bluuebunny/crossref_metadata_2025 huggingface dataset:
Ontology Mapping of PATO to YATO for the improvement of interoperability of quality description
Authors: Masuya Hiroshi , Tanaka Nobuhiko , Waki Kazunori , Kushida Tatsuya , Kozaki Kouji , Mizoguchi Riichiro
Published: July 2009

To facilitate broad interoperability for phenotype information between different ontological frameworks, we developed a reference ontology, PATO2YATO_Quality, with the careful mapping of terms of PATO which is a quality ontology commonly used for biological phenotype annotation to the latest top-level ontology, YATO, which represents advanced modeling of quality-related concepts. As a result, YATO framework enabled to describe changes of phenotypic qualities along the courses of time in ontologically correct way and sophisticated classification and representation of interrelationships among quality-related concepts to provide fully integration of qualitative values and quantitative values obtained from phenotyping experiments and advanced representation of more detailed quality description. Thus, PATO2YATO_Quality will contribute to advanced integration of phenotypic qualities.
A Bayesian Hierarchical Model to Derive Novel Gene Networks from Gene Ontology Fingerprints
Authors: Qin Tingting , Tsoi Lam , Lawson Andrew , Zheng Jim
Published: July 2009

We developed a Bayesian hierarchical model to identify gene networks based on the similarity score generated from comparing the gene ontology fingerprints of gene pairs. Genes in this network were assumed to have similar biological functions that can be indicated by their ontology fingerprints. Our results indicate that different pathways show consistent score threshold that allow us to distinguish biological relevant gene—gene connections in the network.
Concurrent, Collaborative *Ontology Building* with Collaborative Protégé (CP)
Authors: Schober Daniel
Published: July 2009

Creation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by the distribution of the ontology’s developers. An obvious solution therefore is to build collaboration into ontology development tools. Such support necessarily includes both the technical means to perform editing operations upon an ontology, but also support for the communication that makes collaboration such a vital part of much ontology development. To investigate the distributed, collaborative ontology engineering process and the corresponding capabilities of the Collaborative Protege 3 (CP) tool, members of the OntoGenesis network came together and enriched the Ontology of Biomedical Investigations (OBI) with new content. The communications and interactions of the participants with each other, directly or through the tool, were tracked and analyzed. Our initial analysis of the degree to which this new tool fulfills the practical requirements of collaborative ontology engineering suggests the approach is promising. We present some observations and recommendations for CP based upon this experience.
Automated Annotation-Based Bio-Ontology Alignment with Structural Validation
Authors: Joslyn Cliff , Baddeley Bob , Blake Judith , Bult Carol , Dolan Mary , Riensche Rick , Rodland Karin , Sanfilippo Antonio , White Amanda
Published: July 2009

We outline the structure of an automated process to both align multiple bio-ontologies in terms of their genomic co-annotations, and then to measure the structural quality of that alignment. We illustrate the method with a genomic analysis of 70 genes implicated in lung disease against the Gene Ontology.
Expression and Regulation of Soluble Epoxide Hydrolase in Adipose Tissue
Authors: De Taeye Bart M. , Morisseau Christophe , Coyle Julie , Covington Joseph W. , Luria Ayala , Yang Jun , Murphy Sheila B. , Friedman David B. , Hammock Bruce B. , Vaughan Douglas E.
Published: July 2009

Obesity is an increasingly important public health issue reaching epidemic proportions. Visceral obesity has been defined as an important element of the metabolic syndrome and expansion of the visceral fat mass has been shown to contribute to the development of insulin resistance and cardiovascular disease. To identify novel contributors to cardiovascular and metabolic abnormalities in obesity, we analyzed the adipose proteome and identified soluble epoxide hydrolase (sEH) in the epididymal fat pad from C57BL/6J mice that received either a regular diet or a “western diet.” sEH was synthesized in adipocytes and expression levels increased upon differentiation of 3T3‐L1 preadipocytes. Although normalized sEH mRNA and protein levels did not differ in the fat pads from mice receiving a regular or a “western diet,” total adipose sEH activity was higher in the obese mice, even after normalization for body weight. Furthermore, peroxisome proliferator–activated receptor γ (PPARγ) agonists increased the expression of sEH in mature 3T3‐L1 adipocytes in vitro and in adipose tissue in vivo. Considering the established role for sEH in inflammation, cardiovascular diseases, and lipid metabolism, and the suggested involvement of sEH in the development of type 2 diabetes, our study has identified adipose sEH as a potential novel therapeutic target that might affect the development of metabolic and cardiovascular abnormalities in obesity.
Feasibility and Benefit of Parent Participation in a Program Emphasizing Preschool Child Language Development While Homeless
Authors: O'Neil-Pirozzi Therese M.
Published: July 2009

Purpose

This exploratory study examined the feasibility of homeless parents' participation in an intervention to increase use of facilitating language strategies during interactions with their preschool children while residing in family homeless shelters. This study also examined the intervention’s impact on the parents' use of facilitating language strategies, regardless of parent performance on a single-word receptive vocabulary test.

Method

Using a prospective, pretest/posttest comparison group design, 12 parents were randomly assigned to a 4-session experimental group training emphasizing use of facilitating language utterances with children following vocabulary testing. Four parents were randomly assigned to a control group intervention.

