bluuebunny/crossref_metadata_2025 huggingface dataset:
Large eddy simulation of a plane turbulent wall jet
Authors: Dejoan A. , Leschziner M. A.
Published: December 2004

The mean-flow and turbulence properties of a plane wall jet, developing in a stagnant environment, are studied by means of large eddy simulation. The Reynolds number, based on the inlet velocity Uo and the slot height b, is Re=9600, corresponding to recent well-resolved laser Doppler velocimetry and pulsed hot wire measurements of Eriksson et al. The relatively low Reynolds number and the high numerical resolution adopted (8.4 million nodes) allow all scales larger than about 10 Kolmogorov lengths to be captured. Of particular interest are the budgets for turbulence energy and Reynolds stresses, not available from experiments, and their inclusion sheds light on the processes which play a role in the interaction between the near-wall layer and the outer shear layer. Profiles of velocity and turbulent Reynolds stresses in the self-similar region are presented in inner and outer scaling and compared to experimental data. Included are further results for skin friction, evolution of integral quantities and third-order moments. Good agreement is observed, in most respects, between the simulated flow and the corresponding experiment. The budgets demonstrate, among a number of mechanisms, the decisive role played by turbulent transport (via the third moments) in the interaction region, across which information is transmitted between the near-wall layer and the outer layer.
Noise resolution of RuO2-based resistance thermometers
Authors: Ptak Piotr , Kolek Andrzej , Zawislak Zbigniew , Stadler Adam W. , Mleczko Krzysztof
Published: December 2004

Low-frequency noise was measured for RuO2-based thick film resistors at liquid helium temperatures down to 0.36 K. The 1∕f-type spectrum and squared voltage dependence of power spectral density observed at low voltages attribute the noise as coming from equilibrium resistance fluctuations. Measurements carried out at different temperatures show that the magnitude of noise intensity (index) increases significantly as temperature goes down. Due to this fact, the resolution of RuO2 thermometers increases above the instrument resolution. The quantity which describes a sensor resolution is defined and calculated for RuO2 thick film sensor. Some remarks on measurement strategy and sensor optimization are supplied.
A compact and portable PC-based Gundestrup–Langmuir probe diagnostic system
Authors: Sicard P. , Boucher C. , Litnovsky A. , St-Germain J.-P.
Published: December 2004

A compact Gundestrup–Langmuir probe diagnostics system capable of data acquisition as well as data analysis was conceived at INRS-EMT, Canada, and used at IPP-FZJ, Germany. Data acquisition and analysis can be done with this system using several types of probes (Langmuir, double-Langmuir, Mach, Gundestrup,…). The versatility as to the different types of probe that one can use and the relative small size of the whole system makes it advantageous. Using a laptop computer makes the system small size and highly portable. The system acquires data at 1000scans∕s at 12bit resolution on two probe systems simultaneously, using a total of 12 input channels. Bias is done by a DAC-ADC card and is amplified to give a ±100V sweeping range. Measured temperatures ranged from 0.75eVto6.0eV with densities observed as low as 1×1010cm−3 up to 5×1011cm−3, which are the range of conditions to be found in our experimental device. This system is also easy to reproduce since the hardware is commercially available and the scripts can be duplicated and modified according to the specifics of the hardware.
The influence of dietary energy intake on growth performance and tissue deposition in pigs between 80 and 120 kg liveweight
Authors: King R. H. , Campbell R. G. , Smits R. J. , Morley W. C. , Ronnfeldt K. , Butler K. L. , Dunshea F. R.
Published: December 2004

Eighty crossbred pigs of a composite genotype were allocated at 80 kg liveweight to a 2 × 5 factorial experiment involving 2 sexes (boars and gilts) and 5 levels of dietary energy intake ranging from about 55% estimated ad libitum up to 100% ad libitum intake. The diet was formulated to be protein-adequate and contained 14.4 MJ DE/kg and 0.55 g available lysine/MJ DE and the pigs were slaughtered at approximately 120 kg liveweight. Growth rate and food conversion efficiency increased linearly, in response to increasing digestible energy (DE) intake, with boars consistently out-performing gilts at each level of DE intake. Protein deposition rate in the whole empty body of pigs was consistently higher in boars than in gilts and linearly related to DE intake in both sexes, with no evidence of a plateau at high energy intakes, suggesting no intrinsic limit to protein deposition in these pigs up to 120 kg liveweight. When pigs were offered the protein-adequate diet ad libitum between 80 and 120 kg liveweight, boars and gilts consumed 47.7 and 40.9 MJ DE/day, respectively, and protein deposition rates in the whole empty body of pigs reached 247 and 182 g/day, respectively. Maintenance energy requirements were estimated to be 351 kJ DE/kg0.75.day for both boars and gilts [maximal model; including nominal DE level (treated as a 5-level factor), actual DE intake (treated as a continuous variable), and sex (treated as a 2-level factor)] or 506 and 566 kJ DE/kg0.75.day for boars and gilts, respectively [reduced model; including actual DE intake (treated as a continuous variable) and sex (treated as a 2-level factor)]. Statistical analyses show that the maximal model reflects the data more closely than the minimal model, suggesting that the lower maintenance estimate of 351 kJ DE/kg0.75.day could reflect reality better. In conclusion, genetically improved boars, and to a lesser extent gilts, have a high capacity for lean growth, and their upper limit to protein retention might not be reached below about 120 kg liveweight.
Impact of phosphorus application and sheep grazing on the botanical composition of sown pasture and naturalised, native grass pasture
Authors: Hill J. O. , Simpson R. J. , Moore A. D. , Graham P. , Chapman D. F.
Published: December 2004

