bluuebunny/crossref_metadata_2025 huggingface dataset:
Cloud classes and radiative heating profiles at the Manus and Nauru Atmospheric Radiation Measurement (ARM) sites
Authors: Mather James H. , McFarlane Sally A.
Published: October 2009

The tropical western Pacific is a convective regime; however, the frequency and depth of convection is dependent on dynamical forcing which exhibits variability on a range of temporal scales and also on location within the region. Manus Island, Papua New Guinea, lies in the heart of the western Pacific warm pool region and exhibits frequent deep convection much of the time, while Nauru, which lies approximately 20 degrees to the east of Manus, is in a transition zone where the frequency of convection is dependent on the phase of the El Niño−Southern Oscillation. Because of this difference in dynamical regime, the distribution of clouds and the associated radiative heating is quite different at the two sites. Individual cloud types (boundary layer cumulus, thin cirrus, stratiform convective outflow) do occur at both sites, but with different frequencies. In this study we compare cloud profiles and heating profiles for specific cloud types at these two sites using data from the Atmospheric Radiation Measurement (ARM) Climate Research Facility. Results of this comparison indicate that while the frequency of specific cloud types differ between the two sites as one would expect, the characteristics of individual cloud classes are remarkably similar. This information could prove to be very useful for applying tropical ARM data to the broader region.
An objective analysis of the dynamic nature of field capacity
Authors: Twarakavi Navin K. C. , Sakai Masaru , Šimůnek Jirka
Published: October 2009

Field capacity is one of the most commonly used, and yet poorly defined, soil hydraulic properties. Traditionally, field capacity has been defined as the amount of soil moisture after excess water has drained away and the rate of downward movement has materially decreased. Unfortunately, this qualitative definition does not lend itself to an unambiguous quantitative approach for estimation. Because of the vagueness in defining what constitutes “drainage of excess water” from a soil, the estimation of field capacity has often been based upon empirical guidelines. These empirical guidelines are either time, pressure, or flux based. In this paper, we developed a numerical approach to estimate field capacity using a flux‐based definition. The resulting approach was implemented on the soil parameter data set used by Schaap et al. (2001), and the estimated field capacity was compared to traditional definitions of field capacity. The developed modeling approach was implemented using the HYDRUS‐1D software with the capability of simultaneously estimating field capacity for multiple soils with soil hydraulic parameter data. The Richards equation was used in conjunction with the van Genuchten‐Mualem model to simulate variably saturated flow in a soil. Using the modeling approach to estimate field capacity also resulted in additional information such as (1) the pressure head, at which field capacity is attained, and (2) the drainage time needed to reach field capacity from saturated conditions under nonevaporative conditions. We analyzed the applicability of the modeling‐based approach to estimate field capacity on real‐world soils data. We also used the developed method to create contour diagrams showing the variation of field capacity with texture. It was found that using benchmark pressure heads to estimate field capacity from the retention curve leads to inaccurate results. Finally, a simple analytical equation was developed to predict field capacity from soil hydraulic parameter information. The analytical equation was found to be effective in its ability to predict field capacities.
Supervisory Practices in Speech - Language Pathology: Pre-practicum Assessment of Student Clinicians in Graduate Training Programs
Authors: Phillips Daniel E.
Published: October 2009

How do supervisors determine the level of clinical independence of graduate student clinicians before clinic practicum begins and how do supervisors determine the style of supervision used with each student clinician? A qualitative research methodology was used to investigate supervisory practices of clinical educators supervising graduate student clinicians in speech-language pathology graduate training programs. Data was gathered through standardized open-ended interviews with 11 supervisors from five graduate training programs accredited by the American Speech-Language-Hearing Association (ASHA). All 11 supervisors conducted a pre-practicum assessment, but none used a published program or model to assess the student clinicians. All participants met with the student clinicians prior to the start of therapy to discuss the client. Analysis of data revealed three distinct types of meetings: presentation of the client by the clinician, presentation of the clinician to the supervisor, and pre-practicum assessment using a form. Eight of the 11 supervisors interviewed for this study determined the level of clinical independence of the student clinician solely by asking the clinician to present the client to the supervisor. The supervisors then evaluated the manner, organization, accuracy, and completeness of the presentation to estimate the student's level of clinical independence.
Building Teams in Speech-Language Pathology Clinical Education
Authors: Sbaschnig Kristine V.
Published: October 2009

Competition for entry into graduate school in speech-language pathology is intense. Building teams is one way for students to put aside the competitive mindset and learn to collaborate. Building teams is a peer-supervision method of learning that forms a bridge between instructor-driven supervision and self-supervision. Teams meet weekly and include the student clinicians, as well as the clinical educators assigned to the team. The Coordinator of Clinical Services schedules the meetings at a time that is convenient for all members of the team and sets the agenda. The team meetings include two main activities: Case Studies and the Teaching Clinic. The procedures for these activities are discussed. The benefit to students is that it teaches appropriate consultation and advocacy strategies as well as developing knowledge of the clinical process. The benefits to Coordinators of Clinical Services is that it assists them in becoming familiar with the graduate students on a personal level, in knowing the clients and their treatments, and in scheduling to meet each student's professional growth needs.
Reflections on Student Perceptions of Supervisory Needs in Clinical Education
Authors: Fitzgerald Mary Dale T.
Published: October 2009