Results

It was feasible for parents to participate in the intervention. Before the intervention, individual experimental group parents with poor test performance demonstrated relatively high use of facilitating language utterances. After the intervention, the experimental group increased use of facilitating language utterances during interactions with their children.

Conclusions

This exploratory study provides initial evidence that it is feasible for parents to participate in, and benefit from, a brief language-based group intervention while residing in family homeless shelters. Further study of language-based interventions for these at-risk families and of the possible impact of parent language functioning on intervention benefit is needed.
Feeding Tube Placement in Patients With Advanced Dementia: The Beliefs and Practice Patterns of Speech-Language Pathologists
Authors: Sharp Helen M. , Shega Joseph W.
Published: July 2009

Purpose

To describe the beliefs and practices of speech-language pathologists (SLPs) about the use of percutaneous endoscopic gastrostomy (PEG) among patients with advanced dementia and dysphagia.

Method

A survey was mailed to a geographically stratified random sample of 1,050 medical SLPs.

Results

The response rate was 57%, and 326 surveys met inclusion criteria. Fifty-six percent of SLPs recommended PEG for a patient with advanced dementia and dysphagia. Contrary to the evidence, many respondents believed that PEG improves nutritional status and increases survival. Relatively few SLPs believed that PEG improved patients' functional status or quality of life. Patient factors (e.g., age or prognosis) were more often identified as influences on recommendations for PEG than were extrinsic factors (e.g., cost). Nearly 40% believed that PEG was the standard of care, while 15% believed it should be. Very few SLPs (11%) would want a PEG themselves. Perceived standard of care was significantly related to both geographic region and population density (
p
< .05), but self-reported practices were not.

Conclusions

Discrepancies between SLPs' beliefs, the literature, and self-reported practices were observed. The findings suggest the need to connect the evidence base to clinical practice and to include SLPs in local and national discussions about end-of-life care protocols.

Supplemental Material

https://doi.org/10.23641/asha.6170189
Peer Responses to Stuttering in the Preschool Setting
Authors: Langevin Marilyn , Packman Ann , Onslow Mark
Published: July 2009

Purpose

This study investigated peer responses to preschoolers' stuttering in preschool and sought to determine whether specific characteristics of participants' stuttering patterns elicited negative peer responses.

Method

Four outdoor free-play sessions of 4 preschoolers age 3–4 years who stutter were videotaped. Stutters were identified on transcripts of the play sessions. Peer responses to stuttered utterances were judged to be negative or neutral/positive. Thereafter, participants' stuttering behaviors, durations of stutters, and judgments of the meaningfulness of peer-directed stuttered utterances were analyzed.

Results

Between 71.4% and 100% of peer responses were judged to be neutral/positive. In the negative responses across 3 participants, peers were observed to react with confusion or to interrupt, mock, walk away from, or ignore the stuttered utterances. Utterances that elicited negative responses were typically meaningless and contained stutters that were behaviorally complex and/or of longer duration. Other social interaction difficulties also were observed—for example, difficulty leading peers in play, participating in pretend play, and resolving conflicts.

Conclusions

Results indicate that the majority of peer responses to stuttered utterances were neutral/positive; however, results also indicate that stuttering has the potential to elicit negative peer responses and affect other social interactions in preschool.
Using Family Paradigms to Improve Evidence-Based Practice
Authors: Hidecker Mary Jo Cooley , Jones Rebecca S. , Imig David R. , Villarruel Francisco A.
Published: July 2009

Purpose

Evidence-based practice (EBP) describes clinical decision making using research, clinical experience, and client values. For family-centered practices, the client’s family is integral to this process. This article proposes that using family paradigms, a family science framework, may help elicit and understand client/family values within family-centered EBP.

Method

This article describes the family paradigms framework: 4 classic paradigms of “closed,” “random,” “open,” and “synchronous.” Its applicability to family-centered EBP is proposed using augmentative and alternative communication examples.

Results

A family-centered approach to EBP requires families to be an integral part of clinical decision making, but some families may need assistance in enumerating their views and values. Family paradigms (which consider how a family uses its resources of time, space, energy, and material in the pursuit of its goals of control, affect, meaning, and content) may be a way to elicit family values and preferences relevant to clinical decisions.

Conclusions

Family and client values can be incorporated throughout the EBP steps. Considering family paradigms may increase awareness and understanding of how families' views of their goals and resources affect clinical decisions. Further research is needed into both the processes and effectiveness of using family paradigms to conduct family-centered EBP.
The Effects of Color Cues on Typically Developing Preschoolers' Speed of Locating a Target Line Drawing: Implications for Augmentative and Alternative Communication Display Design
Authors: Thistle Jennifer J. , Wilkinson Krista
Published: July 2009

Purpose

This research examined how the presence of color in relation to a target within an augmentative and alternative communication array influenced the speed with which typically developing preschoolers located a target line drawing.

Method

Fifteen children over the age of 4 years (from 4;2 [years;months] to 5;4) and 15 children under the age of 4 years (2;10–3;11) participated. Participants were asked to find a target line drawing of foods (e.g., banana and tomato) among an array of 12. The reaction time of locating the target was measured across 4 conditions in which the foreground color and the background color of the line drawing were manipulated.

