bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential energy surface, kinetics, and dynamics study of the Cl+CH4→HCl+CH3 reaction
Authors: Rangel Cipriano , Navarrete Marta , Corchado Jose C. , Espinosa-García Joaquín
Published: March 2006

A modified and recalibrated potential energy surface for the gas-phase Cl+CH4→HCl+CH3 reaction is reported and tested. It is completely symmetric with respect to the permutation of the four methane hydrogen atoms and is calibrated with respect to updated experimental and theoretical stationary point properties and experimental forward thermal rate constants. From the kinetics point of view, the forward and reverse thermal rate constants and the activation energies were calculated using the variational transition-state theory with semiclassical transmission coefficients over a wide temperature range of 150–2500K. The theoretical results reproduce the available experimental data, with a small curvature of the Arrhenius plot which indicates the role of tunneling in this hydrogen abstraction reaction. A dynamics study was also performed on this PES using quasiclassical trajectory (QCT) calculations, including corrections to avoid zero-point energy leakage along the trajectories. First, we found a noticeable internal energy in the coproduct methyl radical, both in the ground-state [CH4(v=0)] and vibrationally excited [CH4(v=1)] reactions. This CH3 internal energy was directly precluded in some experiments or oversimplified in previous theoretical studies using pseudotriatomic models. Second, our QCT calculations give HCl rotational distributions slightly hotter than those in experiment, but correctly describing the experimental trend of decreasing the HCl product rotation excitation in going from HCl(v′=0) to HCl(v′=1) for the CH4(v=1) reaction. Third, the state specific scattering distributions present a reasonable agreement with experiment, although they tend to make the reaction more forward and backward scattered than found experimentally probably because of the hotter rotational distribution and the deficiencies of the QCT methods.
Calorimeter for measuring the isobaric specific heat capacity of fluids and fluid mixtures by the thermal relaxation method
Authors: Tanaka K. , Uematsu M.
Published: March 2006

We present a new calorimeter for measuring the isobaric specific heat capacity for fluids and fluid mixtures based on the thermal relaxation method. The calorimeter, which is equipped with a metal bellows, works in the temperature range from 250to500K at pressures up to 20MPa and is designed to satisfy the conditions of a lumped system. The calorimeter was calibrated using water and toluene. The isobaric specific heat capacity of methanol was measured at 323.15K and 0.1MPa, which confirms the reliability of the calorimeter. The uncertainty is estimated to be within 2.9% at a 95% confidence level.
Effects of depletion on the emission from individual InGaN dots
Authors: Sherliker B. , Halsall M. P. , Buckle P. D. , Parbrook P. J. , Wang T.
Published: March 2006

We report a photoluminescence (PL) study of the effects of carrier depletion on the electronic states of InGaN quantum dots. Samples were fabricated into mesa devices with top Schottky contacts and back ohmic contacts. Submicrometer apertures were created lithographically. Capacitance-voltage measurements of the devices suggest that the dots are fully depleted when they are unbiased. Micro-PL studies of individual dots show narrow linewidths under zero or reverse bias conditions. Forward biasing of the junction results in broadening of the dot levels due to the populating of nearby conduction band states in the underlying quantum well.
Giant positive magnetoresistance in composite (La0.83Sr0.17MnO3)0.6(ITO)0.4
Authors: Zhang N. , Wang M.
Published: March 2006

We have studied the transport property of the composites (La0.83Sr0.17MnO3)1−x indium tin oxide (ITO)x [ITO=(In2O3)0.95(SnO2)0.05], which were fabricated by mechanically mixing La0.83Sr0.17MnO3 and ITO grains. A giant positive magnetoresistance (PMR) has been observed above the Curie temperature Tc for the samples with x around 0.40 besides the negative magnetoresistance near and below the Tc. The magnetoresistive ratio for the PMR can reach 39.3% under a magnetic field μ0H=2800Oe for (La0.83Sr0.17MnO3)0.6(ITO)0.4. Analysis suggests that the magnetic field-induced broadening of the p-n barrier between both kinds of grains and a suitable density of the p-n heterostructures should be responsible for the PMR behavior.
Mechanism of NO2 detection in carbon nanotube field effect transistor chemical sensors
Authors: Zhang Jian , Boyd Anthony , Tselev Alexander , Paranjape Makarand , Barbara Paola
Published: March 2006

We report an experimental method that clearly determines the sensing mechanism of carbon-nanotube field effect transistors. The nanotube/electrode contacts are covered with a thick and long passivation layer that hinders their exposure to chemicals in a controlled fashion, leaving only the midsection of the nanotube exposed. In the case of nitrogen dioxide, a considerably delayed response is fully consistent with the diffusion of the gas through the passivation layer. The results clearly indicate that nitrogen dioxide detection is due to changes at the interfaces between the nanotube and the electrodes and not to molecules adsorbed on the nanotube surface.
Isoelectronic indium-surfactant-doped Al0.3Ga0.7N∕GaN high electron mobility transistors
Authors: Feng Z. H. , Cai S. J. , Chen K. J. , Lau Kei May
Published: March 2006