Botanical composition (basal cover) was measured in 4 replicated pasture treatments based on Phalaris aquatica and Trifolium subterraneum at Hall, ACT (unfertilised with low and high stocking rate; fertilised with low and high stocking rate) and in 2 unreplicated pasture treatments based on native perennial grasses (Austrodanthonia spp. and Microlaena stipoides) and T. subterraneum at Bookham, NSW (unfertilised and low stocking rate; fertilised and high stocking rate). Current economic pressures are encouraging graziers to increase their use of phosphorus (P) fertiliser and to adopt higher stocking rates. The objective of the research was to determine the changes in botanical composition that may result from these changes in grazing systems management. At Hall, annual species differed in their responses to P fertility. Notably, basal cover of Bromus spp. increased significantly with P application, whereas Vulpia spp. decreased significantly. Basal cover of T. subterraneum also increased significantly with P application when stocking rate was high, but was reduced by P application if stocking rate was low. Basal cover of perennial grasses (P. aquatica and Holcus lanatus) was significantly higher at low stocking rate when P was applied. The botanical composition of high stocking rate treatments was relatively stable over time, which contrasted with less stable composition at low stocking rate. At Bookham, fertilised pasture in unreplicated paddocks appeared to have a higher basal cover of productive annual species (i.e. Bromus spp. and T. subterraneum), but native perennial grasses appeared to have lower basal cover in comparison with the unfertilised area. These results indicated that in some cases, the influence of P fertiliser and high stocking rates on botanical composition was favourable (i.e. increased basal cover of P. aquatica and T. subterraneum) and in others it could be detrimental (i.e. lower basal cover of native perennial grasses).
Effect of physical form of a lucerne hay on rumination and the passage of particles from the rumen of sheep
Authors: Faichney G. J. , Brown G. H.
Published: December 2004

Six 2-year-old Corriedale wethers fitted with rumen and abomasal cannulas were given a lucerne hay, first as chopped (CH) hay then as ground and pelleted (GP) hay. Intake rate increased as dry matter intake (DMI) increased and was greater on GP hay. The time spent eating and ruminating per unit of DMI decreased as DMI increased and was shorter on GP. Ruminating efficiency increased with DMI but did not differ between CH hay and GP hay. The critical size of particles for passage from the rumen was not affected by either DMI or by grinding and pelleting. Most of the overall digestion of large particles (LP) occurred during their retention in the LP pool within the rumen, and retention in the medium particle (MP) pool accounted for much of the rumen mean retention time of particles. The residual digestible material of MP derived from LP by rumination appeared to be less accessible to fermentative activity. Prediction of an animal’s response to the grinding and pelleting of forage must take account of all the determining factors and their interactions.
Photodissociation Dynamics of Vinyl Chloride Investigated with a Pulsed Slit-Jet and Time-Resolved Fourier-Transform Spectroscopy
Authors: Bahou Mohammed , Lee Yuan-Pern
Published: December 2004

Following photodissociation of vinyl chloride seeded in a He supersonic jet at 193 nm, rotationally resolved infrared emission of HCl (v) are recorded to yield nascent rotational and vibrational distributions. Preliminary results show that the rotational distribution of HCl free from rotational quenching deviates slightly from Boltzmann-type distribution and agrees well with trajectory calculations; a portion of the low-J component observed previously in a flow system is attributed to quenching. The implications for photodissociation dynamics are discussed.
Solvation Structure of NaI on the Surface of Ethanol Solution
Authors: Mafuné Fumitaka , Kondow Tamotsu
Published: December 2004

An ethanol solution of sodium iodide (NaI) was introduced into a vacuum as a continuous liquid flow (liquid beam), and the surface of the solution was illuminated by a laser with a wavelength of 118 nm. The kinetic energies of photoelectrons emitted from the surface were measured as a function of NaI concentration in the solution. The photoelectron spectra thus obtained exhibit peaks associated with I− and (NaI)n which are solvated by ethanol. It was concluded that NaI aggregates into clusters, (NaI)n, on the ethanol solution surface, in agreement with previous photo-ion mass spectrometry studies.
DFT Calculations on Group 5 Mixed Metal Tetramers: TaxNbyVz (x + y + z = 4)
Authors: Addicoat Magdalene A. , Buntine Mark A. , Metha Gregory F.
Published: December 2004

We report Density Functional Theory (DFT) calculations on mixed-metal tetramers comprised of the Group 5 (Vb) elements V, Nb, and Ta. Our results show that the lowest energy structures for Nb4 and Ta4 are regular tetrahedra with Td symmetry and singlet multiplicity whereas V4 is a triplet state with C2v symmetry. The monosubstituted isomers, A3B, all have C3v symmetry but several higher energy Cs structures have been found that are approximately 100 kJ mol−1 higher in energy. The disubstituted isomers all posses arachno-butterfly structures; the A2B2 types with C2v symmetry and the A2BC types with Cs symmetry. However, the relative openness of the arachno structures is found to be specific to the composition of the mixed-metal cluster.
Molecular Electronics: From Basic Chemical Principles to Photosynthesis to Steady-State Through-Molecule Conductivity to Computer Architectures
Authors: Reimers Jeffrey R. , Bilić Ante , Cai Zheng-Li , Dahlbom Mats , Lambropoulos Nicholas A. , Solomon Gemma C. , Crossley Maxwell J. , Hush Noel S.
Published: December 2004

