and observers. These variables were examined in helicopter surveys of a suite of medium-sized mammals in a hilly environment in central eastern New South Wales. Maximum-likelihood methods were used to investigate the effects of these variables on detection probability, which was derived using the double-count technique. Significant differences were evident between species in the overall analysis, and group size, vegetation, observer pair and sampling period for various individual species when analysed separately. The implications for monitoring wildlife populations between sites and across time are discussed. This paper emphasises that aerial survey indices may be effective in detecting large differences in population size but can be improved by quantifying detection probabilities for a range of variables.
Developing relative abundance techniques (RATs) for monitoring rodent populations
Authors: Whisson Desley A. , Engeman Richard M. , Collins Kellie
Published: June 2005

Accurate density estimates of rodents are frequently difficult or cost-prohibitive to determine. Thus, a number of techniques (track plates, monitoring blocks, chew cards/sticks, apple slice index, trapping) are often used to index rodent populations. Theoretically, the sensitivity of these indexing techniques could be improved if they applied continuous measurements rather than simple binary measurements (presence/absence). Development of a relative abundance technique that is simple to apply and sensitive to changes in population density is critical for the operational management of rodent pests. In addition to providing a quantitative measure of abundance with statistical parameters, an indexing technique that does not require handling of animals is important in consideration of potential disease issues (for example, hantavirus, arenavirus, etc.). We investigated track plates, chew cards and monitoring blocks and associated continuous measurement methods for calculating indices of rodent abundance. In laboratory and field settings, we tested their effectiveness in detecting different population densities of California meadow voles (Microtus californicus). Chew cards were poorly accepted by meadow voles in pen and field tests. However, track plates and monitoring blocks may provide useful tools for indexing meadow vole populations, and have application for other rodent species.
Wildlife population monitoring: some practical considerations
Authors: Witmer Gary W.
Published: June 2005

The accurate estimation of wildlife population density is difficult and requires considerable investment of resources and time. Population indices are easier to obtain but are influenced by many unknowns and the relationships to actual population densities are usually unclear. Wildlife biologists, whether in the public or private sector, often find themselves in difficult situations where a resource manager or landowner wants good information, quickly, at low cost, and without clear objectives. In many situations, in addition to establishing clear objectives, a budget and timeframe, a biologist must understand and deal with the reality of many logistical concerns that will make the achievement of the objectives difficult or impossible. The situation is often complicated because the biology and ecology of the species of interest may be poorly understood in the specific setting and the species may be very rare or strongly influenced by current or past human activities. Methods to monitor a wildlife population may need to be tested or validated, extending the time and resources needed to complete the assigned task. In this paper, I discuss many of the challenges faced and the decisions to be made when a biologist is requested to provide useful, timely information on the status of a wildlife population.
Improving the efficiency of wildlife monitoring by estimating detectability: a case study of foxes (Vulpes vulpes) on the Eyre Peninsula, South Australia
Authors: Field S. A. , Tyre A. J. , Thorn K. H. , O'Connor P. J. , Possingham H. P.
Published: June 2005

Demonstrating the existence of trends in monitoring data is of increasing practical importance to conservation managers wishing to preserve threatened species or reduce the impact of pest species. However, the ability to do so can be compromised if the species in question has low detectability and the true occupancy level or abundance of the species is thus obscured. Zero-inflated models that explicitly model detectability improve the ability to make sound ecological inference in such situations. In this paper we apply an occupancy model including detectability to data from the initial stages of a fox-monitoring program on the Eyre Peninsula, South Australia. We find that detectability is extremely low (<18%) and varies according to season and the presence or absence of roadside vegetation. We show that simple methods of using monitoring data to inform management, such as plotting the raw data or performing logistic regression, fail to accurately diagnose either the status of the fox population or its trajectory over time. We use the results of the detectability model to consider how future monitoring could be redesigned to achieve efficiency gains. A wide range of monitoring programs could benefit from similar analyses, as part of an active adaptive approach to improving monitoring and management.
Nonlinear protein degradation and the function of genetic circuits
Authors: Buchler Nicolas E. , Gerland Ulrich , Hwa Terence
Published: June 2005

