bluuebunny/crossref_metadata_2025 huggingface dataset:
Nitrogen-doped silicon nanowires: Synthesis and their blue cathodoluminescence and photoluminescence
Authors: Shao Mingwang , Cheng Liang , Zhang Mingliang , Ma Dorthy Duo Duo , Zapien Juan Antonio , Lee Shuit-Tong , Zhang Xiaohong
Published: October 2009

Nitrogen-doped silicon nanowires were obtained via a high temperature oxide assisted method. Both their cathodoluminescence and photoluminescence exhibited blue emissions, which might attributed to the nitrogen doping. Both the elemental mapping analysis and smooth cathodoluminescence image suggested uniform nitrogen doping in the silicon nanowires.
Pressure-temperature phase diagram for shapes of vesicles: A coarse-grained molecular dynamics study
Authors: Liu Ping , Li Ju , Zhang Yong-Wei
Published: October 2009

Coarse-grained molecular dynamics simulations are performed to obtain the phase diagram for shapes of a vesicle with a variation in temperature and pressure difference across the membrane. Various interesting vesicle shapes are found, in particular, a series of shape transformations are observed for a vesicle with an initial spherical shape, which changes to a prolate shape, then an oblate shape, and then a stomatocyte shape, with either increasing temperature or decreasing pressure difference across the membrane.
Decoding cognitive control in human parietal cortex
Authors: Esterman Michael , Chiu Yu-Chin , Tamber-Rosenau Benjamin J. , Yantis Steven
Published: October 2009

Efficient execution of perceptual-motor tasks requires rapid voluntary reconfiguration of cognitive task sets as circumstances unfold. Such acts of cognitive control, which are thought to rely on a network of cortical regions in prefrontal and posterior parietal cortex, include voluntary shifts of attention among perceptual inputs or among memory representations, or switches between categorization or stimulus-response mapping rules. A critical unanswered question is whether task set shifts in these different domains are controlled by a common, domain-independent mechanism or by separate, domain-specific mechanisms. Recent studies have implicated a common region of medial superior parietal lobule (mSPL) as a domain-independent source of cognitive control during shifts between perceptual, mnemonic, and rule representations. Here, we use fMRI and event-related multivoxel pattern classification to show that spatial patterns of brain activity within mSPL reliably express which of several domains of cognitive control is at play on a moment-by-moment basis. Critically, these spatiotemporal brain patterns are stable over time within subjects tested several months apart and across a variety of tasks, including shifting visuospatial attention, switching categorization rules, and shifting attention in working memory.
Single-cell response to stiffness exhibits muscle-like behavior
Authors: Mitrossilis Démosthène , Fouchard Jonathan , Guiroy Axel , Desprat Nicolas , Rodriguez Nicolas , Fabry Ben , Asnacios Atef
Published: October 2009

Living cells sense the rigidity of their environment and adapt their activity to it. In particular, cells cultured on elastic substrates align their shape and their traction forces along the direction of highest stiffness and preferably migrate towards stiffer regions. Although numerous studies investigated the role of adhesion complexes in rigidity sensing, less is known about the specific contribution of acto-myosin based contractility. Here we used a custom-made single-cell technique to measure the traction force as well as the speed of shortening of isolated myoblasts deflecting microplates of variable stiffness. The rate of force generation increased with increasing stiffness and followed a Hill force–velocity relationship. Hence, cell response to stiffness was similar to muscle adaptation to load, reflecting the force-dependent kinetics of myosin binding to actin. These results reveal an unexpected mechanism of rigidity sensing, whereby the contractile acto-myosin units themselves can act as sensors. This mechanism may translate anisotropy in substrate rigidity into anisotropy in cytoskeletal tension, and could thus coordinate local activity of adhesion complexes and guide cell migration along rigidity gradients.
Coin hoards speak of population declines in Ancient Rome
Authors: Turchin Peter , Scheidel Walter
Published: October 2009

In times of violence, people tend to hide their valuables, which are later recovered unless the owners had been killed or driven away. Thus, the temporal distribution of unrecovered coin hoards is an excellent proxy for the intensity of internal warfare. We use this relationship to resolve a long-standing controversy in Roman history. Depending on who was counted in the early Imperial censuses (adult males or the entire citizenry including women and minors), the Roman citizen population of Italy either declined, or more than doubled, during the first century BCE. This period was characterized by a series of civil wars, and historical evidence indicates that high levels of sociopolitical instability are associated with demographic contractions. We fitted a simple model quantifying the effect of instability (proxied by hoard frequency) on population dynamics to the data before 100 BCE. The model predicts declining population after 100 BCE. This suggests that the vigorous growth scenario is highly implausible.
Genetic engineering of human stem cells for enhanced angiogenesis using biodegradable polymeric nanoparticles
Authors: Yang Fan , Cho Seung-Woo , Son Sun Mi , Bogatyrev Said R. , Singh Deepika , Green Jordan J. , Mei Ying , Park Sohyun , Bhang Suk Ho , Kim Byung-Soo , Langer Robert , Anderson Daniel G.
Published: October 2009