Molecular electronics offers many possibilities for the development of electronic devices beyond the limit of silicon technology. Its basic ideas and history are reviewed, and a central aspect of the delocalization of electrons across molecules and junctions is examined. Analogies between key processes affecting steady-state through-molecule conduction and equilibrium geometric and spectroscopic properties of paradigm molecules, such as hydrogen, ammonia, benzene, and the Creutz–Taube ion are drawn, and the mechanisms by which control can be exerted over molecular-electronic processes during biological photosynthesis are examined. Ab initio molecular dynamics and simulations of conductivity are then presented for carbon nanotube flanged to gold(111), and device characteristics are calculated for a molecular shift register clocked by two gold electrodes.
Double Proton Transfer using Dissociable Force Fields
Authors: Lammers Sven , Meuwly Markus
Published: December 2004

The construction, implementation, and use of dissociable classical force fields are discussed. Starting from zeroth-order interaction potentials for O2H5+ and N2H7+ calculated with MP2/6–311++G**, energy scaling of the potential energy surfaces allows adjustment of quantities such as the barrier heights to describe a range of physical situations observed in realistic systems. As an example, ‘potential morphing’ is used to investigate the dynamics of double proton transfer in 2-pyridone · 2-hydroxypyridine for which previous estimates of the barrier to tautomerization are available. Scaling factors to give barrier heights for double proton transfer between 3.6 and 17.6 kcal mol−1 are chosen to demonstrate the utility of the method to describe a range of different barrier heights and shapes. Considerable savings in computing time can be achieved compared to alternative methods such as mixed quantum/classical methods.
Do polyamines modulate the Lotus glaber NADPH oxidation activity induced by the herbicide methyl viologen?
Authors: Cuevas Juan C. , Sánchez Diego H. , Marina María , Ruiz Oscar A.
Published: December 2004

In recent years, there has been a growing interest in NADPH-oxidases which are involved in the active generation of reactive oxygen species (ROS), owing to their role in oxidative burst, signalling and oxidative damage derived from biotic and abiotic stresses. NADPH oxidase activity is enhanced by some environmental cues, such as zinc deficiency and chilling stress, where zinc and polyamines have been suggested to be involved in the modulation of ROS generation. In order to further characterise NADPH oxidation activity during oxidative stress we exposed Lotus glaber Mill. (narrow-leaf trefoil; syn. L. tenuis Waldst. et Kit. ex Wild var. Miller) plants to the herbicide methyl viologen (MV) and evaluated zinc and polyamines as oxidative stress regulatory compounds. For this purpose we conducted in vitro and in vivo experiments, observing that zinc and the higher polyamines spermidine and spermine inhibited the NADPH oxidation activity in vitro while preventing methyl viologen-induced superoxide production in vivo. It is suggested that these substances act through a direct effect on flavin oxidases. However, it was not possible to correlate free polyamine content of L. glaber with their hypothetical inhibitory role during oxidative stress, probably owing to the plant’s natural tolerance to the herbicide tested. Therefore, tobacco, a more sensitive species, was tested for methyl viologen toxicity. High concentrations of methyl viologen induced free polyamine levels in crude extracts and intercellular fluids. However, only free polyamine content in the intercellular fluids was increased in plants treated with low methyl viologen concentrations. These results support the notion that polyamine metabolism in the apoplast is involved in the physiological response to oxidative stress.
Patch use by the greater glider (Petauroides volans) in a fragmented forest ecosystem. I. Home range size and movements
Authors: Pope M. L. , Lindenmayer D. B. , Cunningham R. B.
Published: December 2004

This paper examines home-range attributes of 40 greater gliders (Petauroides volans) in five patches of remnant eucalypt forest surrounded by stands of radiata pine (Pinus radiata) near Tumut in south-eastern Australia. Fixed-kernel smoothing methods were used to estimate home-range size for P. volans. For males, home-range size varied from 1.38–4.10 ha (mean = 2.6 ± 0.8 ha, n = 12) and was significantly larger (P < 0.05) than for females (1.26–2.97 ha, mean = 2.0 ± 0.6 ha, n = 11). Home-range size increased significantly with increasing patch size and reduced patch population density. Thus, small patches had more animals per unit area with smaller home ranges and greater home-range overlap.
Our findings illustrate flexibility in the use of space by P. volans. Such results have not previously been reported for P. volans or any other species of arboreal marsupial. Considerable home-range overlap (at 95th percentile isopleth level) was observed between male and female P. volans. Pairs of females also exhibited home-range overlap. Males tended to maintain home ranges exclusive of other males, although some shared common areas. Contrary to the large variations observed in home-range area, core areas (50th isopleth) remained relatively constant, regardless of patch size, population density or sex. This may indicate that core areas are an essential requirement for individuals and resources they contain cannot be shared with congeners.
Homeostatic cell-cycle control by BLyS: Induction of cell-cycle entry but not G1/S transition in opposition to p18INK4cand p27Kip1
Authors: Huang Xiangao , Di Liberto Maurizio , Cunningham Adam F. , Kang Lin , Cheng Shuhua , Ely Scott , Liou Hsiou-chi , MacLennan Ian C. M. , Chen-Kiang Selina
Published: December 2004