The functions of most genetic circuits require a sufficient degree of cooperativity in the circuit components. Although mechanisms of cooperativity have been studied most extensively in the context of transcriptional initiation control, cooperativity from other processes involved in the operation of the circuits can also play important roles. In this work, we examine a simple kinetic source of cooperativity stemming from the nonlinear degradation of multimeric proteins. Ample experimental evidence suggests that protein subunits can degrade less rapidly when associated in multimeric complexes, an effect we refer to as “cooperative stability.” For dimeric transcription factors, this effect leads to a concentration-dependence in the degradation rate because monomers, which are predominant at low concentrations, will be more rapidly degraded. Thus, cooperative stability can effectively widen the accessible range of protein levelsin vivo. Through theoretical analysis of two exemplary genetic circuits in bacteria, we show that such an increased range is important for the robust operation of genetic circuits as well as their evolvability. Our calculations demonstrate that a few-fold difference between the degradation rate of monomers and dimers can already enhance the function of these circuits substantially. We discuss molecular mechanisms of cooperative stability and their occurrence in natural or engineered systems. Our results suggest that cooperative stability needs to be considered explicitly and characterized quantitatively in any systematic experimental or theoretical study of gene circuits.
Hysteresis in a synthetic mammalian gene network
Authors: Kramer Beat P. , Fussenegger Martin
Published: June 2005

Bistable and hysteretic switches, enabling cells to adopt multiple internal expression states in response to a single external input signal, have a pivotal impact on biological systems, ranging from cell-fate decisions to cell-cycle control. We have designed a synthetic hysteretic mammalian transcription network. A positive feedback loop, consisting of a transgene and transactivator (TA) cotranscribed by TA's cognate promoter, is repressed by constitutive expression of a macrolide-dependent transcriptional silencer, whose activity is modulated by the macrolide antibiotic erythromycin. The antibiotic concentration, at which a quasi-discontinuous switch of transgene expression occurs, depends on the history of the synthetic transcription circuitry. If the network components are imbalanced, a graded rather than a quasi-discontinuous signal integration takes place. These findings are consistent with a mathematical model. Synthetic gene networks, which are able to emulate natural gene expression behavior, may foster progress in future gene therapy and tissue engineering initiatives.
Enhancing calstabin binding to ryanodine receptors improves cardiac and skeletal muscle function in heart failure
Authors: Wehrens Xander H. T. , Lehnart Stephan E. , Reiken Steven , van der Nagel Roel , Morales Raymond , Sun Jie , Cheng Zhenzhuang , Deng Shi-Xiang , de Windt Leon J. , Landry Donald W. , Marks Andrew R.
Published: June 2005

Abnormalities in intracellular calcium release and reuptake are responsible for decreased contractility in heart failure (HF). We have previously shown that cardiac ryanodine receptors (RyRs) are protein kinase A-hyperphosphorylated and depleted of the regulatory subunit calstabin-2 in HF. Moreover, similar alterations in skeletal muscle RyR have been linked to increased fatigability in HF. To determine whether restoration of calstabin binding to RyR may ameliorate cardiac and skeletal muscle dysfunction in HF, we treated WT and calstabin-2-/-mice subjected to myocardial infarction (MI) with JTV519. JTV519, a 1,4-benzothiazepine, is a member of a class of drugs known as calcium channel stabilizers, previously shown to increase calstabin binding to RyR. Echocardiography at 21 days after MI demonstrated a significant increase in ejection fraction in WT mice treated with JTV519 (45.8 ± 5.1%) compared with placebo (31.1 ± 3.1%;P< 0.05). Coimmunoprecipitation experiments revealed increased amounts of calstabin-2 bound to the RyR2 channel in JTV519-treated WT mice. However, JTV519 did not show any of these beneficial effects in calstabin-2-/-mice with MI. Additionally, JTV519 improved skeletal muscle fatigue in WT and calstabin-2-/-mice with HF by increasing the binding of calstabin-1 to RyR1. The observation that treatment with JTV519 improved cardiac function in WT but not calstabin-2-/-mice indicates that calstabin-2 binding to RyR2 is required for the beneficial effects in failing hearts. We conclude that JTV519 may provide a specific way to treat the cardiac and skeletal muscle myopathy in HF by increasing calstabin binding to RyR.
Reversible single-molecule photoswitching in the GFP-like fluorescent protein Dronpa
Authors: Habuchi Satoshi , Ando Ryoko , Dedecker Peter , Verheijen Wendy , Mizuno Hideaki , Miyawaki Atsushi , Hofkens Johan
Published: June 2005