Stem cells hold great potential as cell-based therapies to promote vascularization and tissue regeneration. However, the use of stem cells alone to promote angiogenesis remains limited because of insufficient expression of angiogenic factors and low cell viability after transplantation. Here, we have developed vascular endothelial growth factor (VEGF) high-expressing, transiently modified stem cells for the purposes of promoting angiogenesis. Nonviral, biodegradable polymeric nanoparticles were developed to deliver hVEGF gene to human mesenchymal stem cells (hMSCs) and human embryonic stem cell-derived cells (hESdCs). Treated stem cells demonstrated markedly enhanced hVEGF production, cell viability, and engraftment into target tissues. S.c. implantation of scaffolds seeded with VEGF-expressing stem cells (hMSCs and hESdCs) led to 2- to 4-fold-higher vessel densities 2 weeks after implantation, compared with control cells or cells transfected with VEGF by using Lipofectamine 2000, a leading commercial reagent. Four weeks after intramuscular injection into mouse ischemic hindlimbs, genetically modified hMSCs substantially enhanced angiogenesis and limb salvage while reducing muscle degeneration and tissue fibrosis. These results indicate that stem cells engineered with biodegradable polymer nanoparticles may be therapeutic tools for vascularizing tissue constructs and treating ischemic disease.
Small RNAs serve as a genetic buffer against genomic shock in
Arabidopsis
interspecific hybrids and allopolyploids
Authors: Ha Misook , Lu Jie , Tian Lu , Ramachandran Vanitharani , Kasschau Kristin D. , Chapman Elisabeth J. , Carrington James C. , Chen Xuemei , Wang Xiu-Jie , Chen Z. Jeffrey
Published: October 2009

Small RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), and
trans
-acting siRNAs (tasiRNAs), control gene expression and epigenetic regulation. Although the roles of miRNAs and siRNAs have been extensively studied, their expression diversity and evolution in closely related species and interspecific hybrids are poorly understood. Here, we show comprehensive analyses of miRNA expression and siRNA distributions in two closely related species
Arabidopsis thaliana
and
Arabidopsis arenosa
, a natural allotetraploid
Arabidopsis suecica
, and two resynthesized allotetraploid lines (F
1
and F
7
) derived from
A. thaliana
and
A. arenosa
. We found that repeat- and transposon-associated siRNAs were highly divergent between
A. thaliana
and
A. arenosa. A. thaliana
siRNA populations underwent rapid changes in F
1
but were stably maintained in F
7
and
A. suecica
. The correlation between siRNAs and nonadditive gene expression in allopolyploids is insignificant. In contrast, miRNA and tasiRNA sequences were conserved between species, but their expression patterns were highly variable between the allotetraploids and their progenitors. Many miRNAs tested were nonadditively expressed (deviating from the mid-parent value, MPV) in the allotetraploids and triggered unequal degradation of
A. thaliana
or
A. arenosa
targets. The data suggest that small RNAs produced during interspecific hybridization or polyploidization serve as a buffer against the genomic shock in interspecific hybrids and allopolyploids: Stable inheritance of repeat-associated siRNAs maintains chromatin and genome stability, whereas expression variation of miRNAs leads to changes in gene expression, growth vigor, and adaptation.
Infection of neurons and encephalitis after intracranial inoculation of herpes simplex virus requires the entry receptor nectin-1
Authors: Kopp Sarah J. , Banisadr Ghazal , Glajch Kelly , Maurer Ulrike E. , Grünewald Kay , Miller Richard J. , Osten Pavel , Spear Patricia G.
Published: October 2009

Multiple entry receptors can mediate infection of cells by herpes simplex virus (HSV), permitting alternative pathways for infection and disease. We investigated the roles of two known entry receptors, herpesvirus entry mediator (HVEM) and nectin-1, in infection of neurons in the CNS and the development of encephalitis. Wild-type, HVEM KO, nectin-1 KO, and HVEM/nectin-1 double KO mice were inoculated with HSV into the hippocampus. The mice were examined for development of encephalitis or were killed at various times after inoculation for immunohistological analyses of brain slices. Nectin-1 KO mice showed no signs of disease after intracranial inoculation, and no HSV antigens were detectable in the brain parenchyma. However, HSV antigens were detected in non-parenchymal cells lining the ventricles. In the double KO mice, there was also no disease and no detectable expression of viral antigens even in non-parenchymal cells, indicating that infection of these cells in the nectin-1 KO mice was dependent on the expression of HVEM. Wild-type and HVEM KO mice rapidly developed encephalitis, and the patterns of HSV replication in the brain were indistinguishable. Thus, expression of nectin-1 is necessary for HSV infection via the intracranial route and for encephalitis; HVEM is largely irrelevant. These results contrast with recent findings that (
i
) either HVEM or nectin-1 can permit HSV infection of the vaginal epithelium in mice and (
ii
) nectin-1 is not the sole receptor capable of enabling spread of HSV infection from the vaginal epithelium to the PNS and CNS.
The transcription factors T-bet and GATA-3 control alternative pathways of T-cell differentiation through a shared set of target genes
Authors: Jenner Richard G. , Townsend Michael J. , Jackson Ian , Sun Kaiming , Bouwman Russell D. , Young Richard A. , Glimcher Laurie H. , Lord Graham M.
Published: October 2009

