bluuebunny/crossref_metadata_2025 huggingface dataset:
Jet and hydraulic jump near‐bed stresses below a horseshoe waterfall
Authors: Pasternack Gregory B. , Ellis Christopher R. , Marr Jeffrey D.
Published: July 2007

Horseshoe waterfalls are a common but unexplained feature of bedrock rivers. As a step toward understanding their geomorphology, a six‐component force/torque sensor was used to evaluate clear‐water scour mechanisms in a 0.91‐m broad‐crested horseshoe waterfall built into a 2.75‐m‐wide flume to measure longitudinal, lateral, and temporal profiles of the near‐bed spatially averaged stress vector. Jet impact caused moderate near‐bed stress. Downstream of the impact point, the stress vector shifted into a much more forceful upthrust with peak stress beyond the boil crest. Instantaneous fluctuations in near‐bed lift exceeded drag by 5–10 times and occurred over a wider range of frequencies, suggesting a larger role for particle entrainment. Predictions of bed stress significantly underestimated actual conditions. These results show that horseshoe waterfalls have an extended region of high scour along their centerline corresponding with the three‐dimensional convergent dynamics associated with both jet impact and jump‐enhanced lift fluctuations.
Effects of land use change on soil carbon cycling in the conterminous United States from 1900 to 2050
Authors: Woodbury Peter B. , Heath Linda S. , Smith James E.
Published: July 2007

We developed matrices representing historical area transitions between forest and other land uses. We projected future transitions on the basis of historical transitions and econometric model results. These matrices were used to drive a model of changes in soil and forest floor carbon stocks. Our model predicted net carbon emission from 1900 until 1982, then sequestration until 2030, with little subsequent change. However, the northeast region showed substantial carbon sequestration from 1900 to the present. From 1990 to 2004, afforestation caused sequestration averaging 17 Tg C yr−1: 6 Tg C yr−1 in soil and 11 Tg C yr−1 in forest floor. Deforestation caused emission averaging 12 Tg C yr−1: 3 Tg C yr−1 from soil and 9 Tg C yr−1 from forest floor. However, these effects were only 5% of the total change in carbon stocks in all forestland.
Impacts of Saharan dust as CCN on the evolution of an idealized tropical cyclone
Authors: Zhang Henian , McFarquhar Greg M. , Saleeby Stephen M. , Cotton William R.
Published: July 2007

The impact of dust in the Saharan Air Layer (SAL) acting as cloud condensation nuclei (CCN) on the evolution of a tropical cyclone (TC) was examined by conducting simulations initialized with an idealized pre‐TC mesoscale convective vortex (MCV) using the Regional Atmospheric Modeling System (RAMS). Increasing the background CCN concentration from 100 to 1000 and 2000 cm−3 in a layer between 1 and 5 km led to increases in averaged cloud droplet number concentration, and decreases in cloud droplet mean mass diameter through the entire simulation except during the initial spin‐up. Dust in the SAL as CCN influenced the TC development by inducing changes in the hydrometeor properties, modifying the storm diabatic heating distribution and thermodynamic structure, and ultimately influencing the TC intensity through complex dynamical responses. The simulated storm intensities differed by up to 22 hPa depending on CCN concentration. The impact of CCN on storm intensity was sensitive to the background giant CCN (GCCN) vertical profile and presumably other environmental factors. The physical processes responsible for the impact of dust as nucleating aerosols on TC development need to be examined in the future under a wide range of environmental conditions.
Tropical cyclones over the Mediterranean Sea in climate change simulations
Authors: Gaertner M. A. , Jacob D. , Gil V. , Domínguez M. , Padorno E. , Sánchez E. , Castro M.
Published: July 2007

Tropical cyclones form only under specific environmental conditions. Anthropogenic climate change might alter the geographical areas where tropical cyclones can develop. Using an ensemble of regional climate models, we find an increase in the extremes of cyclone intensity over the Mediterranean Sea under a climate change scenario. At least for the most sensitive model, the increase in intensity is clearly associated with the formation of tropical cyclones. Previous studies did not find evidence of changes in the projected areas of formation of tropical cyclones (Intergovernmental Panel on Climate Change, 2007; Walsh, 2004; Lionello et al., 2002). Those studies were based either on relatively low‐resolution global climate models or on one particular regional climate model. The use of a multi‐model ensemble of relatively high‐resolution regional climate models has allowed us to detect for the first time a risk of tropical cyclone development over the Mediterranean Sea under future climate change conditions.
Identifying the top of the tropical tropopause layer from vertical mass flux analysis and CALIPSO lidar cloud observations
Authors: Fu Qiang , Hu Yongxiang , Yang Qiong
Published: July 2007

We identify the top of the tropical tropopause layer (TTL) by analyzing the vertical mass flux profile based on radiative transfer calculations employing observed atmospheric profiles and cloud information. We find that the top of the TTL is located at ∼18.7 km (70 mb). We have analyzed the CALIPSO lidar cloud observations from June 2006 to February 2007, which indicates that almost no clouds occur above 19 km, consistent with the top of TTL based on vertical mass flux analyses. The total cloud fractions between 20°S and 20°N are about 0.05% at 18.5 km, 0.5% at 18.0 km and 5% at 17.0 km, where the clouds with optical depth larger than 0.5 contribute up to one tenth of these total cloud fractions. The clouds above 17 km mainly originate over the West Pacific, South America, Central Africa, and South Asia.
Stochastic embedding of dynamical systems
Authors: Cresson Jacky , Darses Sébastien
Published: July 2007