Results

For all participants, line drawings featuring foreground color provided greater advantages in the speed of locating the target compared with drawings featuring only background color. Younger participants demonstrated faster reaction times when color was limited to the foreground.

Conclusion

Clinicians should consider incorporating color in the foreground of the line drawing when constructing visual displays. Targets that contain only background color but no foreground color appear to have a negative effect on the speed with which younger children can locate a target. Further research is needed to determine the effects in children with disabilities.
Phonological Accuracy and Intelligibility in Connected Speech of Boys With Fragile X Syndrome or Down Syndrome
Authors: Barnes Elizabeth , Roberts Joanne , Long Steven H. , Martin Gary E. , Berni Mary C. , Mandulak Kerry C. , Sideris John
Published: July 2009

Purpose

To compare the phonological accuracy and speech intelligibility of boys with fragile X syndrome with autism spectrum disorder (FXS-ASD), fragile X syndrome only (FXS-O), Down syndrome (DS), and typically developing (TD) boys.

Method

Participants were 32 boys with FXS-O (3–14 years), 31 with FXS-ASD (5–15 years), 34 with DS (4–16 years), and 45 TD boys of similar nonverbal mental age. We used connected speech samples to compute measures of phonological accuracy, phonological process occurrence, and intelligibility.

Results

The boys with FXS, regardless of autism status, did not differ from TD boys on phonological accuracy and phonological process occurrence but produced fewer intelligible words than did TD boys. The boys with DS scored lower on measures of phonological accuracy and occurrence of phonological processes than all other groups and used fewer intelligible words than did TD boys. The boys with FXS and the boys with DS did not differ on measures of intelligibility.

Conclusions

Boys with FXS, regardless of autism status, exhibited phonological characteristics similar to those of younger TD children but were less intelligible in connected speech. Boys with DS showed greater delays in all phonological measures than the boys with FXS and the TD boys.
Effects of Directional Exercise on Lingual Strength
Authors: Clark Heather M. , O’Brien Katy , Calleja Aimee , Newcomb Corrie Sarah
Published: July 2009

Purpose

To examine the application of known muscle training principles to tongue strengthening exercises and to answer the following research questions: (a) Did lingual strength increase following 9 weeks of training? (b) Did training conducted using an exercise moving the tongue in one direction result in strength changes for tongue movements in other directions? (c) Were differential training effects observed for participants completing exercises sequentially (in isolation) versus concurrently (several exercises in combination)? (d) Were strength gains maintained after exercise was discontinued?

Methods

Participants were 39 healthy adults assigned to sequential or concurrent lingual strength training. Lingual exercise (elevation, protrusion, and/or lateralization) was conducted for 9 weeks, with lingual strength and cheek strength (control variable) assessed weekly.

Results

All lingual strength measures increased with training, but cheek strength remained unchanged. Training effects were not related to training condition (sequential vs. concurrent), nor were specificity effects observed for direction of exercise. Significant decreases in lingual strength were noted 2–4 weeks after exercise was discontinued.

Conclusions

The findings replicate those of earlier studies demonstrating that lingual strength may be increased with a variety of exercise protocols and confirm that detraining effects may be observed when training is discontinued. The findings further suggest that the lingual musculature may demonstrate less dramatic training specificity than what has been reported for skeletal muscles.
Multiscale analysis of thermal field flow fractionation through macrotransport approach
Authors: Song Young Seok , Brenner Howard
Published: July 2009

We introduce the general theory of macrotransport processes to analyze thermal field flow fractionation (ThFFF). Multiscale analysis is carried out by adopting local and total moments. It is shown that the scheme of macrotransport processes is easier to apply and mathematically straightforward than exiting microscopic methods. The mean solute velocity and dispersivity associated with the retention time and standard deviation of a fractogram are calculated considering the temperature dependence of viscosity for ThFFF. A Gaussian distribution function is fitted to the fractogram measured experimentally and then the Soret numbers are calculated by using the retention time and standard deviation.
Gas diffusion ultrabarriers on polymer substrates using Al2O3 atomic layer deposition and SiN plasma-enhanced chemical vapor deposition
Authors: Carcia P. F. , McLean R. S. , Groner M. D. , Dameron A. A. , George S. M.
Published: July 2009

Thin films grown by Al2O3 atomic layer deposition (ALD) and SiN plasma-enhanced chemical vapor deposition (PECVD) have been tested as gas diffusion barriers either individually or as bilayers on polymer substrates. Single films of Al2O3 ALD with thicknesses of ≥10 nm had a water vapor transmission rate (WVTR) of ≤5×10−5 g/m2 day at 38 °C/85% relative humidity (RH), as measured by the Ca test. This WVTR value was limited by H2O permeability through the epoxy seal, as determined by the Ca test for the glass lid control. In comparison, SiN PECVD films with a thickness of 100 nm had a WVTR of ∼7×10−3 g/m2 day at 38 °C/85% RH. Significant improvements resulted when the SiN PECVD film was coated with an Al2O3 ALD film. An Al2O3 ALD film with a thickness of only 5 nm on a SiN PECVD film with a thickness of 100 nm reduced the WVTR from ∼7×10−3 to ≤5×10−5 g/m2 day at 38 °C/85% RH. The reduction in the permeability for Al2O3 ALD on the SiN PECVD films was attributed to either Al2O3 ALD sealing defects in the SiN PECVD film or improved nucleation of Al2O3 ALD on SiN.
Effects of charged impurities and lattice defects on transport properties of nanoscale graphene structures
Authors: Do V. Nam , Dollfus P.
Published: July 2009