Upon detection of antigen, CD4
+
T helper (Th) cells can differentiate into a number of effector types that tailor the immune response to different pathogens. Alternative Th1 and Th2 cell fates are specified by the transcription factors T-bet and GATA-3, respectively. Only a handful of target genes are known for these two factors and because of this, the mechanism through which T-bet and GATA-3 induce differentiation toward alternative cell fates is not fully understood. Here, we provide a genomic map of T-bet and GATA-3 binding in primary human T cells and identify their target genes, most of which are previously unknown. In Th1 cells, T-bet associates with genes of diverse function, including those with roles in transcriptional regulation, chemotaxis and adhesion. GATA-3 occupies genes in both Th1 and Th2 cells and, unexpectedly, shares a large proportion of targets with T-bet. Re-complementation of T-bet alters the expression of these genes in a manner that mirrors their differential expression between Th1 and Th2 lineages. These data show that the choice between Th1 and Th2 lineage commitment is the result of the opposing action of T-bet and GATA-3 at a shared set of target genes and may provide a general paradigm for the interaction of lineage-specifying transcription factors.
Regulation of ciliary polarity by the APC/C
Authors: Ganner Athina , Lienkamp Soeren , Schäfer Tobias , Romaker Daniel , Wegierski Tomasz , Park Tae Joo , Spreitzer Stefan , Simons Matias , Gloy Joachim , Kim Emily , Wallingford John B. , Walz Gerd
Published: October 2009

Planar cell polarity signaling controls a variety of polarized cell behaviors. In multiciliated
Xenopus
epidermal cells, recruitment of Dishevelled (Dvl) to the basal body and its localization to the center of the ciliary rootlet are required to correctly position the motile cilia. We now report that the anaphase-promoting complex (APC/C) recognizes a D-box motif of Dvl and ubiquitylates Dvl on a highly conserved lysine residue. Inhibition of APC/C function by knockdown of the ANAPC2 subunit disrupts the polarity of motile cilia and alters the directionality of the fluid movement along the epidermis of the
Xenopus
embryo. Our results suggest that the APC/C activity enables cilia to correctly polarize in
Xenopus
epidermal cells.
Glucocorticoid regulation of the circadian clock modulates glucose homeostasis
Authors: So Alex Y.-L. , Bernal Teresita U. , Pillsbury Marlisa L. , Yamamoto Keith R. , Feldman Brian J.
Published: October 2009

Circadian clock genes are regulated by glucocorticoids; however, whether this regulation is a direct or secondary effect and the physiological consequences of this regulation were unknown. Here, we identified glucocorticoid response elements (GREs) at multiple clock genes and showed that 3 were directly regulated by the glucocorticoid receptor. We determined that a GRE within the core clock gene Per2 was continuously occupied during rhythmic expression and essential for glucocorticoid regulation of that gene in vivo. We further demonstrated that mice with a genomic deletion spanning this GRE expressed elevated leptin levels and were protected from glucose intolerance and insulin resistance on glucocorticoid treatment but not from muscle wasting. We conclude that Per2 is an integral component of a particular glucocorticoid regulatory pathway and that glucocorticoid regulation of the peripheral clock is selectively required for some actions of glucocorticoids.
Node Security in Hierarchical Sensor Networks: Distribution of Functions versus Keys
Authors: Panja Biswajit , Madria Sanjay
Published: October 2009

Secure communication involving cluster heads in a sensor network is vital as they are responsible for data aggregation and for taking important decisions in their groups. In this article, we propose a scheme for secure communication via such nodes in a sensor network. In our approach, the base station provides a function to the cluster head of each group, which is used to compute the key for the secure communication with the base station. The protocol is first elucidated for a fixed cluster head in each group and later it is extended for dynamic cluster heads. Each function is computed using a certain number of points on the curve using Lagrange's interpolation [ 10 ]. The curve computed from the function intersects the Y axis at a point which is considered as the key of the cluster head. The advantage of this approach in providing secure communication out of a cluster head is that an adversary will not be able to get hold of the function by attacking the cluster head alone. This is because instead of storing the function in the cluster head, sub-functions are generated and distributed among the sensor nodes in each group. After the distribution of the sub-functions, these functions are discarded from each cluster head. When a cluster head wants to communicate with the base station it accumulates sub-functions to compute the function to compute the key used to encrypt/decrypt messages sent and received to and from the base station. For updating the functions, the sub-functions are updated using the information provided by the base station. The key distribution approach requires that the function is to be kept secret all the time. However, since it is present in the cluster head to compute the key, it is difficult to ensure its security. We have experimentally evaluated our scheme through the simulations using TinyOs and TOSSIM and the results show that latency can be improved by using the sub-functions updating approach rather than re-generating the functions and the sub-functions. Also, updating the sub-functions requires reduced computation and bandwidth requirements than updating the sub-keys because updating of the keys needs to be done from scratch whereas updating of the sub-functions are done using an updating parameter.
A Spring–Dashpot System for Modelling Lung Tumour Motion in Radiotherapy
Authors: Wilson P. L. , Meyer J.
Published: October 2009