We report enhanced performance of Al0.3Ga0.7N∕GaN high electron mobility transistors (HEMTs) grown on sapphire substrates incorporating isoelectronic indium surfactant doping in the two-dimensional electron gas channel, the AlGaN spacer, and the AlGaN cap layer. We found that the isoelectronic In doping plays the role of surfactant and can effectively reduce the defect density. The In surfactant also lowers the interface roughness scattering and improves the surface morphology, leading to higher electron mobility at 300 and 77K. More than 30% increase in the drain saturation current and peak transconductance were observed in the In-doped devices that also showed negligible current collapse and high cutoff frequencies. The on-wafer output power, linear gain and power-added efficiency of an unpassivated 1×100μm device measured at 2GHz were 3.01W∕mm, 20.9dB, and 35.7%, respectively.
Metalorganic vapor phase epitaxy grown InGaN∕GaN light-emitting diodes on Si(001) substrate
Authors: Schulze F. , Dadgar A. , Bläsing J. , Diez A. , Krost A.
Published: March 2006

We present GaN-based light emitting diode structures on a Si(001) substrate. The 2.3μm thick, crack-free layers were grown by metalorganic vapor phase epitaxy using a high-temperature AlN seed layer and 4° off-oriented substrates. This allows us to grow a flat, fully coalesced, and single crystalline GaN layer on Si(001). For preventing crack formation, four AlN interlayers were inserted in the buffer structure. The optically active layers consist of five-fold InGaN∕GaN multiple quantum wells showing a bright electroluminescence at 490nm at room temperature. The crystallographic structure was analyzed by x-ray diffraction measurements and the optical properties were determined by photo- and electroluminescence.
Double-perovskite Sr2FeMoO6 epitaxial films with ordered cation structure grown in mixture gas of hydrogen and argon
Authors: Wang Shiqi , Pan Huayong , Zhang Xiaoping , Lian Guijun , Xiong Guangcheng
Published: March 2006

Epitaxial double-perovskite Sr2FeMoO6 films have been grown by pulsed laser deposition (PLD) on SrTiO3 substrates. High-quality metallic Sr2FeMoO6 thin films with low resistivity were obtained by deposited in a mixture gas of hydrogen and argon. Resistivity versus temperature measurements, magnetic measurement, and x-ray diffraction indicate that using a mixture forming gas of hydrogen and argon in PLD is a flexible method for preparing high-quality epitaxial Sr2FeMoO6 films. In (011) cross-section high-resolution transmission electron microscopy images of epitaxial Sr2FeMoO6 films, the clear superlattice structure of ordered cations of Fe and Mo is shown.
Online measurement of the optical anisotropy during the growth of crystalline organic films
Authors: Sun L. D. , Hohage M. , Zeppenfeld P. , Berkebile S. , Koller G. , Netzer F. P. , Ramsey M. G.
Published: March 2006

We report a reflectance difference spectroscopy (RDS) investigation of the growth of para-sexiphenyl (p-6P) on a TiO2(110) single crystal substrate at 100, 300, and 400K. The results demonstrate that RDS is a powerful technique to monitor organic thin film growth from the submonolayer regime to device relevant thicknesses. Based on the polarization dependence of the optical absorption at characteristic wavelengths, the orientation and the crystalline properties of the organic molecules can be directly determined from the RD spectrum with an extremely high sensitivity.
Real-time direct observation of temperature-dependent domain reversal behavior in epitaxial MnAs film on GaAs(001)
Authors: Ryu Kwang-Su , Shin Sung-Chul , Akinaga Hiro , Manago Takashi
Published: March 2006

We have investigated temperature-dependent domain reversal behavior in the MnAs film epitaxially grown on GaAs(001) using a magneto-optical microscope capable of real-time direct observation of domain evolution. Interestingly enough, the domain reversal in the temperature range of 20°C∼35°C shows the domain wall-motion process with the sawtooth type and, then, it changes to the nucleation-dominant process above 37.5°C. This change could be understood by the decrease of the dipolar interaction energy and the disconnection of the ferromagnetic α-MnAs stripes, induced by the decrease of the α-MnAs volume ratio with increasing temperature.
Development pattern of blood oxygen carrying capacity in rainbow bee-eater nestlings
Authors: Eklom Kylie , Lill Alan
Published: March 2006

Growth profile variation among altricial bird species is reflected in variation in development patterns of parameters influencing blood oxygen carrying capacity (O2Cap). Rainbow bee-eater nestlings develop slowly and their asymptotic mass reaches or exceeds adult levels before undergoing prefledging recession (mass overshoot–recession profile, MOR). Erythrocyte count (RBC), blood hemoglobin content (Hb) and hematocrit (Hct) increased 2.5-fold during development. Hatchlings’ erythrocyte volume closely approximated adult levels and decreased by only 1% during development. Erythrocyte hemoglobin content and concentration also increased minimally. RBC and Hb increased throughout development, but Hct increase was restricted to early development, overlapping the mass-gain period by just 37%. Blood parameters influencing O2Cap did not exceed adult levels and then decline during the mass asymptote–recession development stage. Continuing increase in RBC and Hb at this stage contributed to attaining a fledging O2Cap of adult levels. Results were consistent with there being a common mechanism regulating developmental increase in O2Cap in altricial birds. However, features of this development in bee-eater nestlings variously conformed to the patterns of both species with MOR and species with standard growth profiles. Some features shared with other MOR species also differed in timing or pattern in bee-eater nestlings.
Evolution of hearing in moths: the ears of Oenosandra boisduvalii (Noctuoidea:Oenosandridae)
Authors: Fullard James H.
Published: March 2006