Reversible photoswitching of individual molecules has been demonstrated for a number of mutants of the green fluorescent protein (GFP). To date, however, a limited number of switching events with slow response to light have been achieved at the single-molecule level. Here, we report reversible photoswitching characteristics observed in individual molecules of Dronpa, a mutant of a GFP-like fluorescent protein that was cloned from a coral Pectiniidae. Ensemble spectroscopy shows that intense irradiation at 488 nm changes Dronpa to a dim protonated form, but even weak irradiation at 405 nm restores it to the bright deprotonated form. Although Dronpa exists in an acid–base equilibrium, only the photoinduced protonated form shows the switching behavior. At the single-molecule level, 488- and 405-nm lights can be used to drive the molecule back and forth between the bright and dim states. Such reversible photoswitching could be repeated >100 times. The response speed to irradiation depends almost linearly on the irradiation power, with the response time being in the order of milliseconds. The perfect reversibility of the Dronpa photoswitching allows us to propose a detailed model, which quantitatively describes interconversion among the various states. The fast response of Dronpa to light holds great promise for following fast diffusion or transport of signaling molecules in live cells.
An intracellular phosphate buffer filters transient fluctuations in extracellular phosphate levels
Authors: Thomas Melissa R. , O'Shea Erin K.
Published: June 2005

To survive in a dynamic and unpredictable environment, cells must correctly interpret and integrate extracellular signals with internal factors. In particular, internal stores of nutrients must be managed for use during periods of nutrient limitation. To gain insight into this complex process, we combined biochemical and spectroscopic techniques to follow the dynamics of the phosphate responsive signaling pathway in both single yeast cells and populations. We demonstrate that the phosphate-responsive genes
PHO5
and
PHO84
exhibit different kinetics of transcriptional induction in response to phosphate starvation, and that transient phosphate limitation causes induction of
PHO84
but not
PHO5
. This differential kinetic behavior is largely eliminated in cells that lack the ability to store phosphate internally in the form of polyphosphate, but the threshold of external phosphate required for induction of
PHO5
and
PHO84
is unaffected. Our observations indicate that polyphosphate acts as a buffer that can be mobilized during periods of phosphate limitation and enables the phosphate-responsive signaling pathway to filter transient fluctuations in extracellular phosphate levels.
Hypophosphatemia leads to rickets by impairing caspase-mediated apoptosis of hypertrophic chondrocytes
Authors: Sabbagh Yves , Carpenter Thomas O. , Demay Marie B.
Published: June 2005

Rickets is seen in association with vitamin D deficiency and in several genetic disorders associated with abnormal mineral ion homeostasis. Studies in vitamin D receptor (VDR)-null mice have demonstrated that expansion of the late hypertrophic chondrocyte layer, characteristic of rickets, is secondary to impaired apoptosis of these cells. The observation that normalization of mineral ion homeostasis in the VDR-null mice prevents rachitic changes suggests that rickets is secondary to hypocalcemia, hypophosphatemia, or hyperparathyroidism, rather than impaired VDR action. To determine which of these abnormalities is responsible for impaired chondrocyte apoptosis and subsequent rachitic changes, two additional models were examined: diet-induced hypophosphatemia/hypercalcemia and hypophosphatemia secondary to mutations in the
Phex
gene. The former model is associated with suppressed parathyroid hormone levels as a consequence of hypercalcemia. The latter model demonstrates normal calcium and parathyroid hormone levels, but 1,25-dihydroxyvitamin D levels that are inappropriately low for the degree of hypophosphatemia. Our studies demonstrate that normal phosphorus levels are required for growth plate maturation and implicate a critical role for phosphate-regulated apoptosis of hypertrophic chondrocytes via activation of the caspase-9-mediated mitochondrial pathway.
Neighborliness of randomly projected simplices in high dimensions
Authors: Donoho David L. , Tanner Jared
Published: June 2005

Let
A
be a
d
×
n
matrix and
T
=

T
n

-1
be the standard simplex in R

n
.

Suppose that
d
and
n
are both large and comparable:
d
≈ δ
n,
δ ∈ (0, 1). We count the faces of the projected simplex
AT
when the projector
A
is chosen uniformly at random from the Grassmann manifold of
d
-dimensional orthoprojectors of R

n
.

