bluuebunny/crossref_metadata_2025 huggingface dataset:
Sub-tropical astronomy in the southern Andes: the ceque system in Socaire, Atacama, northern Chile
Authors: Moyano Ricardo
Published: July 2011

Sky observation in sub-tropical Andean areas, part of ancient Collasuyu, during the Inca empire (ca. 1470 A.D.) was characterized by the combined use of geographical, social, psychological and natural elements of theentorno(environment or landscape). From a phenomenological perspective, it would be understood as: the place (point of observation), the path (line or relation), the horizon (calendrical marker) and the zenith/anti-zenith (vertical projection) as an expression of ‘dwelling or living in the world’. I present results obtained from a spatio-temporal analysis of mountain worship which took place at the Atacama Indian community of Socaire, northern Chile (23° 35′ 28″S, 67° 52′ 36″W, 3274m AMSL). These indicate the existence of an animistic relationship between astronomical observations, the worship of mountains, and agricultural practices. The psychological phenomena of pareidolia, apophenia and hierophany also contribute to explain the mimetolith of the ‘Hand of God’ (formed by the Tumisa, Lausa, Chiliques, Ipira and Miñiques mountains) and the social categories of space and time in Socaire: ‘above, here, and down’; ‘right and left’; ‘female and male’; ‘noon and midnight’; ‘north and south’; and ‘visible and invisible’ (as complementary opposites oryanantin).
Can nature align? The enigma of Moxos' Lagoons—astronomy and landscape in south-western Amazonia
Authors: Belmonte Juan Antonio , Barba F. Josep
Published: July 2011

In this essay we present a tentative archaeoastronomical analysis of the Moxos' Lagoons, a controversial and huge geographical network in the landscape of the Bolivian Amazon. In the late 1990s, a preliminary analysis of the orientation of a comprehensive and statistically significant number of lagoons showed that only human action could explain the peculiarities of their geometry, and especially their orientation according to a main axis aligned to an azimuth of 50° and its complementary angle. Since then, there has been an open debate on how these orientations could have been determined in practice. The absence of distinctive geographical features on the horizon strongly suggests that this peculiar pattern must have an astronomical justification. This short report presents a first approximation to the problem, suggesting that the lagoons could have been deliberately orientated in accordance with certain stellar positions which may have marked selected moments in the local climatic or economic cycle, a fact that could be corroborated by ethnohistoric references. The implications for new ethnographical research in the region are self-evident.
Cosmogony and prophecy: Maya Era Day cosmology in the context of the 2012 prophecy
Authors: Callaway Carl D.
Published: July 2011

The Maya 2012 prophecy foretells events that will occur at the close of the current Maya ‘era’ and at the end of the 13th BˈAKTUN period of the Maya calendar. This paper explores the mythic and astronomical events that occurred previously at the start of the Maya era in 3114 BC corresponding to the close of the first 13-BˈAKTUN period. These two 13-BˈAKTUN Period Endings, separated by a span of approximately 5125 years, are like two bookends on a single shelf that inextricably link ancient Maya conceptions of time, mythic history and prophecy. The following presentation will demonstrate how in this case, the past is very much prologue. Mythic events and godly actions recorded at the beginning of the era directly parallel those actions that will occur at the end of the era. In addition, new insights will be shared into how ancient Maya scribes linked Era Day events to temple dedications and architecture to reflect the sun's daily solar trek—a journey charted and revered by ancient peoples from all corners of the Americas.
Ancestors and the sun: astronomy, architecture and culture at Chaco Canyon
Authors: Munro Andrew M. , Malville J. McKim
Published: July 2011

Three architectural traditions with astronomical associations have been identified among the ‘Great Houses’ and ‘Great Kivas’ of Chaco Canyon, New Mexico. Great Houses and one Great Kiva built during the height of construction activity (AD 1020–1100), the Bonito Phase, include front-facing south-southeast (SSE) orientations, and cardinal north-south and/or east-west (NS/EW) alignments. We present ethnographic material supporting our previous proposal that the SSE orientation is probably linked to migration traditions and ancestor veneration. We also confirm that a majority of Late Bonito Phase Great Houses (built after A.D. 1100) exhibit a third astronomical tradition: five of the principal in-canyon Great Houses built at that time were positioned at or near observing locations that could have functioned as solstice calendrical stations. Through use of these locations for public ceremonies, the Chacoan elite could demonstrate astronomical knowledge and ritual power. These findings provide support for Van Dyke's hypothesis that construction during this period was intended to reinvigorate a faltering system. One ‘Chaco halo’ Great House, Bis sa'ani, incorporates all three traditions. We suggest that temporal analysis of these traditions improves understanding of migration paths and shifting balances of power and social dominance among ancestral Pueblo culture groups.
Astronomically aligned religious structures on Raiatea and Raivavae and the Matariki festival of 1770 on Easter Island
Authors: Edwards Edmundo
Published: July 2011