A 3D system of springs and dashpots is presented to model the motion of a lung tumour during respiration. The main guiding factor in configuring the system is the spatial relationship between abdominal and lung tumour motion. A coupled, non‐dimensional triple of ordinary differential equations models the tumour motion when driven by a 3D breathing signal. Asymptotic analysis is used to reduce the system to a single equation driven by a 3D signal, in the limit of small lateral and transverse tumour motions. A numerical scheme is introduced to solve this equation, and tested over wide parameter ranges. Real clinical data is used as input to the model, and the tumour motion output is in excellent agreement with that obtained by a prototype tumour tracking system, with model parameters obtained by optimization. The fully 3D model has the potential to accurately model the motion of any lung tumour given an abdominal signal as input, with model parameters obtained from an internal optimization routine.
Ir-CPI, a coagulation contact phase inhibitor from the tick Ixodes ricinus, inhibits thrombus formation without impairing hemostasis
Authors: Decrem Yves , Rath Géraldine , Blasioli Virginie , Cauchie Philippe , Robert Séverine , Beaufays Jérôme , Frère Jean-Marie , Feron Olivier , Dogné Jean-Michel , Dessy Chantal , Vanhamme Luc , Godfroid Edmond
Published: October 2009

Blood coagulation starts immediately after damage to the vascular endothelium. This system is essential for minimizing blood loss from an injured blood vessel but also contributes to vascular thrombosis. Although it has long been thought that the intrinsic coagulation pathway is not important for clotting in vivo, recent data obtained with genetically altered mice indicate that contact phase proteins seem to be essential for thrombus formation. We show that recombinant Ixodes ricinus contact phase inhibitor (Ir-CPI), a Kunitz-type protein expressed by the salivary glands of the tick Ixodes ricinus, specifically interacts with activated human contact phase factors (FXIIa, FXIa, and kallikrein) and prolongs the activated partial thromboplastin time (aPTT) in vitro. The effects of Ir-CPI were also examined in vivo using both venous and arterial thrombosis models. Intravenous administration of Ir-CPI in rats and mice caused a dose-dependent reduction in venous thrombus formation and revealed a defect in the formation of arterial occlusive thrombi. Moreover, mice injected with Ir-CPI are protected against collagen- and epinephrine-induced thromboembolism. Remarkably, the effective antithrombotic dose of Ir-CPI did not promote bleeding or impair blood coagulation parameters. To conclude, our results show that a contact phase inhibitor is an effective and safe antithrombotic agent in vivo.
POWER ASYMMETRY IN COSMIC MICROWAVE BACKGROUND FLUCTUATIONS FROM FULL SKY TO SUB-DEGREE SCALES: IS THE UNIVERSE ISOTROPIC?
Authors: Hansen F. K. , Banday A. J. , Górski K. M. , Eriksen H. K. , Lilje P. B.
Published: October 2009

We repeat and extend the analysis of Eriksen et al. and Hansen et al., testing the isotropy of the cosmic microwave background fluctuations. We find that the hemispherical power asymmetry previously reported for the largest scales ℓ = 2–40 extends to much smaller scales. In fact, for the full multipole range ℓ = 2–600, significantly more power is found in the hemisphere centered at (θ = 107° ± 10°, ϕ = 226° ± 10°) in galactic co-latitude and longitude than in the opposite hemisphere, consistent with the previously detected direction of asymmetry for ℓ = 2–40. We adopt a model selection test where the direction and amplitude of asymmetry, as well as the multipole range, are free parameters. A model with an asymmetric distribution of power for ℓ = 2–600 is found to be preferred over the isotropic model at the 0.4% significance level, taking into account the additional parameters required to describe it. A similar direction of asymmetry is found independently in all six subranges of 100 multipoles between ℓ = 2–600. None of our 9800 isotropic simulated maps show a similarly consistent direction of asymmetry over such a large multipole range. No known systematic effects or foregrounds are found to be able to explain the asymmetry.
Application of homotopy perturbation method in the solution of Fokker–Planck equation
Authors: Jafari M A , Aminataei A
Published: October 2009

In this work, we have generalized the homotopy perturbation method (HPM) and we have shown that methods such as the spectral method, the Adomian decomposition method and the HPM are special cases of the new modified HPM of the present study. At last we apply the HPM to solve the Fokker–Planck equation. To illustrate the method some experiments are provided. The results reveal the efficiency and accuracy of the HPM. The HPM can obtain analytic form of the solution in some cases. The technique (HPM) has been applied with great success to obtain the solution of a large variety of nonlinear problems in both ordinary and partial differential equations, integral equations and integro-differential equations.
Fine-structure energy levels, oscillator strengths and lifetimes in Cu XVIII
Authors: Tayal Vikas , Gupta G P
Published: October 2009