We derive ρ

N
(

δ
)
> 0 with the property that, for any ρ < ρ

N
(

δ
)
, with overwhelming probability for large
d
, the number of
k
-dimensional faces of
P
=
AT
is exactly the same as for
T
, for 0 ≤
k
≤ ρ
d.
This implies that
P
is

\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
\begin{equation*}{\lfloor}{\rho}d{\rfloor}\end{equation*}\end{document}

-neighborly, and its skeleton

\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
\begin{equation*}Skel_{{\lfloor}{\rho}d{\rfloor}}{\mathit{(}}P{\mathit{)}}\end{equation*}\end{document}

is combinatorially equivalent to

\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
\begin{equation*}Skel_{{\lfloor}{\rho}d{\rfloor}}{\mathit{(}}T{\mathit{)}}\end{equation*}\end{document}

. We also study a weaker notion of neighborliness where the numbers of
k
-dimensional faces

f
k
(P)

≥

f
k

(
T
)(1 - ε). Vershik and Sporyshev previously showed existence of a threshold ρ

VS
(

δ
)
> 0 at which phase transition occurs in
k
/
d.
We compute and display ρ

VS

and compare with ρ

N
.

Corollaries are as follows. (
1
) The convex hull of
n
Gaussian samples in

R
d

, with
n
large and proportional to
d
, has the same
k
-skeleton as the (
n
- 1) simplex, for
k
< ρ

N

(
d
/
n
)
d
(1 +

o
P

(1)). (
2
) There is a “phase transition” in the ability of linear programming to find the sparsest nonnegative solution to systems of underdetermined linear equations. For most systems having a solution with fewer than ρ

VS

(
d
/
n
)
d
(1 +
o
(1)) nonzeros, linear programming will find that solution.
Mechanics of receptor-mediated endocytosis
Authors: Gao Huajian , Shi Wendong , Freund Lambert B.
Published: June 2005

Most viruses and bioparticles endocytosed by cells have characteristic sizes in the range of tens to hundreds of nanometers. The process of viruses entering and leaving animal cells is mediated by the binding interaction between ligand molecules on the viral capid and their receptor molecules on the cell membrane. How does the size of a bioparticle affect receptor-mediated endocytosis? Here, we study how a cell membrane containing diffusive mobile receptors wraps around a ligand-coated cylindrical or spherical particle. It is shown that particles in the size range of tens to hundreds of nanometers can enter or exit cells via wrapping even in the absence of clathrin or caveolin coats, and an optimal particles size exists for the smallest wrapping time. This model can also be extended to include the effect of clathrin coat. The results seem to show broad agreement with experimental observations.
Regulating the proton budget of higher plant photosynthesis
Authors: Avenson Thomas J. , Cruz Jeffrey A. , Kanazawa Atsuko , Kramer David M.
Published: June 2005

In higher plant chloroplasts, transthylakoid proton motive force serves both to drive the synthesis of ATP and to regulate light capture by the photosynthetic antenna to prevent photodamage.
In vivo
probes of the proton circuit in wild-type and a mutant strain of
Arabidopsis thaliana
show that regulation of light capture is modulated primarily by altering the resistance of proton efflux from the thylakoid lumen, whereas modulation of proton influx through cyclic electron flow around photosystem I is suggested to play a role in regulating the ATP/NADPH output ratio of the light reactions.
Eutrophication of aquatic ecosystems: Bistability and soil phosphorus
Authors: Carpenter Stephen R.
Published: June 2005

Eutrophication (the overenrichment of aquatic ecosystems with nutrients leading to algal blooms and anoxic events) is a persistent condition of surface waters and a widespread environmental problem. Some lakes have recovered after sources of nutrients were reduced. In others, recycling of phosphorus from sediments enriched by years of high nutrient inputs causes lakes to remain eutrophic even after external inputs of phosphorus are decreased. Slow flux of phosphorus from overfertilized soils may be even more important for maintaining eutrophication of lakes in agricultural regions. This type of eutrophication is not reversible unless there are substantial changes in soil management. Technologies for rapidly reducing phosphorus content of overenriched soils, or reducing erosion rates, are needed to improve water quality.
Hydrophobic hydration from small to large lengthscales: Understanding and manipulating the crossover
Authors: Rajamani Sowmianarayanan , Truskett Thomas M. , Garde Shekhar
Published: June 2005

