bluuebunny/crossref_metadata_2025 huggingface dataset:
Resistance Movements, the State, and National Identities
Authors: Zeghal Malika
Published: July 2011

The uprisings in the Middle East and North Africa (MENA) were primarily centered on profound economic grievances, which protestors addressed directly to state institutions, thereby making the grievances political. As a political scientist, I ask: under what conditions does economic protest transform into political demands? How and why did this happen in the MENA region, and why now? A deep exploration of authoritarian state institutions will be necessary to understand how a young generation that graduated from public educational institutions was unable to find economic opportunities and eventually lost all trust in an inefficient and corrupt state. Workers’ protests and resistance movements had started to organize in the decade before the uprisings and need to be studied as well.
Agencies of Coercion: Armies and Internal Security Forces
Authors: Sayigh Yezid
Published: July 2011

The readiness of army commanders in Egypt and Tunisia to counter the internal security agencies deployed by their own governments against civilian protestors in early 2011 proved decisive in bringing down presidents-for-life Husni Mubarak and Zayn al-ʿAbidin bin ʿAli. This brings into sharp relief questions about how to approach and assess the various coercive agencies of the state. Should we regard them as different branches of a single coercive apparatus, through which the state seeks to exercise a monopoly on the legitimate means of violence? Or should we see them as manifestations of more fragmented political institutions and social forces and consequently as performing distinct, and potentially divergent, functions in constantly evolving relation to each other?
Studying Middle East Militaries: Where Do We Go from Here?
Authors: Barak Oren
Published: July 2011

Research on Middle East militaries is imbalanced. In recent decades, scholarly interest in Israel and Turkey has expanded, while the Arab states have more often than not been overlooked. In this essay, I suggest how to address the “gap” in the study of Arab militaries by drawing parallels with militaries in non-Arab states, which have received considerable attention.
First description of autumn migration of Sooty FalconFalco concolorfrom the United Arab Emirates to Madagascar using satellite telemetry
Authors: JAVED SÁLIM , DOUGLAS DAVID C. , KHAN SHAHID , SHAH JUNID NAZEER , AL HAMMADI ABDULLAH ALI
Published: July 2011

The movement and migration pattern of the ‘Near Threatened’ Sooty FalconFalco concoloris poorly known. Sooty Falcons breed on the islands of the Arabian Gulf after arriving from their non-breeding areas that are mainly in Madagascar. In the first satellite tracking of the species we fitted a 9.5 g Argos solar powered transmitter on an adult breeding Sooty Falcon off the western coast of Abu Dhabi in the United Arab Emirates. The bird successfully undertook autumn migration to Madagascar, a known wintering area for the species. We document the Sooty Falcon’s autumn migration route and stop-over sites. The adult Sooty Falcon initiated its migration at night and with tailwinds, and travelled mainly during daytime hours for 13 days over an inland route of more than 5,656 km. The three stop-over sites in East Africa were characterised by moderate to sparse shrub cover associated with potential sources of water. We discuss the migration pattern of the tracked bird in relation to importance of non-breeding areas for Sooty Falcons and recent declines in numbers in their breeding range.
The youth and old age of Dapi'chi (the Pleiades): frosts, air carnations, and warriors
Authors: Gómez Cecilia Paula
Published: July 2011

Among the Western Tobas of the province of Formosa, Argentina, the asterism called Dapi'chi (the Pleiades) is highly important. Traditionally, it is related to the start of the annual cycle and it is also a very significant figure in terms of its symbolic meaning. In fact, this celestial representation offers a range of insights connected to winter frosts, a type of air carnation (Tillandsia spp.–Bromeliaceae) and also to the role of the warrior.
The Tomárâho conception of the sky
Authors: Sequera Guillermo , Gangui Alejandro
Published: July 2011

The small community of the Tomárâho, an ethnic group culturally derived from the Zamucos, have become known in the South American and world anthropological scenario in recent times. This group, far from the banks of the Paraguay river, remained concealed from organized modern societies for many years. Like any other groups of people in close contact with nature, the Tomárâho developed a profound and rich world-view which parallels other more widely researched aboriginal cultures as well as showing distinctive features of their own. This is also apparent in their imagery of the sky and of the characters that are closely connected with the celestial sphere.

This paper is based on the lengthy anthropological studies of G. Sequera. We have recently undertaken a project to carry out a detailed analysis of the different astronomical elements present in the imagined sky of the Tomárâho and other Chamacoco ethnic groups. We will briefly review some aspects of this aboriginal culture: places where they live, regions of influence in the past, their linguistic family, their living habits and how the advancement of civilization affected their culture and survival. We will later mention the fieldwork carried out for decades and some of the existing studies and publications. We will also make a brief description of the methodology of this work and special anthropological practices. Last but not least, we will focus on the Tomárâho conception of the sky and describe the research work we have been doing in recent times.
Watching the sky from the ushnu: the sukanka-like summit temple in Pueblo Viejo–Pucara (Lurin Valley, Peru)
Authors: Makowski Krzysztof , Ruggles Clive L. N.
Published: July 2011