Clinical supervision is a multi-faceted process involving changing interactions between clinical mentors and supervisees. This paper presents a reflection on students' perspectives from a series of focus groups, surveys, and rating scales completed by students enrolled in residential and distance delivery programs. Qualitative themes which emerged from student focus groups regarding self-identified needs within the clinical education process are examined. Self-assessment surveys and rating scales constructed from focus group data were administered to different cohorts of students during on-campus practica. Participants completed a 5-point rating scale indicating agreement-disagreement with statements of the importance of specific supervisory behaviors and rankings of their five highest priority supervisory needs. Comparisons between students' perceived needs across the developmental continuum and across both delivery modes were examined for differences in the thematic focus of student-identified needs. While the overall patterns of needs were basically similar for the distance education cohort and the beginning, intermediate, and advanced level clinicians in traditional cohorts, differences were observed among the cohorts in terms of patterns of self-identified needs and priorities for emotional support, technical assistance, and collegiality. Implications for accommodating student-identified priority needs for technical knowledge and skills as well as relational interactions with clinical educators are addressed.
Enhancing the nucleation of palladium atomic layer deposition on Al2O3 using trimethylaluminum to prevent surface poisoning by reaction products
Authors: Goldstein D. N. , George S. M.
Published: October 2009

Metal atomic layer deposition (ALD) on oxides can display long nucleation periods and high growth temperatures that may be caused by surface poisoning by reaction products. Exposures of trimethylaluminum (TMA) during Pd ALD using Pd(hfac)2 and formalin on Al2O3 surfaces can shorten the nucleation period and reduce the growth temperatures. Fourier transform infrared spectroscopy studies indicate that TMA removes Al(hfac)∗ species that block surface sites. Pd ALD nucleates more readily and grows at lower temperatures because higher temperatures are not needed to desorb Al(hfac)∗ species. Transmission electron microscopy analysis shows the differences between Pd ALD films deposited with and without TMA.
Spectral and particle dispersion properties of steady two-dimensional multiscale flows
Authors: Priego M. , Vassilicos J. C.
Published: October 2009

The spectral and particle dispersion characteristics of steady multiscale laminar thin-layer flows are investigated through numerical simulations of a two-dimensional layer-averaged model. The model assumes a semiparabolic velocity profile and is solved using a semi-Lagrangian spline method. The main features of the flows are turbulentlike and consistent with previous experimental studies. The Eulerian wavenumber spectra and the Lagrangian frequency spectra oscillate around power laws that reflect the self-similarity of the forcing. In the weak forcing regime, the exponents of these power laws can be related to the multiscale geometry and the intensity scaling of the forcing. The Lagrangian spectra also show low-frequency plateaus, which arise from the slow motions far away from the applied forces. The absolute dispersion of tracer particles in these steady planar flows presents a ballistic stage followed by a diffusive regime, which results from the decorrelated motions of particles lying on streamlines of different periods. Relative dispersion shows an additional intermediate stage consisting of several separation bursts, which originate from the intense strain regions imposed by the different forcing scales. While these bursts can cause locally superquadratic mean square separation, the trapping by steady recirculation regions rules out an intermediate relative dispersion power law regardless of the number of scales in the flow.
Si clusters on reconstructed SiC (0001) revealed by surface extended x-ray absorption fine structure
Authors: Gao Xingyu , Chen Shi , Liu Tao , Chen Wei , Wee A. T. S. , Nomoto T. , Yagi S. , Soda Kazuo , Yuhara Junji
Published: October 2009

The evolution of silicon carbide (0001) surface reconstruction upon annealing has been studied by Si K edge extended x-ray absorption fine structure (EXAFS). Using Si KVV Auger electron yield at different emission angles with different surface sensitivities, EXAFS reveals conclusively that Si–Si bonds exist on the surface for all reconstructions. The existence of Si clusters on the 63×63R30° surface was also confirmed by x-ray photoemission spectroscopy. This finding gives us a better understanding of epitaxial graphene formation on SiC.
Comprehensive investigation about the second order term of thermodynamic perturbation expansion
Authors: Zhou Shiqi , Solana J. R.
Published: October 2009

Monte Carlo simulations are carried out for the second order term in the thermodynamic perturbation expansion around a hard sphere reference fluid. The sample potentials considered cover a wide spectrum: From two frequently employed, namely hard sphere plus square well potential and hard core attractive Yukawa potential, to two kinds of repulsive potentials, namely hard sphere plus square shoulder potential and hard sphere plus triangle shoulder potential; the investigated potential range also extends from extremely short range to rather long range. The obtained simulation data are used to evaluate performance of two theoretical approaches, i.e., a traditional macroscopic compressibility approximation (MCA) and a recent coupling parameter expansion. Extensive comparison shows that the coupling parameter expansion provides a reliable method for accurately calculating the second order term of the high temperature series expansion, while the widely accepted MCA fails quantitatively or even qualitatively for most of the situations investigated.
Multidimensional steric effects for the XeI∗ (B, C) formations in the oriented Xe∗ (P32,MJ=2)+oriented CF3I reaction
Authors: Ohoyama H. , Kubo F. , Kasai T.
Published: October 2009