Cell-cycle entry is critical for homeostatic control in physiologic response of higher organisms but is not well understood. The antibody response begins with induction of naïve mature B cells, which are naturally arrested in G0/G1phase of the cell cycle, to enter the cell cycle in response to antigen and cytokine. BLyS (BAFF), a cytokine essential for mature B cell development and survival, is thought to act mainly by attenuation of apoptosis. Here, we show that BLyS alone induces cell-cycle entry and early G1cell-cycle progression, but not S-phase entry, in opposition to the cyclin-dependent kinase inhibitors p18INK4c. Independent of its survival function, BLyS enhances the synthesis of cyclin D2, in part through activation of NF-κB, as well as CDK4 and retinoblastoma protein phosphorylation. By convergent activation of the same cell-cycle regulators in opposition to p18INK4c, B cell receptor signaling induces cell-cycle entry and G1progression in synergy with BLyS, but also DNA replication. The failure of BLyS to induce S-phase cell-cycle entry lies in its inability to increase cyclin E and reduce p27Kip1expression. Antagonistic cell-cycle regulation by BLyS and p18INK4cis functionally linked to apoptotic control and conserved from B cell activationin vitroto antibody responsein vivo, further indicating a physiologic role in homeostasis.
The origin of the parathyroid gland
Authors: Okabe Masataka , Graham Anthony
Published: December 2004

It has long been held that the parathyroid glands and parathyroid hormone evolved with the emergence of the tetrapods, reflecting a need for new controls on calcium homeostasis in terrestrial, rather than aquatic, environments. Developmentally, the parathyroid gland is derived from the pharyngeal pouch endoderm, and studies in mice have shown that its formation is under the control of a key regulatory gene,
Gcm-2
. We have used a phylogenetic analysis of
Gcm-2
to probe the evolutionary origins of the parathyroid gland. We show that in chicks, as in mice,
Gcm-2
is expressed in the pharyngeal pouches and the forming parathyroid gland. We find that
Gcm-2
is present not only in tetrapods but also in teleosts and chondrichthyans, and that in these species,
Gcm-2
is expressed within the pharyngeal pouches and internal gill buds that derive from them in zebrafish (
Danio rerio
), a teleost, and dogfish (
Scyliorhinus canicula
), a chondrichthyan. We further demonstrate that
Gcm-2
is required for the formation of the internal gill buds in zebrafish. We also have identified parathyroid hormone 1/2-encoding genes in fish and show that these genes are expressed by the gills. We further show that the gills express the calcium-sensing receptor, which is used in tetrapods to monitor serum calcium levels. These results indicate that the tetrapod parathyroid gland and the gills of fish are evolutionarily related structures, and that the parathyroid likely came into being as a result of the transformation of the gills during tetrapod evolution.
A C-terminal translocation signal required for Dot/Icm-dependent delivery of the
Legionella
RalF protein to host cells
Authors: Nagai Hiroki , Cambronne Eric D. , Kagan Jonathan C. , Amor Juan Carlos , Kahn Richard A. , Roy Craig R.
Published: December 2004

The
Legionella pneumophila
Dot/Icm system is a type IV secretion apparatus that transfers bacterial proteins into eukaryotic host cells. The RalF protein is a substrate engaged and translocated into host cells by the Dot/Icm system. In this study, the mechanism of Dot/Icm-mediated translocation of RalF has been investigated. It was determined that RalF translocation into host cells occurs before bacterial internalization. Sequences essential for RalF translocation were located at the C terminus of the RalF protein. A fusion protein consisting of a 20-aa C-terminal RalF peptide appended to the calmodulin-dependent adenylate cyclase domain of the
Bordetella pertussis
adenylate cyclase protein was translocated into host cells by the Dot/Icm system. A leucine (L372) residue at the -3 position in relation to the RalF C terminus was critical for translocation. Consistent with RalF L372 playing an important role in substrate recognition by the Dot/Icm system, most other Dot/Icm substrates were found to have amino acid residues with similar physical properties at their -3 or -4 C-terminal positions. These data demonstrate that the Dot/Icm system can transfer bacterial proteins that modulate host cellular functions before uptake and indicate that substrate recognition involves a C-terminal translocation signal. Thus,
Legionella
has the ability to engage synthesized substrate proteins and transfer them into host cells on contact, enabling
Legionella
to rapidly alter transport of the vacuole in which it resides.
Mitochondrial cytochrome
c
1
is a collapsed di-heme cytochrome
Authors: Baymann Frauke , Lebrun Evelyne , Nitschke Wolfgang
Published: December 2004