Using the nonequilibrium Green’s function theory, transport properties of nanoscale graphene structures deposited on a SiO2/Si substrate have been investigated taking into account the influence of both lattice defects and charged impurities. The calculation argues the metallic lead-graphene coupling responsible for the asymmetric transport of electrons and holes, and shows that the conductivity is generally suppressed by these scattering processes. However, at the charge neutrality point, the screening seems to weaken such a suppression, leading to the minimum conductivity value of 4e2/πh even for the impurity density higher than 1012 cm−2, while it is strongly diminished to zero for the vacancy density of 1011 cm−2. Obtained results for the conductivity and the charge mobility are also discussed to highlight available experimental data.
Two-dimensional (2+n) resonance enhanced multiphoton ionization of HCl: State interactions and photorupture channels via low-energy triplet Rydberg states
Authors: Kvaran Ágúst , Matthiasson Kristján , Wang Huasheng
Published: July 2009

Mass spectra were recorded for (2+n) resonance enhanced multiphoton ionization (REMPI) of HCl as a function of resonance excitation energy in the 81 710–82 870 cm−1 region to obtain two-dimensional REMPI data. Small but significant fragmentations and H+, Cl+, as well as HCl+ formations are found to occur after resonance excitations to the triplet Rydberg states f Δ32(v′=0), f Δ31(v′=0), and g Σ3+(1)(v′=0). Whereas insignificant rotational line shifts could be observed, alterations in relative ion signal intensities, due to perturbations, clearly could be seen, making such data ideal for detecting and analyzing weak state interactions. Model analysis of relative ion signal intensities, taking account of the major ion formation channels following excitations to Rydberg states, its near-resonance interactions with ion-pair states as well as dissociations and/or photodissociations were performed. These allowed verification of the existence of all these major channels as well as quantifications of the relative weights of the channels and estimates of state interaction strengths. The proposed mechanisms were supported by ion signal power dependence studies.
Liquid plug propagation in flexible microchannels: A small airway model
Authors: Zheng Y. , Fujioka H. , Bian S. , Torisawa Y. , Huh D. , Takayama S. , Grotberg J. B.
Published: July 2009

In the present study, we investigate the effect of wall flexibility on the plug propagation and the resulting wall stresses in small airway models with experimental measurements and numerical simulations. Experimentally, a flexible microchannel was fabricated to mimic the flexible small airways using soft lithography. Liquid plugs were generated and propagated through the microchannels. The local wall deformation is observed instantaneously during plug propagation with the maximum increasing with plug speed. The pressure drop across the plug is measured and observed to increase with plug speed, and is slightly smaller in a flexible channel compared to that in a rigid channel. A computational model is then presented to model the steady plug propagation through a flexible channel corresponding to the middle plane in the experimental device. The results show qualitative agreements with experiments on wall shapes and pressure drops and the discrepancies bring up interesting questions on current field of modeling. The flexible wall deforms inward near the plug core region, the deformation and pressure drop across the plug increase with the plug speed. The wall deformation and resulting stresses vary with different longitudinal tensions, i.e., for large wall longitudinal tension, the wall deforms slightly, which causes decreased fluid stress and stress gradients on the flexible wall comparing to that on rigid walls; however, the wall stress gradients are found to be much larger on highly deformable walls with small longitudinal tensions. Therefore, in diseases such as emphysema, with more deformable airways, there is a high possibility of induced injuries on lining cells along the airways because of larger wall stresses and stress gradients.
Exchange bias anisotropy in Co nanowires electrodeposited into polycarbonate membranes
Authors: De La Torre Medina J. , Darques M. , Piraux L.
Published: July 2009

We report on exchange bias effects and time evolution in Co nanowires electrodeposited into the pores of track etched polycarbonate membranes. The slow variation of the exchange bias anisotropy, as extracted from field cooled hysteresis loops, is due to the delayed in time oxidation of the nanowires embedded in the polymer template. A model has been proposed to account for the drop of magnetization due to the presence of an oxide layer at the periphery of the nanowires, within the nanowires/polymer interface. The measured exchange bias energy is about four times smaller than the energy in planar bilayers because of the cylindrical geometry of the wires.
Effect of interlayer coupling in CoFeB/Ta/NiFe free layers on the critical switching current of MgO-based magnetic tunnel junctions
Authors: Lee Kangho , Chen Wei-Chuan , Zhu Xiaochun , Li Xia , Kang Seung H.
Published: July 2009

This paper reports the current-induced magnetization reversal characteristics of MgO-based magnetic tunnel junctions (MTJs) with CoFeB/Ta/NiFe composite free layers designed for spin-transfer-torque magnetoresistive random access memory. As the Ta spacer thickness (≤8 Å) was increased, the MTJs embedded into nanoscale integrated circuits demonstrated not only higher tunneling magnetoresistance ratios but also lower intrinsic critical switching currents. This suggests that promoting weak interlayer exchange coupling between CoFeB and NiFe is desirable for reducing the intrinsic critical switching current of CoFeB/Ta/NiFe. While the energy barrier was also reduced with a thicker Ta spacer, it was maintained at an adequate level (∼57kBT) even for the thickest Ta (8 Å) of this work.
Design and application of differential thermal analysis apparatus in high magnetic fields
Authors: Li Chuanjun , Ren Zhongming , Ren Weili , Deng Kang , Cao Guanghui , Zhong Yunbo , Wu Yuqin
Published: July 2009