Steric effects for the XeI∗ (B) and XeI∗ (C) formations in the oriented Xe∗ (P32,MJ=2)+oriented CF3I reaction have been observed as a function of the mutual configuration between molecular orientation and atomic alignment in the collision frame. The mutual configuration exercises the significant influences on the stereoanisotropy for both the reactivity and the branching to the XeI∗ (B) and XeI∗ (C) channels.
Identification of nitrogen and zinc related vibrational modes in ZnO
Authors: Friedrich Felice , Gluba M. A. , Nickel N. H.
Published: October 2009

Zinc oxide films with natural zinc and isotopically pure Z68n were grown by pulsed laser deposition on sapphire substrates. Prior to and after ion implantation with N2+ the samples were characterized with Raman spectroscopy. After implantation the well-known N-related vibrational modes at 273.9 and 509.5 cm−1 are observed. In the isotopically pure Z68nO samples the vibrational modes exhibit a shift of 5.4 and 1.6 cm−1 to smaller wave numbers. As a result of the experimental data the vibrational modes at 273.9 and 509.5 cm−1 are attributed to a ZnI–NO and ZnI–OI complex, respectively. This is consistent with ab initio calculations based on density functional theory.
Two-dimensional axisymmetric Child–Langmuir scaling law
Authors: Ragan-Kelley Benjamin , Verboncoeur John , Feng Yang
Published: October 2009

The classical one-dimensional (1D) Child–Langmuir law was previously extended to two dimensions by numerical calculation in planar geometries. By considering an axisymmetric cylindrical system with axial emission from a circular cathode of radius r, outer drift tube radius R>r, and gap length L, we further examine the space charge limit in two dimensions. Simulations were done with no applied magnetic field as well as with a large (100 T) longitudinal magnetic field to restrict motion of particles to 1D. The ratio of the observed current density limit JCL2 to the theoretical 1D value JCL1 is found to be a monotonically decreasing function of the ratio of emission radius to gap separation r/L. This result is in agreement with the planar results, where the emission area is proportional to the cathode width W. The drift tube in axisymmetric systems is shown to have a small but measurable effect on the space charge limit. Strong beam edge effects are observed with J(r)/J(0) approaching 3.5. Two-dimensional axisymmetric electrostatic particle-in-cell simulations were used to produce these results.
Field effect on polaron dynamics and charge transport in conducting polymers
Authors: Qiu Yu , Zhu Li-Ping
Published: October 2009

We investigate the formation and motion dynamics of polarons in one-dimensional conjugated polymers within the extended Su–Schrieffer–Heeger model combined with an adiabatic dynamics method. In the presence of external electric fields, the initial location of the polaron is stressed and concerned with the charge transport property of organic semiconductors. Three regimes for the electric fields are categorized in terms of the forming place of the polaron. In the low field strength regime, the polaron is formed around the center of the chain and thus the charge undergoes a long-time travel before being extracted into the electrode because of the strong electron and phonon (e-p) interaction. In the intermediate strength regime, the polaron is formed near the chain end. Due to the chain-end scattering, the electron mobility increases in linear relation with the field strength. In the high strength regime, the polaron is formed at the chain end. This results in a nonlinear enhancement in the electronic mobility, in agreement with the experimental observations on the field dependent transient photocurrent in poly(phenylene vinylene). The electron-electron correlation, as well as the field mode effect on polaron dynamics, is also discussed.
Stoichiometry optimization of homoepitaxial oxide thin films using x-ray diffraction
Authors: LeBeau James M. , Engel-Herbert Roman , Jalan Bharat , Cagnon Joël , Moetakef Pouya , Stemmer Susanne , Stephenson G. Brian
Published: October 2009

Homoepitaxial SrTiO3 thin films grown by molecular beam epitaxy are analyzed using high-resolution x-ray diffraction and transmission electron microscopy. Measured 00L x-ray scans from stoichiometric and nonstoichiometric films are compared with calculations that account for the effects of film thickness, lattice parameter, fractional site occupancy, and an offset between film and substrate at the interface. It is found that thickness fringes, commonly observed around Bragg reflections even in stoichiometric homoepitaxial SrTiO3 films, arise from a film/substrate interface offset. Transmission electron microscopy studies confirm the presence of strain at those homoepitaxial interfaces that show an offset in x-ray diffraction. The consequences for stoichiometry optimization of homoepitaxial films using high-resolution x-ray diffraction and the quality of regrown oxide interfaces are discussed.
Ion distributions, exclusion coefficients, and separation factors of electrolytes in a charged cylindrical nanopore: A partially perturbative density functional theory study
Authors: Peng Bo , Yu Yang-Xin
Published: October 2009