Most physical systems are modeled by an ordinary or a partial differential equation, like the n-body problem in celestial mechanics. In some cases, for example, when studying the long term behavior of the solar system or for complex systems, there exist elements which can influence the dynamics of the system which are not well modeled or even known. One way to take these problems into account consists of looking at the dynamics of the system on a larger class of objects that are eventually stochastic. In this paper, we develop a theory for the stochastic embedding of ordinary differential equations. We apply this method to Lagrangian systems. In this particular case, we extend many results of classical mechanics, namely, the least action principle, the Euler-Lagrange equations, and Noether’s theorem. We also obtain a Hamiltonian formulation for our stochastic Lagrangian systems. Many applications are discussed at the end of the paper.
Effect of methyl rotation on the electronic spectrum of the methyl peroxy radical
Authors: Just Gabriel M. P. , McCoy Anne B. , Miller Terry A.
Published: July 2007

Recent experiments have prompted a theoretical investigation of the effect of methyl rotation on the Ã-X̃ electronic spectrum of the CH3O2 and CD3O2 radicals. Quantum chemistry calculations have mapped the potential for the methyl rotation. Using these results, we calculate the torsional eigenvalues for both the Ã and X̃ states and simulate the Ã-X̃ spectrum. We find that the simulation captures the salient features of the spectrum. These features include torsional sequence structure, whose band contours change dramatically as the lower level nears the barrier, as well as atypical torsional transitions occurring from levels near the top and above the barrier. “Experimental” barrier heights are deduced for both the X̃ and Ã states of methyl peroxy by modestly scaling the calculated potential to best reproduce the observed spectra.
Reappraisal of criticality for two-layer flows and its role in the generation of internal solitary waves
Authors: Bridges Thomas J. , Donaldson Neil M.
Published: July 2007

A geometric view of criticality for two-layer flows is presented. Uniform flows are classified by diagrams in the momentum-massflux space for fixed Bernoulli energy, and cuspoidal curves on these diagrams correspond to critical uniform flows. Restriction of these surfaces to critical flow leads to new subsurfaces in energy-massflux space. While the connection between criticality and the generation of solitary waves is well known, we find that the nonlinear properties of these bifurcating solitary waves are also determined by the properties of the criticality surfaces. To be specific, the case of two layers with a rigid lid is considered, and application of the theory to other multilayer flows is sketched.
On the noncommutative and nonassociative geometry of octonionic space time, modified dispersion relations and grand unification
Authors: Castro Carlos
Published: July 2007

The octonionic geometry (gravity) developed long ago by Oliveira and Marques, J. Math. Phys. 26, 3131 (1985) is extended to noncommutative and nonassociative space time coordinates associated with octonionic-valued coordinates and momenta. The octonionic metric Gμν already encompasses the ordinary space time metric gμν, in addition to the Maxwell U(1) and SU(2) Yang-Mills fields such that it implements the Kaluza-Klein Grand unification program without introducing extra space time dimensions. The color group SU(3) is a subgroup of the exceptional G2 group which is the automorphism group of the octonion algebra. It is shown that the flux of the SU(2) Yang-Mills field strength Fμν through the area-momentum Σμν in the internal isospin space yields corrections O(1∕MPlanck2) to the energy-momentum dispersion relations without violating Lorentz invariance as it occurs with Hopf algebraic deformations of the Poincare algebra. The known octonionic realizations of the Clifford Cl(8), Cl(4) algebras should permit the construction of octonionic string actions that should have a correspondence with ordinary string actions for strings moving in a curved Clifford-space target background associated with a Cl(3, 1) algebra.
Ground-based prototype quantum cascade laser heterodyne radiometer for atmospheric studies
Authors: Weidmann D. , Reburn W. J. , Smith K. M.
Published: July 2007

The advent of quantum cascade lasers has provided matured continuously tunable solid state laser sources emitting from mid-infrared to terahertz wavelengths. Such sources, used as local oscillators, offer the practical prospect of aircraft, high altitude platform, and satellite deployment of compact and shot noise limited heterodyne radiometers for Earth observation and astronomy. A ground-based prototype of a quantum cascade laser heterodyne radiometer operating in the mid-infrared has been developed and is presented. The instrument design and concepts are described, together with evaluation of the instrument in the laboratory and during field measurements of atmospheric ozone. In this study the best performance achieved by the prototype quantum cascade laser heterodyne radiometer was a signal-to-noise ratio of three times the theoretical shot-noise limit. The prototype has allowed the main sources of excess noise to be identified as residual optical feedback in the local oscillator optical path and a lack of mechanical and thermal stability in the local oscillator collimation system. Instrument improvements are currently being implemented and enhanced performance is expected in the near future.
In situ mask designed for selective growth of InAs quantum dots in narrow regions developed for molecular beam epitaxy system
Authors: Ohkouchi Shunsuke , Nakamura Yusui , Ikeda Naoki , Sugimoto Yoshimasa , Asakawa Kiyoshi
Published: July 2007