The differential thermal analysis (DTA) apparatus has been developed for a commercial superconducting magnet. The DTA apparatus could detect the kinetics and thermodynamics of phase transformation with and without a magnetic field. Preliminary results for Al–Al2Cu eutectics are presented. The DTA curves indicate the similarity at several rates regardless of a magnetic field; however, at the same rate, melting transformation seems not to be influenced by a magnetic field, while solidification could be delayed via suppressing nucleation and crystal growth in a magnetic field. It will be believed that the DTA apparatus can be used to investigate the phase transformation of substances of interest in a magnetic field.
Ultraviolet photodissociation of C2F5I with a small and simple photofragment translational spectrometer
Authors: Yu Zijun , Xu Xiling , Cheng Min , Yu Dan , Du Yikui , Zhu Qihe
Published: July 2009

Photodissociation dynamics of C2F5I near 280 and 304 nm has been investigated on a small and simple time-of-flight photofragment translational spectrometer (PTS). On this new PTS, the photolyzed and ionized fragments, not accelerated by electric field, travel freely for a short flight path (<50 mm) and are detected by microchannel plates. In the spectra of the I∗(P21/2) channel at 281.73 and 304.02 nm, vibrational peaks with spacing of ∼350 cm−1 are partially resolved, indicating the preferential excitation of CF2 wag mode (ν11=366 cm−1) of C2F5 photofragment. The fraction of the available energy disposed into the internal energy is higher than 50% for both I∗ channel and I channel, showing the high excitation of vibration in the C2F5 fragments. The fragment recoil anisotropy parameter β(I∗), determined to be 1.70 at 281.73 nm and 1.64 at 304.02 nm, reveals that I∗ atoms are produced predominantly from the parallel Q30←N transition. The anisotropy parameter β(I), determined to be 1.25 at 279.71 nm and 0.88 at 304.67 nm, implies that I atoms are produced from two excited states, i.e., direct dissociation via the perpendicular Q31←N transition, and indirect dissociation via the parallel Q30←N transition then curve crossing to the Q11 potential energy surface. Analysis on the recent studies with vibrational state resolution in the photodissociation of alkyl iodides in the A band reveals that the “symmetric bending” mode on α-carbon of alkyl iodides is the preferential vibrational excitation mode, which can be explained by the classic impulsive model.
Texture inheritance in thin-film growth of Cu2ZnSnS4
Authors: Weber A. , Schmidt S. , Abou-Ras D. , Schubert-Bischoff P. , Denks I. , Mainz R. , Schock H. W.
Published: July 2009

The growth mechanism of Cu2ZnSnS4 thin films is studied starting from highly textured ZnS precursor films. These precursors were converted to Cu2ZnSnS4 by subsequent deposition of Cu, Sn, and S at high temperatures. Orientation measurements revealed that the ⟨111⟩ texture of the ZnS precursor is inherited by the Cu2ZnSnS4 layer. On the basis of texture and transmission electron microscopy measurements, a growth model is proposed. According to this model, the initial formation of Cu2ZnSnS4 nuclei is controlled by a topotactic or epitactic mechanism with respect to the ZnS precursor. The further growth of the Cu2ZnSnS4 grains appears to be independent of the precursor lattice.
Density functional for van der Waals forces accounts for hydrogen bond in benchmark set of water hexamers
Authors: Kelkkanen André K. , Lundqvist Bengt I. , Nørskov Jens K.
Published: July 2009

A recent extensive study has investigated how various exchange-correlation (XC) functionals treat hydrogen bonds in water hexamers and has shown traditional generalized gradient approximation and hybrid functionals used in density-functional (DF) theory to give the wrong dissociation-energy trend of low-lying isomers and van der Waals (vdW) dispersion forces to give key contributions to the dissociation energy. The question raised whether functionals that incorporate vdW forces implicitly into the XC functional predict the correct lowest-energy structure for the water hexamer and yield accurate total dissociation energy is here answered affirmatively for the vdW-DF [M. Dion et al., Phys. Rev. Lett.92, 246401 (2004)].
Displacement flows in horizontal, narrow, eccentric annuli with a moving inner cylinder
Authors: Carrasco-Teja M. , Frigaard I. A.
Published: July 2009