Eastern Polynesian astronomy was practiced by navigators and astronomer-priests who were in charge of adjusting the lunar calendar and their annual ritual cycle of activities known as ‘The Work of the Gods’. The festivity known in Polynesia as Matariki, Matali'i or Matari'i was related to the heliacal and acronical rising and setting of the Pleiades. A study of 75 marae on the island of Raivavae, Austral Islands and of 7 marae in the island of Raiatea, Society Islands shows that there are alignments towards important star positions associated with this ritual cycle. Their use as observatories has not been documented and therefore these alignments could have served solely ritual purposes. On Easter Island all information regarding the Matariki festival coincides with the arrival of a Spanish expedition in 1770.
The sun and fifteen doorways of Phnom Rung
Authors: Komonjinda Siramas
Published: July 2011

Phnom Rung was a Khmer-style Hindu temple complex. It was built in sandstone and laterite on the rim of an extinct volcano between the 10th and 13th centuries. At the beginning, the sanctuary was built as a dedication to Shiva. Following the abandonment of Phnom Rung (which was unrecorded) the sanctuary fell into ruin, and it was not until 1971 that it was restored using anastylosis. Phnom Rung Historical Park, along with the other temples Phimai and Muang Tum, have been on the tentative list for UNESCO World Heritage since 2004.

Walking from the eastern side (front) to the western side of Phnom Rung takes the visitor through 15 doorways—those of the inner cloisters, the annex, the principal tower, and the inner sanctum. The centers of these doorways are perfectly aligned, with an azimuth of 84.5°. Every year thousands of people from Thailand and around the world travel to Phnom Rung to see the sun rising through its all of its 15 doorways. This event happens only twice a year, at the beginning of April and the beginning of September. Sunsets can also be seen through the doorways, in March and October. Each pair of sunrise-sunset events is separated by one lunar month.

The possible meaning of this event has been investigated by both archaeologists and astronomers. Nothing is recorded about sunrise or sunset among the inscriptions at the site. Another issue is that the many and various structures remain within the complex, showing that constructions in this area spanned several centuries. However, it seems that the overall layout did have a significance, both astronomical and religious.
Astronomy and culture in Late Babylonian Uruk
Authors: Steele John M.
Published: July 2011

This article presents three case studies of the role of astronomy within the culture of Late Babylonian Uruk. I argue that in order to fully understand Babylonian astronomy it is necessary to combine technical study of astronomical cuneiform texts with wider cultural study of Babylonian scholarship, archival practice and society.
Astronomical aspects of Kreisgrabenanlagen (Neolithic circular ditch systems)— an interdisciplinary approach
Authors: Zotti Georg , Neubauer Wolfgang
Published: July 2011

Since the 1980s, the entrances of a certain form of monumental Neolithic enclosure (Kreisgrabenanlage, KGA) have been discussed in relation to solstice or lunistice directions. In our current project we analyze astronomical orientations in more than 30 KGAs in Lower Austria, and combine virtual reconstructions based on previous magnetic surveys with horizon surveys and astronomical simulation software.
Astronomy, culture and landscape in the Early Iron Age in the Ebro Basin
Authors: Gutiérrez Manuel Pérez , Fons Jordi Diloli , Castaño David Bea , Seuma Samuel Sardà
Published: July 2011

Archaeological excavations carried out at Turó del Calvari (Tarragona, Spain) have revealed a protohistoric building interpreted as one of the earliest enclosures of power operating during the Early Iron Age in the northeast of the Iberian Peninsula. The structure is exceptional in several respects: the techniques of construction, the materials used, and the topographic situation. The building is perfectly integrated in the landscape and has an exquisite geometrical design, with measurement units based on the Iberian foot. The intended beauty in having used the golden ratio in its construction and an orientation that is both stellar and solar demonstrates the existence at that time of a complete series of mechanisms of representation and territorial control. This was based on the use of rituals and feasts as elements of political cohesion by an emergent elite within a process that reproduced a scaled-down Mediterranean cultural system in an indigenous space.
Traditional rites and their celestial alignments in parts of south-eastern Nigeria
Authors: Urama J. O. , Eze-Uzomaka P. I. , Opata C. C. , Chami F. A. , Obatala J. K.
Published: July 2011

Preliminary investigations at two archaeological sites in south-eastern Nigeria are presented. These sites are the ancient stone circle in Ikom and the crescent shape of an ancient iron slag heap at Lejja, Nsukka. Here, we discuss the celestial alignments of these objects, and other traditional rites in this part of Nigeria, that seem to suggest some possible astronomical connections.
Portal to the heritage of astronomy
Authors: Schultz Rüdiger
Published: July 2011

Following the Starlight meeting held in La Palma in November 2009, members of the IAU Working Group on Astronomy and World Heritage and the Starlight Initative are working together, with the approval of the UNESCO World Heritage Centre, to produce a new integrated web site for the UNESCO–IAU Astronomy and World Heritage Initiative that will act as a Portal to the Heritage of Astronomy. As such, the portal will be the bridge between the Initiative, the scientific community, National Commissions and experts, and the general public.
Closing remarks
Authors: Broda Johanna
Published: July 2011