We have performed large-scale CIV3 (Configuration Interaction Version 3) calculations of excitation energies from ground states for 141 fine-structure levels as well as of oscillator strengths and radiative decay rates for all electric-dipole-allowed and intercombination transitions among the levels of the (1s22s22p6) 3ℓ2, 3ℓ3ℓ′ and 3ℓ4ℓ configurations of Cu XVIII. These states are represented by very extensive configuration–interaction (CI) wavefunctions obtained using the CIV3 computer code of Hibbert. The important relativistic effects are included through the Breit–Pauli approximation. In order to keep our calculated energy splittings as close as possible to the experimental values, we have made small adjustments to the diagonal elements of the Hamiltonian matrices. Since mixing among several fine-structure levels is found to be very strong, it becomes difficult to identify these uniquely. Our excitation energies, including their ordering, are in excellent agreement (better than 1.0%) with the available experimental results. From our calculated radiative decay rates, we have also calculated radiative lifetimes of the fine-structure levels. Our calculated oscillator strengths and radiative decay rates are found to be in good agreement with other theoretical results, while the lifetimes agree very well with the experimental values (wherever available). In this calculation, we also predict new data for several fine-structure levels where no other theoretical and experimental results are available.
Comparison between flux loops and magnetic probes in determination of the Shafranov parameter in an IR-T1 tokamak
Authors: Salar Elahi A , Ghoranneviss M
Published: October 2009

In this paper, we present two comparative techniques for determination of the Shafranov parameter in an IR-T1 tokamak: a poloidal flux loop and magnetic probe techniques. For this purpose, two flux loops were designed and installed on the outer surface of the IR-T1 tokamak chamber, and then a poloidal flux was obtained from them. From the difference of poloidal fluxes on the high-field and low-field sides, the Shafranov parameter was measured. To compare the results, four magnetic probes were designed, constructed and installed on the outer surface of the IR-T1, and again the values of the Shafranov parameter were obtained independently. Experimental results were compared and discussed.
First-principles determination of structural properties of MgO
Authors: Gueddim A , Bouarissa N , Villesuzanne A
Published: October 2009

We present an ab initio calculation of structural properties of MgO in the rocksalt and CsCl structures. We employ the full-potential linearized augmented plane wave (FP-LAPW) method within the density functional theory (DFT) in the generalized gradient approximation (GGA). The agreement between our results and experiment concerning the lattice constant, bulk modulus and pressure derivative of bulk modulus for rocksalt MgO is better than 2, 9 and 2%, respectively. Our results for CsCl MgO are predictions. The pressure for the rocksalt to CsCl transition is found to be 611.12 GPa showing thus a remarkable stability range of MgO in the rocksalt structure.
On the role of electron-driven processes in planetary atmospheres and comets
Authors: Campbell L , Brunger M J
Published: October 2009

After the presence of ionized layers in the Earth's atmosphere was inferred, it took 50 years to quantitatively understand them. The electron density could not be accounted for until Sir David Bates first suggested (along with Sir Harrie Massey) that the main electron-loss process was dissociative recombination with molecular ions, and he and colleagues then developed a theory to predict those rates of dissociative recombination. However, electron impact processes, particularly excitation, have been considered insignificant in most situations, in both planetary and cometary atmospheres. Here we describe cases where recent calculations have shown that electron impact excitation of molecules is important, suggesting that, just as in the time of Sir David Bates, electron-driven processes remain fundamental to our quantitative understanding of atmospheric and cometary phenomena.
Radon transform as a set of probability distributions
Authors: Militello B , Man'ko V I , Man'ko M A , Messina A
Published: October 2009

It is proved that the Radon transform of the Wigner function gives the probability distributions related to measuring the observable operators obtained as linear combinations of position and momentum of the relevant particle. The generalization to an arbitrary number of degrees of freedom is given.
Psychology, The Human Sciences, And Religion
Authors: Paloutzian Raymond F.
Published: October 2009

Three of the five integrative themes in this article seem straightforward: the path of the research, the role of the psychology of religion, and the methods–theory–methods feedback loop. The other two are pivotal. The multilevel interdisciplinary paradigm and the model of religion as a meaning system may be intellectual devices that can foster more expansive research programmes and more visionary theoretical integration. The psychology of religion has developed to such a degree during the past quarter-century that its contributions to the science–religion dialogue are compelling. The boundaries within the subdisciplines of psychology are diminishing, and in their place, people see the rise of research that pulls together ideas from previously isolated lines of work. Similarly, cross-fertilization of psychological research with allied fields has increased, and this trend will continue.
The Scientific Landscape of Religion: Evolution, Culture, and Cognition
Authors: Atran Scott
Published: October 2009