We have developed an in situ mask that enables the selective formation of molecular beam epitaxially grown layers in narrow regions. This mask can be fitted to a sample holder and removed in an ultrahigh-vacuum environment; thus, device structures can be fabricated without exposing the sample surfaces to air. Moreover, this mask enables the observation of reflection high-energy electron diffraction during growth with the mask positioned on the sample holder and provides for the formation of marker layers for ensuring alignment in the processes following the selective growth. To explore the effectiveness of the proposed in situ mask, we used it to grow quantum dot (QD) structures in narrow regions and verified the perfect selectivity of the QD growth. The grown QDs exhibited high optical quality with a photoluminescence peak at approximately 1.30μm and a linewidth of 30meV at room temperature. The proposed technique can be applied for the integration of microstructures into optoelectronic functional devices.
Loss reduction in fully contacted organic laser waveguides using TE2 modes
Authors: Görrn P. , Rabe T. , Riedl T. , Kowalsky W.
Published: July 2007

A strategy to contact organic lasers is proposed. Without the need for thick transport layers that keep the optical mode away from the contacts waveguide losses similar to those of structures without contacts can be achieved. The key to this concept is to position the contacts in the intensity minima of the TE2 waveguide mode. This is accomplished by optical buffers outside the contacted device. Structures based on this idea are demonstrated and the waveguide losses are analyzed. A reduction of the waveguide losses by more than an order of magnitude compared to a device without optical buffers is observed.
Segregation of ion implanted sulfur in Si(100) after annealing and nickel silicidation
Authors: Zhao Q. T. , Breuer U. , Lenk St. , Mantl S.
Published: July 2007

Diffusion of sulfur (S) in S+ ion implanted Si(100) was investigated after rapid thermal annealing as well as after nickel silicidation. At lower S doses, S segregates to the Si(100) surface when the defects created by the S implantation are reduced during annealing. If the S dose exceeds the amorphization threshold, two heavily damaged regions with dislocation loops appear after annealing. It seems that S atoms form stable complexes with dislocation loops that survive even after high-temperature anneals at 900 °C. In contrast, when silicidation comes into play, S atoms appear more mobile. Even during Ni silicidation at 550 °C, segregation yields an enrichment of S at the NiSi/Si interface while the defect density and the S content in the deeper Si regions decrease.
Width-dependent upper threshold field for flux noise in MgB2 strips
Authors: Choi Eun-Mi , Lee Hyun-Sook , Lee Jae Yeap , Lee Sung-Ik , Olsen Å. A. F. , Yurchenko V. V. , Shantsev D. V. , Johansen T. H. , Kim Hyeong-Jin , Cho Moo-Hyun
Published: July 2007

The authors measured magnetization hysteresis curves and used magneto-optical imaging to visualize the flux distributions in superconducting MgB2 films in order to study dendritic flux avalanches. The flux avalanches are found to disappear above some upper threshold field that is typically ∼1kOe, but strongly depends on the film width. If the film is made wider, this threshold field first increases and then tends to saturate. This behavior is quantitatively explained using a thermomagnetic model for the dendritic avalanches and taking into account the field dependence of Jc. The results demonstrate that patterning superconducting films into narrow strips substantially increases the range of magnetic fields for which they can be used for applications.
Organic thin-film transistors using suspended source/drain electrode structure
Authors: Kim Yong-Hoon , Han Sang-Myeon , Lee Woocheul , Han Min-Koo , Lee Yong Uk , Han Jeong-In
Published: July 2007

The electrical properties of triisopropylsilyl pentacene organic thin-film transistors such as field-effect mobility, on/off ratio, threshold voltage, and subthreshold slope were markedly improved by employing suspended source/drain (SSD) electrode structure. The SSD structure was fabricated by using Cr∕Au double layer where Cr was used as a sacrificial layer. Using the SSD structure, the field-effect mobility in the linear region increases from 0.007to0.29cm2∕Vs, on/off ratio from 104 to 107, threshold voltage decreases from +9to−3V, and subthreshold slope decreases from 4.5to0.6V∕decade.
Temperature-power dependence of catastrophic optical damage in AlGaInP laser diodes
Authors: Bou Sanayeh M. , Brick P. , Schmid W. , Mayer B. , Müller M. , Reufer M. , Streubel K. , Tomm J. W. , Bacher G.
Published: July 2007

Facet temperature changes in broad-area red-emitting high-power AlGaInP lasers are analyzed by means of micro-Raman spectroscopy. Measurements as a function of injection current demonstrate that the temperature at the laser output facet rises linearly with optical output power. Temperature profile measurements across the laser stripe show a strong correlation between near field intensity, facet temperature, and catastrophic optical damage (COD). Additionally, temperature-power analyses reveal that a critical facet temperature is needed to induce COD. The consistent results produced by complementary measurement techniques indicate that absorption of stimulated photons at the laser facet is the major source of facet heating.
Change of the kinetics of solidification and microstructure formation induced by convection in the Ni–Al system
Authors: Reutzel S. , Hartmann H. , Galenko P. K. , Schneider S. , Herlach D. M.
Published: July 2007