The ears of Oenosandra boisduvalii (Oenosandridae), as a representative of this heretofore unstudied family of moths, were electrophysiologically examined from specimens captured in South Australia. Male and female moths possess ears with two auditory receptor neurons that are similarly sensitive and tuned to the frequencies emitted by sympatric bats, suggesting that both sexes face equal predation pressures from aerially foraging bats. The two-celled ear of this moth supports the independence of the Oenosandridae from its previous affiliation with the Notodontidae, whose single auditory neuron remains a unique character within the Noctuoidea. The general insensitivity of its ear, however, resembles that of the notodontid moth and is surprising considering the diversity of insectivorous bats that forms its predation potential.
Roosting and thermoregulatory behaviour of male Gould's long-eared bats, Nyctophilus gouldi: energetic benefits of thermally unstable tree roosts
Authors: Turbill Christopher
Published: March 2006

Information about the thermal biology of bats in relation to their roosting behaviour is scant. I used temperature telemetry to locate roosts and record the thermoregulatory behaviour of male long-eared bats, Nyctophilus gouldi (9 g), during late spring in the Northern Tablelands of New South Wales. Bats roosted under bark and in tree cavities, where they typically experienced wide daily fluctuations in ambient temperature (Ta). On 13 out of 16 days, bats employed two torpor bouts per day, during the early morning and late afternoon, coinciding with times of low Ta. Heating of roosts during the day resulted in up to 20°C of passive re-warming before active arousal and provided high Ta around midday when bats were normothermic. By switching between torpor and normothermic thermoregulation according to the daily Ta cycle, male N. gouldi appear to gain an energetic advantage from choosing poorly insulated and often sun-exposed roosts.
Thermoregulatory, metabolic and ventilatory physiology of the eastern barred bandicoot (Perameles gunnii)
Authors: Larcombe Alexander N. , Withers Philip C. , Nicol Stewart C.
Published: March 2006

Thermoregulatory, metabolic and ventilatory parameters measured for the Tasmanian eastern barred bandicoot (Perameles gunnii) in thermoneutrality (ambient temperature = 30°C) were: body temperature 35.1°C, basal metabolic rate 0.55 mL O2 g–1 h–1, wet thermal conductance 2.2 mL O2 g–1 h–1 °C–1, dry thermal conductance 1.4 J g–1 h–1 °C–1, ventilatory frequency 24.8 breaths min–1, tidal volume 9.9 mL, minute volume of 246 mL min–1, and oxygen extraction efficiency 22.2%. These physiological characteristics are consistent with a cool/wet distribution, e.g. high basal metabolic rate (3.33 mL O2 g–0.75 h–1) for thermogenesis, low thermal conductance (0.92 J g–1 h–1 °C–1 at 10°C) for heat retention and intolerance of high ambient temperatures (≥35°C) with panting, hyperthermia and high total evaporative water loss (16.9 mg H2O g–1 h–1).
Collection, focusing, and metering of DNA in microchannels using addressable electrode arrays for portable low-power bioanalysis
Authors: Shaikh Faisal A. , Ugaz Victor M.
Published: March 2006

Although advances in microfluidic technology have enabled increasingly sophisticated biosensing and bioassay operations to be performed at the microscale, many of these applications employ such small amounts of charged biomolecules (DNA, proteins, and peptides) that they must first be preconcentrated to a detectable level. Efficient strategies for precisely handling minute quantities of biomolecules in microchannel geometries are critically needed; however, it has proven challenging to achieve simultaneous concentration, focusing, and metering capabilities with current-generation sample-injection technology. By using microfluidic chips incorporating arrays of individually addressable microfabricated electrodes, we demonstrate that DNA can be sequentially concentrated, focused into a narrow zone, metered, and injected into an analysis channel. This technique transports charged biomolecules between active electrodes upon application of a small potential difference (1 V) and is capable of achieving orders of magnitude concentration increases within a small device footprint. The collected samples are highly focused, with sample zone size and shape defined solely by electrode geometry.
Optophysiology: Depth-resolved probing of retinal physiology with functional ultrahigh-resolution optical coherence tomography
Authors: Bizheva K. , Pflug R. , Hermann B. , Považay B. , Sattmann H. , Qiu P. , Anger E. , Reitsamer H. , Popov S. , Taylor J. R. , Unterhuber A. , Ahnelt P. , Drexler W.
Published: March 2006

Noncontact, depth-resolved, optical probing of retinal response to visual stimulation with a <10-μm spatial resolution, achieved by using functional ultrahigh-resolution optical coherence tomography (fUHROCT), is demonstrated in isolated rabbit retinas. The method takes advantage of the fact that physiological changes in dark-adapted retinas caused by light stimulation can result in local variation of the tissue reflectivity. fUHROCT scans were acquired from isolated retinas synchronously with electrical recordings before, during, and after light stimulation. Pronounced stimulus-related changes in the retinal reflectivity profile were observed in the inner/outer segments of the photoreceptor layer and the plexiform layers. Control experiments (e.g., dark adaptation vs. light stimulation), pharmacological inhibition of photoreceptor function, and synaptic transmission to the inner retina confirmed that the origin of the observed optical changes is the altered physiological state of the retina evoked by the light stimulus. We have demonstrated that fUHROCT allows for simultaneous, noninvasive probing of both retinal morphology and function, which could significantly improve the early diagnosis of various ophthalmic pathologies and could lead to better understanding of pathogenesis.
Conditional and specific NF-κB blockade protects pancreatic beta cells from diabetogenic agents
Authors: Eldor R. , Yeffet A. , Baum K. , Doviner V. , Amar D. , Ben-Neriah Y. , Christofori G. , Peled A. , Carel J. C. , Boitard C. , Klein T. , Serup P. , Eizirik D. L. , Melloul D.
Published: March 2006