Cytochrome
c
1
from mitochondrial complex III and the di-heme cytochromes
c
in the corresponding enzyme from ε-proteobacteria have so far been considered to represent unrelated cytochromes. A missing link protein discovered in the genome of the hyperthermophilic bacterium
Aquifex aeolicus
, however, provides evidence for a close evolutionary relationship between these two cytochromes. The mono-heme cytochrome
c
1
from
A. aeolicus
contains stretches of strong sequence homology toward the ε-proteobacterial di-heme cytochromes. These di-heme cytochromes are shown to belong to the cytochrome
c
4
family. Mapping cytochrome
c
1
onto the di-heme sequences and structures demonstrates that cytochrome
c
1
results from a mutation-induced collapse of the di-heme cytochrome structure and provides an explanation for its uncommon structural features. The appearance of cytochrome
c
1
thus represents an extension of the biological protein repertoire quite different from the widespread innovation by gene duplication and subsequent diversification.
Mechanism and circuitry for clustering and fine discrimination of odors in insects
Authors: Sivan Ehud , Kopell Nancy
Published: December 2004

Odor recognition encompasses both clustering and fine discrimination. Clustering joins together sets of odors, and fine discrimination distinguishes between odors belonging to the same cluster. We hypothesize that these two aspects of odor recognition are encoded in parallel by two brain areas of the insect olfactory system. Population activity of neurons in the lateral horn encodes the odor cluster, and population activity of neurons in the mushroom body encodes the fine identity of the odor. Our mechanism is based on the hypothesis that the underlying network of the insect olfactory system consists of a repetitive, hard-wired substructure whose anatomy we describe. We show that these suggested mechanisms and circuitry explain not only the observed numbers and connections of neurons in the system, but also the observed activity of these neurons, and why oscillations are critical for fine discrimination but not for clustering of odors.
Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA
Authors: Barrett Michael T. , Scheffer Alicia , Ben-Dor Amir , Sampas Nick , Lipson Doron , Kincaid Robert , Tsang Peter , Curry Bo , Baird Kristin , Meltzer Paul S. , Yakhini Zohar , Bruhn Laurakay , Laderman Stephen
Published: December 2004

Array-based comparative genomic hybridization (CGH) measures copy-number variations at multiple loci simultaneously, providing an important tool for studying cancer and developmental disorders and for developing diagnostic and therapeutic targets. Arrays for CGH based on PCR products representing assemblies of BAC or cDNA clones typically require maintenance, propagation, replication, and verification of large clone sets. Furthermore, it is difficult to control the specificity of the hybridization to the complex sequences that are present in each feature of such arrays. To develop a more robust and flexible platform, we created probe-design methods and assay protocols that make oligonucleotide microarrays synthesized
in situ
by inkjet technology compatible with array-based comparative genomic hybridization applications employing samples of total genomic DNA. Hybridization of a series of cell lines with variable numbers of X chromosomes to arrays designed for CGH measurements gave median ratios for X-chromosome probes within 6% of the theoretical values (0.5 for XY/XX, 1.0 for XX/XX, 1.4 for XXX/XX, 2.1 for XXXX/XX, and 2.6 for XXXXX/XX). Furthermore, these arrays detected and mapped regions of single-copy losses, homozygous deletions, and amplicons of various sizes in different model systems, including diploid cells with a chromosomal breakpoint that has been mapped and sequenced to a precise nucleotide and tumor cell lines with highly variable regions of gains and losses. Our results demonstrate that oligonucleotide arrays designed for CGH provide a robust and precise platform for detecting chromosomal alterations throughout a genome with high sensitivity even when using full-complexity genomic samples.
The effect of midazolam on visual search: Implications for understanding amnesia
Authors: Park Heekyeong , Quinlan Joseph , Thornton Edward , Reder Lynne M.
Published: December 2004

The notion of multiple memory systems based on conscious accessibility has been supported largely by neuropsychological patient studies. Specifically, it was widely held that amnesic patients have impaired explicit memory performance but spared implicit memory performance. However, recent patient studies have called the implicit/explicit memory distinction into question. In this study, normal participants were tested on a visual search task, once after an injection of midazolam, an anesthetic that induces temporary amnesia, and once after an injection of saline. Under the influence of midazolam, participants did not show facilitation in search times for repeated configurations (contextual cuing), although there was a general speed-up in performance across blocks in both the midazolam and saline conditions. Neither the contextual-cuing effect nor the procedural-learning effect was available to subjective experience, yet only one of these was affected by midazolam-induced amnesia. These data call into question the notion that memory systems divide on the basis of subjective experience of consciousness or reportability. Rather, the findings support the contention that anterograde amnesia affects learning that depends on building novel associations in memory and that this deficit does not hinge upon accessibility to consciousness.
A quantitative assessment of models for voltage-dependent gating of ion channels
Authors: Grabe Michael , Lecar Harold , Jan Yuh Nung , Jan Lily Yeh
Published: December 2004