The purpose of the present work was to measure the velocity of dendrite growth in undercooled Ni–Al alloy melts as a function of undercooling. The experiments were performed both by containerless electromagnetic levitation on Earth and under reduced gravity conditions during parabolic flight campaigns. While under terrestrial conditions, strong magnetic fields are required to compensate the gravitational force, the forces to compensate disturbing accelerations are decreased by orders of magnitude in reduced gravity. In turn, the alternating electromagnetic fields induce convection, which is strong under terrestrial conditions while much weaker in reduced gravity. The heat and mass transport in front of the solid-liquid interface during solidification controls the dynamics of dendrite growth. By comparing results obtained on Earth and in reduced gravity, it was demonstrated that the change of transport conditions by convection significantly alters the kinetics of solidification and the evolution of grain refined microstructures at undercoolings less than 100K.
Effect of internal electrostatic fields in InGaN quantum wells on the properties of green light emitting diodes
Authors: Wu Z. H. , Fischer A. M. , Ponce F. A. , Lee W. , Ryou J. H. , Limb J. , Yoo D. , Dupuis R. D.
Published: July 2007

Variations in the strength of the piezoelectric field inside InGaN quantum wells have been observed along the growth direction in InGaN-based diodes emitting light in the green region. The internal electrostatic potential distribution across the active region consisting of five InGaN quantum wells has been determined by electron holography in a transmission electron microscope. The strength of the piezoelectric field decreases in the direction towards the p-n junction. Its effect on light emission has been evaluated by depth-profiling cathodoluminescence, where the emission from two peaks becomes increasingly distinct with increasing excitation voltage. The drop in piezoelectric field strength is proposed to be related to the neutralization of piezoelectric charges by hydrogen ions which are initially abundant in the p region and diffuse into the quantum wells during thermal annealing.
All-optical reversible switching of local magnetization
Authors: Shevchenko A. , Korppi M. , Lindfors K. , Heiliö M. , Kaivola M. , Il’yashenko E. , Johansen T. H.
Published: July 2007

The authors demonstrate all-optical reversible switching of the magnetization direction in a uniformly magnetized ferrite-garnet film. The magnetization is switched by locally heating the film with a pulsed laser beam. The direction to which the magnetization flips is controlled by two parameters, the beam diameter and the pulse energy, and not by the direction of the external magnetic field. In the experiments, neither the magnitude nor the direction of the external magnetic field is changed. The results of this work illustrate the richness of optical methods to locally control the properties of magnetic materials and suggest all-optical device applications.
N
O
2
detection by adsorption induced work function changes in In2O3 thin films
Authors: Qazi Muhammad , Koley Goutam , Park Sangmoon , Vogt Thomas
Published: July 2007

A potentiometric sensor platform has been used for NO2 detection at room temperature by measuring the adsorption induced surface work function changes in In2O3 thin films deposited on Si using a solution based process. The highly resistive films were unsuitable for amperometric detection of NO2; however, significant work function changes of ∼30mV were measured for ∼50s of exposure to 70ppm NO2, and detection down to 600ppb (parts per 109) was possible. A model for the transient response was developed, which satisfactorily fits the experimental data. Acceleration of the desorption transient under ultraviolet illumination has also been investigated.
Microstructure and mechanical properties of sputtered intermetallic Al–Au coatings
Authors: Moser M. , Mayrhofer P. H. , Ross I. M. , Rainforth W. M.
Published: July 2007

Intermetallic Al-based coatings such as Al–Ni, Al–Cr, and Al–Pt are widely used as bond coats and/or as oxidation protection of turbine blades. Investigations during earlier work indicated promising thermal stability and oxidation resistance of intermetallic Al2Au-based coatings. Hence, here we study in detail the microstructure and mechanical properties of unbalanced magnetron sputtered Al–Au films with Al∕Au at. % ratios of 1.85, 2.00, and 4.32. The film with an Al∕Au ratio of 2.00 has a single-phase Al2Au dense columnar structure in the as-deposited state and a hardness of ∼8GPa. With increasing Al and Au contents the morphology changes into a more equiaxed structure with additional Al, AlAu, and Au phases, respectively. During growth, excess Al of the film with an Al∕Au ratio of 4.32 forms lamellar nanosegregations (∼3nm thick) in the Al2Au domains. The simultaneous nucleation and growth of Al2Au, AlAu, and Au phases in the coatings with an Al∕Au ratio of 1.85, with their different growth mechanisms, leads to the formation of pores having an average size of ∼150nm. These Al- and Au-rich films, compared to Al2Au, have reduced hardnesses of ∼4 and ∼2GPa, respectively, due to the additional soft metallic phases and pores present. Our results show that within the Al–Au system the single-phase intermetallic Al2Au films exhibit the best structural and mechanical properties for protecting oxidation sensitive materials.
Correlated network activity enhances synaptic efficacy via BDNF and the ERK pathway at immature CA3–CA1 connections in the hippocampus
Authors: Mohajerani Majid H. , Sivakumaran Sudhir , Zacchi Paola , Aguilera Pedro , Cherubini Enrico
Published: July 2007