Seen from the ‘ushnu’ platform in the palatial complex of Pueblo Viejo–Pucará, near Pachacamac, built by the Huarochirí people, the visual axis extends southwards towards two circular structures of the summit temple. Of these structures rising up from a monumental platform, one contains a sacred rock to which gold, silver andSpondylus princeps.were offered and the other housed ahuanca-idol. These structures, and the ushnu, marked points and directions that are relevant for the organization of sacred geography, but whose location does not correspond to orientations that are astronomically relevant for calendrical calculations, contrary to the initial hypothesis.
Lord of the Maya Creations on his jaguar throne: the eternal return of Elder Brother God L to preside over the 21 December 2012 transformation
Authors: Carlson John B.
Published: July 2011

Speculation about what ancient Maya texts have to say about 2012 is becoming a global phenomenon in popular culture. This speculation, largely apocalyptic, is more often based on acquaintance with historical Western interpretations than on familiarity with the texts themselves and their cultural contexts. This paper approaches the 2012 phenomenon through close readings of Maya texts and images considered within the contexts of historical and contemporary Maya culture and Western scholarship. It focuses on images of mythological events depicted on two Late Classic Maya vessels: the ‘Vase of the Seven Gods’ (Kerr no. 2796) and the ‘Vase of the Eleven Gods’ (Kerr no. 7750). These images are interpreted as representing deities, gathered in ‘cosmogonic conclave’, preparing to re-create the world with their sacrifices at the last completion of a great cycle and the beginning of a new 5,125-year 13-Bakˈtun Maya ‘Long Count’. The rites of passage are presided over by an enigmatic Venus-warrior/sacrificer deity previously known only as God L. God L's principal name and nature had remained undeciphered and his identity obscure until the author's researches resulted in the decipherment and ‘reading’ presented here. This study offers an explication of why God L, whom the author has demonstrated is the Maya god of tobacco among his many aspects, takes the senior role in presiding over these 13-Bakˈtun completion rituals and why it is reasonable to hypothesize that the same entities would be back for the fulfillment of the present cycle in 2012.
The God's Grand Costume Ball: a Classic Maya prophecy for the close of the thirteenth Bakˈtun
Authors: MacLeod Barbara
Published: July 2011

In the favored correlation between the Mayan and Gregorian calendars, a time period of a little over 5125 solar years will be completed on the winter solstice of 2012. While numerous Classic Maya hieroglyphic texts feature the previous closing of this era in 3114 BCE, only one text—Monument Six of Tortuguero, Tabasco, Mexico—mentions the future event. The portion of the monument describing the event is damaged, and previous attempts to decipher this part of the text have been inconclusive. These have inadvertently led to popular and far-flung millenniarian speculations about ancient esoteric knowledge. The whole of Tortuguero Monument Six—an exquisite piece of Classic sculpture and literature—addresses the fundamental relationship between royal charter, warfare, captive sacrifice, appeasement of the gods, the ordering of time, and the stability of society for posterity. The author and her colleagues—employing high-resolution photos and great attention to script detail—have brought to light a more accurate interpretation of the damaged text. The results of this effort suggest a distant future ceremony of investiture for a deity of deep-time transitions whose reflexes can be seen in indigenous community celebrations of highland Guatemala.
The diachronic study of orientations: Mérida, a case study
Authors: González-García A. César , Costa-Ferrer Lourdes
Published: July 2011

The study of orientations is a key ingredient in most archaeoastronomical research. Typically, a number of synchronistic monuments belonging to a given culture or cultural horizon are measured and studied in order to see if they share a similar orientation. If an astronomical orientation appears, we may apply other archaeoastronomical procedures to justify further conclusions.

On a few occasions we perform studies that compare, for a given site, monuments of different periods. At most two or three periods are usually compared to verify persistence or to check for evolution in customs of orientation. We argue here that it would also be interesting to study orientations from a diachronic point of view, in order to investigate the persistence/evolution of this particular conception of space through time.

Mérida (Extremadura, Spain) and the neighbouring areas present a rich and highly interesting monumental heritage spanning from the Neolithic to the present, with monuments belonging to several different periods and cultures.

In the present study we will review the orientation of the monuments in that area. We will present some conclusions on the evolution/persistence of customs of orientation and value the applicability of this method to other areas.
Effect of suspended periodic defect structures near a planar microwave ring resonator
Authors: Giri Tulika , Daya K. S.
Published: July 2011

This paper reports the effect of suspended periodic defect structure in switching the frequency of ring resonator. It has been observed in simulations and experiments that this non-intrusive method can switch the frequency by 31 MHz for square lattice of suspended periodic defect and by 124 MHz for a triangular lattice of suspended periodic defect structure.
Modeling the transport of passive tracers in sea ice
Authors: Jeffery N. , Hunke E. C. , Elliott S. M.
Published: July 2011

