bluuebunny/crossref_metadata_2025 huggingface dataset:
Ecological strategies of lichens
Authors: Rogers R. W.
Published: May 2007

Survival strategies of 34 species of lichens from a range of substrata, climates and growth forms were examined using the triangular ordination procedure of Grime. Triangular ordination is apparently an appropriate technique to apply to lichens, all available data falling within a triangle except for two foliicolous species which are probably partial leaf parasites. Statistically significant relationships between survival strategy and growth form, mode of asexual reproduction, substratum preference, family affiliation, and diversity of secondary chemical biosynthetic pathways have been demonstrated.
Japewia Subaurifera, A New Lichen Genus and Species From North-West Europe and Western North America
Authors: Tønsberg T.
Published: May 2007

The genus Japewia Tønsb. is introduced to accommodate three species including J. subaurifera Muhr & Tønsb. sp. nov. based on material from Norway, Sweden, Finland, Scotland, Canada (British Columbia) and U.S.A. (Washington). This species is closely related to Lecidea tornoensis Nyl. but is distinguished in being sorediate and by the production of lobaric acid (accessory) and acetone-soluble pigments. It grows on bark of deciduous and coniferous trees. Lecidea carrollii Coppins & P. James and L. tornoensis Nyl. are transferred to Japewia.
Thermutopsis Jamesii L, A New Member of the Lichinaceae From Antigua
Authors: Henssen Aino
Published: May 2007

Thermutopsis jamesii Henssen gen. et sp. nov. (Lichinaceae) is described from calcareous rocks in Antigua. The new species resembles in habit Thermutis velutina but differs in the internal stucture and development of thallus and fructifications. The cyanobiont is a poorly lichenized species of Tolypothrix; the fructifications arise within the the gelatinous sheath of the algal filaments. The ascocarps are thallinocarps of a special type; the hymenium stains deep blue in iodine; young paraphyses are thick and richly branched; the prototunicate, non-amyloid asci contain 8 simple, colourless spores. The pycnidia are ellipsoid, producing small rod-shaped, acrogenous conidia.
Trebouxia Jamesii and the Question of Multinucleate Cells in the Lichen Photobiont Trebouxia
Authors: Ahmadjian V.
Published: May 2007

The question of whether or not some Trebouxia species have multinucleate cells is a controversial one. Trebouxia jamesii was re-examined and found to have multinucleate cells in cultures grown on rich, organic media. Possible reasons for this condition are discussed.
Chemical and Morphological Variation in The Genus Cetrelia in The soviet Union
Authors: Randlane T. , Saag A.
Published: May 2007

Two hundred and three specimens belonging to the genus Cetrelia from the Soviet Union and also 41 samples from other countries have been analysed by TLC. Eight species were determined in the Soviet Union. In addition two new species, C. orientalis and C. pseudocollata sp. nov. are described. Five morphotypes and six chemotypes have been recognized in the genus: their main characteristics are tabulated in a form that can be used for identification and a key is also included. Evolutionary relationships between the ‘primary’ and ‘secondary’ species related to ‘species-pairs’ are discussed.
Digitothyrea, a new genus in the family Lichinaceae
Authors: Moreno P. P. , Egea J. M.
Published: May 2007

A new genus, Digitothyrea, in the family Lichinaceae, is described. It includes three species formerly placed in Thyrea Massal. Studies on morphology and ascocarp ontogeny show that these are a homogeneous group of closely related species that differ significantly from taxa included in Thyrea.Digitothyrea rotundata is reported for the second time, from Northern Africa, A key is included.
Adaptivity of the thallus structure of Hypogymnia physodes to microclimatic conditions
Authors: Hyvärinen M.
Published: May 2007

The thallus structure of a common epiphytic lichen Hypogymnia physodes growingon the bark of Pinus sylvestris under a variety of microclimatic conditions was studied by means of fluorescence and scanning electron microscopy. The disparity between the thallus layer thicknesses of specimens growing in different habitats proved to be small though obvious, and differences also appeared in the amount of gelatinous substances in the hyphal cell walls ofthe cortex and algal layer. Furthermore, the occurrence of a pored epicortex of H. physodes at dry sites is reported. The size distribution of the thalli, thallus area and the production of soralia showed a complex interaction with microclimate. Against a background of the microclimatic data collected here, humidity is considered to be the most important factor affecting the anatomy and morphology of the thallus.
ASCENT AND DESCENT: THE PHILOSOPHER'S REGRET
Authors: Silverman Allan
Published: May 2007