We analyze the effects of rotation and axial motion of the inner cylinder of an eccentric annular duct during the displacement flow between two Newtonian fluids of differing density and viscosity. The annulus is assumed narrow and is oriented near the horizontal. The main application is the primary cementing of horizontal oil and gas wells, in which casing rotation and reciprocation is becoming common. In this application it is usual for the displacing fluid to have a larger viscosity than the displaced fluid. We show that steady traveling wave displacements may occur, as for the situation with stationary walls. For small buoyancy numbers and when the annulus is near to concentric, the interface is nearly flat and a perturbation solution can be found analytically. This solution shows that rotation reduces the extension of the interface in the axial direction and also results in an azimuthal phase shift of the steady shape away from a symmetrical profile. Numerical solution is used for larger buoyancy numbers. We see that the phase shift results in the positioning of heavy fluid over light fluid along segments of the interface. When the axial extension of the interface is sufficiently large, this leads to a local buoyancy-driven fingering instability, for which a simple predictive theory is advanced. Over longer times, the local fingering is replaced by steady propagation of a diffuse interfacial region that spreads slowly due to dispersion. Slow axial motion of the annulus walls on its own is apparently less interesting. There is no breaking of the symmetry of the interface and hence no instability. However, axial wall motion does generate secondary flows which may combine with those from cylinder rotation resulting in enhanced dispersive effects.
Light-induced EPR study of charge transfer in poly(3-hexylthiophene)/fullerene bulk heterojunction
Authors: Krinichnyi V. I. , Yudanova E. I. , Denisov N. N.
Published: July 2009

The first results of the light-induced EPR study of magnetic, relaxation, and dynamic parameters of charge carriers background photoinduced by optical photons (1.7–3.4 eV) in poly(3-hexylthiophene)/fullerene bulk heterojunctions are described. All magnetic resonance parameters for positively charged polaron and negatively charged fullerene ion-radical in radical pairs photoinduced in the composite were determined separately by the steady-state microwave saturation method. Paramagnetic susceptibility of charge carriers reflects their activation dynamics and exchange interaction. A decay of long-living radical pairs depends on the spatial distance between photoinduced charge carriers. The one-dimensional polaron diffusion along the polymer chain and fullerene rotation near the main molecular axis was shown to follow activation Elliot hopping model and to be governed by photon energy. The difference in activation energies of the charge carriers’ dynamics and in their dependence on the exciting photon energy proves their noninteracting character in the polymer/fullerene composite. Main magnetic, relaxation and dynamics parameters of charge carriers are governed by the photon energy band due to inhomogeneity of distribution of polymer and fullerene domains in the composite.
Non-Born–Oppenheimer calculations of the BH molecule
Authors: Bubin Sergiy , Stanke Monika , Adamowicz Ludwik
Published: July 2009

Variational calculations employing explicitly correlated Gaussian basis functions have been performed for the ground state of the boron monohydride molecule (BH) and for the boron atom (B). Up to 2000 Gaussians were used for each system. The calculations did not assume the Born–Oppenheimer (BO) approximation. In the optimization of the wave function, we employed the analytical energy gradient with respect to the Gaussian exponential parameters. In addition to the total nonrelativistic energies, we computed scalar relativistic corrections (mass-velocity and Darwin). With those added to the total energies, we estimated the dissociation energy of BH. The non-BO wave functions were also used to compute some expectation values involving operators dependent on the interparticle distances.
Bees and white spiders: unravelling the pollination syndrome of Caladenia rigida (Orchidaceae)
Authors: Faast Renate , Farrington Lachlan , Facelli José M. , Austin Andrew D.
Published: July 2009

Orchids of the genus Caladenia have been shown to utilise two quite different pollination strategies, namely species-specific sexual deception of thynnine wasps and a more generalist strategy attracting a larger spectrum of foraging insects. While baiting techniques have enabled the identification of numerous pollinators of sexually deceptive Caladenia, insects that pollinate food-advertising species have received little attention. The present study employed a multidisciplinary approach to better evaluate the pollination syndrome of the white spider orchid, Caladenia rigida R.S.Rogers, a species previously reported to utilise both food and sexual deception. This included the observation and capture of potential pollinators of C. rigida through direct observation, pantraps, Malaise traps and pollinator-baiting experiments, and the use of molecular techniques to identify orchid pollinia isolated from carrier insects. We describe a suite of generalist insects visiting and bearing pollinia from C. rigida. In addition, samples collected from the labellum and column of C. rigida contained sugars at levels comparable to those of a known nectar-producing orchid, Microtis parviflora R.Br. Potential osmophores in the clubs and calli stained positively with neutral red and although this character is often associated with sexual deception, we found no evidence for this secondary pollination syndrome in C. rigida. The present study is the first one to provide a detailed description of the pollinators and pollination syndrome of a non-sexually deceptive species within the genus Caladenia and the first report to provide evidence of nectar production by a species within this genus.
Propagation and reintroduction of Caladenia
Authors: Wright Magali , Cross Rob , Dixon Kingsley , Huynh Tien , Lawrie Ann , Nesbitt Les , Pritchard Andrew , Swarts Nigel , Thomson Richard
Published: July 2009

Many Caladenia species have been reduced to extremely small and/or fragmented populations, and reintroduction/translocation into natural or rehabilitated habitats, by using ex situ propagated plants or via direct seeding, represents an important adjunct in conservation planning. However, Caladenia species are some of the most difficult terrestrial orchid taxa to propagate, in part because of the specificity of the mycorrhizal associations and the need to provide growing conditions that suit both the mycorrhizal fungi and Caladenia plants. The present paper reviews recent advances in Caladenia propagation and reintroduction methods, including in vitro seed germination, transferral from in vitro to nursery environments, ex vitro symbiotic germination (germination in inoculated nursery media), nursery cultivation, the use of nurse plants and reintroduction of Caladenia into natural habitats by using seed, dormant tubers or growing plants. Techniques discussed in the present paper increase the options for future Caladenia conservation programs, especially for those species currently on the brink of extinction.
Biogeography of Caladenia (Orchidaceae), with special reference to the South-west Australian Floristic Region
Authors: Phillips Ryan D. , Backhouse Gary , Brown Andrew P. , Hopper Stephen D.
Published: July 2009