A model for the vertical transport of passive tracers in sea ice is presented. Two Reynolds flux closure approximations are proposed for the tracer velocity dispersion term in the new ice tracer model (IceT). The schemes, “enhanced molecular diffusion” (EMD) and “mixing length diffusion” (MLD), are suggested parameterizations of gravity drainage, the dominant mechanism of desalination in growing sea ice. The performance of IceT using each parameterization is tested against two experimental studies: simulations I compare profiles of brine salinity with passive tracer concentrations during sea ice growth and melt, and simulations II compare bottom boundary salt and brine volume fluxes with passive tracer fluxes and bottom diffusivities. IceT behavior is evaluated under three salinity forcing prescriptions. Both schemes successfully reproduce expected tracer concentrations in simulations I when the salinity forcing evolves logarithmically. However in simulations II, the MLD scheme outperforms EMD in two significant ways: 1) growth rate trends in the MLD diffusivity parallel measurements of brine volume flux, while EMD bottom diffusivities remain almost constant; and 2) MLD bottom tracer concentrations decrease with ice growth rate similar to excluded brine salinity, while EMD trends are contrary. Hence, enhanced molecular diffusion is highly questionable for implementation in models of reactive passive tracers. The IceT mixing length diffusivity is a viable choice in sea ice biogeochemical modeling. It remains a challenge to assess whether MLD can provide quantitative estimates of desalination at each time step for use in forcing IceT or for implementation in a model of sea ice salinity.
Ocean bottom pressure variations estimated from gravity, nonsteric sea surface height and hydrodynamic model simulations
Authors: Siegismund F. , Romanova V. , Köhl A. , Stammer D.
Published: July 2011

Ocean bottom pressure variability is analyzed from three monthly products available from (1) the Gravity Recovery and Climate Experiment (GRACE), (2) sterically corrected altimetry, and (3) from a forward run of the German part of the Estimating the Circulation and Climate of the Ocean (GECCO‐2) model. Results lead to an approximate error estimate for each of the ocean bottom pressure (OBP) maps under the assumption of noncorrelated errors among the three products. The estimated error maps are consistent with the misfits of individual fields against OBP sensor data, with the caveat that a general underestimation of the signal strength, as a common, correlated error in all products, cannot be recovered by the method. The signal‐to‐noise ratio (SNR) increases in all products, when a 3 month running mean filter is applied. Using this filter, we estimate globally averaged errors of 8.6, 11.1, and 5.7 mm of equivalent water height for GRACE, nonsteric altimetry, and GECCO2, respectively. Based on resulting uncertainties, a new OBP product is being produced by merging all three data sets. When validated with bottom pressure observations this new OBP product has a 20% increased SNR compared to the best individual product (GECCO2‐ref). Estimated total ocean mass variations explain a considerable part of OBP variability with a SNR above 1 in most of the ocean. In some regions the nonuniform part is weaker than the estimated error. However, most dynamic ocean models are designed to reproduce only the nonuniform, dynamic, OBP variability, but do not accurately describe total mass variability.
El Niño–Southern Oscillation variability persisted in a warmer world
Authors: Balcerak Ernie
Published: July 2011

Changes in the distribution of sea surface temperature associated with the El Niño–Southern Oscillation (ENSO) cause significant changes in weather. In the past 40 years it has been observed that the frequency and intensity of El Niño events have been increasing. Scientists would like to know what will happen to ENSO variability as the world's climate warms. To find out, some have looked to the mid‐Piacenzian Warm Period (mPWP), a period about 3.26–3.03 million years ago that was approximately 3°C warmer than the present day and that may be analogous to what can be expected in the future if climate continues to warm. Some studies have suggested that during the mPWP, there was actually no ENSO variability but rather a permanent El Niño state. To learn more about ENSO variability during the mPWP, Scroxton et al. analyzed the isotopic composition of planktonic foraminifera from the eastern equatorial Pacific, as well as ENSO simulations conducted with a coupled ocean‐atmosphere climate model. Their proxy and model data suggest that interannual ENSO variability did persist during the mPWP, with a mean state similar to a modern El Niño event. Furthermore, they found that during the mPWP, ENSO events may have been more regular and more intense. (Paleoceanography, doi:10.1029/2010PA002097, 2011)
Integrating genomics, transcriptomics, proteomics, and metabolomics into environmental enzymology: the next frontier or fool's gold?
Authors: Wallenstein Matthew
Published: July 2011

Extracellular enzymes are widely measured as indices of microbial activity, resource allocation, and substrate availability. However, interpretation of enzyme activities is hampered by a limited understanding of controls on enzyme production, turnover, and in-situ activity. In part, this is the consequence of methodological limitations, which require artificial substrates and are conducted under conditions that differ from in situ conditions. Recently, new tools have emerged that have potential to provide new insights into microbial enzymology. Will these methods open a new frontier in enzymology research, or will they only result in the discovery of fool’s gold? I will highlight how genomic, transcriptomic, proteomic, and metabolomic tools might be used to gain new insights into the controls on enzyme production, turnover, and in-situ activity. I will also discuss the potential for significant advancements even without the use of emerging tools. Each of these techniques offers the potential to provide new pieces to the puzzle of environmental enzymology, but progress is most likely through a multi-faceted approach.
Assessing the contribution of inflammation in models of Alzheimer's disease
Authors: Johnston Hannah , Boutin Herve , Allan Stuart M.
Published: July 2011