The purpose of this invited commentary is to present some general closing remarks on the global content of the ‘Oxford IX’ International Symposium on Archaeoastronomy, taking into account how we evaluate the course archaeoastronomy has taken over the past few years. It is significant that the interdisciplinary field of archaeoastronomy has already, by common consent, changed its name into ‘astronomy in culture’ (or ‘cultural astronomy’). This happened several years ago, although it is still the case that the cultural aspect (cosmovision, or vision of the world) is not always taken sufficiently into account. The keynote presentations by Ruggles, Iwaniszewski and McCluskey addressed fundamental issues of method and theoretical concepts that should guide archaeoastronomical studies. The rest of the sessions as well as the posters were dedicated to case studies from different cultural regions of the world. This commentary synthesizes several common themes that were addressed in the many interesting papers from all over the world that were presented in the meeting. Finally I take up the proposition of Gary Urton that future efforts should be concentrated on the study of the production and maintenance of systems of knowledge in complex state societies as well as in more egalitarian rural communities. In my opinion it is an urgent task to begin discourse about the history of pre-Columbian civilizations in the Americas, a discipline of which the history of science and astronomy forms a fundamental part. The ‘Oxford’ International Conferences are a key forum for exchange and encounter regarding comparative studies with other ancient civilizations as well as indigenous traditions from all over the world.
Reply to the comments on ‘Institutions and Economic Development: Theory, Policy and History’
Authors: CHANG HA-JOON
Published: July 2011

This article is a reply to the comments made on my target article, ‘Institutions and Economic Development: Theory, Policy and History’, at the beginning of this issue.
Bayesian calibration and uncertainty analysis of hydrological models: A comparison of adaptive Metropolis and sequential Monte Carlo samplers
Authors: Jeremiah Erwin , Sisson Scott , Marshall Lucy , Mehrotra Rajeshwar , Sharma Ashish
Published: July 2011

Bayesian statistical inference implemented by stochastic algorithms such as Markov chain Monte Carlo (MCMC) provides a flexible probabilistic framework for model calibration that accounts for both model and parameter uncertainties. The effectiveness of such Monte Carlo algorithms depends strongly on the user‐specified proposal or sampling distribution. In this article, a sequential Monte Carlo (SMC) approach is used to obtain posterior parameter estimates of a conceptual hydrologic model using data from selected catchments in eastern Australia. The results are evaluated against the popular adaptive Metropolis MCMC sampling approach. Both methods display robustness and convergence, but the SMC displays greater efficiency in exploring the parameter space in catchments where the optimal solutions lie in the tails of the prescribed prior distribution. The SMC method is also able to identify a different set of parameters with an overall improvement in likelihood and Nash‐Sutcliffe efficiency for selected catchments. As a result of its population‐based sampling mechanism, the SMC method is shown to offer improved efficiency in identifying parameter optimization and to provide sampling robustness, in particular in identifying global posterior modes.
Coordinating standards and applications for optical water quality sensor networks
Authors: Bergamaschi Brian , Pellerin Brian
Published: July 2011

Joint USGS‐CUAHSI Workshop: In Situ Optical Water Quality Sensor Networks; Shepherdstown, West Virginia, 8–10 June 2011; Advanced in situ optical water quality sensors and new techniques for data analysis hold enormous promise for advancing scientific understanding of aquatic systems through measurements of important biogeochemical parameters at the time scales over which they vary. High‐frequency and real‐time water quality data also provide the opportunity for early warning of water quality deterioration, trend detection, and science‐based decision support. However, developing networks of optical sensors in freshwater systems that report reliable and comparable data across and between sites remains a challenge to the research and monitoring community. To address this, the U.S. Geological Survey (USGS) and the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI), convened a 3‐day workshop to explore ways to coordinate development of standards and applications for optical sensors, as well as handling, storage, and analysis of the continuous data they produce.
Want change? Call your representative
Authors: Fischhoff Ilya R.
Published: July 2011

During my tenure as an AGU Congressional Science Fellow, which began in September 2010 and continues until November 2011, my time has been shared between working with the U.S. House of Representatives Natural Resource Committee Democratic staff and in the office of Rep. Ed Markey (D‐Mass., ranking Democrat on the committee). I appreciate getting to work with staff, fellows, and interns who inspire me, make me laugh, and know their issues cold. Much of my work on the committee is related to fish, wildlife, oceans, lands, and water issues and is directly related to my background in ecology and evolutionary biology (I studied zebra ecology and behavior in Kenya). My assignments have included asking the Environmental Protection Agency (EPA) about why it has not changed the allowed usage of certain pesticides that the National Marine Fisheries Service has found to jeopardize the recovery of endangered Pacific salmon; helping to identify research needs and management options to combat the swiftly spreading and catastrophic white nose syndrome in North American bats; and inquiring as to whether a captive‐ape welfare bill, if passed without amendment, could thwart development of a vaccine to stop the Ebola virus from continuing to cause mass mortality in endangered wild apes.
COMBINE and MIRIAM Registry
Authors: Le Novere Nicolas
Published: July 2011

N/A
BioSharing - standards, policies and communication in bioscience
Authors: Sansone Susanna-Assunta
Published: July 2011