The aim of this long essay is to explain why the philosopher-ruler of
Plato's Republic descends “with regret” or having
been “compelled” from his contemplation of the Forms to rule
the state. It offers a new, optimistic interpretation of his goal in so
descending, namely to try to make everyone into a philosopher. After a
brief introductory section, I turn to the argument of the
Republic to show both that the philosopher's understanding of the
Good causes him to try to maximize the amount of good in the cosmos, and
that, since every rational person is capable, in virtue of his rational
soul, of becoming a philosopher, this amounts to adopting the
aforementioned goal. In the third section, I argue that the source of his
regret cannot be that he sacrifices his own happiness in descending. Here
the vehicle is a consideration of the “Plotinian” reading of
the Republic, whose conclusion is that once he has achieved
knowledge of the Forms, the philosopher can neither increase his happiness
by further study, nor lose his happiness. Hence, if he is true to his
goal, he has to try to improve the lot of others. In the next section, I
argue that the Timaeus' account of the Demiurge's construction of the
cosmos helps us to understand both the nature of the ruler's attempts to
make everyone a philosopher and why he also understands that he will
inevitably fail. Here the key idea is to link the Timaeus'
account of Necessity or the Wandering Cause with the circumstances facing
the philosopher in ruling the state. In the conclusion, I sketch how this
account of the philosopher's reason for descending suggests that the best
or ideal city in the Republic is not the tripartite
kallipolis, but is rather a version of the City of Pigs.
THE CLASSICAL ROOTS OF RADICAL INDIVIDUALISM
Authors: Long Roderick T.
Published: May 2007

While the classical Greco-Roman tradition is not ordinarily thought of
as associated with radical individualism, many of the central concerns of
such radical individualists as Frédéric Bastiat, Herbert
Spencer, Benjamin Tucker, Ludwig von Mises, F. A. Hayek, and Ayn
Rand—including their views on human sociality, spontaneous order,
and the relation between self-interest and non-instrumental concern for
others—are shown to be inheritances from and developments of
Platonic, Aristotelian, Epicurean, and Stoic ideas. Hence those working in
the classical tradition have reason to explore the radical individualist
tradition and vice versa.
Incorporating water table dynamics in climate modeling: 1. Water table observations and equilibrium water table simulations
Authors: Fan Ying , Miguez‐Macho Gonzalo , Weaver Christopher P. , Walko Robert , Robock Alan
Published: May 2007

Soil moisture is a key participant in land‐atmosphere interactions and an important determinant of terrestrial climate. In regions where the water table is shallow, soil moisture is coupled to the water table. This paper is the first of a two‐part study to quantify this coupling and explore its implications in the context of climate modeling. We examine the observed water table depth in the lower 48 states of the United States in search of salient spatial and temporal features that are relevant to climate dynamics. As a means to interpolate and synthesize the scattered observations, we use a simple two‐dimensional groundwater flow model to construct an equilibrium water table as a result of long‐term climatic and geologic forcing. Model simulations suggest that the water table depth exhibits spatial organization at watershed, regional, and continental scales, which may have implications for the spatial organization of soil moisture at similar scales. The observations suggest that water table depth varies at diurnal, event, seasonal, and interannual scales, which may have implications for soil moisture memory at these scales.
Mars Climate Sounder: An investigation of thermal and water vapor structure, dust and condensate distributions in the atmosphere, and energy balance of the polar regions
Authors: McCleese D. J. , Schofield J. T. , Taylor F. W. , Calcutt S. B. , Foote M. C. , Kass D. M. , Leovy C. B. , Paige D. A. , Read P. L. , Zurek R. W.
Published: May 2007

Against a backdrop of intensive exploration of the Martian surface environment, intended to lead to human exploration, some aspects of the modern climate and the meteorology of Mars remain relatively unexplored. In particular, there is a need for detailed measurements of the vertical profiles of atmospheric temperature, water vapor, dust, and condensates to understand the intricately related processes upon which the surface conditions, and those encountered during descent by landers, depend. The most important of these missing data are accurate and extensive temperature measurements with high vertical resolution. The Mars Climate Sounder experiment on the 2005 Mars Reconnaissance Orbiter, described here, is the latest attempt to characterize the Martian atmosphere with the sort of coverage and precision achieved by terrestrial weather satellites. If successful, it is expected to lead to corresponding improvements in our understanding of meteorological phenomena and to enable improved general circulation models of the Martian atmosphere for climate studies on a range of timescales.
Finite‐element modeling of subglacial cavities and related friction law
Authors: Gagliardini O. , Cohen D. , Råback P. , Zwinger T.
Published: May 2007

Sliding velocity and basal drag are strongly influenced by changes in subglacial water pressure or subglacial water storage associated with opening and closing of water cavities in the lee of bedrock obstacles. To better understand this influence, finite‐element simulations of ice flowing past bedrock obstacles with cavity formation are carried out for different synthetic periodic bedrock shapes. In the numerical model, the cavity roof is treated as an unknown free surface and is part of the solution. As an improvement over earlier studies, the cases of nonlinear ice rheology and infinite bedrock slopes are treated. Our results show that the relationship between basal drag and sliding velocity, the friction law, can be easily extended from linear to nonlinear ice rheology and is bounded even for bedrocks with locally infinite slopes. Combining our results with earlier works by others, a phenomenological friction law is proposed that includes three independent parameters that depend only on the bedrock geometry. This formulation yields an upper bound of the basal drag for finite sliding velocity and a decrease in the basal drag at low effective pressure or high velocity. This law should dramatically alter results of models of temperate glaciers and should also have important repercussions on models of glacier surges and fast glacier flows.
Transport‐controlled reaction rates under local non‐equilibrium conditions
Authors: Sanchez‐Vila Xavier , Dentz Marco , Donado Leonardo David
Published: May 2007