Voltage-gated ion channels open and close, or “gate,” in response to changes in membrane potential. The electric field across the membrane–protein complex exerts forces on charged residues driving the channel into different functional conformations as the membrane potential changes. To act with the greatest sensitivity, charged residues must be positioned at key locations within or near the transmembrane region, which requires desolvating charged groups, a process that can be energetically prohibitive. Although there is good agreement on which residues are involved in this process for voltage-activated potassium channels, several different models of the sensor geometry and gating motions have been proposed. Here we incorporate low-resolution structural information about the channel into a Poisson–Boltzmann calculation to determine solvation barrier energies and gating charge values associated with each model. The principal voltage-sensing helix, S4, is represented explicitly, whereas all other regions are represented as featureless, dielectric media with complex boundaries. From our calculations, we conclude that a pure rotation of the S4 segment within the voltage sensor is incapable of producing the observed gating charge values, although this shortcoming can be partially remedied by first tipping and then minimally translating the S4 helix. Models in which the S4 segment has substantial interaction with the low-dielectric environment of the membrane incur solvation energies of hundreds of
k
B
T
, and activation times based on these energies are orders of magnitude slower than experimentally observed.
Vesicular reuptake inhibition by a synaptotagmin I C2B domain antibody at the squid giant synapse
Authors: Llinás Rodolfo R. , Sugimori Mutsuyuki , Moran Kimberly A. , Moreira Jorge E. , Fukuda Mitsunori
Published: December 2004

Synaptotagmin (Syt) I, a ubiquitous synaptic vesicle protein, comprises a transmembrane region and two C2 domains. The C2 domains, which have been shown to be essential for both synaptic vesicle exocytosis and endocytosis, are also seen as the Ca
2+
sensors in synaptic vesicular release. In a previous study, we reported that a polyclonal antibody raised against the squid (
Loligo pealei
) Syt I C2B domain, while inhibiting vesicular endocytosis, was synaptic release neutral at the squid giant synapse. Recent reports concerning the C2B requirements for synaptic release prompted us to readdress the role of C2B in squid giant synapse function. Presynaptic injection of another anti-Syt I-C2B antibody (using recombinant whole C2B domain expressed in mammalian cell culture as an antigen) into the presynaptic terminal reproduced our previous results, i.e., reduction of vesicular endocytosis without affecting synaptic release. This set of results addresses the issue of the geometrical arrangement of the Ca
2+
sensor, allowing the C2B domain antibody to restrict Ca
2+
-dependent C2B self-oligomerization without modifying the Ca
2+
-dependent release process.
The crystal structure of yeast copper thionein: The solution of a long-lasting enigma
Authors: Calderone Vito , Dolderer Benedikt , Hartmann Hans-Juergen , Echner Hartmut , Luchinat Claudio , Del Bianco Cristina , Mangani Stefano , Weser Ulrich
Published: December 2004

We report here the crystal structure of yeast copper thionein (Cu-MT), determined at 1.44-Å resolution. The Cu-MT structure shows the largest known oligonuclear Cu(I) thiolate cluster in biology, consisting of six trigonally and two digonally coordinated Cu(I) ions. This is at variance with the results from previous spectroscopic determinations, which were performed on MT samples containing seven rather than eight metal ions. The protein backbone has a random coil structure with the loops enfolding the copper cluster, which is located in a cleft where it is bound to 10 cysteine residues. The protein structure is somewhat different from that of Ag
7
-MT and similar, but not identical, to that of Cu
7
-MT. Besides the different structure of the metal cluster, the main differences lie in the cysteine topology and in the conformation of some portions of the backbone. The present structure suggests that Cu-MT, in addition to its role as a safe depository for copper ions in the cell, may play an active role in the delivery of copper to metal-free chaperones.
Proapoptotic BAX and BAK regulate the type 1 inositol trisphosphate receptor and calcium leak from the endoplasmic reticulum
Authors: Oakes Scott A. , Scorrano Luca , Opferman Joseph T. , Bassik Michael C. , Nishino Mari , Pozzan Tullio , Korsmeyer Stanley J.
Published: December 2004

Proapoptotic BCL-2 family members BAX and BAK are required for the initiation of mitochondrial dysfunction during apoptosis and for maintaining the endoplasmic reticulum (ER) Ca
2+
stores necessary for Ca
2+
-dependent cell death. Conversely, antiapoptotic BCL-2 has been shown to decrease Ca
2+
concentration in the ER. We found that
Bax
-/-
Bak
-/-
double-knockout (DKO) cells have reduced resting ER Ca
2+
levels because of increased Ca
2+
leak and an increase in the Ca
2+
-permeable, hyperphosphorylated state of the inositol trisphosphate receptor type 1 (IP3R-1). The ER Ca
2+
defect of DKO cells is rescued by RNA interference reduction of IP3R-1, supporting the argument that this channel regulates the increased Ca
2+
leak in these cells. BCL-2 and IP3R-1 physically interact at the ER, and their binding is increased in the absence of BAX and BAK. Moreover, knocking down BCL-2 decreases IP3R-1 phosphorylation and ER Ca
2+
leak rate in the DKO cells. These findings support a model in which BCL-2 family members regulate IP3R-1 phosphorylation to control the rate of ER Ca
2+
leak from intracellular stores.
The quality of family relationships within and across generations: A social relations analysis
Authors: Ross Hildy , Stein Nancy , Trabasso Tom , Woody Erik , Ross Michael
Published: December 2004