The structural and thermodynamic properties for charge symmetric and asymmetric electrolytes as well as mixed electrolyte system inside a charged cylindrical nanopore are investigated using a partially perturbative density functional theory. The electrolytes are treated in the restricted primitive model and the internal surface of the cylindrical nanopore is considered to have a uniform charge density. The proposed theory is directly applicable to the arbitrary mixed electrolyte solution containing ions with the equal diameter and different valences. Large amount of simulation data for ion density distributions, separation factors, and exclusion coefficients are used to determine the range of validity of the partially perturbative density functional theory for monovalent and multivalent counterion systems. The proposed theory is found to be in good agreement with the simulations for both mono- and multivalent counterion systems. In contrast, the classical Poisson–Boltzmann equation only provides reasonable descriptions of monovalent counterion system at low bulk density, and is qualitatively and quantitatively wrong in the prediction for the multivalent counterion systems due to its neglect of the strong interionic correlations in these systems. The proposed density functional theory has also been applied to an electrolyte absorbed into a pore that is a model of the filter of a physiological calcium channel.
Local charge transport in nanoscale amorphous and crystalline regions of high-k (Zr2)0.8(Al2O3)0.2 thin films
Authors: Martin Dominik , Grube Matthias , Weber Walter M. , Rüstig Jürgen , Bierwagen Oliver , Geelhaar Lutz , Riechert Henning
Published: October 2009

The charge transport in (Zr02)0.8(Al2O3)0.2 thin films consisting of nanoscale crystallites in an amorphous matrix were investigated by conductive atomic force microscopy. Local current-voltage curves were obtained either from multiple current images for different biases or by ramping the tip bias at a specific location. Comparison of both approaches for amorphous matrix sites implies that they are equivalent. Current-voltage curves for crystallite and amorphous sites are different, but repeated voltage ramps at amorphous sites yield curves as obtained at pristine crystallites. This suggests charge transport through leakage paths along defects at grain boundaries and along stress-induced defects at amorphous sites.
miR-145 directs intestinal maturation in zebrafish
Authors: Zeng Lei , Carter Alyson D. , Childs Sarah J.
Published: October 2009

The rapid specification and differentiation of the embryonic zebrafish gut is essential to provide contractility for the digestion of food. The role of microRNAs in modulating gut epithelial or smooth muscle differentiation is currently not known. Here we show that the microRNA miR-145 is strongly expressed in zebrafish gut smooth muscle and regulates its development. Modulation of miR-145 levels results in gut smooth muscle and epithelium maturation defects. Loss of miR-145 results in defects of smooth muscle function as measured by decreased nitric oxide production but also leads to increased expression of the embryonic smooth muscle markers
sm22
α
-b
,
nm-mhc-b
, and
smoothelin
. Defects in gut epithelial maturation are also present as observed by immature morphology and a complete loss of alkaline phosphatase expression. Loss or gain of miR-145 function phenocopies defects observed with altered
gata6
expression and accordingly, we show that miR-145 directly represses
gata6
, and that
gata6
is a major miR-145 target in vitro and in vivo. miR-145 therefore plays a critical role in promoting the maturation of both layers of the gut during development through regulation of
gata6
.
Folding of electrostatically charged beads-on-a-string as an experimental realization of a theoretical model in polymer science
Authors: Reches Meital , Snyder Phillip W. , Whitesides George M.
Published: October 2009

The “beads-on-a-string” model for folding of polymers is a cornerstone of theoretical polymer science. This communication describes a physical model of beads-on-a-string, based on the folding of flexible strings of electrostatically charged beads in two dimensions. The system comprises millimeter-scale Teflon and Nylon-6,6 (spherical or cylindrical) beads (≈ 6 mm in diameter) separated by smaller (≈3 mm) poly(methyl methacrylate) (PMMA) spherical beads, threaded on a flexible string. The smaller, uncharged beads define the distances between the larger beads, and control the flexibility of the string. During agitation of the sequence of beads on a planar, horizontal paper surface, tribocharging generates opposite electrostatic charges on the larger Nylon and Teflon beads, but leaves the smaller PMMA beads essentially uncharged; the resulting electrostatic interactions cause the string to fold. Examination and comparison of two models—one physical and one theoretical—may offer a new approach to understanding folding, collapse, and molecular recognition at an abstract level, with particular opportunity to explore the influence of the flexibility of the string and the shape of the beads on the pattern and rate of folding. The physical system is, thus, an analog computer, simulating the theoretical beads-on-a-string model in two dimensions; this system makes it possible to test hypotheses connecting “sequence” to “folding”, rapidly and conveniently, while exploring nonlinearities and other complexities omitted from the theoretical model.
Modeling children's early grammatical knowledge
Authors: Bannard Colin , Lieven Elena , Tomasello Michael
Published: October 2009

Theories of grammatical development differ in how much abstract knowledge they attribute to young children. Here, we report a series of experiments using a computational model to evaluate the explanatory power of child grammars based not on abstract rules but on concrete words and phrases and some local abstractions associated with these words and phrases. We use a Bayesian procedure to extract such item-based grammars from transcriptions of 28+ h of each of two children's speech at 2 and 3 years of age. We then use these grammars to parse all of the unique multiword utterances from transcriptions of separate recordings of these same children at each of the two ages. We found that at 2 years of age such a model had good coverage and predictive fit, with the children showing radically limited productivity. Furthermore, adding expert-annotated parts of speech to the induction procedure had little effect on coverage, with the exception of the category of noun. At age 3, the children's productivity sharply increased and the addition of a verb and a noun category markedly improved the model's performance.
Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures
Authors: Cho Samuel S. , Pincus David L. , Thirumalai D.
Published: October 2009