Chemical reactions are driven by non‐equilibrium and can be fully described by the spatio‐temporal distribution of the reaction rate. We present an analytical approach for the computation of reaction rates under local non‐equilibrium conditions for a precipitation/dissolution problem. We derive an original non‐linear partial differential equation for the reaction rate r and present a series expansion of r for large Damköhler numbers, i.e., fast local scale reactions. The impact of local scale non‐equilibrium conditions on the transport‐controlled reaction rate is studied for reactive transport in a column.
Mediterranean Sea level variations during the Messinian salinity crisis
Authors: Gargani Julien , Rigollet Christophe
Published: May 2007

The Mediterranean Basin has not always been connected to the Atlantic Ocean. During the Messinian salinity crisis (MSC), the Mediterranean Sea became progressively isolated by a complex combination of tectonic and glacio‐eustatic processes. When isolated, the Mediterranean water level depends on the hydrological flux and is expected to vary significantly. The amplitude and number of large water level fluctuations in the isolated Mediterranean is still controversial, despite numerous geological investigations. The observation of 3–5 surfaces of erosion in the Nile delta (Eastern Basin) provides new elements for understanding the dynamics of the MSC. Our model demonstrates that numerous water level falls of short duration may explain the preservation of a discontinuous river profile at ∼−500 m and ∼−1500 m in the Western Basin, as well as the existence of deep surfaces of erosion in the Eastern Basin.
Intracellular catalysis of disulfide bond formation by the human sulfhydryl oxidase, QSOX1
Authors: Chakravarthi Seema , Jessop Catherine E. , Willer Martin , Stirling Colin J. , Bulleid Neil J.
Published: May 2007

The discovery that the flavoprotein oxidase, Erv2p, provides oxidizing potential for disulfide bond formation in yeast, has led to investigations into the roles of the mammalian homologues of this protein. Mammalian homologues of Erv2p include QSOX (sulfhydryl oxidases) from human lung fibroblasts, guinea-pig endometrial cells and rat seminal vesicles. In the present study we show that, when expressed in mammalian cells, the longer version of human QSOX1 protein (hQSOX1a) is a transmembrane protein localized primarily to the Golgi apparatus. We also present the first evidence showing that hQSOX1a can act in vivo as an oxidase. Overexpression of hQSOX1a suppresses the lethality of a complete deletion of ERO1 (endoplasmic reticulum oxidase 1) in yeast and restores disulfide bond formation, as assayed by the folding of the secretory protein carboxypeptidase Y.
The molecular structure of human tissue type XV presents a unique conformation among the collagens
Authors: Myers Jeanne C. , Amenta Peter S. , Dion Arnold S. , Sciancalepore Justin P. , Nagaswami Chandrasekaran , Weisel John W. , Yurchenco Peter D.
Published: May 2007

Establishing the structure of the non-fibrillar collagens has provided a unique perspective to understanding their specialized functions in the extracellular matrix. These proteins exhibit very diverse conformations and supramolecular assemblies. Type XV collagen is a large macromolecule distinguished by a highly interrupted collagenous domain and many utilized sites of attachment for CS (chondroitin sulfate) and HS (heparan sulfate) glycosaminoglycan chains. It is present in most basement membrane zones of human tissues, where it is found closely associated with large collagen fibrils. To determine the molecular shape and organization of type XV, the protein was purified from human umbilical cords by salt extraction, and by ion-exchange and antibody-affinity chromatography. The representation of type XV in one of its most abundant tissue sources is estimated at only (1–2)×10−4% of dry weight. The molecules examined by transmission electron microscopy after rotary shadowing were visualized in multiple forms. Relatively few type XV monomers appeared elongated and kinked; most molecules were found in a knot/figure-of-eight/pretzel configuration not previously described for a collagen. Collective measurements of these populations revealed an average length of 193±16 nm. At the N-terminal end, identified by C-terminal antibody binding, were three 7.7 nm-diameter spheres, corresponding to TSPN-1 (N-terminal module of thrombospondin-1) modules, and attached to the collagen backbone by a short linker. The type XV monomers show the ability to self-assemble into higher-order structures. Some were arranged in complex clusters, but simpler oligomers, which may represent intermediates, were observed in a cruciform pattern with intermolecular binding sites that probably originate in the interruption sequences. The morphology of type XV is thus the antithesis of the fibrillar collagens, and the shape attains the required flexibility to form the spectrum of interconnecting links between banded fibrils at the basement membrane/interstitial border. These type XV structures may act as a biological ‘spring’ to stabilize and enhance resilience to compressive and expansive forces, and the multimers, in particular, with selective complements of many localized CS and HS chains, may be instrumental in spatial and temporal recruitment of modulators in growth, development and pathological processes.
Delayed Initiation of the Pharyngeal Swallow: Normal Variability in Adult Swallows
Authors: Martin-Harris Bonnie , Brodsky Martin B. , Michel Yvonne , Lee Fu-Shing , Walters Bobby
Published: May 2007

Purpose

The purpose of this investigation was to determine bolus head timing and location relations with the onset of hyoid movement at the initiation of the pharyngeal swallow and at the onset of swallow-related apnea.

Method

Bolus head timing and location and the timing of swallow-related apnea were recorded from frame-by-frame analyses of 5-ml single liquid swallows using dual-modality videofluoroscopy and nasal airflow recordings in 82 consecutive, healthy volunteers. The presence, depth, and response to airway entry were also recorded and related to the bolus head location and the onset of hyoid movement.