Small and large hydrophobic solutes exhibit remarkably different hydration thermodynamics. Small solutes are accommodated in water with minor perturbations to water structure, and their hydration is captured accurately by theories that describe density fluctuations in pure water. In contrast, hydration of large solutes is accompanied by dewetting of their surfaces and requires a macroscopic thermodynamic description. A unified theoretical description of these lengthscale dependencies was presented by Lum, Chandler, and Weeks [(1999)
J. Phys. Chem. B
103, 4570–4577]. Here, we use molecular simulations to study lengthscale-dependent hydrophobic hydration under various thermodynamic conditions. We show that the hydration of small and large solutes displays disparate dependencies on thermodynamic variables, including pressure, temperature, and additive concentration. Understanding these dependencies allows manipulation of the small-to-large crossover lengthscale, which is nanoscopic under ambient conditions. Specifically, applying hydrostatic tension or adding ethanol decreases the crossover length to molecular sizes, making it accessible to atomistic simulations. With detailed temperature-dependent studies, we further demonstrate that hydration thermodynamics changes gradually from entropic to enthalpic near the crossover. The nanoscopic lengthscale of the crossover and its sensitivity to thermodynamic variables imply that quantitative modeling of biomolecular self-assembly in aqueous solutions requires elements of both molecular and macroscopic hydration physics. We also show that the small-to-large crossover is directly related to the Egelstaff-Widom lengthscale, the product of surface tension and isothermal compressibility, which is another fundamental lengthscale in liquids.
An unusual internal ribosome entry site in the herpes simplex virus thymidine kinase gene
Authors: Griffiths Anthony , Coen Donald M.
Published: June 2005

We have investigated a herpes simplex virus mutant that expresses low levels of thymidine kinase (TK), a phenotype associated with drug resistance and pathogenicity, despite a single-base deletion in the gene. Using a dual-reporter system, a 39-nt sequence including the mutation was shown to direct expression of the downstream reporter gene in reticulocyte lysate. Translation of the downstream reporter was not impaired when the mRNA lacked a 5′ cap or had a stable stem loop 5′ of the upstream reporter and was relatively resistant to edeine, an antibiotic that prevents AUG codon recognition by the 40S-eIF2-GTP/Met-tRNA
i
complex. Twelve nucleotides were as active as the original sequence for translation of the downstream reporter. Surprisingly, this sequence lacks an AUG codon. Analysis of point mutations showed that a CUG codon in the sequence was important. However, many single-base changes had only limited effects, and introduction of AUG codons did not increase translation. A mutant virus containing both the single-base deletion and a mutation that reduced downstream translation
in vitro
had significantly less TK activity than a virus with the single-base deletion alone. Thus, a remarkably short internal ribosome entry site (IRES) that lacks an AUG codon resides in the viral
tk
gene. The IRES appears to be responsible for TK expression from a drug-resistant mutant that would otherwise express no TK, which may contribute to pathogenicity. Because we found numerous short sequences with IRES activity, there might be many hitherto unrecognized polypeptides expressed at low levels from eukaryotic mRNAs.
Recent progress on the boundary rigidity problem
Authors: Stefanov Plamen , Uhlmann Gunther
Published: June 2005

The boundary rigidity problem consists in determining a compact, Riemannian manifold with boundary, up to isometry, by knowing the boundary distance function between boundary points. In this paper we announce the result of our forthcoming article that one can solve this problem for generic simple metrics. Moreover we probe stability estimates for this problem.
Taxol-stabilized Microtubules Can Position the Cytokinetic Furrow in Mammalian Cells
Authors: Shannon Katie B. , Canman Julie C. , Moree C. Ben , Tirnauer Jennifer S. , Salmon E. D.
Published: June 2005