Caladenia contains 376 species and subspecies, of which almost all are endemic to temperate and southern semiarid Australia. Eleven species occur in New Zealand, 10 of which are endemic, and one species is widely distributed in eastern Australia and the western Pacific. Only three species occur in both south-western and south-eastern Australia. At subgeneric level, Drakonorchis is endemic to the South-west Australian Floristic Region (SWAFR), Stegostyla to eastern Australia and New Zealand, whereas three subgenera, Calonema, Phlebochilus and Elevatae occur on both sides of the Nullarbor Plain. Subgenus Caladenia is primarily eastern Australian but also extends to the western Pacific. The largest subgenera (Calonema and Phlebochilus) have radiated extensively, with Calonema exhibiting a greater concentration of species in more mesic parts of the SWAFR than Phlebochilus. Within the SWAFR, the major biogeographic division within Caladenia follows the 600-mm isohyet. Within rainfall zones, biogeographic districts for Caladenia correlate with a combination of underlying geology and surface soils. Areas of high endemism contain diverse edaphic environments. Climatic and edaphic requirements are likely to be key drivers of rarity in Caladenia, although these parameters may be acting in concert with mycorrhizal and pollinator specificity.
Biology and natural history of Caladenia
Authors: Dixon Kingsley , Tremblay Raymond L.
Published: July 2009

The genus Caladenia comprises species that exhibit remarkable consistency in terms of growth form and phenological patterns. All taxa are herbaceous perennials, with the shoot arising annually from a single, usually spheroid, tuber and producing a single, hairy leaf. The tuber is annually replaced either side-by-side with the parent tuber or terminating a descending structure known as a dropper. The dropper is a depth-seeking mechanism that enables placement of the tuber at depth in the soil as a means to avoid predation by surface-foraging native mammals or away from the high temperatures and desiccating conditions during summer dormancy. The 3--5 attenuated roots produced at the junction between the tuber and shoot and produced late in the growing cycle and devoid of mycorrhiza suggest their functional significance may relate to water uptake. Mycorrhizal endophytes are confined to a hypertrophic stem region at the soil surface (collar) subtending the leaf that positions the collar directly in the organically rich zone at the soil surface. This morphology is a unique characteristic of several Australasian orchids in the tribe Diuridae. Mycorrhizal infection occurs rapidly, with maximum colonisation in concert with the onset of breaking rains. Pelotons are restricted to cortical cells, with fully developed pelotons throughout infected tissues within a week or so of soil wetting. Infection occurs as a ‘once-off’ event, with little evidence of secondary infection later in the growth cycle and no evidence of peloton digestion. Some taxa utilise vegetative propagation, often leading to localised clustering as for taxa in the ‘filamentosa’ complex or, extensive clonal mats as found in Caladenia flava and C. latifolia where daughter tubers are produced at the end of extending horizontal outgrowths. For the majority of taxa, plants remain dry-season (summer) dormant from a few months up to 7 months for arid-zone taxa, with shoot emergence from the tuber of temperate species thought to occur in response to a drop in the mean minimum temperature. Pollination biology of Caladenia is apparently through a process of deception, either as food or sexual mimics, with some taxa engaging in self-pollination. Here we review the natural history of Caladenia and acknowledge that much of our understanding is based on assumptions of the biology of terrestrial orchids in general and emphasise areas of research and biological enquiry that will be critical in the development of an effective conservation program for the genus.
Expression of GARP selectively identifies activated human FOXP3+ regulatory T cells
Authors: Wang Rui , Kozhaya Lina , Mercer Frances , Khaitan Alka , Fujii Hodaka , Unutmaz Derya
Published: July 2009

The molecules that define human regulatory T cells (Tregs) phenotypically and functionally remain to be fully characterized. We recently showed that activated human Tregs express mRNA for a transmembrane protein called glycoprotein A repetitions predominant (GARP, or LRRC32). Here, using a GARP-specific mAb, we demonstrate that expression of GARP on activated Tregs correlates with their suppressive capacity. However, GARP was not induced on T cells activated in the presence of TGFβ, which expressed high levels of FOXP3 and lacked suppressive function. Ectopic expression of FOXP3 in conventional T cells was also insufficient for induction of GARP expression in most donors. Functionally, silencing GARP in Tregs only moderately attenuated their suppressive activity. CD25+ T cells sorted for high GARP expression displayed more potent suppressive activity compared with CD25+GARP− cells. Remarkably, CD25+GARP− T cells expanded in culture contained 3–5 fold higher IL-17-secreting cells compared with either CD25+GARP+ or CD25−GARP− cells, suggesting that high GARP expression can potentially discriminate Tregs from those that have switched to Th17 lineage. We also determined whether GARP expression correlates with FOXP3-expressing T cells in human immunodeficiency virus (HIV) −infected subjects. A subset of HIV+ individuals with high percentages of FOXP3+ T cells did not show proportionate increase in GARP+ T cells. This finding suggests that higher FOXP3 levels observed in these HIV+ individuals is possibly due to immune activation rather than to an increase in Tregs. Our findings highlight the significance of GARP both in dissecting duality of Treg/Th17 cell differentiation and as a marker to identify bona fide Tregs during diseases with chronic immune activation.
Functional equivalence of HMGA- and histone H1-like domains in a bacterial transcriptional factor
Authors: García-Heras Francisco , Padmanabhan S. , Murillo Francisco J. , Elías-Arnanz Montserrat
Published: July 2009