Results

The majority of participants—80% on at least 1 trial—produced the onset of hyoid movement at pharyngeal swallow initiation after the bolus head passed the posterior angle of the mandible. There was a trend in older participants for later onset of hyoid movement and onset of apnea relative to bolus head arrival at the posterior angle of the mandible.

Conclusion

Although entry of the bolus head into the pharynx prior to hyoid movement may result in a threat to the laryngeal airway, these data demonstrate that a “delay” by itself cannot be assumed to indicate a disordered swallow without coexisting impairments of swallowing physiology.
Predicting Outcomes of Children Referred for Autism Using the MacArthur–Bates Communicative Development Inventory
Authors: Luyster Rhiannon , Qiu Shanping , Lopez Kristina , Lord Catherine
Published: May 2007

Purpose

Autism spectrum disorders (ASD) are characterized by early impairments in language and related social communication skills. This investigation explored whether scores on the MacArthur–Bates Communicative Development Inventory (CDI) at ages 2 and 3 years predict outcome at age 9 years in children with ASD and developmental delay (DD).

Method

Sixty-two children referred for possible autism at age 2 years, and 19 children with DD, were followed to age 9 years. Vocabulary, prespeech, and gestures scores on CDIs administered at ages 2 and 3 years were used to predict follow-up IQ, language, adaptive skills, and scores on diagnostic measures.

Results

CDI scores at ages 2 and 3 did not predict outcome for the DD group. For the ASD sample, CDI receptive and expressive language and late gestures at ages 2 and 3 years predicted a number of follow-up variables, although scores at age 3 years were generally more predictive than scores at age 2 years.

Conclusions

The CDI yielded scores that were predictive of outcome, suggesting that this parent report measure may be a quick and informative assessment of early verbal and nonverbal skills in children with ASD.
Examining the Language Performances of Children With and Without Specific Language Impairment: Contributions of Phonological Short-Term Memory and Speed of Processing
Authors: Montgomery James W. , Windsor Jennifer
Published: May 2007

Purpose

This study investigated the effects of processing speed and phonological short-term memory (PSTM) on children’s language performance.

Method

Forty-eight school-age children with specific language impairment (SLI) and age peers completed auditory detection reaction time (RT) and nonword repetition tasks, the Clinical Evaluation of Language Fundamentals—Revised (CELF–R; E. Semel, E. Wiig, & W. Secord, 1987), and a word recognition RT task. Correlation and regression were used to determine unique and shared contributions to variance among measures.

Results

Children with SLI were outperformed by age peers on each task. Auditory detection RT was correlated with nonword repetition (NWR) in each group. However, both variables covaried with age, and auditory detection RT did not contribute unique variance to NWR in either group. For the SLI group, NWR predicted unique variance in CELF–R performance (about 15%); auditory detection RT predicted a smaller amount of unique variance in the word recognition RT task (about 9%).

Conclusion

Processing speed and PSTM measures covaried with chronological age. Processing speed was associated with offline language performance only through association with PSTM. Processing speed contributed to online language performance, suggesting that speed is associated with processing more familiar language material (i.e., lexical content and structure) than less familiar material (e.g., various content on the CELF–R).
What Should Chris Say? The Ability of Children With Specific Language Impairment to Recognize the Need to Dissemble Emotions in Social Situations
Authors: Brinton Bonnie , Spackman Matthew P. , Fujiki Martin , Ricks Jenny
Published: May 2007

Purpose

In this study, the authors examined the ability of children with specific language impairment (SLI) and their typical peers to judge when an experienced emotion should be dissembled (hidden) in accord with social display rules.

Method

Participants included 19 children with SLI and19 children with typical language skills, both groups ranging in age from 7;9 (years;months) to 10;10, with a mean age of 9;1. Children were presented with 10 hypothetical social situations in which a character, Chris, experienced an emotion that should be dissembled for social purposes. The participants' responses were categorized as to whether or not they dissembled or displayed the emotion.

Results

Although the task was difficult for many participants, children with SLI indicated that the experienced emotion should be dissembled significantly less often than did their typical peers. Children in the 2 groups did not significantly differ in their judgments of the social display rules governing these situations.

Conclusion

These results suggested that the children with SLI did not understand the impact of displaying emotion on relationships in the same way as did their typical peers. In this respect, they seemed to lag behind the typical children in their developing emotion knowledge.
Ferroelectric interaction and polarization studies in BaTiO3∕SrTiO3 superlattice
Authors: Sarkar Asis , Krupanidhi S. B.
Published: May 2007