At early developmental stages, correlated neuronal activity is thought to exert a critical control on functional and structural refinement of synaptic connections. In the hippocampus, between postnatal day 2 (P2) and P6, network-driven giant depolarizing potentials (GDPs) are generated by the synergistic action of glutamate and GABA, which is depolarizing and excitatory. Here the rising phase of GDPs was used to trigger Schaffer collateral stimulation in such a way that synchronized network activity was coincident with presynaptic activation of afferent input. This procedure produced a persistent increase in spontaneous and evoked α-amino-3-hydroxy-5-methyl-4-isoxadepropionic acid-mediated glutamatergic currents, an effect that required calcium influx through postsynaptic L-type calcium channels. No potentiation was observed when a delay of 3 sec was introduced between GDPs and afferent stimulation. Pairing-induced potentiation was prevented by scavengers of endogenous BDNF or tropomyosin-related kinase receptor B (TrkB) receptor antagonists. Blocking TrkB receptors in the postsynaptic cell did not prevent the effects of pairing, suggesting that BDNF, possibly secreted from the postsynaptic cell during GDPs, acts on TrkB receptors localized on presynaptic neurons. Application of exogenous BDNF mimicked the effects of pairing on synaptic transmission. In addition, pairing-induced synaptic potentiation was blocked by ERK inhibitors, suggesting that BDNF activates the MAPK/ERK cascade, which may lead to transcriptional regulation and new protein synthesis in the postsynaptic neuron. These results support the hypothesis that, during a critical period of postnatal development, GABA
A
-mediated GDPs are instrumental in tuning excitatory synaptic connections and provide insights into the molecular mechanisms involved in this process.
How fast small things become large: Dynamic change in judgment
Authors: Elfering Achim
Published: July 2007

Judgments are context bound. Moreover, in most situations, context is changing; hence judgments often reflect a dynamic adaptation to these changes. This study is on working memory load as a factor that potentially moderates speed of adaptation to new context. Two specific stimulus formats used in generalization tests, simultaneous vs successive presentation, were intended to reflect substantial differences in memory load. Conditions that place a higher memory load on the respondent (successive presentation) should show slower changing effects than do conditions that entail a lower memory load (simultaneous presentation). Sixty participants were trained in two stimulus two forced‐choice visual discriminations of size. Later generalization tests included more extreme visual stimuli. The stimulus that was seen as neither “small” nor “large” (50% ratings each) changed in the direction of the central stimuli within the stimulus series, with both successive and simultaneous stimulus presentation (adaptation). Multilevel regression analyses showed that change increased gradually in successive stimulus presentation, whereas change was immediate in simultaneous presentation. A significant three‐way interaction indicated that generalization was faster with simultaneous presentation of generalization test stimuli than with successive presentation. The results showed that the speed of Point of Subjective Indifference (PSI) shift depends on the mental representation of experience that is strongly related to working memory. The study therefore makes a contribution to the understanding the speed of behavioural change during transition, e.g., the transition from school to work. On a macro‐level, model application may assist rapid learning and behavioural adaptation, for instance when individuals change from one cultural context to another.
Common themes and variations in the rhodanese superfamily
Authors: Cipollone Rita , Ascenzi Paolo , Visca Paolo
Published: July 2007

The rhodanese homology domain is a ubiquitous fold found in several phylogenetically related proteins encoded by eubacterial, archeal, and eukaryotic genomes. Although rhodanese‐like proteins share evolutionary relationships, analysis of their sequences highlights that they are so heterogeneous to form the rhodanese superfamily. The variability occurs at different levels including sequence, active site loop length, presence of a critical catalytic Cys residue, and domain arrangement. Even within the same genome, multiple genes encode rhodanese‐like proteins presenting with variably arranged rhodanese domain(s): as single or tandem domain(s), or combined with other protein domain(s). Given the highly variable organization of the rhodanese domain(s) and the context where it is found, here we review the structural organization and function of the rhodanese‐like proteins. The overview of the most recent findings about rhodanese allow us to depict a superfamily of versatile proteins relying on persulfide chemistry to accomplish cellular functions spanning from resistance to environmental threats, such as cyanide, and key cellular reactions related to sulfur metabolism and progression of cell cycle.
IUBMB Life, 59: 51‐59, 2007
Calcium, iron and neuronal function
Authors: Hidalgo Cecilia , Núñez Marco T.
Published: July 2007

Calcium and iron play dual roles in neuronal function: they are both essential but when present in excess they cause neuronal damage and may even induce neuronal death. Calcium signals are required for synaptic plasticity, a neuronal process that entails gene expression and which is presumably the cellular counterpart of cognitive brain functions such as learning and memory. Neuronal activity generates cytoplasmic and nuclear calcium signals that in turn stimulate pathways that promote the transcription of genes known to participate in synaptic plasticity. In addition, evidence discussed in this article shows that iron deficiency causes learning and memory impairments that persist following iron repletion, indicating that iron is necessary for normal development of cognitive functions. Recent results from our group indicate that iron is required for long‐term potentiation in hippocampal CA1 neurons and that iron stimulates ryanodine receptor‐mediated calcium release through ROS produced via the Fenton reaction leading to stimulation of the ERK signaling pathway. These combined results support a coordinated action between iron and calcium in synaptic plasticity and raise the possibility that elevated iron levels may contribute to neuronal degeneration through excessive intracellular calcium increase caused by iron‐induced oxidative stress.
IUBMB Life, 59: 280‐285, 2007
The tammar wallaby: A model to examine endocrine and local control of lactation
Authors: Brennan Amelia J. , Sharp Julie A. , Digby Matthew R. , Nicholas Kevin R.
Published: July 2007