Understanding how RNA molecules navigate their rugged folding landscapes holds the key to describing their roles in a variety of cellular functions. To dissect RNA folding at the molecular level, we performed simulations of three pseudoknots (MMTV and SRV-1 from viral genomes and the hTR pseudoknot from human telomerase) using coarse-grained models. The melting temperatures from the specific heat profiles are in good agreement with the available experimental data for MMTV and hTR. The equilibrium free energy profiles, which predict the structural transitions that occur at each melting temperature, are used to propose that the relative stabilities of the isolated helices control their folding mechanisms. Kinetic simulations, which corroborate the inferences drawn from the free energy profiles, show that MMTV folds by a hierarchical mechanism with parallel paths, i.e., formation of one of the helices nucleates the assembly of the rest of the structure. The SRV-1 pseudoknot, which folds in a highly cooperative manner, assembles in a single step in which the preformed helices coalesce nearly simultaneously to form the tertiary structure. Folding occurs by multiple pathways in the hTR pseudoknot, the isolated structural elements of which have similar stabilities. In one of the paths, tertiary interactions are established before the formation of the secondary structures. Our work shows that there are significant sequence-dependent variations in the folding landscapes of RNA molecules with similar fold. We also establish that assembly mechanisms can be predicted using the stabilities of the isolated secondary structures.
Identifying genotype-dependent efficacy of single and combined PI3K- and MAPK-pathway inhibition in cancer
Authors: Sos Martin L. , Fischer Stefanie , Ullrich Roland , Peifer Martin , Heuckmann Johannes M. , Koker Mirjam , Heynck Stefanie , Stückrath Isabel , Weiss Jonathan , Fischer Florian , Michel Kathrin , Goel Aviva , Regales Lucia , Politi Katerina A. , Perera Samanthi , Getlik Matthäus , Heukamp Lukas C. , Ansén Sascha , Zander Thomas , Beroukhim Rameen , Kashkar Hamid , Shokat Kevan M. , Sellers William R. , Rauh Daniel , Orr Christine , Hoeflich Klaus P. , Friedman Lori , Wong Kwok-Kin , Pao William , Thomas Roman K.
Published: October 2009

In cancer, genetically activated proto-oncogenes often induce “
upstream
” dependency on the activity of the mutant oncoprotein. Therapeutic inhibition of these activated oncoproteins can induce massive apoptosis of tumor cells, leading to sometimes dramatic tumor regressions in patients. The PI3K and MAPK signaling pathways are central regulators of oncogenic transformation and tumor maintenance. We hypothesized that
upstream
dependency engages either one of these pathways preferentially to induce “
downstream
” dependency. Therefore, we analyzed whether
downstream
pathway dependency segregates by genetic aberrations
upstream
in lung cancer cell lines. Here, we show by systematically linking drug response to genomic aberrations in non-small-cell lung cancer, as well as in cell lines of other tumor types and in a series of in vivo cancer models, that tumors with genetically activated receptor tyrosine kinases depend on PI3K signaling, whereas tumors with mutations in the RAS/RAF axis depend on MAPK signaling. However, efficacy of
downstream
pathway inhibition was limited by release of negative feedback loops on the reciprocal pathway. By contrast, combined blockade of both pathways was able to overcome the reciprocal pathway activation induced by inhibitor-mediated release of negative feedback loops and resulted in a significant increase in apoptosis and tumor shrinkage. Thus, by using a systematic chemo-genomics approach, we identify genetic lesions connected to PI3K and MAPK pathway activation and provide a rationale for combined inhibition of both pathways. Our findings may have implications for patient stratification in clinical trials.
Nonrelatives inherit colony resources in a primitive termite
Authors: Johns Philip M. , Howard Kenneth J. , Breisch Nancy L. , Rivera Anahi , Thorne Barbara L.
Published: October 2009

The evolution of eusociality, especially how selection would favor sterility or subfertility of most individuals within a highly social colony, is an unresolved paradox. Eusociality evolved independently in diverse taxa, including insects (all ants and termites; some bees, wasps, thrips, and beetles), snapping shrimp, and naked mole rats. Termites have received comparatively less focus than the haplodiploid Hymenoptera (ants, bees, and wasps); however, they are the only diploid group with highly complex colonies and an extraordinary diversity of castes. In this study we staged encounters between unrelated colonies of primitive dampwood termites,
Zootermopsis nevadensis
, mimicking natural meetings that occur under bark. During encounters, kings and/or queens were killed and surviving members merged into one colony. After encounters, members of both unrelated colonies cooperated as a single social unit. We determined the colony of origin of replacement reproductives that emerged after death of kings and/or queens. Here, we document that replacement reproductives developed from workers in either or both original colonies, inherited the merged resources of the colony, and sometimes interbred. Because this species shares many characteristics with ancestral termites, these findings demonstrate how ecological factors could have promoted the evolution of eusociality by accelerating and enhancing direct fitness opportunities of helper offspring, rendering relatedness favoring kin selection less critical.
A little bit of lithium does a lot for hydrogen
Authors: Zurek Eva , Hoffmann Roald , Ashcroft N. W. , Oganov Artem R. , Lyakhov Andriy O.
Published: October 2009