How microtubules act to position the plane of cell division during cytokinesis is a topic of much debate. Recently, we showed that a subpopulation of stable microtubules extends past chromosomes and interacts with the cell cortex at the site of furrowing, suggesting that these stabilized microtubules may stimulate contractility. To test the hypothesis that stable microtubules can position furrows, we used taxol to rapidly suppress microtubule dynamics during various stages of mitosis in PtK1 cells. Cells with stabilized prometaphase or metaphase microtubule arrays were able to initiate furrowing when induced into anaphase by inhibition of the spindle checkpoint. In these cells, few microtubules contacted the cortex. Furrows formed later than usual, were often aberrant, and did not progress to completion. Images showed that furrowing correlated with the presence of one or a few stable spindle microtubule plus ends at the cortex. Actin, myosin II, and anillin were all concentrated in these furrows, demonstrating that components of the contractile ring can be localized by stable microtubules. Inner centromere protein (INCENP) was not found in these ingressions, confirming that INCENP is dispensable for furrow positioning. Taxol-stabilization of the numerous microtubule-cortex interactions after anaphase onset delayed furrow initiation but did not perturb furrow positioning. We conclude that taxol-stabilized microtubules can act to position the furrow and that loss of microtubule dynamics delays the timing of furrow onset and prevents completion. We discuss our findings relative to models for cleavage stimulation.
Protein transduction of Rab9 in Niemann‐Pick C cells reduces cholesterol storage
Authors: Narita Keishi , Choudhury Amit , Dobrenis Kostantin , Sharma Deepak K. , Holicky Eileen L. , Marks David L. , Walkley Steven U. , Pagano Richard E.
Published: June 2005

Niemann‐Pick disease type C (NPC) is a genetic disorder in which patient cells exhibit lysosomal accumulation of cholesterol and sphingolipids (SLs) caused by defects in either NPC1 or NPC2 proteins. We previously demonstrated that NPC1 human skin fibroblasts overexpressing endosomal Rab proteins (Rab7 or Rab9) showed a correction in the storage disease phenotype. In the current study, we used protein transduction to further investigate Rab9‐mediated reduction of stored lipids in NPC cells. Recombinant human Rab9 fused with the herpes simplex virus VP22 protein fragment was overexpressed, purified, and added to culture medium to induce protein transduction. When VP22‐Rab9 was transduced into NPC1 fibroblasts, nearly all cells showed significant reduction in cellular free cholesterol levels, with no cytotoxicity up to 5 µM. A fraction of the VP22‐Rab9 that was transduced into the cells was shown to bind to rab GDP dissociation inhibitor, suggesting that this pool of VP22‐Rab9 had become prenylated. The reduction in cellular free cholesterol was associated with correction of abnormal intracellular trafficking of BODIPY‐lactosylceramide and an increase of sterols in the culture media. The clearance of lysosomal free cholesterol was also associated with a decrease in LDL‐receptor levels. In addition, we demonstrated reduction of intracellular cholesterol by VP22‐Rab9 transduction in NPC2 fibroblasts and in cultured mouse NPC1 neurons. These observations provide important new information about the correction of membrane traffic in NPC cells by Rab9 overexpression and may lead to new therapeutic approaches for treatment of this disease.
Haploinsufficiency of the cardiac transcription factor Nkx2‐5 variably affects the expression of putative target genes
Authors: Jay Patrick Y. , Rozhitskaya Olga , Tarnavski Oleg , Sherwood Megan C. , Dorfman Adam L. , Lu Yali , Ueyama Tomomi , Izumo Seigo
Published: June 2005

Heterozygous mutations of the cardiac transcription factor Nkx2‐5 cause congenital heart disease. To elucidate the molecular pathways of transcription factor mutant phenotypes or diseases, direct targets are commonly sought in studies of homozygous null mutant animals and by heterologous promoter‐reporter gene transactivation assays. The expression of putative target genes in a physiologic range of transcription factor concentration, however, is often not examined. Heterozygous Nkx2‐5 knockout (Nkx2‐5+/−) mice have no more than half‐normal levels of Nkx2‐5 protein. We therefore measured the mRNA expression of four putative targets of the cardiac transcription factor Nkx2‐5 in wild‐type and Nkx2‐5+/− animals in a variety of developmental and pathologic states. Wild‐type and Nkx2‐5+/− embryonic hearts expressed similar levels of atrial natriuretic factor (ANF), brain natriuretic peptide (BNP), the RNA helicase Csm, and homeodomain only protein HOP. In the failing adult ventricle, ANF and BNP were up‐regulated to the same extent in wild‐type and Nkx2‐5+/− myocardium. Csm and HOP were down‐regulated in heart failure, and Nkx2‐5+/− hearts expressed about half‐normal levels in healthy and failing states. No consistent relationship existed between the expression of putative transcriptional targets and Nkx2‐5 gene dosage in the physiologically relevant range. Any dependence of gene expression on Nkx2‐5 gene dosage is affected by factors specific to the individual gene and the physiologic context.
Early life immune challenge alters innate immune responses to lipopolysaccharide: implications for host defense as adults
Authors: Ellis Shaun , Mouihate Abdeslam , Pittman Quentin J.
Published: June 2005