Religion has no evolutionary functions per se. Rather, existential anxieties and moral sentiments constitute – by virtue of evolution – ineluctable elements of the human condition; and the cognitive invention, cultural selection, and historical survival of religious beliefs in the supernatural owe much to its success in accommodating these elements. Other factors in the persistence of religion as mankind's provisional evolutionary destiny involve naturally selected elements of human cognition. These include the inherent susceptibility of religious beliefs to modularized conceptual processing systems, such as folk psychology, which favour the survival and recurrence of the supernatural within and across minds and societies.
Toward A Comprehensive Integration Of Science and Religion: A Post‐metaphysical Approach
Authors: Esbjörn‐Hargens Sean , Wilber Ken
Published: October 2009

This article outlines the ways in which Integral Theory, applying Integral Methodological Pluralism (IMP), can provide a successful approach to integrating the disciplines of science and religion. It introduces the Integral approach and the application of IMP. Then, the article draws on IMP to explain some of the important features of both Integral Science and Integral Religion. Finally, it identifies some key considerations for integrating science and religion. Integral Theory provides a comprehensive means of integrating the four dimension-perspectives of objectivity, interobjectivity, subjectivity, and intersubjectivity. It also includes the major methodological families in a way that avoids postulating the existence of pre-existing ontological structures of a Platonic, archetypal, Patanjali, or Yogachara-Buddhist variety.
Science and Theology: Their Relation at the Beginning of the Third Millenium
Authors: Welker Michael
Published: October 2009

A clear perspective on the reductionisms on both sides has been gained through a Theology and Science discourse that has made anthropological research reconsider the relation of God to human beings, revealing that this ‘relation’ is constituted not merely by God's sustenance of human creatures or by their feeling of ‘utter dependence’ on God. The divine creativity has to be differentiated into God's (1) sustaining, (2) rescuing and saving, and, finally, (3) elevating and ennobling work on creation. Naturalistic reductionisms tend to be found on the first level. Anthropologies shaped by social, political, and moral concerns easily come up with reductionisms located on the second level. Typically religious and spiritual perspectives are in danger of creating reductionisms on the third level.
Darwinism
Authors: McGrath Alister E.
Published: October 2009

One of the most vigorous debates within modern Christian thought concerns the implications of Darwinism for religious belief. It is a debate that is by no means limited to Christianity, as is evident from the generally hostile reaction to Darwinism within the Islamic world. While the term is often used to refer specifically to the views set out by Charles Darwin in his Origin of Species, it is more widely used to refer to the theories that emerged from Darwin's work, as they have been received, developed, and modified. Although terms such as the ‘neo-Darwinian synthesis’ are often used to distinguish the present state of evolutionary theory from the earlier forms proposed by Darwin himself, this article follows the widespread convention of using the word ‘Darwinism’ to define a family of theories.
God and Evolution
Authors: Haught John F.
Published: October 2009

On the issue of ‘God and evolution’ it is not helpful to think of God only as a first cause, a final cause, or an intelligent designer. Rather, this article approaches the topic of evolution to bring to the fore what is taken to be the revelatory image of God given in the witness of the author's own religious tradition. Such an image is available to Christians in the picture of Jesus presented in the Gospels and interpreted by other biblical and classic texts throughout the centuries. Therefore, in the world of Christian thought and its engagements with Darwinian biology, the first question must be whether the idea of God as revealed in Christ is able to illuminate the story of life without contradicting or editing the scientific information pertaining to evolution.
The Sacred Emergence of Nature
Authors: Goodenough Ursula , Deacon Terrence W.
Published: October 2009

Scientists have had spectacular success with reductionism. Response to this success has been decidedly mixed. On the one hand, people slurp up the technologies and medicines that spin off from, and thereby validate, these reductionist understandings. On the other hand, they often decry the Humpty-Dumpty fragments that appear to be all that remains of their whole-egg world where the human is the point. This article first gives an overview of the emergentist view of nature, and then uses these concepts to outline an emergentist view of the religious quest. It suggests that much of what religious persons seek is grounded in a thirst for the very emergent phenomena that in fact surround us. The concept of emergence, more than any other concept we have encountered, puts Humpty-Dumpty back together again in ways that are wonderfully resonant with our existential and religious yearnings.
Theology, Ecology, and Values
Authors: Deane‐Drummond Celia
Published: October 2009

The nexus between ecology and religious reflection has been on the agenda for discussion among theologians since the 1970s, which were characterized by an increased social, public, and political awareness of environmental questions arising specifically from human activities. This article engages with the values that arise within ecology to offer an illustrative analysis of current ecological challenges, and to highlight debates within Christian theological ethics as to how best to respond to such challenges. It argues for a virtue-ethics approach to complex questions in ecology, drawing specifically on the classical tradition of Thomas Aquinas and including the virtues of wisdom, prudence, justice, and fortitude alongside the theological virtues of faith, hope, and charity. Finally, the article offers pointers towards the way the field might develop in the future.
Concluding Reflections: Dover Beach Revisited
Authors: Midgley Mary
Published: October 2009