From detailed assessments of electronic structure, we find that a combination of significantly quantal elements, six of seven atoms being hydrogen, becomes a stable metal at a pressure approximately 1/4 of that required to metalize pure hydrogen itself. The system, LiH
6
(and other LiH

n

), may well have extensions beyond the constituent lithium. These hypothetical materials demonstrate that nontraditional stoichiometries can considerably expand the view of chemical combination under moderate pressure.
Transient dwarfism of soil fauna during the Paleocene–Eocene Thermal Maximum
Authors: Smith Jon J. , Hasiotis Stephen T. , Kraus Mary J. , Woody Daniel T.
Published: October 2009

Soil organisms, as recorded by trace fossils in paleosols of the Willwood Formation, Wyoming, show significant body-size reductions and increased abundances during the Paleocene–Eocene Thermal Maximum (PETM). Paleobotanical, paleopedologic, and oxygen isotope studies indicate high temperatures during the PETM and sharp declines in precipitation compared with late Paleocene estimates. Insect and oligochaete burrows increase in abundance during the PETM, suggesting longer periods of soil development and improved drainage conditions. Crayfish burrows and molluscan body fossils, abundant below and above the PETM interval, are significantly less abundant during the PETM, likely because of drier floodplain conditions and lower water tables. Burrow diameters of the most abundant ichnofossils are 30–46% smaller within the PETM interval. As burrow size is a proxy for body size, significant reductions in burrow diameter suggest that their tracemakers were smaller bodied. Smaller body sizes may have resulted from higher subsurface temperatures, lower soil moisture conditions, or nutritionally deficient vegetation in the high-CO
2
atmosphere inferred for the PETM. Smaller soil fauna co-occur with dwarf mammal taxa during the PETM; thus, a common forcing mechanism may have selected for small size in both above- and below-ground terrestrial communities. We predict that soil fauna have already shown reductions in size over the last 150 years of increased atmospheric CO
2
and surface temperatures or that they will exhibit this pattern over the next century. We retrodict also that soil fauna across the Permian-Triassic and Triassic-Jurassic boundary events show significant size decreases because of similar forcing mechanisms driven by rapid global warming.
Contour Guided Dissemination for Networked Embedded Systems
Authors: Chu I-Hsien , Duan Minlan , Sastry Shivakumar
Published: October 2009

Networked Embedded Systems have come to occupy an important role in emerging applications. Nodes in such a system are interconnected by a mesh topology. Despite the availability of multiple shortest paths between pairs of nodes, simulation results revealed that these paths cannot be effectively exploited by spreading the messages over the paths in a uniform method. We define the union of all the shortest paths between a pair of nodes as a contour. We present results that characterize the structure of contours when each node communicates directly with eight immediate neighbors. Heuristic rules that effectively disseminate messages over the available paths are presented. Simulation results demonstrate that the new method for dissemination ensures that nodes in a contour, which are at the same distance from the source, handle roughly the same number of messages. In the future, such techniques can be extended to general topologies.
An Enhanced CPA Algorithm for Real-Time Target Tracking in Wireless Sensor Networks
Authors: Yang Qing , Lim Alvin , Casey Kenan , Neelisetti Raghu-Kisore
Published: October 2009

Real-time tracking of moving targets using wireless sensor networks has been a challenging problem because of the high velocity of the targets and the limited resources of the sensors. CPA (closest point of approach) algorithms are appropriate for tracking fast-moving targets since the tracking error is roughly inversely proportional to the square root of the target velocity. However, this approach requires a specific node configuration with reference to the target trajectory which may not always be possible in randomly deployed sensor networks. Moreover, our mathematical analysis of the original CPA algorithm shows that it suffers from huge localization errors due to inaccuracies in sensor location and measured CPA times. To address these issues, we propose an enhanced CPA (ECPA) algorithm which requires only five sensors around the target to achieve the reliability and efficiency we want for computing the bearing of the target trajectory, the relative position between the sensors and the trajectory, and the velocity of the target. To validate the ECPA algorithm, we designed and implemented this algorithm over an actual data-centric acoustic sensor network as well as simulating it in an NS-2 simulator. The results of our field experiments and simulations show that we can achieve our goals of detecting the target and predicting its location, velocity and direction of travel with reasonable accuracy.
Mathematical Identification of a Neuronal Network Consisting of GABA and DA in Striatal Slices of the Rat Brain
Authors: Ramrath L. , Levering J. , Conrad M. , Thuemen A. , Fuellgraf H. , Moser A.
Published: October 2009