Ferroelectric superlattice structures consisting of alternating layers of BaTiO3 and SrTiO3 with variable interlayer thickness were grown on Pt (111)∕TiO2∕SiO2∕Si (100) substrates by pulsed laser deposition. The presence of superlattice reflections in the x-ray diffraction pattern clearly showed the superlattice behavior of the fabricated structures over a range of 6.4–20nm individual layer thicknesses. Depth profile conducted by secondary ion mass spectrometry analysis showed a periodic concentration of Ba and Sr throughout the film. Polarization hysteresis and the capacitance-voltage characteristics of these films show clear size dependent ferroelectric characteristics. The spontaneous (Ps) and remnant (Pr) polarizations increase gradually with decreasing periodicity, reach a maximum at a finite thickness and then decrease. The competition between the size effect and long-range ferroelectric interaction is suggested as a possible reason for this phenomenon. The temperature dependence of Ps and Pr shows a single ferroelectric phase transition, and the Curie temperature is estimated to be about 316K. The curve shows that the ferroelectric superlattice tends to form an artificial material, responding as a single structure with an averaged behavior of both the parent systems.
The effect of subgrid-scale models on the near wall vortices: A priori tests
Authors: Hauët Gwenaël , da Silva Carlos B. , Pereira José C. F.
Published: May 2007

Direct numerical simulation of a turbulent channel flow at Reτ=180 is used to analyze the resolved enstrophy dissipation caused by the subgrid-scale (SGS) models. The SGS enstrophy dissipation attains a minimum (forward scatter) at about y+≈8 and a backscatter region for y+<6, and is correlated with the high-speed streaks. A priori tests show that in the buffer layer, of all the models considered, the dynamic Smagorinsky, filtered structure function, and scale-similarity models display the smallest amount of resolved enstrophy dissipation, whereas the Smagorinsky and mixed models are the most dissipative.
Parametric instability of the helical dynamo
Authors: Peyrot Marine , Plunian Franck , Normand Christiane
Published: May 2007

We study the dynamo threshold of a helical flow made of a mean plus a fluctuating part. Two flow geometries are studied: (i) solid body and (ii) smooth. Two well-known resonant dynamo conditions, elaborated for stationary helical flows in the limit of large magnetic Reynolds numbers, are tested against lower magnetic Reynolds numbers and for fluctuating flows with zero mean. For a flow made of a mean plus a fluctuating part, the dynamo threshold depends on the frequency and the strength of the fluctuation. The resonant dynamo conditions applied on the fluctuating (respectively, mean) part seems to be a good diagnostic to predict the existence of a dynamo threshold when the fluctuation level is high (respectively, low).
Direct correlation between ferrite microstructure and electrical resistivity
Authors: Cernik R. J. , Freer R. , Leach C. , Mongkolkachit C. , Barnes P. , Jacques S. , Pile K. , Wander A.
Published: May 2007

Variations in the composition and microstructure of Mn-Zn soft ferrites have been directly correlated with spatial variations in electrical resistivity, which were both observed to occur on a length scale of approximately 500 μm. Tomographic energy dispersive diffraction imaging (TEDDI) was used to determine the nonsystematic change in the lattice parameter across the sample volume (8.48±0.05 Å) at a spatial resolution of 50 μm. We have used a microprobe contact technique to measure the local electrical resistivity (∼35 Ω cm) and density functional theory to model the band structure. The band structure calculations directly utilized the experimentally measured lattice parameters from the TEDDI measurements and were in good agreement with the measured resistivity. The mean band gap shrinkage was found to be 0.02 eV. This value for Eg was found to account well for the observed 10−20 Ω cm resistivity variations.
First and second order Raman scattering spectroscopy of nonpolar a-plane GaN
Authors: Gao Haiyong , Yan Fawang , Zhang Huixiao , Li Jinmin , Wang Junxi , Yan Jianchang
Published: May 2007

Nonpolar a-plane [(112¯0)] GaN samples have been grown on r-plane [(11¯02)] sapphire substrates by low-pressure metal-organic chemical-vapor deposition. The room-temperature first and second order Raman scattering spectra of nonpolar a-plane GaN have been measured in surface and edge backscattering geometries. All of the phonon modes that the selection rules allow have been observed in the first order Raman spectra. The frequencies and linewidths of the active modes have been analyzed. The second order phonon modes are composed of acoustic overtones, acoustic-optical and optical-optical combination bands, and optical overtones. The corresponding assignments of second order phonon modes have been made.
Study of electro-osmotic flows in microchannels packed with variable porosity media via lattice Boltzmann method
Authors: Chai Zhenhua , Guo Zhaoli , Shi Baochang
Published: May 2007

In this article, electro-osmotic flow (EOF) in microchannels packed with a variable porosity medium is studied using the lattice Boltzmann method (LBM). The present lattice Boltzmann model is constructed based on the generalized porous medium equation for EOF and validated by comparing the numerical solution with the approximate analytical solution. A detailed parametric study has been presented for EOF in microchannels filled with a variable porosity medium. It is found that the variations of porosity, particle size, ζ potential, applied electric field strength, and tortuosity significantly affect the flow pattern. Numerical results also indicate that the variation of the porosity near the wall has an important influence on the velocity profile, and should not be neglected in practice.
Long-term stability of nanostructured systems with negative heats of mixing
Authors: Nathani H. , Wang J. , Weihs T. P.
Published: May 2007