Inflammation has long been proposed as having a role in AD (Alzheimer's disease), although it remains unclear whether inflammation represents a cause or consequence of AD. Evidence from the clinical setting in support of a role for inflammation in AD includes increased expression of inflammatory mediators and microglial activation in the post-mortem AD brain. Also, epidemiological studies on AD patients under long-term treatment with non-steroidal anti-inflammatory drugs suggest some benefits, although recent prospective trials showed no effect. Furthermore, in AD patients, infection and other systemic inflammatory events worsen symptoms. Finally, several inflammatory genes are associated with increased risk of AD. Therefore, to elucidate the underlying mechanisms of AD and the role of inflammation, researchers have turned to experimental models and here we present a short overview of some key findings from these studies. Activation of microglia is seen in various transgenic models of AD, with both a protective role and a detrimental role being ascribed to it. Early microglial activation is probably beneficial in AD, through phagocytosis of amyloid β-peptide. At later stages however, pro-inflammatory cytokine release from microglia could contribute to neuronal demise. A better understanding of microglial phenotype at the various stages of AD is therefore still required. Although most studies suggest a detrimental role for pro-inflammatory cytokines such as interleukin-1 and tumour necrosis factor in AD, contradictory findings do exist. Age-related and differential cellular expression of these inflammatory mediators is probably a key determinant of their exact contribution to AD. In conclusion, there is no doubt that inflammatory processes are part of the pathophysiology of AD, but a better understanding of the exact contribution at different stages of the disease process is still required before appropriate treatment strategies can be devised.
Can neurodegeneration be separated from neuropathological hallmarks of chronic idiopathic human neurodegenerative disease? A perspective from modelling!
Authors: Paine Simon , Lowe James , Bedford Lynn , Mayer R. John
Published: July 2011

Chronic neurodegenerative disease is characterized by extensive regional loss of neurons in the brain and neuropathological hallmarks in surviving neurones. Genetic modelling by overexpression of hallmark proteins does not produce extensive neurodegeneration, whereas genetic deletion of neuronal 26S proteasomes does, as well as some hallmarks of human disease.
An expanded family of proteins with BPI/LBP/PLUNC-like domains in trypanosome parasites: an association with pathogenicity?
Authors: Gluenz Eva , Barker Amy R. , Gull Keith
Published: July 2011

Trypanosomatids are protozoan parasites that cause human and animal disease. Trypanosoma brucei telomeric ESs (expression sites) contain genes that are critical for parasite survival in the bloodstream, including the VSG (variant surface glycoprotein) genes, used for antigenic variation, and the SRA (serum-resistance-associated) gene, which confers resistance to lysis by human serum. In addition, ESs contain ESAGs (expression-site-associated genes), whose functions, with few exceptions, have remained elusive. A bioinformatic analysis of the ESAG5 gene of T. brucei showed that it encodes a protein with two BPI (bactericidal/permeability-increasing protein)/LBP (lipopolysaccharide-binding protein)/PLUNC (palate, lung and nasal epithelium clone)-like domains and that it belongs to a multigene family termed (GR)ESAG5 (gene related to ESAG5). Members of this family are found with various copy number in different members of the Trypanosomatidae family. T. brucei has an expanded repertoire, with multiple ESAG5 copies and at least five GRESAG5 genes. In contrast, the parasites of the genus Leishmania, which are intracellular parasites, have only a single GRESAG5 gene. Although the amino acid sequence identity between the (GR)ESAG5 gene products between species is as low as 15–25%, the BPI/LBP/PLUNC-like domain organization and the length of the proteins are highly conserved, and the proteins are predicted to be membrane-anchored or secreted. Current work focuses on the elucidation of possible roles for this gene family in infection. This is likely to provide novel insights into the evolution of the BPI/LBP/PLUNC-like domains.
Systematic nomenclature for the PLUNC/PSP/BSP30/SMGB proteins as a subfamily of the BPI fold-containing superfamily
Authors: Bingle Colin D. , Seal Ruth L. , Craven C. Jeremy
Published: July 2011

We present the BPIFAn/BPIFBn systematic nomenclature for the PLUNC (palate lung and nasal epithelium clone)/PSP (parotid secretory protein)/BSP30 (bovine salivary protein 30)/SMGB (submandibular gland protein B) family of proteins, based on an adaptation of the SPLUNCn (short PLUNCn)/LPLUNCn (large PLUNCn) nomenclature. The nomenclature is applied to a set of 102 sequences which we believe represent the current reliable data for BPIFA/BPIFB proteins across all species, including marsupials and birds. The nomenclature will be implemented by the HGNC (HUGO Gene Nomenclature Committee).
Plasma PLTP (phospholipid-transfer protein): an emerging role in ‘reverse lipopolysaccharide transport’ and innate immunity
Authors: Gautier Thomas , Lagrost Laurent
Published: July 2011

Plasma PLTP (phospholipid-transfer protein) is a member of the lipid transfer/LBP [LPS (lipopolysaccharide)-binding protein] family, which constitutes a superfamily of genes together with the short and long PLUNC (palate, lung and nasal epithelium clone) proteins. Although PLTP was studied initially for its involvement in the metabolism of HDL (high-density lipoproteins) and reverse cholesterol transport (i.e. the metabolic pathway through which cholesterol excess can be transported from peripheral tissues back to the liver for excretion in the bile), it displays a number of additional biological properties. In particular, PLTP can modulate the lipoprotein association and metabolism of LPS that are major components of Gram-negative bacteria. The delayed association of LPS with lipoproteins in PLTP-deficient mice results in a prolonged residence time, in a higher toxicity of LPS aggregates and in a significant increase in LPS-induced mortality as compared with wild-type mice. It suggests that PLTP may play a pivotal role in inflammation and innate immunity through its ability to accelerate the ‘reverse LPS transport’ pathway.
Nutritional influences on the gut microbiota and the consequences for gastrointestinal health
Authors: Scott Karen P. , Duncan Sylvia H. , Louis Petra , Flint Harry J.
Published: July 2011