High frequency stimulation (HFS) has been used to treat various neurological and psychiatric diseases. Although further disorders are under investigation to extend the clinical application of HFS, the complex effect of HFS within a neuronal network is still unknown. Thus, it would be desirable to find a theoretical model that allows an estimation of the expected effect of applied HFS. Based on the neurochemical analysis of effects of the γ‐aminobutyric acid (GABA)A receptor antagonist bicuculline, the D2‐like receptor antagonist sulpiride and the D1‐like receptor antagonist SCH‐23390 on HFS evoked GABA and dopamine (DA) release from striatal slices of the rat brain, a mathematical network model is proposed including the neurotransmitters GABA, DA and glutamate (GLU). The model reflects inhibitory and excitatory interactions of the neurotransmitters outflow in the presence of HFS. Under the assumption of linear interactions and static measurements, the model is expressed analytically. Numerical identification of inhibition and excitation is performed on a basis of real outflow levels of GABA and DA in the rat striatum. Results validate the nature of the proposed model. Therefore, this leads to an analytical model of the interactions within distinct neural network components of the rat striatum.
The Dynamics of an HIV/AIDS Model with Screened Disease Carriers
Authors: Hove-Musekwa S. D. , Nyabadza F.
Published: October 2009

The presence of carriers usually complicates the dynamics and prevention of a disease. They are not recognized as disease cases themselves unless they are screened and they usually spread the infection without them being aware. We argue that this has been one of the major causes of the spread of human immunodeficiency virus (HIV). We propose, in this paper, a model for the heterogeneous transmission of HIV/acquired immunodeficiency syndrome in the presence of disease carriers. The model allows us to assess the role of screening, as an intervention program that can slow the epidemic. A threshold value ψ*, for the screening rate is obtained. It is shown numerically that if 80% or more of the carrier population is screened, the epidemic can be contained. The qualitative analysis is done in terms of the model reproduction number R. The model has two equilibria, the disease free equilibrium and a unique endemic equilibrium. The disease free equilibrium is globally stable of R < 1 and the endemic equilibrium is is locally stable for R > 1. A detailed discussion of the model reproduction number is given and numerical simulations are done to show the role of some of the important model parameters.
A Mixed‐Culture Model of a Probiotic Biofilm Control System
Authors: Eberl Hermann J. , Khassehkhan Hassan , Demaret Laurent
Published: October 2009

We present a mathematical model and computer simulations for the control of a pathogenic biofilm by a probiotic biofilm. This is a substantial extension of a previous model of control of a pathogenic biofilm by microbial control agents that are suspended in the aqueous bulk phase (H. Khassehkhan and H.J. Eberl, Comp. Math. Meth. Med, 9(1) (2008), pp. 47–67). The mathematical model is a system of double‐degenerate diffusion–reaction equations for the microbial biomass fractions probiotics, pathogens and inert bacteria, coupled with convection–diffusion–reaction equations for two growth controlling substrates, protonated lactic acids and hydrogen ions (pH). The latter are produced by the bacteria and become detrimental at high concentrations. In simulation studies, we find that the site of attachment of probiotics in the flow channel is crucial for success and efficacy of the probiotic control mechanism.
Phosphoinositide-dependent kinase 1 controls migration and malignant transformation but not cell growth and proliferation in PTEN-null lymphocytes
Authors: Finlay David K. , Sinclair Linda V. , Feijoo Carmen , Waugh Caryll M. , Hagenbeek Thijs J. , Spits Hergen , Cantrell Doreen A.
Published: October 2009

In normal T cell progenitors, phosphoinositide-dependent kinase l (PDK1)–mediated phosphorylation and activation of protein kinase B (PKB) is essential for the phosphorylation and inactivation of Foxo family transcription factors, and also controls T cell growth and proliferation. The current study has characterized the role of PDK1 in the pathology caused by deletion of the tumor suppressor phosphatase and tensin homologue deleted on chromosome 10 (PTEN). PDK1 is shown to be essential for lymphomagenesis caused by deletion of PTEN in T cell progenitors. However, PTEN deletion bypasses the normal PDK1-controlled signaling pathways that determine thymocyte growth and proliferation. PDK1 does have important functions in PTEN-null thymocytes, notably to control the PKB–Foxo signaling axis and to direct the repertoire of adhesion and chemokine receptors expressed by PTEN-null T cells. The results thus provide two novel insights concerning pathological signaling caused by PTEN loss in lymphocytes. First, PTEN deletion bypasses the normal PDK1-controlled metabolic checkpoints that determine cell growth and proliferation. Second, PDK1 determines the cohort of chemokine and adhesion receptors expressed by PTEN-null cells, thereby controlling their migratory capacity.
Loss of matrix metalloproteinase 2 in platelets reduces arterial thrombosis in vivo
Authors: Momi Stefania , Falcinelli Emanuela , Giannini Silvia , Ruggeri Loredana , Cecchetti Luca , Corazzi Teresa , Libert Claude , Gresele Paolo
Published: October 2009