This paper investigates the long-term stability of nanostructured systems with negative heats of mixing using differential scanning calorimetry (DSC) and sputter deposited Al∕Ni nanolaminate foils as a model system. Changes in the intermixing between nanoscale layers were investigated using DSC after three years of storage at room temperature. Using the heats measured for the total formation reaction the average thicknesses of intermixing between alternating Al and Ni layers were determined to be 6.75±1.23nm shortly after deposition and 6.99±1.16nm after three years of storage, suggesting no decrease in stored energy. However, using the much smaller heats evolved during the shoulder prior to the first exotherm, the increase in average intermixing thickness was determined to be 1.19±0.34nm after three years of storage. For multilayer foils with bilayer thicknesses as thin as 15nm, this increase in intermixing can produce a measurable drop in stored energy (74.77J∕g). However, for foils with bilayers greater than 30nm, the decrease in stored energy is small and difficult to detect by DSC, suggesting that nanostructure systems with negative heats of mixing can have long-term stability.
Thermal stability of metal organic vapor phase epitaxy grown AlInN
Authors: Gadanecz A. , Bläsing J. , Dadgar A. , Hums C. , Krost A.
Published: May 2007

AlInN layers with a thickness of 100nm were grown by metal organic vapor phase epitaxy on GaN buffer layers on Si(111) substrates. By varying the growth temperature, In and NH3 flows, and reactor pressure, three series with different In contents were produced and thermally treated in the temperature range from 30to960°C. The as grown and annealed layers were investigated by x-ray diffraction in standard and grazing incidence geometry. Nearly lattice matched samples with an indium concentration of 17%–18% show long time stability at annealing temperatures as high as 960°C. At higher temperatures, the onset of severe Ga–Si meltback etching prevents further measurements. Nonlattice matched samples consist of pseudomorphic and relaxed parts. In the latter, a redistribution and loss of indium is observed upon annealing.
Photoacoustic imaging of early inflammatory response using gold nanorods
Authors: Kim Kang , Huang Sheng-Wen , Ashkenazi Shai , O’Donnell Matthew , Agarwal Ashish , Kotov Nicholas A. , Denny Michael F. , Kaplan Mariana J.
Published: May 2007

Gold nanorods have unusually strong absorption in near infrared, which can be utilized for an optical imaging with nanocolloids. The feasibility of photoacoustic imaging of inflammatory responses using bioconjugated gold nanorods is demonstrated. To target the stimulated cells, gold nanorods were conjugated to anti-intercellular adhesion molecule-1 (ICAM-1) which binds to cell surfaces over expressing ICAM-1. A monolayer of stimulated endothelial cells labeled with bioconjugated gold nanorods was scanned using a high frequency transducer. Photoacoustic images differentiated inflamed cells from control cells and matched well with fluorescence images. This technology may permit identification of critical inflammation sites such as blood vessels.
Structural studies of single crystalline In2O3 films epitaxially grown on InN(0001)
Authors: Wang Ch. Y. , Lebedev V. , Cimalla V. , Kups Th. , Tonisch K. , Ambacher O.
Published: May 2007

Single crystalline In2O3 is a prospective material to be used as a gate dielectric in InN based field effect transistors (FETs). This work addresses structural investigations of In2O3∕InN heterostuctures for metal-oxide-semiconductor FET devices. Single crystalline cubic In2O3 (111) films were epitaxially grown on hexagonal InN (0001) epilayers. The epitaxial relationship between the film and the template was determined as In2O3[111]‖InN[0001] and In2O3[101¯]‖InN⟨112¯0⟩ with an effective lattice mismatch of 2.14%. On the basis of the structural investigations, a phenomenological model for the growth of In2O3 on InN (0001) is proposed.
Hydrogen adsorption by tungsten carbide nanotube
Authors: Pan Hui , Feng Yuan Ping , Lin Jianyi
Published: May 2007

First-principles calculations based on density functional theory were carried out to investigate single-wall tungsten carbide nanotubes and their applications to energy storage, such as hydrogen storage and fuel cell. The pristine tungsten carbide nanotube was metallic. The W atop site is the most stable adsorption site for hydrogen atom, with a binding energy of 3.94eV and a binding distance of 1.7Å. Hydrogen molecule also favors the W atop site energetically. The calculated binding energy and distance are 0.44eV and 1.85Å, respectively. The authors’ studies demonstrate that the tungsten carbide nanotube could be a promising material for energy storage.
Protein structure determination from NMR chemical shifts
Authors: Cavalli Andrea , Salvatella Xavier , Dobson Christopher M. , Vendruscolo Michele
Published: May 2007

NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules. Chemical shifts are the most readily and accurately measurable NMR parameters, and they reflect with great specificity the conformations of native and nonnative states of proteins. We show, using 11 examples of proteins representative of the major structural classes and containing up to 123 residues, that it is possible to use chemical shifts as structural restraints in combination with a conventional molecular mechanics force field to determine the conformations of proteins at a resolution of 2 Å or better. This strategy should be widely applicable and, subject to further development, will enable quantitative structural analysis to be carried out to address a range of complex biological problems not accessible to current structural techniques.
The induced prostaglandin E
2
pathway is a key regulator of the respiratory response to infection and hypoxia in neonates
Authors: Hofstetter Annika O. , Saha Sipra , Siljehav Veronica , Jakobsson Per-Johan , Herlenius Eric
Published: May 2007