Fever is the most common manifestation of the innate immune response to invading pathogens. Animals prevented from developing fever have increased morbidity and mortality to infection. We now show that early life events can program this innate immune response, in that rats that have been challenged neonatally with the immune stimulant lipopolysaccharide (LPS) have both suppressed febrile responses to LPS as adults and significantly reduced nuclear factor (NF)‐κB activation in peripheral immune organs. This was associated with reduced levels of proinflammatory cytokines tumor necrosis factor (TNF)‐α, and interleukin‐6 (IL‐6) in the plasma after adult LPS challenge, compared with animals that have received saline neonatally. In contrast, adult LPS challenge elicited higher corticosterone levels in the animals that had been treated neonatally with LPS. When this increased corticosterone response was negated by adrenalectomy or by administration of the glucocorticoid receptor antagonist RU‐486, both the cytokine and febrile responses were normalized. This study indicates that the innate immune response can be programmed by a neonatal LPS challenge, whereby an amplified hypothalamic‐pituitary‐adrenal response causes reduced cytokine synthesis and an attenuated febrile response to an adult immune challenge. In light of the importance of fever in the host defense response, these alterations may have deleterious consequences on an individual's ability to combat disease later in life.
Stability of an elastic rod buckling into a soft wall
Authors: Manning Robert S , Bulman George B
Published: June 2005

The conjugate point theory of the calculus of variations is extended to apply to the buckling of an elastic rod in an external field. We show that the operator approach presented by Manning (Manning
et al
. 1998
Proc. R. Soc. A
454
, 3047–3074) can be used when the second-variation operator is an integrodifferential operator, rather than a differential operator as in the classical case. The external field is chosen to model two parallel ‘soft’ walls. We consider the examples of two-dimensional buckling under both pinned–pinned and clamped–clamped boundary conditions, as well as the three-dimensional clamped–clamped problem, where we consider the importance of the rod cross-section shape as it ranges from circular to extreme elliptical. For each of these problems, we find that in the appropriate limit, the soft-wall solutions approach a ‘hard-wall’ limit, and thus we make conjectures about these hard-wall contact equilibria and their stability. In the two-dimensional pinned–pinned case, this allows us to assign stability to the configurations reported by Holmes (Holmes
et al
. 1999
Comput. Methods Appl. Mech. Eng.
170
, 175–207) and reconsider the experimental results discussed therein.
On the complete integrability and linearization of certain second-order nonlinear ordinary differential equations
Authors: Chandrasekar V.K , Senthilvelan M , Lakshmanan M
Published: June 2005

A method for finding general solutions of second-order nonlinear ordinary differential equations by extending the Prelle–Singer (PS) method is briefly discussed. We explore integrating factors, integrals of motion and the general solution associated with several dynamical systems discussed in the current literature by employing our modifications and extensions of the PS method. We also introduce a novel way of deriving linearizing transformations from the first integrals to linearize the second-order nonlinear ordinary differential equations to free particle equations. We illustrate the theory with several potentially important examples and show that our procedure is widely applicable.
The Schwarz–Christoffel mapping to bounded multiply connected polygonal domains
Authors: Crowdy Darren
Published: June 2005

A formula for the generalized Schwarz–Christoffel mapping from a bounded multiply connected circular domain to a bounded multiply connected polygonal domain is derived. The theory of classical Schottky groups is employed. The formula for the derivative of the mapping function contains a product of powers of Schottky–Klein prime functions associated with a Schottky group relevant to the circular pre-image domain. The formula generalizes, in a natural way, the known mapping formulae for simply and doubly connected polygonal domains.
Analytical formulae for the Kirchhoff–Routh path function in multiply connected domains
Authors: Crowdy Darren , Marshall Jonathan
Published: June 2005

Explicit formulae for the Kirchhoff–Routh path functions (or Hamiltonians) governing the motion ofN-point vortices in multiply connected domains are derived when all circulations around the holes in the domain are zero. The method uses the Schottky–Klein prime function to find representations of the hydrodynamic Green's function in multiply connected circular domains. The Green's function is then used to construct the associated Kirchhoff–Routh path function. The path function in more general multiply connected domains then follows from a transformation property of the path function under conformal mapping of the canonical circular domains. Illustrative examples are presented for the case of single vortex motion in multiply connected domains.