Type 1 diabetes is characterized by the infiltration of inflammatory cells into pancreatic islets of Langerhans, followed by the selective and progressive destruction of insulin-secreting beta cells. Islet-infiltrating leukocytes secrete cytokines such as IL-1β and IFN-γ, which contribute to beta cell death.In vitroevidence suggests that cytokine-induced activation of the transcription factor NF-κB is an important component of the signal triggering beta cell apoptosis. To study thein vivorole of NF-κB in beta cell death, we generated a transgenic mouse line expressing a degradation-resistant NF-κB protein inhibitor (ΔNIκBα), acting specifically in beta cells, in an inducible and reversible manner, by using the tet-on regulation system.In vitro, islets expressing the ΔNIκBα protein were resistant to the deleterious effects of IL-1β and IFN-γ, as assessed by reduced NO production and beta-cell apoptosis. This effect was even more strikingin vivo, where nearly complete protection against multiple low-dose streptozocin-induced diabetes was observed, with reduced intraislet lymphocytic infiltration. Our results showin vivothat beta cell-specific activation of NF-κB is a key event in the progressive loss of beta cells in diabetes. Inhibition of this process could be a potential effective strategy for beta-cell protection.
Genetic independence of mouse measures of some aspects of novelty seeking
Authors: Kliethermes Christopher L. , Crabbe John C.
Published: March 2006

High novelty seeking is a complex personality attribute correlated with risk for substance abuse. There are many putative mouse models of some aspects of novelty seeking, but little is known of genetic similarities among these models. To assess the genetic coherence of “novelty seeking,” we compared the performance of 14 inbred strains of mice in five tests: activity in a novel environment, novel environment preference, head dipping on a hole-board, object preference, and a two-trial version of the spontaneous alternation task. Differences among strains were observed for all tasks, but performance in any given task was generally not predictive of performance in any other. To evaluate similarities among these tasks further, we selectively bred lines of mice for high or low head dipping on the hole-board. Similar to results from the inbred strain experiments, head dipping was not correlated with performance in the other measures but was genetically correlated with differences in locomotor activity. Using two approaches to estimating common genetic influences across tasks, we have found little evidence that these partial models of novelty seeking reflect the influence of common genes or measure a single, unified construct called novelty seeking. Based on the substantial influence of genetic factors, ease of implementation, and relative independence from general locomotion, head dipping on a hole-board is a good task to use in the domain of novelty seeking, but multiple tasks, including others not tested here, would be needed to capture the full genetic range of the behavioral domain.
Disruption of axo–glial junctions causes cytoskeletal disorganization and degeneration of Purkinje neuron axons
Authors: Garcia-Fresco German P. , Sousa Aurea D. , Pillai Anilkumar M. , Moy Sheryl S. , Crawley Jacqueline N. , Tessarollo Lino , Dupree Jeffrey L. , Bhat Manzoor A.
Published: March 2006

Axo–glial junctions (AGJs) play a critical role in the organization and maintenance of molecular domains in myelinated axons. Neurexin IV/Caspr1/paranodin (NCP1) is an important player in the formation of AGJs because it recruits a paranodal complex implicated in the tethering of glial proteins to the axonal membrane and cytoskeleton. Mice deficient in either the axonal protein NCP1 or the glial ceramide galactosyltransferase (CGT) display disruptions in AGJs and severe ataxia. In this article, we correlate these two phenotypes and show that both
NCP1
and
CGT
mutants develop large swellings accompanied by cytoskeletal disorganization and degeneration in the axons of cerebellar Purkinje neurons. We also show that αII spectrin is part of the paranodal complex and that, although not properly targeted, this complex is still formed in
CGT
mutants. Together, these findings establish a physiologically relevant link between AGJs and axonal cytoskeleton and raise the possibility that some neurodegenerative disorders arise from disruption of the AGJs.
Variations in liver and blood copper concentrations in young beef cattle raised in north-west Spain: associations with breed, sex, age and season
Authors: Miranda M. , Cruz J. M. , López-Alonso M. , Benedito J. L.
Published: March 2006

The aim of the present study was to evaluate the influence of breed and other factors (age, sex and season) on copper (Cu) accumulation by calves reared in a region in north-west Spain where pig slurry is widely used for slurry fertilization, and where cattle typically have hepatic Cu concentrations above the generally accepted safe-adequate levels. In December 2000 and August 2001, paired liver and blood samples were obtained at slaughter from 532 male and female Galician Blond, Holstein-Friesian and Galician Blond×Holstein-Friesian calves, aged between 6 and 10 months, from 434 different farms. Samples were acid-digested and Cu concentrations determined by ICP-OES. Holstein-Friesian calves showed significantly higher mean Cu concentrations both in the liver (80·6 mg/kg fresh weight) and blood (0·891 mg/l) than Galician Blond calves (50·4 mg/kg and 0·748 mg/l respectively) and crosses between the two breeds (61·3 mg/kg and 0·829 mg/l respectively). Holstein-Friesian was the breed with the highest percentage (42%) of calves with hepatic Cu concentrations above safe-adequate levels (25 to 100 mg/kg fresh weight) and Galician Blond the breed with the highest proportion (29%) of hypocupraemia during the winter sampling. Considering all breeds, hepatic Cu levels were higher in males (63·8 mg/kg) than in females (53·5 mg/kg) and significantly increased with age in summer. A significant three-way breed×sex×age interaction was observed for liver Cu but this may be attributable to the small number of animals in some groups, having a confounding effect on the analysis. A significant sex×age×season interaction was also observed which could indicate greater male dominance in summer, so that they consume more forage (and thus more Cu) than females. Calves slaughtered in winter showed significantly lower mean blood Cu concentration (0·703 mg/l) than calves slaughtered in summer (0·940 mg/l).
Interaction before conflict and conflict resolution in pre‐school boys with language impairment
Authors: Horowitz Laura , Jansson Liselotte , Ljungberg Tomas , Hedenbro Monica
Published: March 2006