Infection during the neonatal period commonly induces apnea episodes, and the proinflammatory cytokine IL-1β may serve as a critical mediator between these events. To determine the mechanism by which IL-1β depresses respiration, we examined a prostaglandin E
2
(PGE
2
)-dependent pathway in newborn mice and human neonates. IL-1β and transient anoxia rapidly induced brainstem-specific microsomal prostaglandin E synthase-1 (mPGES-1) activity in neonatal mice. Furthermore, IL-1β reduced respiratory frequency during hyperoxia and depressed hypoxic gasping and autoresuscitation in mPGES-1 wild-type mice, but not in mPGES-1 knockout mice. In wild-type mice, PGE
2
induced apnea and irregular breathing patterns
in vivo
and inhibited brainstem respiratory rhythm generation
in vitro
. Mice lacking the EP3 receptor (EP3R) for PGE
2
exhibited fewer apneas and sustained brainstem respiratory activity, demonstrating that PGE
2
exerts its respiratory effects via EP3R. In human neonates, the infectious marker C-reactive protein was correlated with elevated PGE
2
in the cerebrospinal fluid, and elevated central PGE
2
was associated with an increased apnea frequency. We conclude that IL-1β adversely affects breathing and its control by mPGES-1 activation and PGE
2
binding to brainstem EP3 receptors, resulting in increased apnea frequency and hypoxia-induced mortality.
Sex chromosome silencing in the marsupial male germ line
Authors: Namekawa Satoshi H. , VandeBerg John L. , McCarrey John R. , Lee Jeannie T.
Published: May 2007

In marsupials, dosage compensation involves silencing of the father's X-chromosome. Because no
XIST
orthologue has been found, how imprinted X-inactivation occurs is unknown. In eutherians, the X is subject to meiotic sex chromosome inactivation (MSCI) in the paternal germ line and persists thereafter as postmeiotic sex chromatin (PMSC). One hypothesis proposes that the paternal X is inherited by the eutherian zygote as a preinactive X and raises the possibility of a similar process in the marsupial germ line. Here we demonstrate that MSCI and PMSC occur in the opossum. Surprisingly, silencing occurs before X–Y association. After MSCI, the X and Y fuse through a dense plate without obvious synapsis. Significantly, sex chromosome silencing continues after meiosis, with the opossum PMSC sharing features of eutherian PMSC. These results reveal a common gametogenic program in two diverse clades of mammals and support the idea that male germ-line silencing may have provided an ancestral form of mammalian dosage compensation.
Docosahexaenoic acid alters bilayer elastic properties
Authors: Bruno Michael J. , Koeppe Roger E. , Andersen Olaf S.
Published: May 2007

At low micromolar concentrations, polyunsaturated fatty acids (PUFAs) alter the function of many membrane proteins. PUFAs exert their effects on unrelated proteins at similar concentrations, suggesting a common mode of action. Because lipid bilayers serve as the common “solvent” for membrane proteins, the common mechanism could be that PUFAs adsorb to the bilayer/solution interface to promote a negative-going change in lipid intrinsic curvature and, like other reversibly adsorbing amphiphiles, increase bilayer elasticity. PUFA adsorption thus would alter the bilayer deformation energy associated with protein conformational changes involving the protein/bilayer boundary, which would alter protein function. To explore the feasibility of such a mechanism, we used gramicidin (gA) analogues of different lengths together with bilayers of different thicknesses to assess whether docosahexaenoic acid (DHA) could exert its effects through a bilayer-mediated mechanism. Indeed, DHA increases gA channel appearance rates and lifetimes and decreases the free energy of channel formation. The appearance rate and lifetime changes increase with increasing channel-bilayer hydrophobic mismatch and are not related to differing DHA bilayer absorption coefficients. DHA thus alters bilayer elastic properties, not just lipid intrinsic curvature; the elasticity changes are important for DHA's bilayer-modifying actions. Oleic acid (OA), which has little effect on membrane protein function, exerts no such effects despite OA's adsorption coefficient being an order of magnitude greater than DHA's. These results suggest that DHA (and other PUFAs) may modulate membrane protein function by bilayer-mediated mechanisms that do not involve specific protein binding but rather changes in bilayer material properties.
Discovery of parasite virulence genes reveals a unique regulator of chromosome condensation 1 ortholog critical for efficient nuclear trafficking
Authors: Frankel Matthew B. , Mordue Dana G. , Knoll Laura J.
Published: May 2007

Eukaryotic parasites are a leading cause of morbidity and mortality worldwide, yet little is known about the genetic basis of their virulence. Here, we present a forward genetic screen to study pathogenesis in the protozoan parasiteToxoplasma gondii. By using modified signature-tagged mutagenesis, the growth of 6,300T. gondiiinsertional mutants was compared in cell culture and murine infection to identify genes required specificallyin vivo. One of the 39 avirulent mutants is disrupted in a divergent ortholog of the regulator of chromosome condensation 1 (RCC1), which is critical for nuclear trafficking in model systems. Although this RCC1 mutant grows similar to wild type in standard tissue culture conditions, it is growth-impaired under nutrient limitation. Genetic complementation of mutant parasites with theT. gondiiRCC1 gene fully restores both virulence in mice and growth under low-nutrient conditions. Further analysis shows that there is a significant defect in nuclear trafficking in the RCC1 mutant. These findings suggest that the rate of nuclear transport is a critical factor affecting growth in low-nutrient conditionsin vivoandin vitro. Additionally, we observed that although RCC1 proteins are highly conserved in organisms from humans to yeast, no protozoan parasite encodes a characteristic RCC1. This protein divergence may represent a unique mechanism of nucleocytoplasmic transport. This study illustrates the power of this forward genetics approach to identify atypical virulence mechanisms.
Conformational variability of the intracellular domain of
Drosophila
Notch and its interaction with Suppressor of Hairless
Authors: Kelly Deborah F. , Lake Robert J. , Walz Thomas , Artavanis-Tsakonas Spyros
Published: May 2007