Using a passage from Matthew Arnold's poetry which writes sadly of the receding Sea of Faith, this article holds that the loss of Christian metaphysics drained away all the normal meaning from life, leaving people desperately trying to make sense of a dead, empty world. The nihilistic message draws its power from exploiting the unreal split that Descartes introduced between human minds and the rest of nature. We ourselves are unearthly, supernatural entities, God's colonists sent to supervise the Earth. The Newtonian age could use this crude dualism because the Christian God still kept the two elements together. The inert particle model itself no longer makes any sense because it is contrary to modern physics. The behaviourists, misguidedly obsessed with parsimony, had tried to explain human life entirely from the outside, ignoring the inner experience that lies at the heart of all human action.
Bragg scattering and wave-power extraction by an array of small buoys
Authors: Garnaud Xavier , Mei Chiang C.
Published: October 2009

Future designs of systems for power extraction from ocean waves will likely involve a periodic array of absorbing units. We report an asymptotic theory of scattering and radiation by a linear array of heaving buoys in a channel and attached to power-takeoff devices. The spacing between buoys is assumed to be comparable to the incident wavelength and sea depth but much greater than the buoy size. The effects of extraction rate on the buoy motion, transmission and reflection coefficients for a range of frequencies in and outside the band gap are studied. It is found that strong reflection for frequencies inside the band gap of Bragg resonance reduces the extraction efficiency significantly. For comparison an alternate theory for the efficiency away from the band gap is derived using Froude–Krylov approximation. The predictions confirms and complements the asymptotic theory.
Phylogenetic structure of angiosperm communities during tropical forest succession
Authors: Letcher Susan G.
Published: October 2009

The phylogenetic structure of ecological communities can shed light on assembly processes, but the focus of phylogenetic structure research thus far has been on mature ecosystems. Here, I present the first investigation of phylogenetic community structure during succession. In a replicated chronosequence of 30 sites in northeastern Costa Rica, I found strong phylogenetic overdispersion at multiple scales: species present at local sites were a non-random assemblage, more distantly related than chance would predict. Phylogenetic overdispersion was evident when comparing the species present at each site with the regional species pool, the species pool found in each age category to the regional pool or the species present at each site to the pool of species found in sites of that age category. Comparing stem size classes within each age category, I found that during early succession, phylogenetic overdispersion is strongest in small stems. Overdispersion strengthens and spreads into larger size classes as succession proceeds, corroborating an existing model of forest succession. This study is the first evidence that succession leaves a distinct signature in the phylogenetic structure of communities.
Mechanical implications of pneumatic neck vertebrae in sauropod dinosaurs
Authors: Schwarz-Wings Daniela , Meyer Christian A. , Frey Eberhard , Manz-Steiner Hans-Rudolf , Schumacher Ralf
Published: October 2009

The pre-sacral vertebrae of most sauropod dinosaurs were surrounded by interconnected, air-filled diverticula, penetrating into the bones and creating an intricate internal cavity system within the vertebrae. Computational finite-element models of two sauropod cervical vertebrae now demonstrate the mechanical reason for vertebral pneumaticity. The analyses show that the structure of the cervical vertebrae leads to an even distribution of all occurring stress fields along the vertebrae, concentrated mainly on their external surface and the vertebral laminae. The regions between vertebral laminae and the interior part of the vertebral body including thin bony struts and septa are mostly unloaded and pneumatic structures are positioned in these regions of minimal stress. The morphology of sauropod cervical vertebrae was influenced by strongly segmented axial neck muscles, which require only small attachment areas on each vertebra, and pneumatic epithelia that are able to resorb bone that is not mechanically loaded. The interaction of these soft tissues with the bony tissue of the vertebrae produced lightweight, air-filled vertebrae in which most stresses were borne by the external cortical bone. Cervical pneumaticity was therefore an important prerequisite for neck enlargement in sauropods. Thus, we expect that vertebral pneumaticity in other parts of the body to have a similar role in enabling gigantism.
A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae
Authors: Berchowitz Luke E. , Hanlon Sean E. , Lieb Jason D. , Copenhaver Gregory P.
Published: October 2009

During meiosis, chromatin undergoes extensive changes to facilitate recombination, homolog pairing, and chromosome segregation. To investigate the relationship between chromatin organization and meiotic processes, we used formaldehyde-assisted isolation of regulatory elements (FAIRE) to map open chromatin during the transition from mitosis to meiosis in the budding yeast Saccharomyces cerevisiae. We found that meiosis-induced opening of chromatin is associated with meiotic DSB hotpots. The positive association between open chromatin and DSB hotspots is most prominent 3 h into meiosis, when the early meiotic genes DMC1 and HOP1 exhibit maximum transcription and the early recombination genes SPO11 and RAD51 are strongly up-regulated. While the degree of chromatin openness is positively associated with the occurrence of recombination hotspots, many hotspots occur outside of open chromatin. Of particular interest, many DSB hotspots that fell outside of meiotic open chromatin nonetheless occurred in chromatin that had recently been open during mitotic growth. Finally, we find evidence for meiosis-specific opening of chromatin at the regions adjacent to boundaries of subtelomeric sequences, which exhibit specific crossover control patterns hypothesized to be regulated by chromatin.
Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
Authors: Reddy Timothy E. , Pauli Florencia , Sprouse Rebekka O. , Neff Norma F. , Newberry Kimberly M. , Garabedian Michael J. , Myers Richard M.
Published: October 2009