The human colonic microbiota degrades dietary substrates that are indigestible in the upper GIT (gastrointestinal tract), releasing bacterial metabolites, some of which are important for gut health. Advances in molecular biology techniques have facilitated detailed analyses of the composition of the bacterial community resident in the lower GIT. Such analyses have indicated that more than 500 different bacterial species colonize an individual, and that, although there is much functional consistency in the resident bacterial groups, there is considerable inter-individual variation at the species/strain level. The bacterial community develops during early childhood until it reaches an adult-like composition. Whereas colonization and host factors influence the species composition, dietary factors also have an important impact, with specific bacterial groups changing in response to specific dietary interventions. Since bacterial species have different metabolic activities, specific diets have various consequences for health, dependent on the effect exerted on the bacterial population.
Impeded protein folding and function in active inflammatory bowel disease
Authors: Deuring J. Jasper , Peppelenbosch Maikel P. , Kuipers Ernst J. , van der Woude C. Janneke , de Haar Colin
Published: July 2011

The intestinal tract is covered by a total of 300 square metres of IECs (intestinal epithelial cells) that covers the entire intestinal mucosa. For protection against luminal xenobiotics, pathogens and commensal microbes, these IECs are equipped with membrane-bound transporters as well as the ability to secrete specific protective proteins. In patients with active IBD (inflammatory bowel disease), the expression of these proteins, e.g. ABC (ATP-binding cassette) transporters such as ABCG2 (ABC transporter G2) and defensins, is decreased, thereby limiting the protection against various luminal threats. Correct ER (endoplasmic reticulum)-dependent protein folding is essential for the localization and function of secreted and membrane-bound proteins. Inflammatory triggers, such as cytokines and nitric oxide, can impede protein folding, which causes the accumulation of unfolded proteins inside the ER. As a result, the unfolded protein response is activated which can lead to a cellular process named ER stress. The protein folding impairment affects the function and localization of several proteins, including those involved in protection against xenobiotics. In the present review, we discuss the possible inflammatory pathways affecting protein folding and eventually leading to IEC malfunction in patients with active IBD.
Evolution of symmetric reconnection layer in the presence of parallel shear flow
Authors: Lu Haoyu , Cao Jinbin
Published: July 2011

The development of the structure of symmetric reconnection layer in the presence of a shear flow parallel to the antiparallel magnetic field component is studied by using a set of one-dimensional (1D) magnetohydrodynamic (MHD) equations. The Riemann problem is simulated through a second-order conservative TVD (total variation diminishing) scheme, in conjunction with Roe’s averages for the Riemann problem. The simulation results indicate that besides the MHD shocks and expansion waves, there exist some new small-scale structures in the reconnection layer. For the case of zero initial guide magnetic field (i.e., By0 = 0), a pair of intermediate shock and slow shock (SS) is formed in the presence of the parallel shear flow. The critical velocity of initial shear flow Vzc is just the Alfven velocity in the inflow region. As Vz∞ increases to the value larger than Vzc, a new slow expansion wave appears in the position of SS in the case Vz∞ < Vzc, and one of the current densities drops to zero. As plasma β increases, the out-flow region is widened. For By0 ≠ 0, a pair of SSs and an additional pair of time-dependent intermediate shocks (TDISs) are found to be present. Similar to the case of By0 = 0, there exists a critical velocity of initial shear flow Vzc. The value of Vzc is, however, smaller than the Alfven velocity of the inflow region. As plasma β increases, the velocities of SS and TDIS increase, and the out-flow region is widened. However, the velocity of downstream SS increases even faster, making the distance between SS and TDIS smaller. Consequently, the interaction between SS and TDIS in the case of high plasma β influences the property of direction rotation of magnetic field across TDIS. Thereby, a wedge in the hodogram of tangential magnetic field comes into being. When β → ∞, TDISs disappear and the guide magnetic field becomes constant.
Gyrokinetic study of electromagnetic effects on toroidal momentum transport in tokamak plasmas
Authors: Hein T. , Angioni C. , Fable E. , Candy J. , Peeters A. G.
Published: July 2011

The effect of a finite βe = 8πneTe/B2 on the turbulent transport of toroidal momentum in tokamak plasmas is discussed. From an analytical gyrokinetic model as well as local linear gyrokinetic simulations, it is shown that the modification of the parallel mode structure due to the nonadiabatic response of passing electrons, which changes the parallel wave vector k∥ with increasing βe, leads to a decrease in size of both the diagonal momentum transport as well as the Coriolis pinch under ion temperature gradient turbulence conditions, while for trapped electron modes, practically no modification is found. The decrease is particularly strong close to the onset of the kinetic ballooning modes. There, the Coriolis pinch even reverses its direction.
Transform and relax sampling for highly anisotropic systems: Application to protein domain motion and folding
Authors: Kitao Akio
Published: July 2011