The Notch receptor is the central element in an evolutionarily conserved signal transduction pathway that controls cell fates in metazoans. Receptor–ligand interactions trigger a cascade of proteolytic events that release the entire Notch intracellular domain (NICD) from the membrane, permitting its translocation into the nucleus and participation in a transcriptionally active complex. Using electron microscopy, we examined the structure of NICD and its interaction with the DNA-binding effector of Notch signaling, Suppressor of Hairless [Su(H)]. In conjunction with biochemical analyses, we found that
Drosophila
NICD is monomeric and exists in two primary conformational states, only one of which can bind Su(H). Furthermore, we show that changes in divalent cation concentrations lead to NICD self-association, which seems to be mediated by the polyglutamine-containing, opa-repeat region of NICD. Our study suggests that conformational modulation of NICD may define a mechanism of Notch pathway control.
Information flow between subspaces of complex dynamical systems
Authors: Majda Andrew J. , Harlim John
Published: May 2007

The quantification of information flow between subspaces in ensemble predictions for complex dynamical systems is an important practical topic, for example, in weather prediction and climate change projections. Although information transfer between dynamical system components is an established concept for nonlinear multivariate time series, the specific nature of the nonlinear dynamics generating the observed flow of information is ignored in such statistical analysis. Here, a general mathematical theory for information flow between subspaces in ensemble predictions of a dynamical system is developed, which accounts for the specific underlying dynamics. The results below also include potentially useful approximation strategies for practical implementation in dynamical systems with many degrees of freedom. Specific elementary examples are developed here with both stable and unstable dynamics to both illustrate facets of the theory and to test Monte Carlo solution strategies.
Lithocholic acid can carry out
in vivo
functions of vitamin D
Authors: Nehring Jamie A. , Zierold Claudia , DeLuca Hector F.
Published: May 2007

The physiological ligand for the vitamin D receptor (VDR) is 1,25-dihydroxyvitamin D
3
. Lithocholic acid (LCA), a bile acid implicated in the progression of colon cancer, was recently shown to bind to VDR with low affinity and increase expression of the xenobiotic enzymes of the CYP3A family. Thus, LCA can induce its own catabolism through the VDR. We have now found that LCA can substitute for vitamin D in the elevation of serum calcium in vitamin D-deficient rats. Further, LCA in the diet will also replace vitamin D in the mobilization of calcium from bone. Further, LCA induces CYP24-hydroxylase mRNA gene expression in the kidney of vitamin D-deficient rats. It is clear, therefore, that LCA can be absorbed into the circulation to bind to the VDR at extra-intestinal sites. These findings lend support for the idea that the VDR may have evolved from an original role in detoxification.
The B″/PR72 subunit mediates Ca
2+
-dependent dephosphorylation of DARPP-32 by protein phosphatase 2A
Authors: Ahn Jung-Hyuck , Sung Jee Young , McAvoy Thomas , Nishi Akinori , Janssens Veerle , Goris Jozef , Greengard Paul , Nairn Angus C.
Published: May 2007

In dopaminoceptive neurons, dopamine- and cAMP-regulated phosphoprotein of 32 kDa (DARPP-32) plays a central role in integrating the effects of dopamine and other neurotransmitters. Phosphorylation of DARPP-32 at Thr-34 by protein kinase A results in inhibition of protein phosphatase 1 (PP1), and phosphorylation at Thr-75 by Cdk5 (cyclin-dependent kinase 5) results in inhibition of protein kinase A. Dephosphorylation at Thr-34 involves primarily the Ca
2+
-dependent protein phosphatase, PP2B (calcineurin), whereas dephosphorylation of Thr-75 involves primarily PP2A, the latter being subject to control by both cAMP- and Ca
2+
-dependent regulatory mechanisms. In the present study, we have investigated the mechanism of Ca
2+
-dependent regulation of Thr-75 by PP2A. We show that the PR72 (or B″ or PPP2R3A) regulatory subunit of PP2A is highly expressed in striatum. Through the use of overexpression and down-regulation by using RNAi, we show that PP2A, in a heterotrimeric complex with the PR72 subunit, mediates Ca
2+
-dependent dephosphorylation at Thr-75 of DARPP-32. The PR72 subunit contains two Ca
2+
binding sites formed by E and F helices (EF-hands 1 and 2), and we show that the former is necessary for the ability of PP2A activity to be regulated by Ca
2+
, both
in vitro
and
in vivo
. Our studies also indicate that the PR72-containing form of PP2A is necessary for the ability of glutamate acting at α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid and NMDA receptors to regulate Thr-75 dephosphorylation. These studies further our understanding of the complex signal transduction pathways that regulate DARPP-32. In addition, our studies reveal an alternative intracellular mechanism whereby Ca
2+
can activate serine/threonine phosphatase activity.