Background: Children with language impairment (LI) experience social difficulties, including conflict management. The factors involved in peer‐conflict progression in pre‐school children with LI, and which of these processes may differ from pre‐school children with typical language development (TL), is therefore examined.

Aims: To describe the relationship between opponents interacting before conflict, aberrant conflict causes, the conflict‐resolution strategy reconciliation (i.e. friendly contact between former opponents shortly following conflict termination), and conflict outcome in the form of social interaction after a conflict has run its course. It is hypothesized that without social interaction before conflict, children with LI will experience increased difficulties attaining reconciliation.

Methods & Procedures: Unstructured play of 11 boys with LI (4–7 years old), at a specialized language pre‐school, and 20 boys with TL (4–6 years old), at mainstream pre‐schools, were video filmed. Conflicts were identified and recorded according to a validated coding system. Recorded conflict details include social interaction between conflict in the pre‐conflict period, behavioural sequences constituting conflict cause (conflict period), reconciliatory behaviours in the post‐conflict period, and social interaction between former opponents in the succeeding non‐conflict period. The group's mean proportion of individual children's conflicts in which specific behavioural sequences occurred were calculated and compared between and within the groups.

Outcomes & Results: When conflicts with and without pre‐conflict social interaction were analysed separately, aberrant caused conflicts occurred more often in LI group conflicts than in TL group conflicts. However, in conflicts without social interaction in the pre‐conflict period, boys with LI exhibit reconciliatory behaviours in, and reconcile a comparatively smaller proportion of, conflicts. Social interaction in the succeeding non‐conflict period was proportionately less for boys with LI. This appears to stem from lower reconciliation rates in LI conflicts that do not begin with social interaction in the pre‐conflict period. It was also confounded by the larger number of aberrant caused LI conflicts that were rarely reconciled. In turn, non‐reconciliation and aberrant caused conflicts were independently associated with comparatively less social interaction in the succeeding non‐conflict period.

Conclusions: The results suggest that in addition to traditional psycholinguistic training, children with LI may gain from interventions that support concluding behavioural turns, as in aberrant caused conflicts; and in initiating contact in conflict situations, even when a frame of reference is not immediately available, as was the case when opponents have not established social interaction in the pre‐conflict period.
Inferring causal relationships among intermediate phenotypes and biomarkers: a case study of rheumatoid arthritis
Authors: Li Wentian , Wang Mingyi , Irigoyen Patricia , Gregersen Peter K.
Published: March 2006

Motivation: Genetic association analysis is based on statistical correlations which do not assign any cause-to-effect arrows between the two correlated variables. Normally, such assignment of cause and effect label is not necessary in genetic analysis since genes are always the cause and phenotypes are always the effect. However, among intermediate phenotypes and biomarkers, assigning cause and effect becomes meaningful, and causal inference can be useful.

Results: We show that causal inference is possible by an example in a study of rheumatoid arthritis. With the help of genotypic information, the shared epitope, the causal relationship between two biomarkers related to the disease, anti-cyclic citrullinated peptide (anti-CCP) and rheumatoid factor (RF) has been established. We emphasize the fact that third variable must be a genotype to be able to resolve potential ambiguities in causal inference. Two non-trivial conclusions have been reached by the causal inference: (1) anti-CCP is a cause of RF and (2) it is unlikely that a third confounding factor contributes to both anti-CCP and RF.

Contact:  wli@nslij-genetics.org
DRTF: a database of rice transcription factors
Authors: Gao Ge , Zhong Yingfu , Guo Anyuan , Zhu Qihui , Tang Wen , Zheng Weimou , Gu Xiaocheng , Wei Liping , Luo Jingchu
Published: March 2006

Summary: DRTF contains 2025 putative transcription factors (TFs) in Oryza sativa L. ssp. indica and 2384 in ssp. japonica, distributed in 63 families, identified by computational prediction and manual curation. It includes detailed annotations of each TF including sequence features, functional domains, Gene Ontology assignment, chromosomal localization, EST and microarray expression information, as well as multiple sequence alignment of the DNA-binding domains for each TF family. The database can be browsed and searched with a user-friendly web interface.