WORTH A SECOND LOOK
From time to time we republish review articles from the Australian Biochemist, the magazine of the Australian Society for Biochemistry and Molecular Biology Inc. This exposes these excellent reviews to a much wider and different readership. Here we republish a review on the tammar wallaby that originally appeared in the Australian Biochemist, volume 57, no. 2, August 2006.
We are most grateful for the permission of the authors and of Rebecca Lew, the Editor of the Australian Biochemist, to republish the review. Dr Lew is also an IUBMB Life Editor.
Marsupials, such as the tammar wallaby (Macropus eugenii), have adopted a reproductive strategy that is very different to eutherians. Both the rate of production and the composition of milk changes progressively during the lactation cycle to meet the nutritional demands of an altricial young. The tammar therefore provides a valuable model to study changes in milk composition, and in particular the genes that code for proteins secreted in the milk, to more accurately assess the role of gene products regulating either development of the young or mammary function.
IUBMB Life, 59: 146‐150, 2007
Gene response elements, genetic polymorphisms and epigenetics influence the human dietary requirement for choline
Authors: Zeisel Steven H.
Published: July 2007

Recent progress in the understanding of the human dietary requirement for choline highlights the importance of genetic variation and epigenetics in human nutrient requirements. Choline is a major dietary source of methyl‐groups (one of choline's metabolites, betaine, participates in the methylation of homocysteine to form methionine); also choline is needed for the biosynthesis of cell membranes, bioactive phospholipids and the neurotransmitter acetylcholine. A recommended dietary intake for choline in humans was set in 1998, and a portion of the choline requirement can be met via endogenous de novo synthesis of phosphatidylcholine catalyzed by phosphatidylethanolamine N‐methyltransferase (PEMT) in the liver. Though many foods contain choline, many humans do not get enough in their diets. When deprived of dietary choline, most adult men and postmenopausal women developed signs of organ dysfunction (fatty liver, liver or muscle cell damage, and reduces the capacity to handle a methionine load, resulting in elevated homocysteine). However, only a portion of premenopausal women developed such problems. The difference in requirement occurs because estrogen induces expression of the PEMT gene and allows premenopausal women to make more of their needed choline endogenously. In addition, there is significant variation in the dietary requirement for choline that can be explained by common polymorphisms in genes of choline and folate metabolism. Choline is critical during fetal development, when it alters DNA methylation and thereby influences neural precursor cell proliferation and apoptosis. This results in long term alterations in brain structure and function, specifically memory function.
IUBMB Life, 59: 380 ‐ 387, 2007
Heme binding to albuminoid proteins is the result of recent evolution
Authors: Fasano Mauro , Fanali Gabriella , Leboffe Loris , Ascenzi Paolo
Published: July 2007

We hypothesize that the structure of the heme binding site of paralogous albuminoids alpha‐fetoprotein and serum albumin has evolved from the ancestor vitamin D binding protein through the 'phylogenetic intermediate' afamin, the most recently discovered albuminoid. Heme binding to plasma proteins should serve not only as a buffer for heme homeostasis, avoiding heme binding to lipoproteins with the consequent oxidative stress, but also for heme transfer to the liver, complementing the function of hemopexin.
iubmb Life, 59: 436‐440, 2007
INK4 proteins, a family of mammalian CDK inhibitors with novel biological functions
Authors: Cánepa Eduardo T. , Scassa María E. , Ceruti Julieta M. , Marazita Mariela C. , Carcagno Abel L. , Sirkin Pablo F. , Ogara María F.
Published: July 2007

The cyclin D‐Cdk4‐6/INK4/Rb/E2F pathway plays a key role in controlling cell growth by integrating multiple mitogenic and antimitogenic stimuli. The members of INK4 family, comprising p16INK4a, p15INK4b, p18INK4c, and p19INK4d, block the progression of the cell cycle by binding to either Cdk4 or Cdk6 and inhibiting the action of cyclin D. These INK4 proteins share a similar structure dominated by several ankyrin repeats. Although they appear to be structurally redundant and equally potent as inhibitors, the INK4 family members are differentially expressed during mouse development. The striking diversity in the pattern of expression of INK4 genes suggested that this family of cell cycle inhibitors might have cell lineage‐specific or tissue‐specific functions. The INK4 proteins are commonly lost or inactivated by mutations in diverse types of cancer, and they represent established or candidate tumor suppressors. Apart from their capacity to arrest cells in the G1‐phase of the cell cycle they have been shown to participate in an increasing number of cellular processes. Given their emerging roles in fundamental physiological as well as pathological processes, it is interesting to explore the diverse roles for the individual INK4 family members in different functions other than cell cycle regulation. Extensive studies, over the past few years, uncover the involvement of INK4 proteins in senescence, apoptosis, DNA repair, and multistep oncogenesis. We will focus the discussion here on these unexpected issues.
iubmb Life, 59: 419‐426, 2007
Let's stick together: The role of the Fras1 and Frem proteins in epidermal adhesion
Authors: Short Kieran , Wiradjaja Fenny , Smyth Ian
Published: July 2007