Histone H1 and high-mobility group A (HMGA) proteins compete dynamically to modulate chromatin structure and regulate DNA transactions in eukaryotes. In prokaryotes, HMGA-like domains are known only in
Myxococcus xanthus
CarD and its
Stigmatella aurantiaca
ortholog. These have an N-terminal module absent in HMGA that interacts with CarG (a zinc-associated factor that does not bind DNA) to form a stable complex essential in regulating multicellular development, light-induced carotenogenesis, and other cellular processes. An analogous pair, CarD
Ad
and CarG
Ad
, exists in another myxobacterium,
Anaeromyxobacter dehalogenans
. Intriguingly, the CarD
Ad
C terminus lacks the hallmark HMGA DNA-binding AT-hooks and instead resembles the C-terminal region (CTR) of histone H1. We find that CarD
Ad
alone could not replace CarD in
M. xanthus
. By contrast, when introduced with CarG
Ad
, CarD
Ad
functionally replaced CarD in regulating not just 1 but 3 distinct processes in
M. xanthus
, despite the lower DNA-binding affinity of CarD
Ad
versus CarD in vitro. The ability of the cognate CarD
Ad
–CarG
Ad
pair to interact, but not the noncognate CarD
Ad
–CarG, rationalizes these data. Thus, in chimeras that conserve CarD–CarG interactions, the H1-like CTR of CarD
Ad
could replace the CarD HMGA AT-hooks with no loss of function in vivo. More tellingly, even chimeras with the CarD AT-hook region substituted by human histone H1 CTR or full-length H1 functioned in
M. xanthus
. Our domain-swap analyses showing functional equivalence of HMGA AT-hooks and H1 CTR in prokaryotic transcriptional regulation provide molecular insights into possible modes of action underlying their biological roles.
CD14-Mac-1 interactions inBacillus anthracisspore internalization by macrophages
Authors: Oliva Claudia , Turnbough Charles L. , Kearney John F.
Published: July 2009

Anthrax, a potentially lethal disease of animals and humans, is caused by the Gram-positive spore-forming bacteriumBacillus anthracis. The outermost exosporium layer ofB. anthracisspores contains an external hair-like nap formed by the glycoprotein BclA. Recognition of BclA by the integrin Mac-1 promotes spore uptake by professional phagocytes, resulting in the carriage of spores to sites of spore germination and bacterial growth in distant lymphoid organs. We show that CD14 binds to rhamnose residues of BclA and acts as a coreceptor for spore binding by Mac-1. In this process, CD14 induces signals involving TLR2 and PI3k that promote inside-out activation of Mac-1, thereby enhancing spore internalization by macrophages. As observed with mice lacking Mac-1, CD14−/−mice are also more resistant than wild-type mice to infection byB. anthracisspores. Additionally, afterB. anthracisspore challenge of CD14−/−mice, interference with the CD14-mediated signaling pathways results in increased mortality. Our results show that the binding and uptake ofB. anthracisspores by phagocytic cells is a dynamic process and involves multiple receptors and signaling pathways.
Innovations in host and microbial sialic acid biosynthesis revealed by phylogenomic prediction of nonulosonic acid structure
Authors: Lewis Amanda L. , Desa Nolan , Hansen Elizabeth E. , Knirel Yuriy A. , Gordon Jeffrey I. , Gagneux Pascal , Nizet Victor , Varki Ajit
Published: July 2009

Sialic acids (Sias) are nonulosonic acid (NulO) sugars prominently displayed on vertebrate cells and occasionally mimicked by bacterial pathogens using homologous biosynthetic pathways. It has been suggested that Sias were an animal innovation and later emerged in pathogens by convergent evolution or horizontal gene transfer. To better illuminate the evolutionary processes underlying the phenomenon of Sia molecular mimicry, we performed phylogenomic analyses of biosynthetic pathways for Sias and related higher sugars derived from 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids. Examination of ≈1,000 sequenced microbial genomes indicated that such biosynthetic pathways are far more widely distributed than previously realized. Phylogenetic analysis, validated by targeted biochemistry, was used to predict NulO types (i.e., neuraminic, legionaminic, or pseudaminic acids) expressed by various organisms. This approach uncovered previously unreported occurrences of Sia pathways in pathogenic and symbiotic bacteria and identified at least one instance in which a human archaeal symbiont tentatively reported to express Sias in fact expressed the related pseudaminic acid structure. Evaluation of targeted phylogenies and protein domain organization revealed that the “unique” Sia biosynthetic pathway of animals was instead a much more ancient innovation. Pathway phylogenies suggest that bacterial pathogens may have acquired Sia expression via adaptation of pathways for legionaminic acid biosynthesis, one of at least 3 evolutionary paths for de novo Sia synthesis. Together, these data indicate that some of the long-standing paradigms in Sia biology should be reconsidered in a wider evolutionary context of the extended family of NulO sugars.