Availability: DRTF is available at

Contact:  drtf@mail.cbi.pku.edu.cn
Site-specific phosphorylation of a checkpoint mediator protein controls its responses to different DNA structures
Authors: Yoo Hae Yong , Jeong Seong-Yun , Dunphy William G.
Published: March 2006

The checkpoint mediator protein Claspin is indispensable for the ATR-dependent phosphorylation of Chk1 in response to stalled DNA replication forks in Xenopus egg extracts. We show that Claspin also participates in the detection of chromosomal double-stranded DNA breaks (DSBs) in this system. Significantly, removal of Claspin from egg extracts only partially abrogates the activation of Chk1 in response to chromatin with DSBs, whereas depletion of both Claspin and BRCA1 completely abolishes this activation. The function of Claspin in this DSB-triggered pathway depends on phosphorylation of T817 and S819 by ATR. Conversely, neither phosphorylation of Claspin on these sites nor the presence of BRCA1 is necessary for activation of Chk1 in response to stalled replication forks. Thus, site-specific phosphorylation of a checkpoint mediator protein is a crucial determinant in the discrimination between various checkpoint-inducing structures. Furthermore, checkpoint mediator proteins exhibit functional overlap that varies depending on the nature of the checkpoint-triggering DNA signal.
High-resolution ChIP–chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome
Authors: Alekseyenko Artyom A. , Larschan Erica , Lai Weil R. , Park Peter J. , Kuroda Mitzi I.
Published: March 2006

X-chromosome dosage compensation in Drosophila requires the male-specific lethal (MSL) complex, which up-regulates gene expression from the single male X chromosome. Here, we define X-chromosome-specific MSL binding at high resolution in two male cell lines and in late-stage embryos. We find that the MSL complex is highly enriched over most expressed genes, with binding biased toward the 3′ end of transcription units. The binding patterns are largely similar in the distinct cell types, with ∼600 genes clearly bound in all three cases. Genes identified as clearly bound in one cell type and not in another indicate that attraction of MSL complex correlates with expression state. Thus, sequence alone is not sufficient to explain MSL targeting. We propose that the MSL complex recognizes most X-linked genes, but only in the context of chromatin factors or modifications indicative of active transcription. Distinguishing expressed genes from the bulk of the genome is likely to be an important function common to many chromatin organizing and modifying activities.
Anions in metallic matrices model: application to the aluminium crystal chemistry
Authors: Vegas Ángel , Santamaría-Pérez David , Marqués Miriam , Flórez Manuel , García Baonza Valentín , Recio J. Manuel
Published: March 2006

We introduce and discuss an interpretative model of the structure and bonding of inorganic crystals containing metallic elements. The central idea is the conception of the crystal structure of such an inorganic compound as a metallic matrix whose geometric and electronic structures govern the formation and localization of the anions in the lattice. This is the reason for labelling the model anions in metallic matrices (AMM). Taking the AlX
3 crystal family (X = F, Cl, OH) as a suitable test-bed class of compounds, we illustrate how this approach gives a direct interpretation of the crystalline structures and explains the variable coordination that Al exhibits in crystalline materials. An exhaustive analysis of the topology of the electron density allows us to provide a quantum-mechanical assessment of the main hypotheses of the AMM model and to uncover, using microscopic arguments, the behavior of anions as chemical pressure agents.
(Z,2R,3R,4aR,7R,12aS)-2,3,7,8,12,12a-Hexahydro-2,3-dimethoxy-2,3,7-trimethyl-4aH-[1,4]dioxino[2,3-c]oxecin-5(11H)-one: a commensurate occupationally modulated structure revealing a condition for diffraction symmetry enhancement for non-parent reflections
Authors: Rae A. David , Willis Anthony C. , Loong David T. J. , Banwell Martin G.
Published: March 2006

(Z,2R,3R,4aR,7R,12aS)-2,3,7,8,12,12a-Hexahydro-2,3-dimethoxy-2,3,7-trimethyl-4aH-[1,4]dioxino[2,3-c]oxecin-5(11H)-one (C16H26O6) crystallizes in the space group P3
1
and approximates the conditions necessary for diffraction symmetry enhancement without twinning for the h − k ≠ 3N reflections. The structure may be described as an occupancy modulation of a 1:1 disordered P3
1
21 parent structure with Z = 3 that would only contribute to the h − k = 3N reflections. The crystal studied was a 0.717 (2):0.283 twin, but also had a stacking fault that on average caused the (1 − p

j

):p

j

population ratio for the alternative orientations of ordered columns along the three non-equivalent screw axes (j = 1, 2 or 3) of P3
1
to be describable by p
1 = 0.068 (3), p
2 = p
3 = 0.960 (3). The effect of these stacking faults could be simulated using global parameters that modify an ordered prototype structure. The structure reveals that the ten-membered lactone ring incorporates a Z-configured double bond and that the methoxy-substituted stereogenic centers created during a trans-diol protection step each possess the R-configuration.
Single-crystal X-ray and neutron powder diffraction investigation of the phase transition in tetrachlorobenzene
Authors: Barnett Sarah A. , Broder Charlotte K. , Shankland Kenneth , David William I. F. , Ibberson Richard M. , Tocher Derek A.
Published: March 2006

The polymorphic phase transition of 1,2,4,5-tetrachlorobenzene (TCB) has been investigated using neutron powder diffraction and single-crystal X-ray diffraction. The diffraction experiments show a reversible phase change that occurs as a function of temperature with no apparent loss of sample quality on transition between the two phases. Neutron powder diffraction gives detailed information on the molecular structural changes and lattice parameters from 2 K to room temperature. The structure of the low-temperature form has been elucidated for the first time using single-crystal X-ray diffraction. Comparison of the α and β structures show that they are both based on the same sheet motif, with the differences between the two being very subtle, except in terms of crystal symmetry. Detailed analysis of the structures revealed the changes required for inter-conversion. A computational polymorph search showed that these two sheet structures are more thermodynamically stable than alternative herringbone-type structures.
Spatial arrangement of molecules in homomolecular Z' = 2 structures
Authors: Pidcock Elna
Published: March 2006