The Fras1 and Frem extracellular matrix proteins play critical roles in epithelial‐mesenchymal interaction during embryonic development. Loss of function in humans results in a recessive embryonic blistering disorder called Fraser syndrome. Inactivation of these proteins, or the proteins with which they interact (e.g., Grip1) has also been shown to underlie members of the 'bleb' family of classic mouse mutants which provide a valuable model of Fraser syndrome. Recent studies supporting direct interactions between the Fras1 and Frem proteins, combined with more rigorous elucidation of their developmental regulation, have shed new light on their activity. We summarize the findings to date, bringing new insight into their role in the regulation of epidermal‐basement membrane adhesion and organogenesis during development.
iubmb Life, 59: 427‐435, 2007
Blocking SCF/c‐Kit signal did not inhibit the proliferation of cultured liver progenitor cells
Authors: Jin Caixia , Li Wenlin , Xu Fang , Zhu Ji , He Zhiying , Hu Yiping
Published: July 2007

Oval cells are the putative liver stem cells that proliferate during hepatocarcinogenesis and chemically‐induced severe liver injury. Antigens traditionally associated with haematopoietic cells, such as c‐Kit, have been reported to be expressed by oval cells. Previous studies suggested that stem cell factor (SCF) and c‐Kit were critical to oval cell development. However, the role of SCF/c‐Kit signals in oval cell proliferation still remains unclear. Recently, we reported the establishment of oval cell‐derived liver epithelial progenitor cells (LEPCs). In this work, we showed LEPCs co‐expressed c‐Kit and its ligand SCF. The involvement of SCF/c‐Kit signals in LEPCs proliferation was investigated either by exposing LEPCs to c‐Kit inhibitors (STI571 and AG1296), SCF, anti‐SCF neutralized antibody or by using small interfering RNA to knock‐down c‐Kit expression. Our data demonstrate that blocking SCF/c‐Kit signal did not inhibit the proliferation of LEPCs, which suggest SCF/c‐Kit is not necessary for the proliferation of oval cells, at least for the cultured oval cell counterpart LEPCs.
iubmb Life, 59: 458‐464, 2007
Optimal Layout of Multicast Groups Using Network Embedded Multicast Security in Ad Hoc Sensor Networks
Authors: Brooks R. R. , Pillai Brijesh , Weigle Michele C. , Pirretti Matthew
Published: July 2007

This paper considers the security of sensor network applications. Our approach creates multicast regions that use symmetric key cryptography for communications. Each multicast region contains a single keyserver that is used to perform key management and maintain the integrity of a multicast region. Communications between two multicast regions is performed by nodes that belong to both regions. To ease the network management burden, it is desirable for the networks to self-organize into regions and dynamically select their keyservers. This paper shows how to determine the number of keyservers ( k) to use and the size in the number of hops ( h) of their multicast regions. We find that power consumption issues provide a natural trade-off that determines optimal values for these parameters. Analysis of one application shows an increase in system security with 70-80% less power overhead than existing security approaches.
Estimation of the Hyperexponential Density with Applications in Sensor Networks
Authors: Singh Larry N. , Dattatreya G. R.
Published: July 2007

This paper solves the problem of estimation of the parameters of a hyperexponential density and presents a practical application of the solution in sensor networks. Two novel algorithms for estimating the parameters of the density are formulated. In the first algorithm, an objective function is constructed as a function of the unknown component means and an estimate of the cumulative distribution function (cdf) of the hyperexponential density. The component means are obtained by minimizing this objective function, using quasi-Newtonian techniques. The mixing probabilities are then computed using these known means and linear least squares analysis. In the second algorithm, an objective function of the unknown component means, mixing probabilities, and an estimate of the cdf is constructed. All the 2M parameters are computed by minimizing this objective function, using quasi-Newtonian techniques. The developed algorithms are also compared to the basic EM algorithm, and their relative advantages over the EM algorithm are discussed. The algorithms developed are computationally efficient and easily implemented, and hence, are suitable for low-power and sensor nodes with limited storage and computational capacity. In particular, we demonstrate how the structure of these algorithms may be exploited to be effectively utilized in practical situations, and are hence ideal for sensor networks.
The healthcare of older inmates in the correctional setting
Authors: Potter Emily , Cashin Andrew , Chenoweth Lynn , Jeon Yun‐Hee
Published: July 2007

Australia, like other western nations, is experiencing a new trend within its prison population ‐ the ageing inmate. This ‘greying’ of the population presents a unique challenge for the correctional environment. Specific needs of this population may not be well met within a correctional facility due to the physical environment layout and surroundings, restricted health service access and unaccommodating facilities and programmes. This is compounded by limited visits from family and friends. This paper outlines some of the general needs of the older male inmate and the difficulties this poses for correctional and health services. Current international initiatives and programmes used to address the ageing population’s needs are briefly examined, as are the implications for Australian and international correctional and health services wishing to implement such schemes. The
applicability of Government Legislation, pertaining to the standards of care in the community, to correctional aged care programmes and facilities is discussed.
Evaluation of a prison‐based naltrexone program
Authors: Shearer James , Wodak Alex D. , Dolan Kate A.
Published: July 2007