Parents and two children (average ages: 81/2 and 51/2 years) in 76 families each appraised the quality of their relationships with one another. Family members described generally positive relationships, both from their own perspectives (e.g., “I am often nice to my mother”) and from the perspectives of their relationship partners (e.g., “My mother is often nice to me”). Sibling relationships were rated less positively than other family relationships. The Social Relations Model was utilised to examine the patterning of family relationships. Actor effects, indicating consistent relationship qualities for each individual family member, were found, especially for ratings of self. Partner effects, indicating consistency in relationships as assessed by others in the family, were present for ratings of the children as relationship partners. Relationship effects were pervasive, indicating that specific family relationships had distinct qualities. Participants’ own ratings suggested that reciprocity would characterise all family relationships, in that strong correlations were found between each person’s rating of self and other, but only the marital and the sibling relationship evidenced relational reciprocity, as assessed by correlations between relationship effects found for relationship partners.
Gynecologists′ Attitudes Regarding Human Papilloma Virus Vaccination: A Survey of Fellows of the American College of Obstetricians and Gynecologists
Authors: Raley Janice C. , Followwill Kristen A. , Zimet Gregorgy D. , Ault Kevin A.
Published: December 2004

Background: Human papilloma virus (HPV) is the causative agent of cervical neoplasia and genital warts. A vaccine has recently been developed that may prevent infection with HPV. Vaccination for HPV may become a
routine part of office gynecology. We surveyed members of the American College of Obstetricians and Gynecologists (ACOG) to determine their attitudes to HPV vaccination.

Methods: A survey was sent to Fellows of ACOG to evaluate gynecologists′ attitudes. Vaccine acceptability was analyzed using 13 scenarios with the following dimensions and respective attributes: age of patient (3, 17 and 22 years); efficacy of vaccine (50% or 80%); ACOG recommendation (yes or no); and disease targeted (cervical cancer, warts or both). Each scenario was rated by means of an 11‐point response format (0 to 100). Responses were evaluated using conjoint analysis.

Results: Of 1200surveys that were sent out, 181 were returned and included in our analysis. ACOG recommendation was considered the most important variable in vaccine distribution (importance score = 32.2), followed by efficacy (24.5), age (22.4) and, lastly, disease targeted (20.9). Of these variables, higher efficacy was
favored; preference was given to age 17 years, with a strong disinclination to vaccinate at age 13 years; and protection against cervical cancer, or genital warts, or both, was significantly favored over a vaccine against genital warts alone. Demographic characteristics of the gynecologists (i.e., age of physician, gender, practice setting and community size) did not play an important role in the decision to recommend vaccination.

Conclusion: Professional society recommendation is important for acceptability of a potential HPV vaccine. Gynecologists are willing to include this vaccine in their office practice.
Interaction of Microbiology and Pathology in Women Undergoing Investigations for Infertility
Authors: Debattista Joseph , Gazzard Caroline M. , Wood Robyn N. , Allan John A. , Allan Janet M. , Scarman Anthony , Mortlock Miranda , Timms Peter , Knox Christine L.
Published: December 2004

Background: Cases of endometriosis with no tubal damage are associated with infertility, suggesting an immunological rather than mechanical barrier to reproduction. Laparoscopy and falloposcopy results of clinically
asymptomatic women undergoing investigation of infertility were correlated with the outcomes of microbiological screening for Chlamydia trachomatis, Mycoplasma pneumoniae, Mycoplasma hominis, ureaplasma species, Neisseria gonorrhoeae, Neisseria meningitidis and Chlamydia pneumoniae.

Methods: A total of 44 women presenting to a hospital IVF service for laparoscopic or laparoscopic/ falloposcopic investigation of infertility provided endocervical swabs, fallopian tube washings, and peripheral whole blood for analysis.

Results: Of these 44 women, 15.9% (7) showed evidence of C. trachomatis infection as detected by either PCR or EIA serology. Of these 7 women, 5 (71%) had no or mild endometriosis and 2 (29%) had moderate or
severe endometriosis. Of the remaining 37 women who showed no evidence of chlamydial infection, 15 (40.5%) had no or mild endometriosis.

Conclusion: Women with infertility, but without severe endometriosis at laparoscopy, showed a trend towards tubal damage and a higher rate of previous C. trachomatis infection. Although not statistically significant, this trend would suggest that, where moderate to severe tubal damage is found to be the primary cause of infertility, C. trachomatis infection could be a likely cause for such tubal damage.
Accentuating the Positive: The ‘Selling Arrangement’, The First Decade, and Beyond
Authors: Connor Tim
Published: December 2004

The ‘selling arrangement’ is a judicial device which removes national law from thescrutiny of European Community law relating to the free movement of goods. National provisions affecting the marketing of products may fall for consideration as ‘selling arrangements’ where the treatment of the domestic and imported goods has been even handed. Measures relating to the substance of the goods remain subject to Community law rules on the free movement of goods. The prime example of the selling arrangement is the advertisement, but in the years since creation, other areas of national activity with respect to the free movement of goods have been enveloped inthe selling arrangement. Certain measures which have related to the conduct of business may also fall for similar treatment as selling arrangements. A recent development would appear tomean that the concept of the selling arrangement may apply where the obligation imposed by the national measure has beenidentified as being general, as opposed to specific in nature. Were this to be so, the selling arrangement would have the potential to break free of the traditional boundaries established for itunder Criminal Proceedings against Bernard Keck and Daniel Mithouard.1
Exploring the Feasibility of Farmers' Rights
Authors: Srinivasan C. S.
Published: December 2004