The Box Model of crystal packing describes unit cells in terms of a limited number of arrangements of molecular building blocks. An analysis of Z′ ≤ 1 structures has shown that cell dimensions are related to molecular dimensions in a systematic way and that the spatial arrangement of molecules in crystal structures is very similar, irrespective of Z or space group. In this paper it is shown that the spatial arrangement of molecules in Z′ = 2 structures are, within the context of the Box Model, very similar to that found for Z′ ≤ 1 structures. The absence of crystallographic symmetry does not appear to affect correlations between molecular dimensions and cell dimensions, or between the packing patterns and the positions of molecules in the unit cell, established from the analysis of Z′ ≤ 1 structures. The preference shown by Z′ = 2 structures for low surface-area packing patterns and the observation that strong energetic interactions are most often found between the large faces of the independent molecules reaffirms the importance of molecular shape in crystal packing.
Experimental charge-density study on the nickel(II) coordination complex [Ni(H3
L)][NO3][PF6] [H3
L = N,N′,N′′-tris(2-hydroxy-3-methylbutyl)-1,4,7-triazacyclononane]: a reappraisal
Authors: Farrugia L. J. , Frampton C. S. , Howard J. A. K. , Mallinson P. R. , Peacock R. D. , Smith G. T. , Stewart B.
Published: March 2006

The experimental charge density in the title complex has been re-examined. The original work, reported some 8 years ago [Smith et al. (1997). J. Am. Chem. Soc.
119, 5028–5034], was undertaken using a very early version of the XD software, which contained serious programming errors. A re-refinement, using the original data and a recent version of the XD software, shows that many of the unusual aspects of this earlier study are artefacts due to these programming errors. The topological properties of the newly obtained experimental density compare well with those calculated from a theoretical DFT (density-functional theory) UHF-SCF (unrestricted Hartree Fock–self-consistent field) density. This report corrects several erroneous conclusions regarding the charge density in the title complex – in particular, the highly unusual diffuse Laplacian distribution about the Ni atom, and the trifurcated bond path from the Ni atom to the alcohol oxygen donor atoms are no longer observed. An examination of a range of topological properties of the metal–ligand bonds leads to the conclusion that the Ni—N and Ni—O bonds have an intermediate character, with a significant shared interaction, but with a substantial ionic component. This new study also reveals a previously unrecognized intramolecular H...H interaction in the macrocyclic ligand.
Structural investigations of phosphorus–nitrogen compounds. 7. Relationships between physical properties, electron densities, reaction mechanisms and hydrogen-bonding motifs of N3P3Cl(6 − n)(NHBu
t
)
n
derivatives
Authors: Bartlett Stewart W. , Coles Simon J. , Davies David B. , Hursthouse Michael B. , İbişogˇlu Hanife , Kiliç Adem , Shaw Robert A. , Ün İlker
Published: March 2006

A series of compounds of the N3P3Cl(6 − n)(NHBu
t
)
n
family (where n = 0, 1, 2, 4 and 6) are presented, and their molecular parameters are related to trends in physical properties, which provides insight into a potential reaction mechanism for nucleophilic substitution. The crystal structures of N3P3Cl5(NHBu
t
) and N3P3Cl2(NHBu
t
)4 have been determined at 120 K, and those of N3P3Cl6 and N3P3Cl4(NHBu
t
)2 have been redetermined at 120 K. These are compared with the known structure of N3P3(NHBu
t
)6 studied at 150 K. Trends in molecular parameters [phosphazene ring, P—Cl and P—N(HBu
t
) distances, PCl2 angles, and endo- and exocyclic phosphazene ring parameters] across the series are observed. Hydrogen-bonding motifs are identified, characterized and compared. Both the molecular and the hydrogen-bonding parameters are related to the electron distribution in bonds and the derived basicities of the cyclophosphazene series of compounds. These findings provide evidence for a proposed mechanism for nucleophilic substitution at a phosphorus site bearing a PCl(NHBu
t
) group.
Temperature dependence of the silver distribution in the crystal structure of natural pearceite, (Ag,Cu)16(As,Sb)2S11
Authors: Bindi Luca , Evain Michel , Menchetti Silvio
Published: March 2006