Research communities, funding agencies, and journals participate in the development of reporting standards for the bioscience domain to ensure that shared experiments are reported with enough information to be comprehensible and (in principle) reproducible, compared or integrated (Field, Sansone et al., Science, 2009). Similar trends exist in both the regulatory arena and commercial science.Proliferation of standards is a positive sign of stakeholders’ engagement, but how much do we know about these standards? Which ones are mature and stable enough to use or recommend? Which tools and databases implement which standard? Etc...The BioSharing catalogue (www.biosharing.org) aims to1. centralize community-developed bioscience standards, linking to policies, other portals, open access resources and lists of tools and databases implementing the standards;1.1 The International Society for Biocuration (ISB) and the BioSharing initiative have produced BioDBcore, a community-defined, uniform system for describing these bio-resources, in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement(www.biodbcore.org).2. develop and maintain a set of criteria for assessing the usability and popularity of the standards, also the interoperability and relations among them;3. foster interoperability, addressing overlaps and duplication of efforts that hamper their wider uptake and interfere with the creation of standards-compliant systems.
Models of Dementia: an introductory overview
Authors: Graham Lindsay , Sutherland Calum
Published: July 2011

The analysis of the molecular development of AD (Alzheimer's disease) is technically challenging, due to the chronic nature of the disease, the lack of early and definitive clinical diagnosis, and the fact that the abnormal molecular pathology occurs in the brain. Therefore appropriate animal models of AD are essential if we are to dissect the processes leading to molecular pathology, and ultimately to test the efficacy of potential therapies before clinical studies. Unfortunately, there is controversy over the benefits of the available models, the only consensus of opinion being that no perfect model currently exists. The investigation of animal models is extremely costly and time-consuming, therefore researchers tend to focus on one or two models. For scientists entering the AD research field, it can be difficult to identify the most appropriate model for their needs. Therefore the Models of Dementia: the Good, the Bad and the Future Biochemical Society Focused Meeting provided a platform for discussion and debate on the use and limitations of current models, the most appropriate methods for their characterization and identification of the most pressing needs of the field in general.
Systemic inflammation and Alzheimer's disease
Authors: Holmes Clive , Butchart Joe
Published: July 2011

A number of studies demonstrate disturbances of the central innate immune system in AD (Alzheimer's disease). In animal and human studies, there is evidence of close communication between systemic and central innate immune systems. Animal models of neurodegeneration show evidence of an exaggerated central innate immune response following systemic inflammation. Clinical studies of AD show evidence of increased cognitive decline and exaggerated sickness behaviour in response to systemic inflammation. Recognition of this communication pathway offers alternative explanations for a number of recognized risk factors in the development and progression of AD and highlights the potential of the manipulation of systemic innate immunity as a novel therapeutic approach.
Old and new findings on lipopolysaccharide-binding protein: a soluble pattern-recognition molecule
Authors: Schumann Ralf R.
Published: July 2011

LBP [LPS (lipopolysaccharide)-binding protein] was discovered approximately 25 years ago. Since then, substantial progress has been made towards our understanding of its function in health and disease. Furthermore, the discovery of a large protein family sharing functional and structural attributes has helped in our knowledge. Still, key questions are unresolved, and here an overview on the old and new findings on LBP is given. LBP is an acute-phase protein of the liver, but is also synthesized in other cells of the organism. While LBP is named after the ability to bind to LPS of Gram-negative bacteria, it also can recognize other bacterial compounds, such as lipopeptides. It has been shown that LBP is needed to combat infections; however, the main mechanism of action is still not clear. New findings on natural genetic variations of LBP leading to functional consequences may help in further elucidating the mechanism of LBP and its role in innate immunity and disease.
The Molecular Biology of Inflammatory Bowel Diseases
Authors: Corfield Anthony P. , Wallace Heather M. , Probert Chris S.J.
Published: July 2011

IBDs (inflammatory bowel diseases) are a group of diseases affecting the gastrointestinal tract. The diseases are multifactorial and cover genetic aspects: susceptibility genes, innate and adaptive responses to inflammation, and structure and efficacy of the mucosal protective barrier. Animal models of IBD have been developed to gain further knowledge of the disease mechanisms. These topics form an overlapping background to enable an improved understanding of the molecular features of these diseases. A series of articles is presented based on the topics covered at the Biochemical Society Focused Meeting The Molecular Biology of Inflammatory Bowel Diseases.
Dislocation pinning effects induced by nano-precipitates during warm laser shock peening: Dislocation dynamic simulation and experiments
Authors: Liao Yiliang , Ye Chang , Gao Huang , Kim Bong-Joong , Suslov Sergey , Stach Eric A. , Cheng Gary J.
Published: July 2011

Warm laser shock peening (WLSP) is a new high strain rate surface strengthening process that has been demonstrated to significantly improve the fatigue performance of metallic components. This improvement is mainly due to the interaction of dislocations with highly dense nanoscale precipitates, which are generated by dynamic precipitation during the WLSP process. In this paper, the dislocation pinning effects induced by the nanoscale precipitates during WLSP are systematically studied. Aluminum alloy 6061 and AISI 4140 steel are selected as the materials with which to conduct WLSP experiments. Multiscale discrete dislocation dynamics (MDDD) simulation is conducted in order to investigate the interaction of dislocations and precipitates during the shock wave propagation. The evolution of dislocation structures during the shock wave propagation is studied. The dislocation structures after WLSP are characterized via transmission electron microscopy and are compared with the results of the MDDD simulation. The results show that nano-precipitates facilitate the generation of highly dense and uniformly distributed dislocation structures. The dislocation pinning effect is strongly affected by the density, size, and space distribution of nano-precipitates.
Effects of polarization-field tuning in GaInN light-emitting diodes
Authors: Xu Jiuru , Schubert Martin F. , Zhu Di , Cho Jaehee , Schubert E. Fred , Shim Hyunwook , Sone Cheolsoo
Published: July 2011