Transform and relax sampling (TRS) is proposed as a conformational sampling method to enhance “soft” fluctuation in highly anisotropic systems using molecular dynamics simulation. This method consists of three stages; transform, relax, and sampling. In the transform stage, molecular dynamics simulation is performed with randomly assigned force bias to enhance the fluctuations along relatively soft collective movements, as expected from the linear response theory. After relaxing the heated system to equilibrium without force bias in the relax stage, Monte Carlo-type determination is made as to whether the generated state is accepted or not. The sampling stage is then conducted for conformational sampling by conventional molecular dynamics simulation. TRS is first applied for the idealized multidimensional double-well Cα model to mimic protein open-close transition. Subsequently, it is applied to three different all-atom protein systems in an explicit solvent model; T4 lysozyme, glutamine binding protein, and a mini-protein chignolin. Investigation of structural variations in the hinge angle of T4 lysozyme in crystals is demonstrated by TRS. The liganded close structure of the glutamine binding protein is sampled starting from the unliganded open form. Chignolin is shown to fold into a native structure multiple times starting from highly extended structures within 100 ns. It is concluded that TRS sampled a reasonable conformational space within a relatively short simulation time in these cases. Possible future extensions of TRS are also discussed.
Quantum efficiency of GaN photocathode under different illumination
Authors: Wang Xiaohui , Chang Benkang , Du Yujie , Qiao Jianliang
Published: July 2011

GaN samples are activated by Cs/O under illumination of deuterium lamp, 300 nm monochromatic light with power of 70 μW and 300 nm monochromatic light with power of 35 μW, respectively. Photocurrent is detected before activation under illumination of deuterium lamp. Quantum efficiency (QE) is tested after activation. The results indicate that GaN activated under 300 nm monochromatic light have higher QE than that under deuterium lamp, and no obvious difference is detected between different power 300 nm monochromatic light. The photocurrent before activation inhibits the adsorption of Cs on the GaN surface, which decrease the QE of GaN.
Camelback channel for fast decay of LO phonons in GaN heterostructure field-effect transistor at high electron density
Authors: Šermukšnis E. , Liberis J. , Ramonas M. , Matulionis A. , Leach J. H. , Wu M. , Avrutin V. , Morkoç H.
Published: July 2011

Fluctuation technique is used to measure hot-phonon lifetime in dual channel GaN-based configuration proposed to support high-power operation at high frequencies. The channel is formed of a composite Al0.1Ga0.9N/GaN structure situated in an Al0.82In0.18N/AlN/Al0.1Ga0.9N/GaN heterostructure. According to capacitance–voltage measurements and simultaneous treatment of Schrödinger–Poisson equations, the mobile electrons in this dual channel configuration form a camelback density profile at elevated hot-electron temperatures. The hot-phonon lifetime was found to depend on the shape of the electron profile rather than solely on its sheet density. The camelback channel with an electron sheet density of 1.8 × 1013 cm−2 demonstrates ultrafast decay of hot phonons at hot-electron temperatures above 600 K: the hot-phonon lifetime is below ∼60 fs in contrast to ∼600 fs at an electron sheet density of 1.2 × 1013 cm−2 obtained in a reference Al0.82In0.18N/AlN/GaN structure at 600 K. The results suggest a suitable method to increase the electron sheet density without the deleterious effect caused by inefficient hot-phonon decay observed in a standard design at similar electron densities.
Note: Heated sample platform for in situ temperature-programmed XPS
Authors: Samokhvalov Alexander , Tatarchuk Bruce J.
Published: July 2011

We present the design, fabrication, and performance of the multi-specimen heated platform for linear in situ heating during the Temperature-Programmed XPS (TPXPS). The platform is versatile, compatible with high vacuum (HV) and bakeout. The heater platform is tested under in situ linear heating of typical high surface area sorbent/catalyst support – nanoporous TiO2. The platform allows the TPXPS of multiple samples located on specimen disk that can be transferred in and out of the TPXPS chamber. Electric characteristics, temperature and pressure curves are provided. Heating power supply, PID temperature controller, data-logging hardware and software are described.
Fluctuating hydrodynamics for multiscale simulation of inhomogeneous fluids: Mapping all-atom molecular dynamics to capillary waves
Authors: Shang Barry Z. , Voulgarakis Nikolaos K. , Chu Jhih-Wei
Published: July 2011

We introduce a multiscale framework to simulate inhomogeneous fluids by coarse-graining an all-atom molecular dynamics (MD) trajectory onto sequential snapshots of hydrodynamic fields. We show that the field representation of an atomistic trajectory is quantitatively described by a dynamic field-theoretic model that couples hydrodynamic fluctuations with a Ginzburg-Landau free energy. For liquid-vapor interfaces of argon and water, the parameters of the field model can be adjusted to reproduce the bulk compressibility and surface tension calculated from the positions and forces of atoms in an MD simulation. These optimized parameters also enable the field model to reproduce the static and dynamic capillary wave spectra calculated from atomistic coordinates at the liquid-vapor interface. In addition, we show that a density-dependent gradient coefficient in the Ginzburg-Landau free energy enables bulk and interfacial fluctuations to be controlled separately. For water, this additional degree of freedom is necessary to capture both the bulk compressibility and surface tension emergent from the atomistic trajectory. The proposed multiscale framework illustrates that bottom-up coarse-graining and top-down phenomenology can be integrated with quantitative consistency to simulate the interfacial fluctuations in nanoscale transport processes.
Aging of the cerebral cortex differs between humans and chimpanzees
Authors: Sherwood Chet C. , Gordon Adam D. , Allen John S. , Phillips Kimberley A. , Erwin Joseph M. , Hof Patrick R. , Hopkins William D.
Published: July 2011