The study evaluated the introduction of naltrexone in an Australian prison system for imprisoned male heroin users. Treatment outcomes were analysed for two sub‐samples taken from an unsuccessful randomised controlled trial. The first sample comprised 68 participants who were randomly allocated to naltrexone treatment. The second sample comprised 47 participants who commenced opioid pharmacotherapy during the study period. Thirteen per cent of subjects started naltrexone, with only 7% retained in treatment at six months. Six‐month retention was significantly lower in naltrexone compared to methadone (p = 0.0007). Poor patient acceptability and retention did not support oral naltrexone maintenance in this treatment group.
Time‐dependent inhibition of human drug metabolizing cytochromes P450 by tricyclic antidepressants
Authors: Polasek Thomas M. , Miners John O.
Published: July 2007

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Much of the literature evidence for mechanism‐based inactivation (MBI) of CYP by tricyclic antidepressants is limited to studies in rat liver microsomes.

• One report from this laboratory characterized MBI of human recombinant CYP2C8 by nortriptyline.

WHAT THIS STUDY ADDS

• Tricyclic antidepressants form alkylamine metabolite‐intermediate complexes with human recombinant CYP enzymes (expressed inEscherichia coli) relatively easily, resulting in time‐dependent inhibition.

• Evidence to support similar irreversible inhibition using human liver microsomal (HLM) fractions is limited.

• HLM and recombinant CYP (expressed inE. coli) are not equivalent enzyme sources for evaluating the time‐dependent inhibition of human drug metabolizing CYP that is associated with some drugs.

AIMS

To investigate time‐dependent inhibition (TDI) of human drug metabolizing CYP enzymes by tricyclic antidepressants (TCAs).

METHODS

CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A/CYP3A4 activities were investigated following co‐ and preincubation with TCAs using human liver microsomes (HLM) and human recombinant CYP proteins (expressed inEscherichia coli) as the enzyme sources. A two‐step incubation method was employed to examine thein vitromechanism‐based inactivation (MBI) criteria. Potential metabolite–intermediate complex (MIC) formation was studied by spectral analysis.

RESULTS

TCAs generally exhibited significant TDI of recombinant CYP1A2, CYP2C19 and CYP2D6 (>10% positive inhibition differences between co‐ and preincubation conditions). TDI of recombinant CYP2C9 was minor (<10%), and was minor or absent in experiments utilizing recombinant CYP3A4 or HLM as the enzyme sources. Where observed, TDI of recombinant CYP occurred via alkylamine MIC formation, but evidence to support similar behaviour in HLM was limited. Indeed, only secondary amine TCAs reduced the apparent P450 content of HLM (3–6%) consistent with complexation. As a representative TCA, nortriptyline fulfilled thein vitroMBI criteria using recombinant CYP2C19 and CYP3A4 (KIandkinactvalues of 4 µmand 0.19 min−1, and 70 µmand 0.06 min−1), but not with the human liver microsomal enzymes.

CONCLUSIONS

TCAs appear to have minimal potential for MBI of human liver microsomal CYP enzymes involved in drug metabolism. HLM and recombinant CYP (expressed inE. coli) are not equivalent enzyme sources for evaluating the TDI associated with some drugs.
Adverse drug reaction monitoring in a secondary care hospital in South India
Authors: Arulmani R. , Rajendran S.D. , Suresh B.
Published: July 2007

What is already known about this subject

• The benefits of adverse drug reaction (ADR) monitoring are well‐known.

• Poor awareness and nonavailability of a central co‐ordinating body resulted in lack of ADR monitoring in India.

• The National Pharmacovigilance Programme was recently initiated, encouraging ADR monitoring in selected centres, including our centre.

What this study adds

• This is the first study of its kind at GHQH, Ootacamund that has provided insight into the burden of ADRs here.

• The incidence and severity of ADRs documented in our study is lower than those reported in comparable populations in Western studies but more than those reported in India.

Aims

To ascertain the current burden of ADRs at a Government hospital in Ooty and to assess the severity of reported ADRs and the additional financial burden associated with ADRs.

Methods

A prospective, spontaneous reporting study was conducted over a period of 9 months of inpatient admissions to the medical wards, co‐ordinated by clinical pharmacists. The WHO definition of an ADR was adopted. The Naranjo algorithm scale was used for causality assessment. Confirmed ADRs were classified according to the Wills & Brown [7] method and assessed for severity and patient outcomes. The average cost incurred in treating the ADRs was calculated.

Results

Of the total of 187 adverse drug events (ADEs) reported, 164 reports from 121 patients were confirmed as ADRs, giving an overall incidence of 9.8%. This included 58 (3.4%) ADR related admissions and 63 (3.7%) ADRs occurring during the hospital stay. About two thirds of the reactions (102, 62.2%) were classified as probable. The majority of the reactions (88, 53.7%) were mild. Most patients (119, 72.6%) recovered from the incidence. The majority of the reactions were of type H (100, 61%) which indicates that they were not predictable and not potentially preventable. An average cost of 481 rupees (£6) was spent on each patient to manage ADRs.

Conclusions

The incidence and severity of ADRs documented in our study are lower than those reported in comparable populations in Western studies but more than those reported in India.