III-V nitrides form the backbone of light-emitting diode (LED) technology. However, the relevance of the very strong polarization fields in III-V nitride LEDs remains unclear. Here, we demonstrate the tuning of polarization fields by mechanical force. For compressive strain in a GaInN LED epitaxial layer, we find: (i) redistribution of intensity within the electroluminescence spectrum; (ii) a decrease in the peak efficiency at low current densities; and (iii) an increase in light-output power at high current densities. These findings show the relevance of transport effects in the efficiency droop.
Coulomb singularities in scattering wave functions of spin-orbit-coupled states
Authors: Bogdanski P. , Ouerdane H.
Published: July 2011

We report on our analysis of the Coulomb singularity problem in the frame of the coupled channel scattering theory including spin-orbit interaction. We assume that the coupling between the partial wave components involves orbital angular momenta such that Δl = 0, ±2. In these conditions, the two radial functions, components of a partial wave associated to two values of the angular momentum l, satisfy a system of two second-order ordinary differential equations. We examine the difficulties arising in the analysis of the behavior of the regular solutions near the origin because of this coupling. First, we demonstrate that for a singularity of the first kind in the potential, one of the solutions is not amenable to a power series expansion. The use of the Lippmann-Schwinger equations confirms this fact: a logarithmic divergence arises at the second iteration. To overcome this difficulty, we introduce two auxilliary functions which, together with the two radial functions, satisfy a system of four first-order differential equations. The reduction of the order of the differential system enables us to use a matrix-based approach, which generalizes the standard Frobenius method. We illustrate our analysis with numerical calculations of coupled scattering wave functions in a solid-state system.
Prospects for electricity from renewable resources in the United States
Authors: Holmes K. John , Papay Larry
Published: July 2011

In 2009, the National Research Council issued Electricity from Renewables: Status, Prospects, and Impediments the study report of the Panel on Electricity from Renewable Sources. As part of the larger America’s Energy Future study undertaken by the National Academies, the panel was asked to examine the technical potential for development and deployment of renewable electricity technologies. This paper summarizes the report by this panel. The panel noted that renewable electricity generation technologies represent a tremendous opportunity to provide low net carbon dioxide (CO2)-emitting electricity generation from domestic resources and to generate new economic opportunities for the United States. The panel found that there are sufficient domestic renewable resources and technologies to allow renewable electricity to play a significant role in future electricity generation. However, although wind and solar electricity in particular have exhibited very large growth rates, non-hydropower renewables still provide a small percentage of total US electricity generation. The study considered the size and distribution of the resource base; the status of renewable electricity technologies; the economics of renewable electricity in light of various policy options; the environmental impacts of electricity from renewable resources; and the issues related to scaling up deployment. The panel concluded that an aggressive but achievable future for renewables could have non-hydroelectric renewables contributing 10% of the nation’s electricity generation by 2020 and 20% or more by 2035. To reach these levels, significant and sustained actions, involving a combination and coordination of policy, technology, and capital, will be essential. The panel emphasizes policy, technology, and capital equally because the scale of the effort required to reach such levels brings significant challenges beyond simple resource availability or technical capabilities.
Secondary threshold amplitudes for sinuous streak breakdown
Authors: Cossu Carlo , Brandt Luca , Bagheri Shervin , Henningson Dan S.
Published: July 2011

The nonlinear stability of laminar sinuously bent streaks is studied for the plane Couette flow at Re = 500 in a nearly minimal box and for the Blasius boundary layer at Reδ*=700. The initial perturbations are nonlinearly saturated streamwise streaks of amplitude AU perturbed with sinuous perturbations of amplitude AW. The local boundary of the basin of attraction of the linearly stable laminar flow is computed by bisection and projected in the AU – AW plane providing a well defined critical curve. Different streak transition scenarios are seen to correspond to different regions of the critical curve. The modal instability of the streaks is responsible for transition for AU = 25%–27% for the considered flows, where sinuous perturbations of amplitude below AW ≈ 1%–2% are sufficient to counteract the streak viscous dissipation and induce breakdown. The critical amplitude of the sinuous perturbations increases when the streamwise streak amplitude is decreased. With secondary perturbations amplitude AW ≈ 4%, breakdown is induced on stable streamwise streaks with AU ≈ 13%, following the secondary transient growth scenario first examined by Schoppa and Hussain [J. Fluid Mech. 453, 57 (2002)]. A cross-over, where the critical amplitude of the sinuous perturbation becomes larger than the amplitude of streamwise streaks, is observed for streaks of small amplitude AU < 5%–6%. In this case, the transition is induced by an initial transient amplification of streamwise vortices, forced by the decaying sinuous mode. This is followed by the growth of the streaks and final breakdown. The shape of the critical AU – AW curve is very similar for Couette and boundary layer flows and seems to be relatively insensitive to the nature of the edge states on the basin boundary. The shape of this critical curve indicates that the stability of streamwise streaks should always be assessed in terms of both the streak amplitude and the amplitude of spanwise velocity perturbations.
Robust room temperature ferromagnetism in Cu doped ZnO thin films
Authors: Ahmed Khan Zaheer , Ghosh Subhasis
Published: July 2011