Several biological changes characterize normal brain aging in humans. Although some of these age-associated neural alterations are also found in other species, overt volumetric decline of particular brain structures, such as the hippocampus and frontal lobe, has only been observed in humans. However, comparable data on the effects of aging on regional brain volumes have not previously been available from our closest living relatives, the chimpanzees. In this study, we used MRI to measure the volume of the whole brain, total neocortical gray matter, total neocortical white matter, frontal lobe gray matter, frontal lobe white matter, and the hippocampus in a cross-sectional sample of 99 chimpanzee brains encompassing the adult lifespan from 10 to 51 y of age. We compared these data to brain structure volumes measured in 87 adult humans from 22 to 88 y of age. In contrast to humans, who showed a decrease in the volume of all brain structures over the lifespan, chimpanzees did not display significant age-related changes. Using an iterative age-range reduction procedure, we found that the significant aging effects in humans were because of the leverage of individuals that were older than the maximum longevity of chimpanzees. Thus, we conclude that the increased magnitude of brain structure shrinkage in human aging is evolutionarily novel and the result of an extended lifespan.
HIGH NITROGEN INSENSITIVE 9 (HNI9)-mediated systemic repression of root NO
3
−
uptake is associated with changes in histone methylation
Authors: Widiez Thomas , El Kafafi El Sayed , Girin Thomas , Berr Alexandre , Ruffel Sandrine , Krouk Gabriel , Vayssières Alice , Shen Wen-Hui , Coruzzi Gloria M. , Gojon Alain , Lepetit Marc
Published: July 2011

In plants, root nitrate uptake systems are under systemic feedback repression by the N satiety of the whole organism, thus adjusting the N acquisition capacity to the N demand for growth; however, the underlying molecular mechanisms are largely unknown. We previously isolated the
Arabidopsis high nitrogen-insensitive 9-1
(
hni9-1
) mutant, impaired in the systemic feedback repression of the root nitrate transporter NRT2.1 by high N supply. Here, we show that
HNI9
encodes
Arabidopsis
INTERACT WITH SPT6 (AtIWS1), an evolutionary conserved component of the RNA polymerase II complex. HNI9/AtIWS1 acts in roots to repress
NRT2.1
transcription in response to high N supply. At a genomic level, HNI9/AtIWS1 is shown to play a broader role in N signaling by regulating several hundred N-responsive genes in roots. Repression of
NRT2.1
transcription by high N supply is associated with an HNI9/AtIWS1-dependent increase in histone H3 lysine 27 trimethylation at the
NRT2.1
locus. Our findings highlight the hypothesis that posttranslational chromatin modifications control nutrient acquisition in plants.
Network-based prediction for sources of transcriptional dysregulation using latent pathway identification analysis
Authors: Pham Lisa , Christadore Lisa , Schaus Scott , Kolaczyk Eric D.
Published: July 2011

Understanding the systemic biological pathways and the key cellular mechanisms that dictate disease states, drug response, and altered cellular function poses a significant challenge. Although high-throughput measurement techniques, such as transcriptional profiling, give some insight into the altered state of a cell, they fall far short of providing by themselves a complete picture. Some improvement can be made by using enrichment-based methods to, for example, organize biological data of this sort into collections of dysregulated pathways. However, such methods arguably are still limited to primarily a transcriptional view of the cell. Augmenting these methods still further with networks and additional -omics data has been found to yield pathways that play more fundamental roles. We propose a previously undescribed method for identification of such pathways that takes a more direct approach to the problem than any published to date. Our method, called latent pathway identification analysis (LPIA), looks for statistically significant evidence of dysregulation in a network of pathways constructed in a manner that implicitly links pathways through their common function in the cell. We describe the LPIA methodology and illustrate its effectiveness through analysis of data on (
i
) metastatic cancer progression, (
ii
) drug treatment in human lung carcinoma cells, and (
iii
) diagnosis of type 2 diabetes. With these analyses, we show that LPIA can successfully identify pathways whose perturbations have latent influences on the transcriptionally altered genes.
Evolution of direct reciprocity under uncertainty can explain human generosity in one-shot encounters
Authors: Delton Andrew W. , Krasnow Max M. , Cosmides Leda , Tooby John
Published: July 2011

Are humans too generous? The discovery that subjects choose to incur costs to allocate benefits to others in anonymous, one-shot economic games has posed an unsolved challenge to models of economic and evolutionary rationality. Using agent-based simulations, we show that such generosity is the necessary byproduct of selection on decision systems for regulating dyadic reciprocity under conditions of uncertainty. In deciding whether to engage in dyadic reciprocity, these systems must balance (i) the costs of mistaking a one-shot interaction for a repeated interaction (hence, risking a single chance of being exploited) with (ii) the far greater costs of mistaking a repeated interaction for a one-shot interaction (thereby precluding benefits from multiple future cooperative interactions). This asymmetry builds organisms naturally selected to cooperate even when exposed to cues that they are in one-shot interactions.
Flexibility of the C-terminal, or CII, ring of KaiC governs the rhythm of the circadian clock of cyanobacteria
Authors: Chang Yong-Gang , Kuo Nai-Wei , Tseng Roger , LiWang Andy
Published: July 2011