The crystal structure of the mineral pearceite, (Ag,Cu)16(As,Sb)2S11, has been solved and refined at 300, 120 and 15 K. At room temperature pearceite crystallizes with trigonal symmetry, space group P\bar 3m1; the refinement of the structure leads to a residual factor of R = 0.0464 for 1109 independent observed reflections and 92 variables. The crystal structure consists of sheets stacked along the c axis. The As atoms form isolated (As,Sb)S3 pyramids, which typically occur in sulfosalts, copper cations link two S atoms in a linear coordination, and the silver cations are found in a fully occupied position and in various sites corresponding to the most pronounced probability density function locations (modes) of diffusion-like paths. These positions correspond to low-coordination (2, 3 and 4) sites, in agreement with the preference of silver for such environments. d
10 silver-ion distribution has been determined by means of a combination of a Gram–Charlier description of the atomic displacement factors and a split-atom model. To analyse the crystal chemical behaviour of the silver cations as a function of temperature, a structural study was carried out at 120 K (R = 0.0450). The refinement indicates that the mineral exhibits the same structural arrangement as the room-temperature structure (space group P\overline 3m1) and shows that the silver cations are still highly disordered. In order to investigate a possible ordering scheme for the silver cations, a data collection at ultra-low temperature (15 K) was performed. The structural skeleton was found to be similar to that of the room-temperature and 120 K atomic structures, but the best solution was achieved with a fully split-atom model of five silver positions, giving an R value of 0.0449 for 651 observed reflections and 78 parameters. Although the silver cation densities condense into better defined modes, the joint probability density function still exhibits a strong overlapping of neighbouring sites.
Structure determination and phase transition behaviour of dimethyl sulfate
Authors: Ibberson Richard M. , Telling Mark T. F. , Parsons Simon
Published: March 2006

The crystal structures of phase I and phase II of dimethyl sulfate, (CH3O)2SO2, have been determined using complementary high-resolution neutron powder and single-crystal X-ray diffraction techniques. Below its melting point of 241 K dimethyl sulfate crystallizes in an orthorhombic structure (I) in the space group Fdd2. On cooling below ∼175 K the crystal transforms to a monoclinic structure (II) in the space group I2/a. The molecule is located on a twofold axis (Z′ = 1/2) in both structures. The phase transition is of first order with strong hysteresis. The phase transition results in changes to both the intra- and the intermolecular coordination environment.
Packing and polytypism in 1,10-phenanthrolin-1-ium (2-carboxyethyl)(2-carboxylatoethyl)dichlorostannate(IV)
Authors: Somphon Weenawan , Haller Kenneth J. , Rae A. David , Ng Seik Weng
Published: March 2006

The 1:1 adduct of [SnCl2(C2H4COOCH3)2] and 1,10-phenanthroline, (C12H8N2), which was set aside for 25 years, when recrystallized from ethanol was found to be the salt [C12H9N2]+·[SnCl2(C2H4COO)(C2H4COOH)]−. The SnIV atom in the anion has pseudo-octahedral coordination with two cis Cl atoms, two C atoms and two O atoms trans to the Cl atoms. The possibility of alternative stacking of layers perpendicular to c* offers an explanation for observed twinning and polytypism. An ordered, untwinned, Z = 2 crystal structure was determined. Pairs of adjacent anions are linked together by strong intermolecular O—H...O− hydrogen bonds, and the cation contains a strong intramolecular N—H...N hydrogen bond between its two N atoms. The protonated ring of the cation exhibits increased Lewis acidity and is linked into a network with the anions using a strong N—H...O and weak C—H...O and C—H...Cl interactions. The remaining rings of the cation form weaker C—H...O and C—H...Cl interactions. The cations stack in columns along a with an interplanar spacing of 3.24 Å for separations between cations inversion-related about (1, 1\over2, 1\over2) and 3.34 Å for separations between cations inversion-related about (1\over2, 1\over2, 1\over2).
Crystal chemical information to be obtained from the bond-number equality concept
Authors: Parthé Erwin
Published: March 2006

Based on the bond-number equality concept an equation is derived for anion complexes of normal valence compounds with triangularly and/or tetrahedrally coordinated central atoms and anions having one, two, three and four bonds to central atoms: %Δ = 4 − (n/m′) × [2 − %A
[1] + %A
[3] + 2 × %A
[4]]. %Δ is the ratio of the number of central atoms with triangular anion coordination to the sum of all central atoms in the anion complex. n/m′ is the ratio of the number of all A anions to the number of all central atoms C′ in the anion complex. %A
[1] is the ratio of the number of anions with one bond to a central atom to the sum of all anions in the anion complex. %A
[3] and %A
[4] are defined accordingly. The equation can be used to formulate the possible crystal chemical formulae, which are characterized by partitions of central atoms and anions according to their bond numbers. Nitridosilicates and selected oxoborates are treated as examples of applications of the equation.
Production and characterization of auxin‐insensitive rice by overexpression of a mutagenized rice IAA protein
Authors: Nakamura Ayako , Umemura Iichiro , Gomi Kenji , Hasegawa Yasuko , Kitano Hidemi , Sazuka Takashi , Matsuoka Makoto
Published: March 2006

Since auxin was first isolated and characterized as a plant hormone, the underlying molecular mechanism of auxin signaling has been elucidated primarily in dicot plants represented by Arabidopsis. In monocot plants, the molecular mechanism of auxin signaling has remained unclear, despite various physiological experiments. To understand the function and mechanism of auxin signaling in rice (Oryza sativa), we focused on the IAA gene, a well‐studied gene in Arabidopsis that serves as a negative regulator of auxin signaling. We found 24 IAA gene family members in the rice genome. OsIAA3 is one of these family members whose expression is rapidly increased in response to auxin. We produced transgenic rice harboring mOsIAA3‐GR, which can overproduce mutant OsIAA3 protein containing an amino acid change in domain II to cause a gain‐of‐function phenotype, by treatment with dexamethasone. The transgenic rice was insensitive to auxin and gravitropic stimuli, and exhibited short leaf blades, reduced crown root formation, and abnormal leaf formation. These results suggest that, in rice, auxin is important for development and its signaling is mediated by IAA genes.