In many developing countries, there is concern that a conventional system of plant breeders' rights provides no rewards to farmers for their role in the conservation and enhancement of agro‐biodiversity. To redress this imbalance, developing countries are incorporating farmers' rights provisions in their plant variety protection legislation. This article examines the feasibility of farmers' rights provisions based on intellectual property rights. It argues that the farmers' rights provisions crafted by some developing countries will involve enormous operational difficulties, while IPR‐based farmers' rights are unlikely to provide significant economic returns to farmers or farming communities. At the same time, farmers' rights provisions, as currently conceived, are likely significantly to dilute the incentives for innovation provided to institutional plant breeders.
Growth and Poverty Reduction in Uganda, 1999–2000: Panel Data Evidence
Authors: Deininger Klaus , Okidi John
Published: December 2004

To explore factors underlying growth and poverty reduction in Africa while overcoming some of the limitations of cross‐country analysis, this article uses micro‐level survey and panel‐data evidence from Uganda spanning 1992–2000. The high elasticity of both income growth and poverty reduction with respect to agricultural output (coffee) prices confirms the benefits from Uganda's decisive liberalisation of output markets. It also suggests the importance of product diversification to protect the poor against price shocks and the potential of cotton‐market improvements in tackling persistent poverty in the North. The importance of improving access to basic education and health care emerges more clearly than in cross‐country analysis, but benefits depend on complementary investments in electricity and other infrastructure, and reductions in civil strife.
The origins and evolution of links between word learning and conceptual organization: new evidence from 11‐month‐olds
Authors: Waxman Sandra , Booth Amy
Published: December 2004

How do infants map words to their meaning? How do they discover that different types of words (e.g. noun, adjective) refer to different aspects of the same objects (e.g. category, property)? We have proposed that (1) infants begin with a broad expectation that novel open‐class words (both nouns and adjectives) highlight commonalities (both category‐ and property‐based) among objects, and that (2) this initial expectation is subsequently fine‐tuned through linguistic experience. We examine the first part of this proposal, asking whether 11‐month‐old infants can construe the very same set of objects (e.g. four purple animals) either as members of an object category (e.g. animals) or as embodying a salient object property (e.g. four purple things), and whether naming (with count nouns vs. adjectives) differentially influences their construals. Results support the proposal. Infants treated novel nouns and adjectives identically, mapping both types of words to both category‐ and property‐based commonalities among objects.
On the origins of age‐of‐acquisition effects in the perception of printed words
Authors: Nazir Tatjana A. , Decoppet Nathalie , Aghababian Valérie
Published: December 2004

Children from different grades were tested in a lexical decision task. Word‐stimuli consisted of words acquired in their respective grades, and in grades previous to their own. The results showed that the proportion of errors for newly acquired words increased steadily with grade (i.e. first graders made fewer errors with words of grade one than fifth graders with words of grade five). However, the proportion of errors for words acquired in a given grade remained constant throughout the following grades (fifth graders made as many errors with words acquired in grade one as first graders did). These results indicate that the strong impact that age‐ or order‐of‐acquisition of words has on the way words will be recognized is in place at a very young age.
Is a false belief statement a lie or a truthful statement? Judgments and explanations of children aged 3 to 8
Authors: Berthoud‐Papandropoulou Ioanna , Kilcher Helga
Published: December 2004

Attribution of a false belief is usually taken to indicate that children distinguish between a real world state of affairs and its representation by a subject. But how do they conceive of the properties of such a mental entity? Do they understand that false belief necessarily goes hand in hand with good faith? Our study explores to what extent children conflate false beliefs with lies. Sixty children aged 3 to 8 were presented with an FB situation and then asked whether the character having an FB was lying or not. Results show that up to 6 years, although correctly attributing the FB, children systematically judge the FB statement to be a lie, since it does not correspond to the real world state of affairs. Older children succeed in the lie judgment, invoking the false believer's not knowing the world state. Discussion bears on the relation between false belief and more general epistemic states.
Theory of mind: is training contagious?
Authors: Melot Anne‐Marie , Angeard Nathalie
Published: December 2004

In this study, preschool children were successfully trained in theory of mind tasks, namely false belief inference and appearance–reality distinction. Results show that both types of training had a direct effect, as measured by the improvement of performance on the FB and AR delayed post‐tests. Both types of training also had an indirect effect, as measured by transfer of the benefits of the training to the task that was not in the training. Finally, both types of training were effective even when the children were trained in a task they had already mastered.
Two‐month‐old infants match phonetic information in lips and voice
Authors: Patterson Michelle L. , Werker Janet F.
Published: December 2004

Infants aged 4.5 months are able to match phonetic information in the face and voice (Kuhl & Meltzoff, 1982; Patterson & Werker, 1999); however, the ontogeny of this remarkable ability is not understood. In the present study, we address this question by testing substantially younger infants at 2 months of age. Like the 4.5‐month‐olds in past studies, the 2‐month‐old infants tested in the current study showed evidence of matching vowel information in face and voice. The effect was observed in overall looking time, number of infants who looked longer at the match, and longest look to the match versus mismatch. Furthermore, there were no differences based on male or female stimuli and no preferences for the match when it was on the right or left side. These results show that there is robust evidence for phonetic matching at a much younger age than previously known and support arguments for either some kind of privileged processing or particularly rapid learning of phonetic information.