The glucocorticoid steroid hormone cortisol is released by the adrenal glands in response to stress and serves as a messenger in circadian rhythms. Transcriptional responses to this hormonal signal are mediated by the glucocorticoid receptor (GR). We determined GR binding throughout the human genome by using chromatin immunoprecipitation followed by next-generation DNA sequencing, and measured related changes in gene expression with mRNA sequencing in response to the glucocorticoid dexamethasone (DEX). We identified 4392 genomic positions occupied by the GR and 234 genes with significant changes in expression in response to DEX. This genomic census revealed striking differences between gene activation and repression by the GR. While genes activated with DEX treatment have GR bound within a median distance of 11 kb from the transcriptional start site (TSS), the nearest GR binding for genes repressed with DEX treatment is a median of 146 kb from the TSS, suggesting that DEX-mediated repression occurs independently of promoter-proximal GR binding. In addition to the dramatic differences in proximity of GR binding, we found differences in the kinetics of gene expression response for induced and repressed genes, with repression occurring substantially after induction. We also found that the GR can respond to different levels of corticosteroids in a gene-specific manner. For example, low doses of DEX selectively induced PER1, a transcription factor involved in regulating circadian rhythms. Overall, the genome-wide determination and analysis of GR:DNA binding and transcriptional response to hormone reveals new insights into the complexities of gene regulatory activities managed by GR.
Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome
Authors: Salehi-Ashtiani Kourosh , Lin Chenwei , Hao Tong , Shen Yun , Szeto David , Yang Xinping , Ghamsari Lila , Lee HanJoo , Fan Changyu , Murray Ryan R. , Milstein Stuart , Svrzikapa Nenad , Cusick Michael E. , Roth Frederick P. , Hill David E. , Vidal Marc
Published: October 2009

Although a highly accurate sequence of the Caenorhabditis elegans genome has been available for 10 years, the exact transcript structures of many of its protein-coding genes remain unsettled. Approximately two-thirds of the ORFeome has been verified reactively by amplifying and cloning computationally predicted transcript models; still a full third of the ORFeome remains experimentally unverified. To fully identify the protein-coding potential of the worm genome including transcripts that may not satisfy existing heuristics for gene prediction, we developed a computational and experimental platform adapting rapid amplification of cDNA ends (RACE) for large-scale structural transcript annotation. We interrogated 2000 unverified protein-coding genes using this platform. We obtained RACE data for approximately two-thirds of the examined transcripts and reconstructed ORF and transcript models for close to 1000 of these. We defined untranslated regions, identified new exons, and redefined previously annotated exons. Our results show that as much as 20% of the C. elegans genome may be incorrectly annotated. Many annotation errors could be corrected proactively with our large-scale RACE platform.
Dependence of small-angle neutron scattering contrast on the difference in thermal expansions of phases in two-phase alloys
Authors: Strunz Pavel , Gilles Ralph , Mukherji Debashis , Hofmann Michael , del Genovese Dominique , Roesler Joachim , Hoelzel Markus , Davydov Vadim
Published: October 2009

Theoretical expressions describing small-angle neutron scattering (SANS) contrast dependence on temperature in the region where no phase-composition changes occur were derived for two-phase Ni superalloys. The theory is based on the difference in thermal expansion of the two primary phases, γ and γ′. The simulations show that the scattering contrast temperature evolution is significant enough to be considered inin situSANS experiments with superalloys at elevated temperatures. The simulations performed show that the magnitude of the scattering contrast at room temperature is firmly connected with the particular shape of the scattering contrast temperature dependence. This fact can be used for determination of the scattering contrast without a knowledge of the compositions of the individual phases. The theoretical expressions derived for scattering contrast were proven experimentally on an Ni–Fe-base alloy, DT706. The evolution of lattice parameters of both the matrix and the precipitate phases was obtained from anin situwide-angle neutron diffraction experiment. The theoretical scattering contrast dependence was then successfully fitted to the measured SANS integral intensity.
Test tube for obtaining crystals
Authors: Cabric Branislav , Danilovic Nebojsa
Published: October 2009

A design for an air-cooled test tube with a series of sockets and plugs (`crystallization socket-outlet adaptor') installed in a laboratory furnace is presented. The setup allows easy regulation and simultaneous crystallization tests of a series of different crystallization parameters and substances, enabling fast studies of single-crystal growth.
A method for the indexation of back-reflection Laue X-ray photographs
Authors: Sidokhine F. A. , Sidokhine E. F. , Sidokhine A. F.
Published: October 2009

This article presents a variation of the traditional method for indexing and determining the crystal orientation from Laue back-photographs with a demonstration of its applicability to low-quality diffraction patterns from imperfect metallic single crystals.