Platelet activation at a site of vascular injury is essential for the arrest of bleeding; however, excessive platelet activation at a site of arterial damage can result in the unwarranted formation of arterial thrombi, precipitating acute myocardial infarction, or ischemic stroke. Activation of platelets beyond the purpose of hemostasis may occur when substances facilitating thrombus growth and stability accumulate. Human platelets contain matrix metalloproteinase 2 (MMP-2) and release it upon activation. Active MMP-2 amplifies the platelet aggregation response to several agonists by potentiating phosphatidylinositol 3-kinase activation. Using several in vivo thrombosis models, we show that the inactivation of the MMP-2 gene prevented thrombosis induced by weak, but not strong, stimuli in mice but produced only a moderate prolongation of the bleeding time. Moreover, using cross-transfusion experiments and wild-type/MMP-2−/− chimeric mice, we show that it is platelet-derived MMP-2 that facilitates thrombus formation. Finally, we show that platelets activated by a mild vascular damage induce thrombus formation at a downstream arterial injury site by releasing MMP-2. Thus, platelet-derived MMP-2 plays a crucial role in thrombus formation by amplifying the response of platelets to weak activating stimuli. These findings open new possibilities for the prevention of thrombosis by the development of MMP-2 inhibitors.
Mast cell–derived particles deliver peripheral signals to remote lymph nodes
Authors: Kunder Christian A. , St. John Ashley L. , Li Guojie , Leong Kam W. , Berwin Brent , Staats Herman F. , Abraham Soman N.
Published: October 2009

During infection, signals from the periphery are known to reach draining lymph nodes (DLNs), but how these molecules, such as inflammatory cytokines, traverse the significant distances involved without dilution or degradation remains unclear. We show that peripheral mast cells, upon activation, release stable submicrometer heparin-based particles containing tumor necrosis factor and other proteins. These complexes enter lymphatic vessels and rapidly traffic to the DLNs. This physiological drug delivery system facilitates communication between peripheral sites of inflammation and remote secondary lymphoid tissues.
Buddhism and Science
Authors: Wallace B. Alan
Published: October 2009

While Buddhism is often referred to as a ‘non-theistic religion’, it has the potential to play a unique mediating role between theistic religions, with their emphasis on faith and divine revelation, and the natural sciences, with their ideals of empiricism, rationality, and scepticism. The main body of this article focuses on Buddhist approaches to cultivating eudaimonic well-being, probing the nature of consciousness, and understanding reality at large. In each case, religious, scientific, and philosophical elements are blended in ways that may not only lend themselves to dialogue with Western science, but push forward the frontiers of scientific research as well as interdisciplinary and cross-cultural inquiry. The article also argues that Buddhism has developed a science of consciousness, with a few exceptions regarding sciences with no controlled experiments.
Judaism and Science
Authors: Samuelson Norbert M.
Published: October 2009

This article discusses the role of science in Judaism using familiar terms in unfamiliar ways, such as creation, revelation, redemption, God, world, humanity, belief, wisdom, philosophy, and science. Judaism is the formal expression of the faith of the Jewish people from its origins in the land of Israel almost 4,000 years ago to the present. Judaism and Christianity share a common textual origin; much of what they believe at least shares a common religious terminology. Furthermore, the centre for Jewish intellectual life for at least the past 500 years has been in Western European Christian civilization. However, Jewish intellectual development took place over more than 1,000 years, in lands where the dominant religion became Islam, and where Christianity consequently had little importance.
Islam And Science
Authors: Nasr Seyyed Hossein
Published: October 2009

The issue of Islam and modern science, along with its progeny, modern technology, continues today as one of the most crucial faced by the Islamic community. It has been, and continues to be, addressed by numerous scholars and thinkers, covering nearly the whole gamut of the spectrum of Islamic intellectual activity since the last century. This article analyses modern science and subjects it to an in-depth criticism from the Islamic point of view, drawing from the Islamic intellectual tradition. It holds that any science that could legitimately be called Islamic science, and not be disruptive of the whole Islamic order, must be one that remains aware of the ‘vertical cause’ of all things, along with the horizontal, a science that issues from and returns to the Real (al-Haqq), who is the cause of all things.
Molecular Biology and Religion
Authors: Hewlett Martinez
Published: October 2009

This article introduces the background, assumptions, and kinds of descriptive models used in molecular biology. It aims to provide a way to navigate through the jargon-spiked waters of this field and examine how and where these places of overlap between this field and religion exist, as well as where the controversies lie. Molecular biology as a discipline has had a short and tumultuous history. It has risen to become the pre-eminent paradigm of the life sciences and, from that position, has dominated the research agenda of the last half of the twentieth century in disciplines far removed from the pure study of genes. With the massive complexity issues that arise from the ultimate reductionist project, the Human Genome Project, molecular biology has been offered a chance for humility and introspection.
Sociology and Religion
Authors: Fenn Richard K.
Published: October 2009

In studying social order, sociologists of religion investigate the sacred. When a social system begins to emerge from the flux of everyday life, it develops boundaries that separate it from those outside. To signify the continuity of certain relationships over time, to give them an identity, and to mark their difference from other relationships, social systems define themselves in symbols, construct themselves through rituals, and realize themselves through practices. Whether it is called the numinous or the holy, charisma or mana, the sacred is always somewhat mysterious. In all of its manifestations, whether personal or social, natural or supernatural, the sacred provides only a limited embodiment of unfulfilled possibilities. What might well be called the upper-case Sacred, then, or the Sacred itself, comprises the set of all possibilities that any social system must necessarily exclude.