We report the growth of high quality Cu doped ZnO thin films by magnetron sputtering. High level of Cu doping has been achieved at higher growth temperature. Room temperature ferromagnetism, with magnetic moment initially increasing and then decreasing with Cu content, has been observed in the thin film without post growth annealing. Observed ferromagnetism is robust and does not disappear upon annealing.
Photonic THz generation in GaAs via resonantly enhanced intracavity multispectral mixing
Authors: Vodopyanov K. L. , Hurlbut W. C. , Kozlov V. G.
Published: July 2011

We generate tunable (1.5–2 THz) terahertz output with up to 200 μW average power in periodically inverted GaAs using resonantly enhanced multispectral frequency mixing inside the cavity of a type-0 optical parametric oscillator operating at degeneracy. The optical parametric oscillator was synchronously pumped by a 1064-nm picosecond Yb-fiber laser and produced, due to the presence of an intracavity Fabry-Pérot etalon, a set of optical frequency peaks spaced at the desired THz interval that allows efficient THz wave production via difference frequency generation. The proposed method is well adapted for cascaded THz generation, where the quantum conversion limit can be significantly surpassed.
Evolution of a derived protein–protein interaction between HoxA11 and Foxo1a in mammals caused by changes in intramolecular regulation
Authors: Brayer Kathryn J. , Lynch Vincent J. , Wagner Günter P.
Published: July 2011

Current models of developmental evolution suggest changes in gene regulation underlie the evolution of morphology. Despite the fact that protein complexes regulate gene expression, the evolution of regulatory protein complexes is rarely studied. Here, we investigate the evolution of a protein-protein interaction (PPI) between Homeobox A11 (HoxA11) and Forkhead box 01A (Foxo1a). Using extant and “resurrected” ancestral proteins, we show that the physical interaction between HoxA11 and Foxo1a originated in the mammalian stem lineage. Functional divergence tests and coimmunoprecipitation with heterologous protein pairs indicate that the evolution of interaction was attributable to changes in HoxA11, and deletion studies demonstrate that the interaction interface is located in the homeodomain region of HoxA11. However, there are no changes in amino acid sequence in the homeodomain region during this time period, indicating that the origin of the derived PPI was attributable to changes outside the binding interface. We infer that the amino acid substitutions in HoxA11 altered Foxo1a's access to the conserved binding interface at the HoxA11 homeodomain. We also found an expansion in the number of paired Hox/Fox binding sites in the genomes of mammalian lineage species suggesting the complex has a biological function. Our data indicate that the physical interaction between HoxA11 and Foxo1a evolved through noninterface changes that facilitate the PPI, which prevents inappropriate interactions, rather than through the evolution of a novel binding interface. We speculate that evolutionary changes of intramolecular regulation have limited pleiotropic effects compared with changes to interaction domains themselves.
Engineering hepatocyte growth factor fragments with high stability and activity as Met receptor agonists and antagonists
Authors: Jones Douglas S. , Tsai Ping-Chuan , Cochran Jennifer R.
Published: July 2011

The Met receptor tyrosine kinase and its ligand hepatocyte growth factor (HGF) play an important role in mediating both tumor progression and tissue regeneration. The N-terminal and first Kringle domains (NK1) of HGF comprise a naturally occurring splice variant that retains the ability to activate the Met receptor. However, NK1 is a weak agonist and is relatively unstable, limiting its therapeutic potential. Here, we engineered NK1 mutants with improved biochemical and biophysical properties that function as Met receptor agonists or antagonists. We first engineered NK1 for increased stability and recombinant expression yield using directed evolution. The NK1 variants isolated from our library screens acted as weak Met receptor antagonists due to a mutation at the NK1 homodimerization interface. We introduced point mutations that restored this NK1 homodimerization interface to create an agonistic ligand, or that further disrupted this interface to create more effective antagonists. The rationally engineered antagonists exhibited melting temperatures up to approximately 64 °C, a 15 °C improvement over antagonists derived from wild-type NK1, and approximately 40-fold improvement in expression yield. Next, we created disulfide-linked NK1 homodimers through introduction of an N-terminal cysteine residue. These covalent dimers exhibited nearly an order of magnitude improved agonistic activity compared to wild-type NK1, approaching the activity of full-length HGF. Moreover, covalent NK1 dimers formed from agonistic or antagonistic monomeric subunits elicited similar activity, further signifying that NK1 dimerization mediates agonistic activity. These engineered NK1 proteins are promising candidates for therapeutic development and will be useful tools for further exploring determinants of Met receptor activation.
Crystal structure of human CD1e reveals a groove suited for lipid-exchange processes
Authors: Garcia-Alles Luis F. , Giacometti Gaelle , Versluis Cees , Maveyraud Laurent , de Paepe Diane , Guiard Julie , Tranier Samuel , Gilleron Martine , Prandi Jacques , Hanau Daniel , Heck Albert J. R. , Mori Lucia , De Libero Gennaro , Puzo Germain , Mourey Lionel , de la Salle Henri
Published: July 2011