In the cyanobacterial circadian oscillator, KaiA and KaiB alternately stimulate autophosphorylation and autodephosphorylation of KaiC with a periodicity of approximately 24 h. KaiA activates autophosphorylation by selectively capturing the A loops of KaiC in their exposed positions. The A loops and sites of phosphorylation, residues S431 and T432, are located in the CII ring of KaiC. We find that the flexibility of the CII ring governs the rhythm of KaiC autophosphorylation and autodephosphorylation and is an example of dynamics-driven protein allostery. KaiA-induced autophosphorylation requires flexibility of the CII ring. In contrast, rigidity is required for KaiC-KaiB binding, which induces a conformational change in KaiB that enables it to sequester KaiA by binding to KaiA’s linker. Autophosphorylation of the S431 residues around the CII ring stabilizes the CII ring, making it rigid. In contrast, autophosphorylation of the T432 residues offsets phospho-S431-induced rigidity to some extent. In the presence of KaiA and KaiB, the dynamic states of the CII ring of KaiC executes the following circadian rhythm:

. Apparently, these dynamic states govern the pattern of phosphorylation, ST → SpT → pSpT → pST → ST. CII-CI ring-on-ring stacking is observed when the CII ring is rigid, suggesting a mechanism through which the ATPase activity of the CI ring is rhythmically controlled. SasA, a circadian clock-output protein, binds to the CI ring. Thus, rhythmic ring stacking may also control clock-output pathways.
Extraordinary neoteny of synaptic spines in the human prefrontal cortex
Authors: Petanjek Zdravko , Judaš Miloš , Šimić Goran , Rašin Mladen Roko , Uylings Harry B. M. , Rakic Pasko , Kostović Ivica
Published: July 2011

The major mechanism for generating diversity of neuronal connections beyond their genetic determination is the activity-dependent stabilization and selective elimination of the initially overproduced synapses [Changeux JP, Danchin A (1976)
Nature
264:705–712]. The largest number of supranumerary synapses has been recorded in the cerebral cortex of human and nonhuman primates. It is generally accepted that synaptic pruning in the cerebral cortex, including prefrontal areas, occurs at puberty and is completed during early adolescence [Huttenlocher PR, et al. (1979)
Brain Res
163:195–205]. In the present study we analyzed synaptic spine density on the dendrites of layer IIIC cortico–cortical and layer V cortico–subcortical projecting pyramidal neurons in a large sample of human prefrontal cortices in subjects ranging in age from newborn to 91 y. We confirm that dendritic spine density in childhood exceeds adult values by two- to threefold and begins to decrease during puberty. However, we also obtained evidence that overproduction and developmental remodeling, including substantial elimination of synaptic spines, continues beyond adolescence and throughout the third decade of life before stabilizing at the adult level. Such an extraordinarily long phase of developmental reorganization of cortical neuronal circuitry has implications for understanding the effect of environmental impact on the development of human cognitive and emotional capacities as well as the late onset of human-specific neuropsychiatric disorders.
Essential role of Stat3 in PI3K-induced oncogenic transformation
Authors: Hart Jonathan R. , Liao Lujian , Yates John R. , Vogt Peter K.
Published: July 2011

Cells transformed by the p110α-H1047R mutant of PI3K show increased tyrosine phosphorylation of Stat3. This activation of Stat3 is important for the transformation process, because a dominant-negative mutant of Stat3 interferes with PI3K-induced oncogenesis. GDC-0941, a specific inhibitor of PI3K reduces the level of Stat3 phosphorylation. The effect of PI3K on Stat3 appears to be mediated by a member of the Tec kinase family. The Tec kinase inhibitor LFM-A13 blocks Stat3 phosphorylation in H1047R-transformed cells. The Janus kinase inhibitor AG490 and the Src kinase inhibitor Src-1, as well as rapamycin, have no effect on Stat3 phosphorylation in H1047R-transformed cells. The H1047R-transformed cells also release a factor that induces Stat3 phosphorylation in normal cells with possible effects on the cellular microenvironment. In some human tumor cell lines, the enhanced phosphorylation of Stat3 is inhibited by both PI3K and by Tec kinase inhibitors, suggesting that the link between PI3K and Stat3 is significant in human cancer.
Genomic loss of the putative tumor suppressor gene E2A in human lymphoma
Authors: Steininger Anne , Möbs Markus , Ullmann Reinhard , Köchert Karl , Kreher Stephan , Lamprecht Björn , Anagnostopoulos Ioannis , Hummel Michael , Richter Julia , Beyer Marc , Janz Martin , Klemke Claus-Detlev , Stein Harald , Dörken Bernd , Sterry Wolfram , Schrock Evelin , Mathas Stephan , Assaf Chalid
Published: July 2011

The transcription factor E2A is essential for lymphocyte development. In this study, we describe a recurrent E2A gene deletion in at least 70% of patients with Sézary syndrome (SS), a subtype of T cell lymphoma. Loss of E2A results in enhanced proliferation and cell cycle progression via derepression of the protooncogene MYC and the cell cycle regulator CDK6. Furthermore, by examining the gene expression profile of SS cells after restoration of E2A expression, we identify several E2A-regulated genes that interfere with oncogenic signaling pathways, including the Ras pathway. Several of these genes are down-regulated or lost in primary SS tumor cells. These data demonstrate a tumor suppressor function of E2A in human lymphoid cells and could help to develop new treatment strategies for human lymphomas with altered E2A activity.