CD1e is the only human CD1 protein existing in soluble form in the late endosomes of dendritic cells, where it facilitates the processing of glycolipid antigens that are ultimately recognized by CD1b-restricted T cells. The precise function of CD1e remains undefined, thus impeding efforts to predict the participation of this protein in the presentation of other antigens. To gain insight into its function, we determined the crystal structure of recombinant CD1e expressed in human cells at 2.90-Å resolution. The structure revealed a groove less intricate than in other CD1 proteins, with a significantly wider portal characterized by a 2 Å-larger spacing between the α1 and α2 helices. No electron density corresponding to endogenous ligands was detected within the groove, despite the presence of ligands unequivocally established by native mass spectrometry in recombinant CD1e. Our structural data indicate that the water-exposed CD1e groove could ensure the establishment of loose contacts with lipids. In agreement with this possibility, lipid association and dissociation processes were found to be considerably faster with CD1e than with CD1b. Moreover, CD1e was found to mediate in vitro the transfer of lipids to CD1b and the displacement of lipids from stable CD1b–antigen complexes. Altogether, these data support that CD1e could have evolved to mediate lipid-exchange/editing processes with CD1b and point to a pathway whereby the repertoire of lipid antigens presented by human dendritic cells might be expanded.
How the binding of human transferrin primes the transferrin receptor potentiating iron release at endosomal pH
Authors: Eckenroth Brian E. , Steere Ashley N. , Chasteen N. Dennis , Everse Stephen J. , Mason Anne B.
Published: July 2011

Delivery of iron to cells requires binding of two iron-containing human transferrin (hTF) molecules to the specific homodimeric transferrin receptor (TFR) on the cell surface. Through receptor-mediated endocytosis involving lower pH, salt, and an unidentified chelator, iron is rapidly released from hTF within the endosome. The crystal structure of a monoferric N-lobe hTF/TFR complex (3.22-Å resolution) features two binding motifs in the N lobe and one in the C lobe of hTF. Binding of Fe
N
hTF induces global and site-specific conformational changes within the TFR ectodomain. Specifically, movements at the TFR dimer interface appear to prime the TFR to undergo pH-induced movements that alter the hTF/TFR interaction. Iron release from each lobe then occurs by distinctly different mechanisms: Binding of His349 to the TFR (strengthened by protonation at low pH) controls iron release from the C lobe, whereas displacement of one N-lobe binding motif, in concert with the action of the dilysine trigger, elicits iron release from the N lobe. One binding motif in each lobe remains attached to the same α-helix in the TFR throughout the endocytic cycle. Collectively, the structure elucidates how the TFR accelerates iron release from the C lobe, slows it from the N lobe, and stabilizes binding of apohTF for return to the cell surface. Importantly, this structure provides new targets for mutagenesis studies to further understand and define this system.
Hyperprolinemic larvae of the drosophilid fly,
Chymomyza costata
, survive cryopreservation in liquid nitrogen
Authors: Koštál Vladimír , Zahradníčková Helena , Šimek Petr
Published: July 2011

The larva of the drosophilid fly,
Chymomyza costata
, is probably the most complex metazoan organism that can survive submergence in liquid nitrogen (-196 °C) in a fully hydrated state. We examined the associations between the physiological and biochemical parameters of differently acclimated larvae and their freeze tolerance. Entering diapause is an essential and sufficient prerequisite for attaining high levels of survival in liquid nitrogen (23% survival to adult stage), although cold acclimation further improves this capacity (62% survival). Profiling of 61 different metabolites identified proline as a prominent compound whose concentration increased from 20 to 147 mM during diapause transition and subsequent cold acclimation. This study provides direct evidence for the essential role of proline in high freeze tolerance. We increased the levels of proline in the larval tissues by feeding larvae proline-augmented diets and found that this simple treatment dramatically improved their freeze tolerance. Cell and tissue survival following exposure to liquid nitrogen was evident in proline-fed nondiapause larvae, and survival to adult stage increased from 0% to 36% in proline-fed diapause-destined larvae. A significant statistical correlation was found between the whole-body concentration of proline, either natural or artificial, and survival to the adult stage in liquid nitrogen for diapause larvae. Differential scanning calorimetry analysis suggested that high proline levels, in combination with a relatively low content of osmotically active water and freeze dehydration, increased the propensity of the remaining unfrozen water to undergo a glass-like transition (vitrification) and thus facilitated the prevention of cryoinjury.
Inflammatory chemokine receptors regulate CD8+ T cell contraction and memory generation following infection
Authors: Kohlmeier Jacob E. , Reiley William W. , Perona-Wright Georgia , Freeman Michael L. , Yager Eric J. , Connor Lisa M. , Brincks Erik L. , Cookenham Tres , Roberts Alan D. , Burkum Claire E. , Sell Stewart , Winslow Gary M. , Blackman Marcia A. , Mohrs Markus , Woodland David L.
Published: July 2011

The development of T cell memory from naive precursors is influenced by molecular cues received during T cell activation and differentiation. In this study, we describe a novel role for the chemokine receptors CCR5 and CXCR3 in regulating effector CD8+ T cell contraction and memory generation after influenza virus infection. We find that Ccr5−/− Cxcr3−/− cells show markedly decreased contraction after viral clearance, leading to the establishment of massive numbers of memory CD8+ T cells. Ccr5−/− Cxcr3−/− cells show reduced expression of CD69 in the lung during the peak of infection, which coincides with differential localization and the rapid appearance of memory precursor cells. Analysis of single chemokine receptor–deficient cells revealed that CXCR3 is primarily responsible for this phenotype, although there is also a role for CCR5 in the enhancement of T cell memory. The phenotype could be reversed by adding exogenous antigen, resulting in the activation and contraction of Ccr5−/− Cxcr3−/− cells. Similar results were observed during chronic Mycobacterium tuberculosis infection. Together, the data support a model of memory CD8+ T cell generation in which the chemokine-directed localization of T cells within infected tissues regulates antigen encounter and controls the extent of CD8+ T cell activation and differentiation, which ultimately regulates effector versus memory cell fate decisions.
Charge density and plasmon modes in a triangular quantum well model for doped and undoped gated AlGaN/GaN HEMTs
Authors: Rabbaa S , Stiens J
Published: July 2011

We have calculated the plasmon frequency of the two-dimensional electron gas (2DEG) in AlGaN/GaN high electron mobility transistors (HEMT). The impact of HEMT's parameters on the plasmon frequency and the sheet charge density of the 2DEG is discussed in detail. The charge density in the HEMT's channel is calculated by means of a triangular quantum well model. It has been found that the AlGaN/GaN heterostructure induces plasmon oscillations in the THz range with larger frequencies compared with other semiconductor compounds. The sensitivity of the tunability of these frequencies is considerable, especially using a variable applied gate voltage. We have derived optimal structure parameters for obtaining a maximum plasmon frequency for a given doping concentration. We will show that the accuracy of this optimized frequency value is dependent on the average position Δd of charge density in the triangular shaped (quantum well) channel. The interaction between radiation and plasmons has many applications such as detectors, mixers and generators of THz waves.
Superprism effect in a deformed triangular sonic crystal
Authors: Kaya Olgun Adem , Cicek Ahmet , Yilmaz Mukremin , Ulug Bulent
Published: July 2011

The superprism effect in a two-dimensional sonic crystal composed of lead cylinders in water aligned on a lattice obtained by varying the angle between the primitive vectors of triangular lattice is numerically investigated. Symmetry breaking influences the equi-frequency contours to reflect the lattice symmetry, so that compression along a direction leads to smaller critical angles of incidence. The whole 0°–90° range is spanned by the refracted waves at the water/sonic crystal interface for frequencies between 165 and 183 kHz, in the third band, and angles of incidence between 0° and 15°. The studied superprism behaviour can be used to achieve both spectral and angular resolution. The refraction angle varies linearly for small angles of incidence below 3° at a constant frequency, while its frequency dependence at a given angle of incidence is quadratic for small frequencies. Finite-element computations reveal that waves are refracted into the angles calculated from the equi-frequency contours with small beam divergence at any frequencies and angles of incidence.
Nondegeneracy of the saddle solution of the Allen-Cahn equation
Authors: Kowalczyk Michał , Liu Yong
Published: July 2011

A solution of the Allen-Cahn equation in the plane is called a saddle solution if its nodal set coincides with the coordinate axes. Such solutions are known to exist for a large class of nonlinearities. In this paper we consider the linear operator obtained by linearizing the Allen-Cahn equation around the saddle solution. Our result states that there are no nontrivial, decaying elements in the kernel of this operator. In other words, the saddle solution of the Allen-Cahn equation is nondegenerate.
Lessons from the long-term management plan for northern hake: could the economic assessment have accepted it?
Authors: Da Rocha José-María , Gutiérrez María-José
Published: July 2011

Da Rocha, J-M., and Gutiérrez, M-J. 2011. Lessons from the long-term management plan for northern hake: could the economic assessment have accepted it? – ICES Journal of Marine Science, 68: 1937–1941. An economic working group was convened by the EU's Scientific, Technical and Economic Committee for Fisheries (STECF) in 2007 to evaluate the potential economic consequences of the long-term management plan for the northern hake (Merluccius merluccius) stock. An analysis of all the scenarios proposed by the biological assessment using the Economic Interpretation of ACFM Advice (EIAA) model showed that F at the status quo level was the best policy for both yield and profits, in terms of net present values. This result is counter-intuitive because it seems to suggest that effort costs do not influence economic indicators, whereas it is widely accepted that including costs negatively affects economic indicators. A dynamic age-structured model is applied to northern hake and shows that the optimal fishing mortality that maximizes the net present value of profits is  Fmax is also shown.